Donating money to scientific research after my death

Funding people instead of projects is in fact a good idea if you are interested in a supporting fundamental research problems to be addressed. There are multiple ways to go about this, and it's a reasonably well established principle, so you might want to search around a bit how other funding organizations and (non-profit) foundations approach this.

Lump sum vs. funding from interest is really a choice between aiming at one or two breakthroughs within a period of 5 to 10 years vs. continuously supporting research in a specific field, on a smaller scale, over 50 to 100 years. This relates to the answer of the next questions...
Amount to give to a single professor: A strategy for short term funding (using up the capital) would be to fund the establishment of a new research group, i.e., pay the salary of someone early in their career (assistant or associate professor level) plus some funds for research staff (PhD students and post-docs). I would recommend a funding level of $2M (that is what the Consolidator Grant of the European Research Council provides for a period of 5 years) to $5M per professor, depending on how much expensive equipment and materials are needed to do this research. That means you could fund 2 to 5 such groups. After the period of funding at that level, these persons should have achieved sufficient research results to be self-sustainable, though you cannot be sure that they will continue working on the kind of questions you aimed to fund.
For long term funding, I would recommend donating the whole sum as a Financial endowment (see Endowed professorships) to one university. If you assume an interest rate of 1 %, it will pay $100k per year, which might be just enough to pay a professor's salary, or, if the university agrees to pay the professor, could be used to fund 1 - 2 PhD students or post-docs working with the professor.
How to spend the money: Don't transfer that money to a professor's private account. Professors get research budgets from their universities, and if the funder wants to, the spending restrictions can be extremely flexible while still making sure that the money is only used on research related costs. So you either need to make an agreement with a university for them to administer the money according to the stipulations you agree on, or set up a foundation that administers the money and pays it to universities, who then put it in the research budget of the professors that it's meant to support. For the first option, you may want to contact a university's alumni or financial office, or maybe the dean of a department in the area you'd like to support.
Don't plan to select the persons you're funding yourself. First, it's better to fund young researchers, and if you talk to potential candidates while you still can do it, I'd hope that these will be old, or at least senior researchers, by the time the money becomes available. Instead, choose the persons that will do the selection. In the endowment case, that would be the university department that gets the endowment. Make sure that the general research direction and overall functioning of the department fits to your aims, and only select them if you're reasonably confident that they will use the money according to your aims. In the non-profit foundation case, I'd suggest setting up an advisory board with reputable scientists in the field you'd like to fund, and let them run the selection. Keep in mind that the composition of this group (institutions they come from, character, etc.) will be an important factor in who they select for funding. If this is going to operate over a longer time, make sure that there are regulations in place how new persons can enter the advisory board when you won't be there anymore.


MOOC's certificates on graduate admissions

You're free to mention the certificate in your application.  How much weight to give to it is presumably up to individual committee members.  I think unless the certificate pertains to a specific skill that's in demand for the program, you shouldn't expect to get much of a boost from having one.  At the moment, people don't have much experience with such certificates, and will be more inclined to look at indicators they know better, like grades and GREs.  It's possible this will change a bit in the future, but it will likely move pretty slowly.


What is meant by the term "research interest", when asked to provide a brief description of research interests on an application?

Trivially, your research interests refer to what you are interested in doing research on should you be admitted to grad school. For instance, in computer science, your interests might be in the human aspects of software engineering, in applying machine learning to the optimization of business processes, or in finding a polynomial-time algorithm for the travelling salesman problem (although I don't recommend the latter).

Note that your instructions specifically say that this is not the same as your statement of purpose. That is, "I want to do research to better mankind" is not a research interest, and neither is "I will do whatever my advisor wants me to do" or "I will do research that is publishable at top venues". The question here really is that you tell the admission committee what research content you want  to work on, why you think it is relevant and interesting, and what in your previous studies enables you to do that kind of research.

If you already have a potential advisor in mind, you want to look at what kind of research her or his current students are working on, and draft your research statement along similar lines (of course taking your own interests into account, but if your interests and the interests of your prospective advisor don't match, you should keep on looking anyway). It generally pays to be as specific as you can - even if you end up not doing exactly what you wrote in your research statement (most people don't), providing concrete details will indicate that you know and understand the work that your future advisor is doing, and that you have thought extensively about how you will fit into it.


Is it unethical writing two papers addressing two aspects of the same research project

Not necessarily. However, the following would be unethical:

Submitting two papers with any overlapping material without one citing the other and explaining the parts that overlap (giving credit to where the idea was originally proposed)
Submitting essentially the same idea to two different venues at the same time (farming to see if one of them gets accepted)
Submitting two papers with exactly the same idea, but making it sound like they are two different ideas

Basically the rule of thumb here is: be honest. It is fine to split an idea across multiple papers; my advisor has suggested doing this a few times, and it's worked out well. But if you are doing anything to mislead the reviewers, then you have a problem of misconduct.

  I have realized that, the systematic framework I have applied in Paper 1 can be a more generic framework, applying to different scenarios for different application purposes...I have written another Paper 2 discussing this generality aspect of the framework, with the simplified yet slightly different experimental setting as a case study for the framework.

Congratulations on this realization!
This sounds like a significant advancement over your Paper 1, and it constitutes research progress. So there is no ethical issue with writing the second paper.

  Also, while paper 1's still under review, I have submitted an ArXiv preprint. All similarities in paper 2 compared to paper 1 are properly cited, noted and discussed if necessary, when writing paper 2.

Great! It sounds like you have already taken the right steps here.

  So the question is, is it OK to have this paper 2 submitted to another conference (an automation conference vs. the previous cs one) for review? Is paper 2 considered to be an "unethical salami slicing"?

It is OK, since you have cited paper 1 and made it clear this builds on it. Now, it is up to the reviewers to decide whether it is too much overlap to be novel. You may find that the reviewers love the idea, or maybe they will say it's not clear to them how it is an advancement over paper 1. Either way, it is perfectly ethical to submit and see what they think, assuming you have been honest and professional.

For comparison, here are some examples of ethical behavior (roughly taken from experience):

We have a new idea, which we write up in Paper A and submit as an invited contribution. At the same time, we are working on an application that uses the idea from A, and in order to make the paper self-contained we need to explain some things about that idea. We write Paper B which applies the idea, and we put Paper A on arXiv and cite it in Paper B. Paper B has a section on the new idea and explains clearly that this idea was originally proposed in Paper A.
We have a paper which is too long and needs better motivation, so we decide to split it into two papers instead as part of the paper is not really helping the reviewers like it anyway. We write Paper A which basically contains the bulk of the original paper minus one section which studies a particular theoretical aspect. Then we write Paper B which studies the theoretical aspect. We rephrase Paper B to only contain the parts that were specific to that aspect, and remove parts related to Paper A, so that the papers no longer have any overlap.


Can I present the results of a paper that is currently under review?

The only problem of presenting results that are not published is if someone else steals the results and writes their own paper about them. (Though this probably more likely only happens with ideas that are shared too prematurely.)

It is generally considered a good thing to promote one’s own work, and one way of doing this is by giving presentations at other universities.

Even if this work is under review at a different conference, I don’t think it is problematic. When presenting a paper at a conference, you are not necessarily obliged to talk about precisely the contents of the paper. You are advertising the paper, and more generally, your own work, so that people will read it and cite it. If you have bigger and better results, then these will help with your promotion of your own work.

Of course it would be weird, though probably not wrong, to talk entirely about a different paper when presenting at a conference.


How to tell my current project adviser that I want to try working with someone else next semester?

There is a famous quote "The bitterest truth was always better than the sweetest lie". You should always the truth, just tell the whole stories about how you are interested in prof 2 but still want prof 1 for your current project that you initiated together. As a professor, he is a professional academician, so he should be able to accept whatever you said as long as you convey it truthfully. Academician always know that working with different people is always better than sticking to only one. Do your best and good luck.


Usage of a web application that I sold for an academic project: Copyright issues?

After your clarifications, I don't see that from the point of view of the company, you did anything wrong. Since you sold them the application and not the source code and since you didn't transfer your copyrights to them, or signed any contract saying you will not resell/reuse the app, there is no issue.

From the point of view of your university, it really depends. You reused previous work for your project and you will find people arguing on both sides of whether that's ethical (check Is reusing old code for a new assignment considered self plagiarism? How to protect yourself if you consider it to be, and a group partner does not?). In my opinion, it is not the best thing you can do because you are supposed to learn something new in your master thesis, but personally I don't find it unethical.

Moreover, your supervisor(s) must have realized it when you showed up with a finished/polished product, with a designer on the acknowledgments and without asking him/her any questions on how to get there. If he/she didn't realize, then he/she didn't really care.

If this is really eating you up, you can have someone else (maybe a current student at the same institute) send an email to your past supervisor and asking if it's OK to use material from previous work in ones master thesis. In any case, don't beat up yourself.


Should students have access to past exams or an exam bank?

As a professor, one has to assume that all past exam questions are available to students. Some student organizations debrief members after exams and capture the questions for such an exam bank.

Some professors realize this and take action accordingly, not reusing questions, or not using enough of them to matter substantially. Others think, probably mistakenly, that they can set rules forbidding the use of such "resources". The rules will be broken by at least some of the students. I don't know of any effective way to actually prevent access to old questions. So, just assume that they are available.

My own opinion is that the professor should just assume that it will happen and, if they want to make the test taking "fair" will make old exams available for study. Some even go so far as to give out the final exam on the first day of class, to be taken later, though I suspect that not many do that.

But old exams are useful for honest students to study from if they don't expect to get those questions on their own exams.

Of course, coming up with new questions each term/year adds a bit of work, but if the course is so "stagnant" that an exam from a few years ago is still being reused then the prof needs to do a better job.


Is it possible to be known in academia by a different name?

My answer to another question applies equally here:

Regardless of what your ID card says, you can publish your papers under whatever name you want. Some people use pseudonyms. Much more common is that many women continue to publish under their maiden name when they marry and change their surname.
There's no reason you can't publish papers as [Jake].


Do I call my supervisor “dean” or “professor”?

If you don't want to ask him directly (the easy solution), you could always ask other students what they do.  In general, I would stick to "Professor Smith."  People don't have be called by their full titles (I would never want or expect to be called "Associate Professor Webster").


Citing propositions etc. in a master's thesis

Including propositions from elsewhere with just a generic remark at the start of the chapter is risky, and I would strongly advise against it.

In particular when it comes to proofs this makes it very difficult to see what is going on: Are you providing your own proofs for statements deemed to be "obvious" in the paper? Are you expanding a proof from the source? Are you merely paraphrasing?

For propositions, a rather elegant way that does not impact the writing flow would be:

\begin{proposition}[\cite[Proposition XX]{source}]

...

\end{proposition}

For proofs, you can just put a sentence outlining the extent of your contribution at the start, where it also does not break the flow.


faculty position: personal statement in the cover letter of a job application

Yes.  Search committees are very sensitive to what are called "two-body problems".


How to get my humanities paper published in the short timeframe before admissions deadline?

Journal review times in the humanities tend to be longish and I doubt that you'd have a paper accepted in a journal of sufficient quality to impress anybody. (I just got back yesterday a round of comments from a paper I submitted in September.) If I were you, I'd maybe try to submit a paper to a graduate conference instead. Look around for Ph.D. granting programs in your field in the area and send them a paper/abstract. It's much less work for you to write up an abstract, and a much higher likelihood of actually getting something accepted in a reasonable timeframe. An undergrad getting something into a grad conference is probably sufficient to make the committees think you've got potential as a researcher. Maybe it isn't quite as impressive to have a presentation as a publication, but I doubt that'd be a big factor here. To get accepted to a grad program, you just have to get past a threshold of potential, and doing something that puts you way, way above that threshold (publication in a reputable professional journal) just isn't really any more helpful to getting accepted than doing something that just barely puts you above that threshold (a grad conference presentation).

One exception here: if you have a paper or something that one of your profs was just raving about and told you that you just have to publish it in Such And Such Journal, then yeah, maybe shoot it off, but don't expect it to get picked up in time to make a difference in your apps.


How to earn a Bachelor or Master without attendance?

It is already possible to do that to some extent in many US universities, these are called majors and minors, in your case it would be having multiple majors. Yes you can use the same credits for different degrees but there are only a limited amount of overlapping credits in our related fields. Additionally, I think it will be more complicated to have majors across colleges. Bottom line is that you can only "reuse" a limited amount of credits, so you will still have to take many exams to get the additional credits, regardless of whether attendance is required or not, because you also have distance learning that doesn't require attendance.


PhD student, issued contract at year 3 which will sign over intellectual property. Is it legal?

Legally, you can't be made to sign a retrospective, retroactive contract.

Professionally, if your supervisor or the university person responsible for the CASE studentships decided to be obnoxious about it, they could make the completion of your PhD uncomfortable.

As long as you don't need the CASE money or the on-site experience, this looks like a useless deal for you; in your shoes, I'd be minded to talk to my supervisors, then the faculty graduate tutor. Explain without emotion that you didn't sign up for a CASE studentship; ask if they can give you a good reason why you should sign up, because from where you are, it's hard to see any value in it.

They won't want to stop you finishing. You're EPSRC-funded, and having EPSRC-funded students fail to finish causes a problem for the department when it seeks a renewal of the funding. So you do hold quite a lot of the cards, here.

Ultimately, it's going to be a negotiation. It would be very surprising, and rather irregular, if they did sign up with the sponsor having given the sponsor the belief that this contract will retroactively apply to all current PhD students: I've only seen the terms and conditions apply to those students who start their PhD as CASE students. My hunch is that it's more that someone is just trying to get something for nothing - a free rider.


She's been really nice after this, and complimenting me on small things, but I'm not sure how to go forward.

It shows that she realized you have been stressed out, and she is willing to be helpful to make you feel better as a new student. Do not think too much. Work well. Respect her and be nice to her (really mean that. not pretend).

As time passes, the event will be forgotten and forgiven (if needed). Since you are fairly new, you will eventually get to know her more. At that time, you will be in a better position to see what went wrong and what made you lose your cool.

Also offer to proactively fix the situation. Apologies by word mean nothing. Show it in action.


From whom do I get references when my original advisor leaves academia?

Your current advisor's letters are killing you.  Do not ask him for any more letters.  Do not list him as a reference in your CV.  Don't walk; run.

  I will add here that I have a number of publications (>5) including single authored ones-which for my field is significant- as well as an excellent track record of funding and in presenting my research.

In that case, you really should have no trouble finding enough other good references to overcome any concerns raised by not having a letter from either of your advisors.  Everyone reads advisor letters with a grain of salt anyway; strong letters from well-known senior researchers outside your home department have much bigger impact.

Of course, if anyone asks why your current advisor isn't writing you letters, you should answer honestly, but I think adding an explanatory note in advance is unnecessarily defensive.


How can I deal with a significant flaw I found in my previous supervisor’s paper?

Two suggestions:

You found that someone was wrong in a good journal.  The fact that the error was published in a good journal does not mean that it is worth working on.  You should decide if this error is really worthy of your research efforts.  It might be better for you to work on something more important.
If you decide to pursue the error, you can choose to present your correction as a new idea.  If you tell people that you have found a new idea that advances the state of the art, that makes you look good.  If you tell people you have found someone else's error, that makes the other person look bad but may fail to make you look good.  The actual substance of the research can be the same, but the way you present it makes a world of difference in how it is viewed.


How credible is an application for a PhD in Computational Fluid Dynamics from an MSc in Computer Science?

If at the moment you didn't take any courses in physics and fluid mechanics yet then I think your chances are close to zero.

However, you mentioned that you still have 2 years to go on your MSc program. In that case you still have 2 years to 'reshape' yourself for such a position. I would approach this endeavor in 3 steps:

Talk to professors with (open) PhD positions in CFD and ask them what courses they think are prerequisite for the positions that they have. Also ask what courses would be desirable/helpful.
Take ALL of the prerequisite courses they mentioned and as many of the desirable ones as possible. Either take them as electives for your current program or just on top of it. This might seem like a lot of work, and it probably is, but if you are serious about the PhD in CFD then this will actually help in your application process, because it shows that you are committed.
In many MSc programs you will have some big project at the end. If that is the case for you as well, make it a CFD project for a professor with PhD projects available. Give it your all and you might be able to 'network' your way into one of his/her positions.


I don't see much value in a letter from an old relationship that is no longer relevant. Your recent work will almost certainly be considered more heavily than anything you did as an undergraduate. (Extraordinary cases aside.)
Get letters from those who know your work and can make a (positive) prediction about your likelihood of success in the new program. That probably means professors and/or advisors from your MS program.


How to find the best journal to submit a paper to (when having written the title, abstact and full text)?

You need to know your field.  Part of knowing your field is reading lots of papers.  This should give you an idea of what kinds of papers each of the major journals publishes, and what journal may be best suited to you.  If you're a good researchers, you ought to already know what are the main journals that publish research in your area.  If you don't already know that, then maybe you need to spend more time reading published work first.

In particular, the best way to figure out if a particular journal is a good fit for your paper is to read a bunch of papers published at that journal.  That will give you a pretty good sense.  You can use the "call for papers" as a further sanity check, but nothing substitutes for reading what else they have published.

There is no shortcut.  If you are a knowledgeable about your field, a random webpage is not going to know your field better than you do.  If you are not knowledgeable about your field, then the first thing you need to do is to fix that.


Same citation in multiple paragraphs (undergrad paper)

How about, assuming that [1] was written by Smith:

Smith notes, that ....... [1, p. 42]

Furthermore, Smith asserts that .... [1, p. 13]

Smith is also of the opinion that .... [1, p. 92]

You want to give the EXACT reference so that your reader can find it. And you want to clearly mark what is from you and what is from Smith. It goes without saying that the text in your paragraphs MUST be in your own words and not copied from Smith. Otherwise you need quotation marks.


Is it good to publish a research paper with many partially answered questions with sub-optimal results?

This depends on many things. Most important is the significance of the questions themselves and whether the partial solutions add anything beyond standard techniques. The questions can be "challenging" without being significant, of course. Do they lead to other things, for example.

If your solution techniques are standard, then they won't add much either, but if you have developed a new way of looking at such problems, then it could be very important.

"Almost half a year" doesn't sound very long, actually, for the stage you are at.

Your advisor should give you good advice here. He or she is more familiar with your problem and your attack and degree of attainment.

However, I come down a bit on the side of waiting to publish. For one thing, if you publish partial results it may lead others to join the search for solutions in competition with you, perhaps denying you a more significant publication (or even a dissertation) in the future.

If it makes sense to separate them, having four or five papers, each with a complete solution would be much better for you than rushing now. The publishing venue is likely to be more prestigious, and also more likely to accept complete results.

Carry on.


How deal with an innovation from outside academia

I would recommend e-mailing the authors of the original paper. (In general contact information for academics can be very easily found via googling.) Briefly explain your discovery and pose your questions.

In general, such e-mails are quite welcome in academia. There is some possibility you might get no response, but I think it is likely that you will get a polite response, and that the authors will be encouraging and helpful if your work is worth publishing.

If you don't want to do much of the grunt work yourself, you may be able to coauthor the paper with the authors and/or others whom the authors might put you in touch with. (But don't propose this until you get an initial positive response.)

Good luck!


How do I specify my affiliation/contact information when I changed institutions and fields?

If you have the opportunity to be clear (that is, some limited online form doesn't prevent it) explain the transition "Jon Barker, formerly of Acme Corp, now with Zypppy Inc. JB@Zypppy.com". Or something similar.

The reason for the email is so that people can contact you, so use the current one even if it seems weird. Using an obsolete mail does no one any good.

If the former employer/institution contributed funds to the project it is usually good etiquette to indicate that you were associated with them then. But for identification purposes, your current affiliation is more valuable. But if it is a paper with multiple authors, some still at Acme, then it is less important to list an old affiliation (my opinion only).

There may even be reasons that you must not imply an affiliation that no longer exists, but that is fairly rare. If you can only give a single affiliation, it is probably best in most cases to list your current one. I suspect such a rule has many possible exceptions, but I'd suggest thinking about why you think you have an exceptional case.


This is a really important question, and it's one that isn't asked enough.

From reading your question, though, it sounds like you are rushing a bit. Renowned physicist and biologist Uri Alon (34k+ citations) has written an excellent paper on 'How To Choose a Good Scientific Problem' and one of his main points is that one, however cliché it sounds, should take ones time to conceive a good project.

I strongly suggest you read his paper. It's not exhaustingly long, and reads like a good talk. He also has a TED talk that challenges the 'A to B' dogma in science, which has helped me a lot.


Advice needed : Reaching out to your past PhD advisor for a post doc opportunity

I think that reaching out and asking never hurts. The worst case is that they say no. Just explain your current situation, and why you're reaching out so late.
Do expect a rejection, not because of any issues they may have had with you in the past, but rather because postdocs are not cheap, and taking on an unplanned group member is never easy to do. This has nothing to do with your performance, just that hiring someone requires a budget and time to work with them.
If they agree to interview you and discuss your options, explain your plan for how to make things work this time around: alleviate any concerns they might have about hiring you. Treat this like you would any other interview, and come prepared.
You should not expect them to take you out of the kindness of their heart.
Show them how you can make their research better.
If you do an impressive enough job at that interview, and they have no opening, they may still offer you options that do not require them to hire you. For example, there may be teaching positions in the university or relevant industry jobs that they may be aware of and whose profile you fit.
Good luck!


spending time to get into top school PhD vs getting done with PhD

I think you are vastly overestimating the value of ratings from a popular magazine as they apply to doctoral education and vastly underestimating the quality of doctoral education at any R1 in Texas.

Frankly the real difference, in an individual field between a school rated 180 and one rated, say, 40 is likely to be a mix of random and the value of a given helpful advisor.

Frankly, I think you would be wasting your time to do much of anything but take what looks like a very nice offer. You'd be halfway through a doctorate at the Texas place before you had a chance to start if you go another route. If you read a lot of questions on this site you'd notice how lucky you would be to have found a good and supportive advisor. Many are not so lucky. Who can say whether you'd have a better time of it if you look elsewhere?

And it is you that makes your career, not the journalist/researchers at US News rating places on general criteria.


Rights of authors who withdraw peer reviewed manuscript due to refusal to transfer copyright

The authors should check when the journal transfers copyright. As mentioned by Andrés E. Caicedo in the comments, some journals assume the authors transfer copyright once a paper is submitted, not after acceptance.

If the authors withdraw a paper because they do not want to transfer the copyright, the journal's likely reaction would be to remind the author about the possibility of publishing open access. If the authors decline that too, then the journal will probably think, "why did you submit it to us then?" Getting the paper reviewed involves a nontrivial amount of effort. If the journal decides the authors submitted the paper knowing that they will withdraw it if it's accepted, effectively wasting the journal's time, they might blacklist the authors.

As for what happens to the peer reviews, from the journal's perspective, nothing. The reviews are left on the manuscript's record, of course, but nothing beyond that. The authors will still have access to them, and they can do whatever they want with them (such as use it to improve their manuscript). They should not, however, present them to another journal. As I wrote in an answer to another question, these reviews don't help the new journal:

  We can't use the original journal's reviewer comments & your responses. We don't know who the reviewers are. We can't tell if the reports are legitimate. We can't see if confidential comments were submitted.


Why is getting your PhD in Iran invalid for obtaining a post-doc position in the US?

I think the answer is simple: your premise is false. There are no rules/regulations forbidding an Iranian earned PhD from being a postdoc in the US.

It might be hard to get a postdoc in the US for anyone whose academic background, and PhD earning institution, is not perceived as highly ranked.

Note: I have answered this a year and a half ago. Things may have changed since then through the presidential ban against Iranians entering the US. I have no specific knowledge of the current situation with respect to Iranian students.


Should I include proofs for known theorems in a doctoral thesis in mathematics?

This is something you should discuss with your adviser. It really should depend on the theorems; how important is including their proofs to the understanding of what one has done? Also, how long are their proofs? And how much is your own work using proofs which build off of those theorems? There's no simply response here. You'll see both dissertations and papers where relevant theorems have their proofs included, and others where they are referenced.


Should I tell an editor that I believe an article I'm reviewing is not good enough for the journal?

Referees and/or editors should not invite the authors to submit a revised version unless there's a real chance that the revision will be accepted.  Also, most things could be made significantly better than they are.  If your feeling is that the paper, even though not flawed in any way, does not meet the standards of the journal, then I think you should recommend rejection unless you can identify explicitly which improvements would change your mind.  Even then, in a field with a sufficiently large number of reputable/good/great/... journals (my own field, mathematics, is certainly like this), it would be reasonable to suggest improvements that could make the paper suitable for a journal of the caliber submitted to while rejecting the paper.  A top journal is going to get more than enough papers that are good in every way than it can publish.   And finally, if you revise and improve your paper enough then at a certain point you can justly claim that it's not the same paper.  Nothing stops authors from submitting the new, better paper to the same journal.  (Once I was added as a coauthor on a paper after the first version was rejected by a strong journal in the field.  I saw how to improve the paper so significantly that I thought: why not send it back to the same journal?  They accepted it.)

Having said all that: from the comments it doesn't sound like the authors spent much time and effort making significant improvements to their paper.  So while there may have been a miscommunication of some sort among you, the editors and the authors, it doesn't seem to have caused much harm to them.  In my opinion you should reject the paper for the reasons that you say: there's nothing wrong with it, but it's not good enough for the journal.  A top journal must reject many papers for this reason -- that's what makes it a top journal.

(If they had spent a lot of time and effort: well, I would feel bad about it if I were you, but it doesn't really change the decision to reject the paper.  Anyway the time they spent improving their paper did after all result in an improved paper, which they can then submit to another journal.)

Maybe the lesson is to be more clear in the future.  It feels nice to give people a chance, but in fact you're being asked to apply your professional judgment in a way that's going to have a negative outcome much of the time.  When your judgment is negative, the nicest you can be is to deliver the bad news relatively quickly and with sufficient justification.

Finally, the fact that the editors asked you to referee it again might or might not mean that they are more positive about the paper than you -- you have no way of knowing.  Anyway, their opinions are their opinions, but they're asking you for yours.  Once or twice I have been asked to referee a second draft of a paper that I recommended for rejection the first time.  I did look at the revised versions, quickly, but my answer was essentially: "I told you that I didn't think the paper was suitable for your journal.  If you disagree, okay: ask someone else to look at it."


Is is possible to study mathematics PHD with another bachelor degree like Business Administration?

The short answer is: "yes, but it won't automatically be easy"

First, every department of every school in every major has a set of preferences - things they like to see in an applicant. This list includes GPA, GRE, sometimes subject-specific GRE, specific coursework, specific reference letters, and the rarely-ever-listed undergraduate research/term papers that lots of people here give great advice about but that I didn't previously know was a 'thing'.

Looking over the admittance pages of prospective programs can give you an idea of this at times. In your case, I looked at a few schools math departments I'm familiar with, and using this one as an example because its not terribly atypical (but you should research your own preferred institutions): University of Wisconsin Mathematics

  1) A GPA of at least 3.0 overall and substantially higher in mathematics courses.

  2) 18 or more credits of mathematics beyond calculus. The 18 credits should include at least one semester of both rigorous analysis
  (sometimes called advanced calculus) and abstract algebra, and
  preferably two semesters. Advanced undergraduate courses in other
  topics further strengthen your application.

  6) A “Supplemental Application Form” is required after submitting your
  online Graduate School application. It is important that you include
  all advanced mathematics courses you have completed, are currently
  enrolled in, or intend to take...

  7) Three letters that address the question of mathematical promise.
  These letters should be from mathematics faculty, or other faculty
  familiar with the demands of graduate work in mathematics...

Now keep in mind that any published outlines are a "wishlist", and they don't automatically toss anyone. But every area you don't fit requires explanation or some other counter-balancing factor. Some programs give a list of x requirements, then say they'll waive 1-2 of them without further explanation needed, etc.

If you are missing all of these, then you need to look at a different program, but you might find no program that's a fit. If this happens, that doesn't mean you can't do something, just that you might have to go about it sideways or backtrack a bit.

If you are missing just a few things, like a course or two, some programs have probation where they'll tentatively admit you on the demand you complete X courses on your first semester and get at least Y GPA, etc.

Alternatively, you might need to make arrangements to take advanced math courses at an undergrad/graduate level. It's harder to get financial aid for this sort of thing (you can't qualify for a Pell grant anymore, etc), but you can still get loans or pay for it outright. If you need this route, you need to talk personally with professors in advance to discuss what your goals are and make any possible arrangement to do extra work, write an academic research paper, etc. You need to find people you can have enough contact with to be willing to go to bat for you in writing strong reference letters if you don't already have math professors who are familiar with your past work. Join math clubs, go to math study labs, volunteer, whatever you can manage.

Before you go running off and doing any of this, however, you should make contact with math faculty at your present school and/or at a target school, and get an opportunity to talk with them about what you want to do and get their advice. Sometimes just showing "mathematical promise" can get a magic wand waived over your application, which maybe you already have - but only someone familiar with what you've done can tell you that. If you have a piece of mathematical "best work" from your most advanced class, bring it with you to such a meeting.

Once you've gotten a few honest appraisals of where you stand, be kind to yourself in looking for programs that will fit YOU, not some imaginary ideal program for someone else.

Finally, one last piece of advice. Keep your mind open to hybrid possibilities. There are whole fields of study you might really like that you aren't aware of, including applied mathematics study offered by business schools, economic fields that emphasize mathematical theory and/or application, etc.

Sometimes we have to try to mold ourselves to fit an existing mold a little better, but sometimes its trying to fit a square peg into a round hole. Talk to people and investigate the possibilities, get a clearer understanding of your relative shape, and seek out openings with geometry congruent to yours. Good luck in your journey!


Is the idea of "boarding university" still a formal policy?

In the United States, it tends to depend strongly on the particular university and the population that it aims to serve.  In general, the more local and "non-traditional" that students are expected to be, the less that a university will feel obligated to assist in the arrangement of housing and board.

Thus, for example, a place like Williams College, where the students are mostly "traditional" undergraduates coming from far away to a small isolated town in the mountains, expects to house, board, and provide a full campus life for essentially all of its students.

At the opposite end of the spectrum there are places like Suffolk University, which is in the middle of a big city (Boston) and historically focused strongly on professional postgraduate education and on students enhancing their education later in life.  Suffolk doesn't even have a campus per se---it just has about a dozen buildings scattered around the center of Boston, and until quite recently did not have any dormitories at all.

Across the whole spectrum, most administrations will consider it their responsibility to provide a rich intellectual environment for students both inside and outside of the classroom, e.g., by supporting student groups.  The degree to which this happens "on campus" and with direct university investment varies greatly depending on circumstance.  No university in America, however, will attempt to confine students to a campus---some merely recognize that geography makes it more difficult for their students to leave.


Asking for a recommendation letter from an open source repository mentor

Go for it.

I had the doubts like you earlier. But changed my mind after talking to one of my mentors. He fits all your above descriptions. He said, he would be happy to give a recommendation letter to his Google Summer of Code (a remote open source summer internship sponsored by Google) students who performed exceptionally.

While you do not have a student-professor relationship, he might be the only professor that ever witnessed you coding in a professional environment. He might have noticed your positive sides that other professors will never have the chance to find (except on academic projects).

Just ask. It won't hurt. If the professor feels he does not know you enough, he will let you know.


Does peer-reviewing for journals/conferences which advertise to attract reviewers; harm one's academic reputation?

I am hard-pressed to imagine a situation in which reviewing would hurt your reputation. It does pay, as your question hints, to check up on the journal you'd be reviewing for to be sure it isn't scammy, but asking for reviewers isn't much indication one way or the other -- almost every journal needs a stable of willing reviewers, and what harm does asking do?

Yes, editors do choose reviewers for a given paper as carefully as we can, but we mostly haven't the luxury of "who's the most famous person working in this area?" because Most Famous Person is swamped. So we keep a stable of folks who have signed up with us, and we look through it for potential reviewers.


Reviewers and incorrect article references - Do they adjust them?

Peer reviewers never make changes to the paper they review. It is not their task to do so, and they do not have the means anyway.

If they do notice mistakes, they will ask the author(s) to fix them. For mistakes such as minor errors in references, I consider it unlikely that the reviewers will notice them at all. If I want to check out a reference, I will either go by doi or the provided link, or simply google author + title -- thus, I wouldn't notice a wrong volume number.

In some journals, the editing staff might check and adjust references. They would then just make a note of that in the page proofs, such that the author(s) can check that the changes are indeed correct.


What can I do if I wrote a grant proposal with a professor, and now that it is funded he refuses to hire me?

There are at least three possible explanations as why the professor told you he was not going to hire you for the up-coming project,

He wants to do it by himself.
He wants to hire somebody else who has similar qualifications and research capabilities to do it with less salary.
He wants to hire you with the salary less than listed on the proposal budget section to do it.

The first possibility is unlikely because he has no idea what you are doing.

The second one and the third one are equally likely. Both are for the reason that he wants a bigger share of the pie. I cannot tell which one is more likely because you did not get his explanation.

If he did not have a candidate to replace you yet, I guess the reason he said he was not going to hire you was an attempt to negotiate the salary. In other words, he wants you to take a pay cut.

I would suggest you to approach him by a face-to-face meeting if you really want to work with him on this project. During the meeting, politely ask him to explain to you why he was not going to hire you for the project. If he ever expresses the desire to cut your salary, then it's up to you whether to accept the offer.

There could be a fourth possibility that he did not want to hire you because the relationship between you is bad. I exclude this one for now because there is no strong indication in your question that this is the case (otherwise he would not ask you to write the proposal in the first place). If indeed the relationship is bad, you'll need to figure out how to repair it if you want to work with him.


What is a proper balance between reading research papers and reading books?

I make a simple distinction based on what I'm looking for. Essentially, am I tackling a problem that I know about, or am I looking for a new problem/area to expand into?

I'd suggest you to have atleast this broad an idea before dipping into any material, otherwise you may easily get lost in the sea of information available today. The risk of getting too deep into something and forgetting why you got there on the first place is very real.

EDIT: For this problem, I'd recommend taking a look at this question.

Now, if a problem is known, I'd go straight to research papers and get an idea of what approach people follow, what is being tried, what gap areas exist, and so on. I'd go to a book only if (a) it is referenced in a part of the paper I find relevant, or (b) the explanation proposed hinges on something I know very little of. In (b), a book is good because typically it is written in a more pedagogical style and hence easier to understand.

On the other hand, if I'm looking for an area to expand into, I'd first consult books on related topics to acquire some understanding before jumping in to literature. Yes, it is time consuming, and reading papers directly seems like a shortcut ('you anyway need to read them once you select your problem, so why not start there'). Nevertheless, I personally believe that a firm understanding at the beginning is necessary to attempt formulating your problem.

Just to reinforce, let us consider these two situations and see what happens if we reverse the approaches.

(a) You know the problem already, but start off with a textbook- you will spend a lot of time reading. Since a good book is engaging, you will find it hard to put down, and may start jumping from the chapter you were interested in to another chapter that is referenced somewhere (another quality of good books). At the end, you've spent a lot of time, gathered a lot of information and hopefully some knowledge, but you are no further on your research problem.

(b) You don't know a field, but start reading literature- you may get lost in jargon. Also, you may think a contextual statement is generally valid, leading to misconceptions. Finally, you will rely completely on the approach and methodology of a particular author with a particular agenda (i.e. to advance a particular viewpoint/theory) and therefore adopt all his/her biases. A book will generally be written in a neutral way (the agenda is to disseminate information), which will help you to critically analyse any research result.


Google Scholar Public Access new feature and lost citations

I did the same yesterday, with exactly the same effect.
The good news: One day later, the lost citations are back.


Does equipment purchased with grants stay with the PI?

The fate of equipment purchased with research funds generally follows one of three trajectories:

Small common equipment below a certain threshold of cost is typically categorized as something like "office/lab supplies" and is effectively treated as part of the overhead costs of doing research.  Different organizations have different ways of categorizing and budgeting such equipment, but it generally includes things like laptops, pipettes, staplers, etc.  These items will be owned by the research organization, but below some threshold they are ignored and treated as being owned by individual researchers (they care about your pipette, but nobody's going to track your pencils).
Specialized and/or costly equipment typically belongs to the funder of the project, unless specified otherwise as part of the contract.  For example, the US government almost always retains ownership of equipment purchased using research contract funds.  After a research contract ends, one of two things happens with such equipment:

A. The equipment remains in the hands of the organization, either rolled over into use by another contract or simply ignored and abandoned by the funder.  In my experience, this is by far the most common outcome with research equipment, since it is generally useless to others and/or difficult to transfer, and the funder is often not interested in holding it in inventory.

B. The funder requests that the equipment be shipped back to it.  This is most likely to happen when the funder is concerned about alternate uses that the equipment might be put to (e.g., supporting an industrial competitor) or is planning to give it to another organization.

One of the common frustrations is that it's often difficult to tell whether you're dealing with 2A or 2B, especially when dealing with the government, which may take years to get around to requesting something back.  In the meantime, the organization still needs to track and maintain custody as though expecting the funder to want the equipment back.

Now, in all cases, the PI does not own the equipment, but if it is worthwhile to transfer a piece of funder-owned equipment to a new organization, the funder may be quite willing to do so, just as they may be willing to transfer funds to follow the PI.


Can I negotiate an acceptance to print delay, post acceptance?

It's hard to tell from the outside why they aren't posting online versions of your accepted paper now. If the publisher is the root cause, you could conceivably change their mind by negotiation. I would not be hopeful because they're likely to keep to the status quo purely out of inertia, but your objection would probably be filed away as a data point for when they finally decide to modernize.

On the other hand if the editor-in-chief is the root cause, the publisher is not likely to overrule the editor-in-chief, and you'll have to convince the EiC. Chances are the EiC has entrenched views of this (as opposed to the publisher who's more likely to simply be doing what they've always been doing), which makes convincing him/her harder. Still, you could try. Be sure to mention you have follow-up work already lined up.

It's unlikely that there'll be negative consequences for trying and failing. Your paper's already accepted; they're not going to rescind it for non-academic reasons.

One thing I would definitely check is whether you are permitted to upload preprints. You mention there's an embargo, but quite often the embargo is only on the accepted manuscript. You can still post preprints. Some publishers (e.g. Elsevier) allow you to post the accepted manuscript as well, on a non-commercial personal homepage or blog.

Edit: based on that paragraph, negotiation is the only way out, because they're preventing you from making anything else publicly available. If you have transferred your copyright then they can actually publish without your consent now (still, they might let you withdraw anyway as a gesture of goodwill). You say you haven't signed any copyright transfer, but that's not sufficient; the journal might have policies that say the copyright is automatically transferred upon acceptance or even upon submission. You'll have to check. If you haven't transferred the copyright, then you could withdraw and submit elsewhere. It's a decision you'll have to make.


To include only academic titles in business cards of researchers with many positions?

I am thinking to exlude all positions, and just having your academic titles because I do not want to carry a pile of different business cards and in many languages

That seems like a somewhat bad idea. The main goal of a business card is to serve as a reminder for the recipient of the card who you were once the conference or event where the card was given out is over. Hence, the more specific the information on it is, the better. "PhD" or "MD" usually carries really little information, as many people at the events that you frequent will have the same titles. "Works at IBM" or "Associate Prof at UCLA" is much, much better in that sense. Your job title(s) are also a much more fine-grained representation of your seniority than your academic titles. The holder of a PhD can be anything from a freshly-minted graduate to a senior professor, while saying "Associate Prof" transports a lot more meaning.

Further, many employers will actually not be thrilled about you rolling your own business cards. Employers typically have a specific corporate identity, and expect you to use that (and not mention your other gigs on their cards).

So what do you do?

Get separate business cards for all your major affiliations. These may include all your titles if customary, and only the job title and branding of this specific affiliation. You probably don't need a card for company X just because you are in the advisory board, or for university Y because you teach a course as external lecturer once a year. If you have multiple major affiliations, decide who you represent in any specific event, and use these cards (a good proxy for this might be who you are charging the event to, time-wise and financially). You can always verbally add your other major job(s) when handing out the card.


How long does it take for a citation to show up online?

Google Scholar, Web of Knowledge, Scopus and other indexing services have their own ways how the papers get into their database. For Scopus, the journal has to be registered there, and then actively send the data. It's similar for Web of Knowledge I think. Google gets the data from who-knows-where and I doubt you can control it efficiently. In general, it takes couple weeks to several months.

As dgraziotin pointed out in comments, Google Scholar indexes citations from arXiv quite quickly, in couple days. However, by many people and many institutions, arXiv papers are not considered at all regarding citations, unless they are published properly elsewhere and properly Journal-ref'ed; even then, many people don't trust that the arXiv version is correct, because nobody makes any check of this (I mean, you can put whatever Journal-ref to whatever your arXiv paper, so it's not trusted).


MS student in CS meeting advisor for the first time in person (USA). What should I wear? (male)

I've never even visited any universities in that part of the country, but I think your comfortable shorts/T-shirt should be perfect for a cookout in any part of the country.  For the first impression, make sure you choose something comfortable.  I think dress shoes would probably be overkill.  However, a short-sleeved button shirt (i.e. tailored shirt with a collar) would be a nice touch.  Do you have some sort of sports shoes?  That would be a happy medium between dress shoes and flip flops.  If not, I'd go with the dress shoes.

If you ask what food to take to the cookout, I'll chime in on that one too.


There is another option for you, of course, which is a regular position in a non-research oriented institution. In the US, most undergraduate colleges require some research but with lower intensity than at research institutions. Teaching is highly valued and helping undergraduates get started in research, even if not  publishable is also important.

There are, in fact, many fine such colleges and they do send students to graduate school as well as into industry. You might spend some of your effort in exploring such opportunities.

But, in general, institutions don't depend on narrow criteria in hiring. There are a lot of things that can influence a decision. Your current experience as an assistant professor can be a help if it is successful. Depending on your field and the level at which you enter employment, your past publication record may have more or less impact.


Is it okay to upload the PDF of my non-open access papers in academia.edu or research gate?

The current best source for answers to this question is the SHERPA/RoMEO database, which categorizes all journals by their policies.

This tells you, for most respectable journals, what you are legally allowed to do in terms of posting versions of the paper on other sites (this may, of course, be modified by local laws; for example, documents produced by US government employees are not generally protected by copyright).

For a large number of journals, you are at least legally allowed to post preprints.  In such a case, I see no advantage in flouting the law by publishing the journal's final version instead: I believe a preprint is generally sufficient to make your work more readily accessible and gain you the open access citation benefits.

As for journals that do not allow you to post preprints: you need to make your own moral and personal judgement on whether you will submit to such journals at all, and if so, the degree to which you will comply with the law.


Is it rude not to attend courses which have no attendance requirements?

I think the question is not "Is it rude?" but "Do lecturers find it ok?" as the answer to the latter is not universal but varies a lot.

Here is what I think about students skipping classes: Personally, I also do not have any attendance requirements (actually, where I am it is currently forbidden to have such requirements) for my classes and there are students who skip some or most classes. Since I do not have such requirement, I am not mad at them, but I note that they miss opportunities to get into a dialogue about the contents which help them learning the material deeper. I do get mad when these students come to office hours asking for clarifications of stuff I treated in the lecture since this basically amounts to unnecessarily teaching the stuff double. When I note that students skip many classes I get thinking "Hmm, let's see how they manage to grasp all the material…". When it comes to exams and I note that the students missed some point which has been stressed in the lectures over and over, I feel like the students really missed a crucial point (even if it is just one) just by skipping the lectures and I do not give any benefit of doubt. It's like "it was obvious that I considered this to be a central point, and you did not get it - sorry for you." However, some bright students that skipped classes managed to impress me during an exam and scored great grades.

As for not greeting students: If you haven't shown up in classes that often, your face may probably not be that familiar to the lecturer… Here in Germany we often have hundreds of students every semester so it is impossible to know the all students who are enrolled but did not show up.

As for the question What can I do to turn it around?: Show that you learned a lot by being great at exams and show that you deeply grasped the material. Do not go to office hours with questions that have likely been answered during the lectures.


How do US grad schools interpret international GPAs?

1) How do grad schools in the US interpret international GPAs?

Exactly the same way we interpret domestic GPAs!  We rely on our previous experience with applicants from your institution and our (Google-enhanced) knowledge of the content and rigor of your degree program.  After all, there's no universal interpretation of grades even within a particular country.

And as others have already said, your GPA is only one component of your application, and not necessarily even the most important.

  2) Would it be okay to address the reasons for my low GPA in SOP)personal statement briefly, like in a line or two? If so, how should I subtly go about doing it? I don't want to make an excuse and of course, don't want to blame others.

You're assuming your GPA is low enough to require explaining, but that assumption is based on a naive numerical conversion, which really isn't appropriate.  Whether your grades are actually "low" is a good question for the people who will write you letters, who presumably have some experience with the type of PhD programs you're applying to.  (Otherwise, how would they know what they're recommending you for?)  In particular: Would your GPA prevent you from getting a PhD at your current institution?

However, I do think you need to explain your lack of formal research experience ("My university didn't offer courses and a supervisor directly in my area of interest"), both as justification for your current research record and as motivation for pursuing a PhD elsewhere.

  3) Should I just give up on applying for PhDs then and focus more on the masters program, say in some Canadian universities?

No!  Never throw away opportunities until you're sure you don't have them!  If you know you want a PhD, and you believe you are qualified for a PhD, and enough people are willing to write you strong recommendation letters for PhD programs, then you should apply to PhD programs!  But if you're still worried about your chances of admission, you should also apply to some masters programs as backup.


Can't shake doubts about quality of research, but want to continue

If I have understood your question correctly, you are doubting that the methods used in Paper A (and followed in Paper B) are "correct." The question of whether or not Paper A's methods are "good enough" to get the "right" answer to this problem is an empirical one you can investigate.

You should consider proposing and writing a paper where you look at a similar problem as Paper A with two methodologies and see if there are different results. You could do what your advisor wants and also solve the problem a different way and compare. This would be a valuable contribution and would make your point for you (or not).

You could do this while also starting Paper C to make your advisor happy. You may also consider publishing Paper C with a simple method as a "first pass" and including caveats about the method and how it may be affecting the results. Then when you get the results to the comparison paper it will become obvious if Paper C also needs to use the new method, and you could publish a follow-up paper (or add to Paper C if it is not yet submitted).


Journal's website states different and much higher impact factor than what I found on Scopus. What do I do?

Short answer: Scopus have their own database of publications  calcuating citations per year, which is different to the trademarked "impact factor". There are also variations between years and between citescore and 2-year values.

Note on predatory publishers: It is common for predatory publishers to fabricate an impact factor, or come up with some variant of an official impact factor (e.g., "google impact factor"), when they do not have an official impact factor.

However, your case is different. The journal does have an official impact factor (or scopus citescore) which suggests that it probably passes some basic quality threshold. The website is simply listing a different impact factor than what you have found.

While it could be a typo, or even fraud, the most likely answer is that there are many different "impact factors".

Official impact factor: First, I believe impact factor is a trademark traditionally of ISI. But the main point is that "impact factor" in this sense refers to 2-year impact factor using a particular bibliometric database (the Web of Science, I think).
Even here, the impact factor is updated each year and there is a 2-year and a 5-year impact factor that is commonly reported (although without clarification, it should be the 2-year impact factor). So, occasionally, a journal website might be showing a slightly out of date impact factor.

Impact factor more broadly: There is a boarder concept of impact factor that relates to the general formula of dividing citations by publications over a given period. There are subtle ways that this formula can be tweaked based on what counts as a publication. In particular, the choice of database dramatically influences what publications contribute towards citation counts. The more inclusive the database, the more citations a given publication will receive, and the higher the "impact factor" will be.

The scopus metric is typically called citescore. I think the scopus metrics focus on a three year period and uses a different database (i.e.,Scopus rather than web of science) for generating citation counts. https://journalmetrics.scopus.com/ . Also see http://www.scimagojr.com/ for another set of rankings also based on Scopus.

In general, the original ISI impact factor has a certain influence in the market. Various reasons include quality control of their database of citations and the fact that they were the first big player in this space. They have also trademarked the term "impact factor", which is interesting given that the concept of dividing citations by publications is a pretty straightforward idea.

Nonetheless, the meaning of an index of citations per year is often based on benchmarks within a field. For example, researchers in a field get to know the impact factors of the journals in a given field and they form rules of thumb about what is poor, good, and great. In this sense, if you change the index, then the rules of thumb may change. For example, if you used Google Scholar to calculate impact factors, then impact factors would probably increase massively (e.g., by a factor of 2, 3, or more more), because Google Scholar is highly inclusive. So for example, a bunch of journals that had an ISI impact factor or 2, now has a GS impact factor of 6 or 7. So some care is required when using a new index to ensure that relative benchmarks are recalibrated.

Check out this review of the mapping of scopus citescores with ISI impact factors.


Refuted papers: do they belong in a literature review?

Based on the background you gave, particularly that you are writing a detailed review article, then I think you should definitely include this article.

Part of the function of a good review article is that it documents the history of scholarly thinking on the topic of question. From your explanation, this article presented an idea so apparently true that not only did some intelligent researchers study it and present it as fact, but it even passed peer review in a high-quality journal and was cited by subsequent researchers (though, of course, many people might have cited it to contradict its results). This indicates that it has played an important role in the evolution of knowledge in the area.

Think of it this way: suppose some researchers read your review article that omits this idea, and then they independently get that same idea as their own original idea. Without knowing that it has already been refuted, they waste their time conducting a study based on their ideas, and probably get negative results, to their disappointment. (Or worse, they get positive results, submit them for publication, and then get slammed in peer review for not knowing the literature.) By documenting the full body of knowledge, you can spare these hypothetical researchers all that pain.

Although my area has nothing to do with biology, I still remember in secondary school biology class learning about spontaneous generation as an early theory of genetics. I was deeply impressed by the explanation of how such a popular theory was eventually refuted by better science. That case was an important educational milestone in developing my scientific thinking. By including the refuted work in some detail (in correspondance with the amount of scholarly work spent developping and then refuting it), you could help your readers in a similar way.


Colleague demanding to add additional participant to funded grant

The grant has been awarded to you, so you are responsible for making decisions on how to allocate the funding. If a bad choice results in less success or output, this will reflect badly on you much more than it will on other grant participants. So if you do not consider that adding this person will positively contribute to the results, you should not add them.

As others mentioned in the comments, you should discuss this with your department chair, and make sure that you clearly state your opinion and give enough reasons. Your chair might have additional motivations and it could happen that they want to add this person for different reasons (which would make your situation more complicated), but likely (hopefully) they will support you in your decision.


How can I address a fail in course when applyin graduate schools?

Since 3.53 is a rather good GPA, I would say nothing about the failed course. To say something would draw attention to it, whereas with the 3.53 GPA, many evaluators would not even notice that you failed one course.

If I were a careful evaluator who noticed that one failed course, I would also notice your above-3.53 average on everything else, and would probably consider that very atypical (in the sense that I would guess that something unusually bad happened in that one case). If I really cared, then I would ask you about it in an interview; otherwise, the rest of your good record would lead me to give you the benefit of a doubt.

Of course, you cannot assume that every evaluator would take the same attitude as me, a random person on Academia Stack Exchange, but I do think that if you said anything at all (e.g. trying to excuse yourself in your motivation letter), you risk drawing attention to a negative detail that many people would not notice anyway.

Regardless, best wishes on your applications.


How to encourage administration to handle plagiarism?

It is harder to deal with plagiarism in oriental countries than in the western world. It's even harder when your employer is a national lab.

To answer your question, how to encourage the administration to handle plagiarism?

There is something you need to know (I suspect you already know it to some extent), orientals tend to treat their faces much more seriously than anything else. This is the key.

Things may not be that serious as you would think. So far, he only presented the idea and the work as if they were his. But I agree that it's a bad sign. You need to deal with it as soon as possible before he goes any further.

Edit (I would like to argue that we do not have sufficient information to tell if plagiarism will happen or already happened.)
 End of Edit

From what you described in the comments, your supervisor seems to have personal issue with you. You might have some conflicts with him without you even knowing it. The key word face is the most probable reason I could think of. There is probably some cultural thing buried somewhere you would need to figure out if you want to resolve it. It may not be that serious as you think, could be just misunderstanding.

There is some different thinkings between oriental and western world. In the western world, people take individual ownership for what they think and do. In the oriental world, some tend to think the ideas and the works are products of the whole team/group. Thus, the head of the group would present the idea and the work as the head of the group. This could be construed as plagiarism in the western world

You said they are powerless to do anything about it. This is probably due to that thinking. I must say that changing a culture takes huge efforts and long time. If you want to talk to them to encourage them to handle plagiarism, you need to

  Talk to them politely, professionally and discreetly.


How much domain expertise and network does a special issue guest editor need?

I've edited journals without holding a PhD in the past (don't ask). Doing a mediocre job is not that hard - to invite reviewers for example you just need to do a literature survey of the paper's field, which is standard Masters-level work. You can then invite reviewers even if you don't know them. The success rate is quite good - I think roughly 50% of the reviewers I invited responded to the invitation (although a substantial number decline). Doing just this, it's possible to keep the journal operating, although of course it will not do well. Since you know something about the field you should be able to do better: for example you can desk reject with more confidence, make sure every accepted paper has something interesting to say, and so on. If you can understand what the papers are saying on a high level, you should not have to worry about not being able to do a good job.

However, there are several potential problems I can see:

You've said it's an open access publisher based in Switzerland, which pretty much identifies which publisher it is. It doesn't have a great reputation. You could meet people who disapprove of you working with that publisher.
More concerningly, you are very likely to be asked to help solicit submissions. This is very different from reviewing submissions, and here a wide network will be helpful. You may also feel like the publisher is exploiting you - viewed one way, you are using your contacts to help them make money. If this troubles you, then that feeling could be exacerbated by the low response rate from other potential editors.
Yet another potential problem is "The title is broad enough to be its own journal". I would guess from this that the initiative for the special issue came from the publisher's staff, not the editor-in-chief. Although this isn't a red flag - there's a good chance the publisher got the editor-in-chief's approval before approaching you - it is something to keep in mind. Another issue is the broad scope could make it difficult for you to even put together a special issue since so many topics would be relevant. You could talk to the publisher and/or the editor-in-chief to narrow down the topic, if you feel it's appropriate.

One more thing probably worth mentioning is that you'll likely have a lot of scope to define what you want the special issue to look like. If the initiative really is from the publisher, chances are they will be willing to defer to your expertise, and the editor-in-chief won't object.

So, what to do now? If you don't care about doing a good job, you can go ahead. Leave the scope, invitations, marketing, etc to the publisher (they'll undoubtedly do a mediocre job at best, since they have no domain expertise) and just review any papers that actually are submitted. The special issue will not be pretty, but the amount of non-review work you need to do will be minimal. If you care about doing a good job, I'd suggest thinking it through before committing. Talk to the editor-in-chief, talk to a senior colleague, think about what you want the special issue to be about and who you might invite to contribute.

By the way: if you do go ahead, I'd recommend asking the publisher if they can offer free open access for your invited submissions.


How should I take a potential PhD supervisor's age into account, when planning to follow PhD with habilitation?

First: a few people commented that thinking about your postdoc/Habilitation before even starting your Ph.D. is premature. I disagree. I have seen too many people coast along during their Ph.D. time without ever knowing what they are going to do afterwards, and certainly not preparing for their post-Ph.D. time, whether in academia or in industry. So I would say you demonstrate good long-term thinking. Already thinking about your academic career will help you prepare to work out a research program, network (more on this below) etc.

Second: there is no problem whatsoever with changing advisors between the Ph.D. and the postdoc period. To the contrary! If you stay at the same place for almost ten years, you will need to explain why you never moved, never checked out other places to work, other approaches to research. Many, many (most?) people will switch advisors at least once, or possibly even do postdocs in two different places.

Incidentally, this is why I think it is a good thing you are already thinking about your long-term future now, because it is never too early to start meeting people at conferences with your future in mind. You may just meet someone at your first conference who you could collaborate with or spend your postdoc time with.

So I would definitely recommend that you consider the older potential advisor. He sounds like he could introduce you to lots of people, and you will likely not need to pack up and move somewhere else during your Ph.D. period, which seems possible with the younger professor and which could somewhat mess up your personal life.

Of course, these considerations are all not the highest priority. You should definitely keep other aspects in mind in choosing where to do your Ph.D., like the kind of project you would be doing for either of the two professors, or whether the two of you "click" on a personal level, or what financing there is, or lots of other things you should discuss with your potential advisor ahead of time.

Finally, there is no Habilitation in Germany any more. Nowadays, Germany has moved to a more American style in academic careers. You will do a Ph.D., then a postdoc, then usually a Juniorprofessur (roughly, assistant professorship - not tenured and limited to six years), then get your Ruf to a tenured position. It's quite possible to skip the Juniorprofessur, though.


Academically dismissed from grad school but want to reapply

For the poster, I recommend you take this very carefully, and perhaps read it a few times. I hate telling people that their dream may not be achievable, because I was in those shoes at one point, too. However, I can't advocate blindly trudging forward and not giving up because that wastes both your money and your time if you don't objectively evaluate whether or not your goal is still achievable.

A while ago, I was in a Master's Program in Biological Sciences, with the ultimate goal of eventually going to medical school. I struggled as much as I could, but in the end, failed to meet academic standards and was told that I was no longer in the program. BAM! Just like that, my dream of going to medical school was over. What seemed achievable, in a year, became a flight of fancy, and a disappointment that I took deeply for a while.

Needless to say, when you fail out of one program, the chances of you continuing in the same field drop dramatically, even if you can explain it as a medical issue, because the onus of proof points to the fact that you were unable to complete your original program.

I gave up my dream of applying to medical school and started working on a Master's in Computer Science. I had some experience, and I knew I could do it. It wasn't brain surgery, but it was something I was good at. I've been done with the Master's for a few years, and have been VERY happy with what I am currently doing. If you had told me right after I failed my first Master's that I would find something better to enjoy doing, I would probably have just flopped over like a fish and not cared.

I now call this event my "early-life crisis." A lot earlier than the mid-life crises that people feel regarding their work, because we reach the point where our dream not being attainable actually becomes a plausible or even likely scenario.

I hate to say it, some of us aren't really prepared or capable of achieving our "dream" jobs. I say "dream" because dreams can change, and they certainly should, given how your life plays out. Lots of people want to become the next Lebron James, but very few can. You can take 24/7 basketball courses and weight training, but sometimes, we just don't have the traits we need to reach that level. We make do, and we should course-correct if we know that making do is not sufficient for us.

You state that you were uncomfortable participating in group discussions regarding the subject of your Master's, mental health counseling. I'm somewhat familiar with this by prior trade, but communication is a big part of that field, and unless you get around the issues preventing you from participating, the same failure is likely to happen. Given what you've said, I would like to put to question whether or not you feel that you are a good fit for the program you're enrolled in.

Instead of jumping immediately in and trying again, you definitely evaluate your short-term and long-term career goals with your therapist. You should seriously consider additional programs and subject fields as well.


How to make a great first impression at a conference?

Don't try too hard. You will have plenty of time later to build a solid reputation.

First impressions are way overrated. They will not be the basis of any serious (as in "costs real money") decisions, least of all concerning some complete newbie.

Enjoy the conference, get to know people, mingle. Play your rôle of newcomer who is just joining the club. Check out what is going on in the sidetracks, you might be quite wrong about their importance (or totally right).


Two PhD programs simultaneously in different countries

I think it would be a serious mistake to try and deceive either institution. You could wind up ostracized by both and expelled. If both agree that you can do this then the only problem is being able to accomplish the task.
But, of course, you would need to work on separate problems as you can't get two doctorates for the same work. Your advisors in both places need to have the possibility of contacting one another.
All in all it seems like a poor plan. If your home country is in turmoil, make an exit plan, certainly, but this doesn't seem like the correct one.
And one doctoral research program is usually plenty for anyone.


Why not include both?

Blablabla  (A, 1999, and B, 1998).


Can I send an IEEE paper that I downloaded using my institutional access to a person? Is it personal use or copyright infringement?

Check your institution's policies. Here are three examples:
University of Auckland:

Data may not be copied in any format for sale or any other commercial purpose, nor may it be copied or reproduced for the benefit of any third party external to the University of Auckland.

So assuming the person you are sending the file to is not affiliated with the University of Auckland, you may not send the file.
National University of Singapore:

The following limits on the copying or reproduction of any Work for the purpose of research or study must be strictly observed:

Electronic Materials:
Not more than, in total,

10% of the total number of bytes in the Work, or
10% of the total number of words in the Work or, where it is not practical to use the
total number of words as a measure, 10% of the contents of the Work, or
One chapter of the Work, where it exceeds any of the limits.

So you may not send the full file.
University College London

You MUST NOT:

provide print or electronic copies of material to anyone;

Read strictly, this is more stringent than the University of Auckland's policies; however presumably if the person you are sending to is also affiliated with UCL, then they can use their own access to get the paper. I'd guess then that UCL presumably meant the same thing as UoA, you can still send to someone affiliated with the university but not anyone external to it.
Exception: if you are one of the authors of the manuscript, you typically have more leeway with sharing. IEEE's policies are vague (see Section 8.1.4, page 76):

In return for the transfer of authors’ copyrights, the IEEE shall grant authors and their employer’s permission to make copies and otherwise reuse the accepted versions of their articles under terms approved by the Board of Directors.

But they don't say what those terms are, and I couldn't find them in the document. If you want an authoritative answer then you should email them at copyrights@ieee.org and ask.
However if we use Elsevier's policies as a proxy (I'm using Elsevier because it's so big), then:

If you are an author, you may also share your Published Journal Article (PJA) privately with known students or colleagues for their personal use

So you are free to send the paper to this person, if they are your colleague in research.
If IEEE sent you a copy of the paper after they published it (the publishers I worked with did), the email might also detail their sharing policies and/or where to find them.


Is your advisor allowed to read your emails?

What is the method of the email access?  If it is provided through the university or accessed on a university-provided computer, then it may be the case that they have a legal right to those contents.  This was the case at at least one of my workplaces in the USA.  If you are using your own email address, and your own computer, then I don't see how they could have the rights to access it.

Either way, it is best to have a separate email for all personal/private communication rather than risk it on your school email.


Is it right to submit a conference abstract knowing that I will not attend but my advisor will give my talk instead?

I think it can be acceptable if and only if it is clearly communicated in the submission that the former supervisor is the intended presenter.  Deliberately misrepresenting who will present at the conference is dishonest.  If in doubt, contact someone at the conference.


Mathematicians publishing philosophy papers and essays

Just randomly browsed Philosophia Mathematica and found To Diagram, to Demonstrate: To Do, To See, and To Judge in Greek Geometry written by Montelle, who lists his employment as in the department of mathematics. It's from Feb 2012, so recent.


Two ideas that might help.

The first is that you are new at this. Like any skill it is likely to improve with practice and time. As you progress you get insights that lead to further insights. But those insights don't come at regular intervals, can't be scheduled, and are harder for beginners. Frustration is common.

Second is that if you are really doing research then you are exploring the unknown and it is, well, unknown. Three months on a problem without success is not very long really. It is hard to predict how hard any given problem is. It might take years to crack any given nut. But it is also true that it isn't helpful to become so obsessive about a given problem that you ignore the possibility of progress on other, related, problems. That other work can lead to the insight you need on the harder problem.

“If we knew what it was we were doing, it would not be called research, would it?” ~~Albert Einstein


do's and don'ts of networking for a PhD student in a conference?

One could easily make a long list of obvious don'ts relating to basic conduct at the conference.  However, given your stated goals, here are some things I would recommend:

  Do present your own work in a clear and simple way that allows the audience to understand your topic and get interested in your problem.  Be prepared to discuss your problem (and other research interests) afterwards and form collaborations if you find them useful.

  Don't try to impress people by making your talk sound complicated - make it as simple and clear as you possibly can.  Impress people by your clarity rather than trying to bamboozle them with complexity and obfuscation.

  Don't restrict your goals to meeting only the "elite" researchers.  Try to network broadly and talk to anyone else who has shared interests.  Focus on talking to people who have shared interests with you, who can have a clear and fruitful conversation with that imparts value.  You might find that your most fruitful interactions are with people closer to your own research level rather than the most elite researchers.


Getting into new field after tech career / PhD in STEM, should i start a new degree as undergrad or at postgrad level

I don't see any reason to formally do another undergraduate degree. And you may not even need a credential at a higher level if you already have a doctorate and some publications in your new field.
My perspective is the US, where an undergraduate degree has a lot of things not related to the "major" subject. That is different elsewhere, of course.
But there may be some gaps in your education. If you are at a university, there is little reason why you can't ask a professor in some other field if you can "sit in" on one of their courses. I've done this, actually. The professor even agreed to give me ordinary student feedback (but no posted grade) on the homework assignments and exams. It was all informal and just let me "scratch an itch" in his field.
Once you think you have the knowledge gaps plugged you can, if you need the credential, apply for some higher level degree. You probably need to ask for special treatment in the admissions process, I suppose, but can probably justify it.


Should I tell my situation or request a possibly negative recommendation letter?

"Too busy" means "I won't write a letter you'd like."

"Describing conflicts" with your supervisor will raise flags you do not want to raise.

Your choice 2 is the correct one.  If you are asked why you don't have a letter from a current faculty member, say your working relationship with your thesis supervisor was "difficult."  Do not say anything more except to answer further questions as briefly and politely as possible.  Let your transcript speak for itself.


What's the point in a "list of figures"?

A list of figures allows one to find the figures contained in a book. This could be useful, for example, when you want to quickly find one of the figures you recall seeing in the book, but you can't remember which page it is on. You could also use the list of figures when buying the book to see whether it has lots of figures or only a few.


Are software engineers with PhD in demand in Academia?

tl;dr: Yes, some universities do value software engineers with a research background.
University College London (UCL), for example, has a Research Software Development Team (RSDT), which specialises in providing software engineering by programmers with a science-research background.
From the first of those links:

This is a team of professional software developers with particular expertise in designing, constructing and maintaining software for academic research.
Our goal is to enhance UCL’s capacity to produce high quality scientific software, from the simplest scripts to complex simulations running on state of the art high performance computers. We do this by collaborating with researchers who are creating their own software

How is it funded?
The work can be funded in one of several ways. It can be funded through university core funding. The work can be bid for as part of a research funding proposal or consultancy contract. It can be funded as part of a research grant for generic research software development.
What do they do?
The UCL RSDT team work alongside researchers on scientific projects. They co-author papers with them, transfer best practice & skills into the team, and hand over well-crafted, well-documented software (and its version-control history) for research.
The team do have research backgrounds themselves. They help select / develop the algorithms. When starting a new project, they read some of the background literature to the project - particularly that relating to the algorithms - to get enough grounding to enable them to ask meaningful questions of the researchers who they're working with.
And (touching on a comment by dgraziotin), the team host Software Carpentry Boot Camps for research staff and doctoral students. This gives the attendees an introduction to key concepts that they might otherwise not be exposed to, such as unit testing, version control, and working from the command-line.
Do many universities do this?
At the moment, this isn't an initiative at many universities that I'm aware of. However, given the success of UCL RSDT to date (the team is now expanding again), and the growing awareness of the concept of the Research Software Developer ("a new type of hero", as described by Neil P Chue Hong, Director of the Software Sustainability Institute), this is probably an idea whose time has come.
Disclosure
I am a little involved with the research software development effort linked to above.


Include Acknowledgements while submitting PhD thesis for review

Yes, include them. I don't find it arrogant at all that you believe at review time that you will do well and pass even if there are changes to be made. Lots of people are asked for some minor revisions, and your committee members know that. Your supervisor should not let you submit it for review if they don't believe that your work is sufficient to pass review. They should also not allow you to have a defense or viva or whatever it's called in your locale unless they think you will pass. It's fine, but you could also ask your supervisor their opinion.

Believing in your work is OK. How would you ever publish a journal or conference paper after your PhD if you didn't think it would be accepted? You have to start believing in your own work, on your own, at some point soon. That's part of being an independent researcher which is what your near future is about.


Should I inform my thesis adviser about current situation

As a rule of thumb, if you tell someone you'll be doing stuff with them at time X, and then change your mind, let them know!

More specifically, I would recommend an email such as:

"Dear Advisor,

we had planned for me to start my thesis in September, but because of REASONS I'll only be able to start on October. I apologize bla bla
In the meantime, I'm planning to do EXERCISES. Please let me know if you have any other suggestions on how to prepare."

I don't see a point in telling this to your advisor in person anyway, and this should keep you safe from being made to sign stuff.


How to ask my advisor from another department for research assistantship?

Just ask.  Generalities from the Internet are not going to be so helpful here.

  Would you be willing to consider me for a research assistantship at some point?

  What would you expect me to accomplish to get to that point?

  If I had an assistantship, what would you expect me to work on?  Would it be part of my dissertation research?  If not, how should I plan to balance the two?

  Given that I'm enrolled in another department, are there any bureaucratic obstacles to this, and is there anything I can do to help with them?


What is the academic degree of medical school graduate after 6 years of study, plus 1 year intern?

Huh. According to this table (PDF), an entry-to-practice degree that requires licensure is credited the same as a master's level, 23 points.

  University-level credential at the Master’s level OR an
  entry-to-practice professional degree. CIC only accepts as an
  entry-to-practice professional degree, those degrees issued in
  relation to an occupation listed at NOC Skill level A and for which
  licensing by a provincial regulatory body is required.

This section includes:

various master's, medicine, veterinary medicine, dentistry, podiatry, chiropractic medicine, optometry, law, and pharmacy.


Citing article where listed author is pseudonym

Always use the name that is used on the article/book you are referring to.

If someone searches for an article referred to as being written by Dwork, but the name on the article is Boyarsky it will only cause confusion about whether this is the article they are looking for.

Regarding the pseudonym: I would not mention it at all. It is up to the author when or where they reveal that they use a pseudonym. Even when it is commonly known I would still not do this, except when you have explicit permission from the user of the pseudonym. This way you avoid spreading awareness of the use of the pseudonym in a situation where the user may not desire this. One exception could be when there is suspicion of the pseudonym being used with ill intent. Generally though I think it is good to be cautious about such revelations.


How to find out if a conference submission deadline is likely to be extended?

Just look at past editions and see if there was indeed an extension. If they always do it, there will be another one; if they never extend, there is no reason to believe they will start this year.

If they don't, you could always give a shot to a polite email to the organizers and explain your situation. Perhaps you can submit a tentative proposal, with the uncertain data, and submit a refined version later (provided it doesn't change much).