Is it unethical to apply to/attend a PhD program knowing you MIGHT end up leaving it under a particular circumstance?

It is not unethical to apply to both programs.

However, for most advanced degree programs, the possibility of doing multiple programs simultaneously is remote, unless the departments have already established a method for undertaking work between the disciplines. For instance, there may be an interdisciplinary program or a "joint degree" program. In such cases, though, you will find it very difficult to find a funded program that will pay for your studies to complete a degree in another department.


When in Rome, do as the Roman's do. Observe how your peers interact with their peers, superiors, and subordinates. Emulate them and you'll do fine. Note in what circumstances they are formal and when they are not. For instance, I addressed my professor by his first name in private but by his title in public. Also, don't be too shy to ask someone!


Lots of people would object to this. LOTS. I think somewhat differently. If this section doesn't cite the original, I think that's pretty bad. I don't think that it's career-ending, but I also don't think that we should be slavish to not copying ourselves when the material is rote or nearly so. Methodology sections that don't change much from paper to paper are places where I think reproducing text and saying so and citing yourself are particularly acceptable to me, but lots of people disagree vehemently with me. I'm aware of this propensity, so I don't copy text in my own papers as much as possible. I rewrite such sections and cite my old work for alternative descriptions.

In the case you mention, both articles appear to have been published, so unless you have a vendetta with this author and want to try to ruin their career, it's probably not worth saying anything to anyone about it. In other words, what would you do if we all said it was bad self-plagiarism? The only thing you can really do is tell the journal or their department chair and hope for a retraction or firing. If it doesn't change the result, then there's not much point in bringing it up. That being said, it's probably best if you don't follow their example. It's  also probably worth being wary of future articles from this group of authors since there might be other aspects that aren't exactly above board.


CV and/or resume for PhD Student with industry experience?

I would say there are a couple ways to attack this. You could list academic experience as a separate section to industry experience, this would show that you consider them very separate.

You could also make a section titled " (Relevant) Experience" and list everything you have in chronological order. This would give the impression to whoever is reading it that you consider all of your experience relevant in the position that you are applying to.

In either case, make sure you highlight the relevant portions of your background to the position you are applying.


How to structure a proof by induction in a maths research paper?

As you probably have observed by now, by reading articles, people generally do not write steps down explicitly when those steps are considered "obvious." This trend is not special to proofs by induction.
In fact, this is true at any level, but what is considered "obvious" to an audience of people holding a PhD or with significant progress towards a PhD is different from what is "obvious" to someone taking first year calculus.
Think about it this way: people reading research articles know math quite well already. What they are interested in is what is new in your paper; demonstrating "obvious" facts is just a distraction. And, if you are at the stage where you will read several papers in a week, you generally want those papers to get to the point.
For people who are learning math, it's entirely different: you're probably only reading 1 textbook at a time, and the whole thing is new to you. So, you want everything explained in lots of detail because you've never seen it before. But again, if you're reading a calculus book, you probably don't need an explanation on solving a quadratic; you already know that. If you're learning induction, you want it spelled out; if you've seen proofs by induction ten thousand times, you don't need it spelled out for you.
Since you are a bit new to this, I would like to give some more examples about how proofs by induction are typically structured in upper undergraduate/graduate/research levels. Now, when it comes to proofs by induction, there are generally two categories: proofs where the induction step is "obvious" and proofs where the base-case is "obvious." Sometimes both are easy, but it's very rare in my experience to find a proof by induction where both the base case and the induction step require a lot of work to prove.
I suppose on the rare instance where both the base case and the induction step are non-obvious, I might split the proof into two lemmas or possibly I would call these "claims." In every other case, I write statements such as "the base case is trivial" or "the general case (the induction step) follows by induction."
I would also point out that there are even times where a proof will "prove" something by induction without the author ever writing that induction is being used. For instance:

Let f(n + 1) = 2f(n) and f(0) = 1. Then f(n) = 21 f(n - 1) = 22 f(n - 2) = . . . = 2k f(n - k) = . . . = 2n.

Induction is being used implicitly within the ellipses, but it hasn't been written explicitly so. I, personally, like to write "by induction" at the end of such a statement, but not everyone does.
I think your intuition of generally following how other people write mathematics is appropriate. You can deviate slightly, sure, but it's also good to understand why things are written the way they are and so it is great that you are asking this question.


Methods to track behind cheating on exams using on-line sites?

I can think of a few approaches that might help. I'm not sure pursuing the sites used will be very fruitful. There are always disposable emails they can sign up with, Tor exit nodes they can route traffic through etc. It's a fool's errand.

Oral interviews post-exam

Ask a random sample of students for an interview after they've submitted their answers. With the script in front of both of you, ask them about their thought process when answering the question and evaluate the extent to which they can confidently discuss the subject.

Cons: time-consuming, potential for false positives from students who forget most of the content after taking the exam/have other assessments to study for/don't cope well with the interview pressure.

Issue unique questions per student

If you have control over the online assessment platform, you may be able to issue unique questions per student to catch out blatant copy-pasting of the question text in order to publicly outsource an answer. I am not proposing that a paper is manually put together per student; this seems like something you'd want to automate.

Cons: the ability to do this well will vary from subject to subject. It might be easy to generate lots of linear programming problems of comparable difficulty if your exam e.g. assesses the student's ability to apply the Simplex algorithm. But, explanation questions may be more difficult and lead to a perception that some students unfairly get 'easier' or 'harder' papers.


Overcoming nerves from anticipating conference questions

There are a few obvious questions to ask yourself in planning for questions:

What are the inherent weaknesses in the current work? (Almost no research is completely "airtight," so figuring out where the weak spots are will make a difference.)
What are the ramifications of whatever assumptions I have made? Are they logical? What happens if I strengthen, relax, or eliminate some of those assumptions? Will everything still work in the more general (or more restricted) case?
How would I apply this work to other problems? How will it help others in the field?

And then, with respect to the presentation:

Have I left anything out in the interests of time that would potentially interest the user? Is the research methodology clear?

If there's anything in the last point, you may want to plan on having additional "backup" slides which highlight that info, but that aren't part of the "main" talk.


Can I use my university email address for job applications?

I, personally, wouldn't use anything else.  This might depend a little on the culture of your field (see Should I use my university's letterhead for a cover letter for a job application? for a similar discussion), but exactly as you say, using your professional email address might well cause someone to give your email an extra second of attention.


Cheated on an exam when I was eight years old. Should I tell graduate admissions?

As noted in the comments, actions committed long ago as a child are (and should be) entirely irrelevant to graduate admissions.

It is well understood that children do not have same ability as adults to comprehend the consequences on their actions.  As a result, many legal systems wipe a child's record clean of most or all juvenile offenses upon reaching adulthood.

I would thus similarly argue that any academic offense predating your undergraduate education should generally neither be reported nor considered in an application for graduate school.


Firstly, a tip: as currently written, your question is not a good match for the format of the site and is likely to be closed. You need to ask a question that can be answered in an objective (or at least good-subjective) way.

That said, I will try to answer the question as it stands.

Firstly, be sure that you actually want to do a doctorate. It is long, hard work and you need to be fully committed. Honestly, your plans sound too vague at the moment. The whole point of a doctorate is to show that you have initiative and can work independently.
Next, you need to clarify your subject. At a bare minimum you need to identify a particular group, region and/or period of interest and justify why this is a particularly important focus.
Next, you need to do some research online and identify one or more potential supervisors with a track record and interests in this or a very closely related field, at an institution which would be happy with you doing a part-time distance learning doctorate. This will be difficult. There is an interdisciplinary science and religion doctoral programme at Boston but it doesn't sound to me like they would accept part-time or distance learners.
Next, you now need to contact them to find out if they are potentially interested in taking you on to do a project in the area you have identified.
Finally, you need a source of funding. You need to pay university fees (depending on which instiution you end up at) and potentially living costs (if you are planning to reduce your working hours to allow time for study; if you are planning to continue working full-time you are probably underestimating the amount of work a doctorate takes). A supportive supervisor might be able to help identify some charities, scholarships, bursaries etc that could help with this, or some students self-fund using savings. This is inevitably much more expensive than you think and most of the students I know of who go down this route end up in financial difficulties at some point. If you're lucky (I don't know the situation in the Seychelles) your government may offer funding for study.


What should be included when inquiring about the status of my application?

As someone who has been participating in more of these hiring discussions recently, and been responsible for filling some of them myself, I would encourage you to use extreme caution before sending out such emails.

Faculty search committees usually consist of faculty members who are already quite overworked, and who have to deal with potentially many candidates who may all want to pester them with questions. If somebody starts acting like a nuisance, they might consider that person "not a team player" and reject the application on those grounds alone.

However, there are a few times when it is appropriate to ask about such deadlines:

When you have received an offer from another institution, but the institution you're writing to is a higher-perference choice. Then you are doing two things: you're making sure that you get an informed decision, plus you're also letting the other guys know that if they're interested in you, they'll need to make a move quickly.
If you have a major update to announce. This might include a change in location (new position, new mailing address, etc.) as well as status updates—you've earned a promotion or a major award. Then it would be OK to mention this in an email.
It is well past the "standard" deadline, or a promised deadline. Then you're just following up on an arrangement, and it's hard to argue against this.

However, you should never ask if you are included on the list of finalists. That's considered both rude, as well as unfair to everybody else involved. Like eykanal, I think the last paragraph in your excerpt is always superfluous, and should not be included in an email requesting a status update. (You could and perhaps should send it as part of a thank-you note to the interviewer.)


What is the percentage of Latino/Hispanic females with a Ph.D. degree?

The NSF releases analysis on such data regularly: https://ncses.nsf.gov/pubs/nsf19304/

You can find a digest, as well as the source data, in case your particular question isn't answered by the digest.


I work for a literature archive, and this is a very important question for me. Here is an example of how restrictive licensing affects our work. We host a large collection of biomedical publications. We developed a tool that identifies mentions of research data in the text. The tool highlights these mentions for readers to find it easier. If the article is licensed as CC-BY-ND (no derivatives) we cannot display the highlight, because it changes the article.
We are a publicly funded, free service that offers free open tools for researchers. But we can only develop new functionalities based on public data. The more restrictive you go, the less value we can provide for the benefit of all.


How should one address negative circumstances with past advisor in a Statement of Purpose?

Congratulations on the switch, I'm so glad to hear your update.

There will be an ongoing need to heal from the trauma you underwent.  The SOP will be separate from that.

If you are concerned that an admissions committee might raise a red flag for the extra time you spent in your program, you may address that briefly in a cover letter.  For example, "You might notice that I spent longer than customary on my degree.  That was due to some health issues exacerbated by an uncomfortable advisor fit."  That's enough.

You might also alert your new advisor to your concern, so that s/he may choose to consider this when writing letter of recommendation.


What should I put in the introduction chapter of my thesis?

Talk to your advisor and look into student services provided by your university.  The department should have pretty clear guidance on document structure and format.  You will also learn a lot by reading some of the dissertations of previous (successful) candidates.


What is the most effective way to take notes in class?

I'm a PhD candidate from Caltech and here are my tips:

If it's a Math/Stat class, you should always bring a notebook and a pen to drop down the derivations and you have to review the notes immediately after the class; You should always make sure you are not lost in the middle of this type of classes.
If it's a Bio/Chem or any class focusing on stories and concepts, you should always print out the powerpoints in advance and bring a laptop. So that you can highlight on the hardcopy and type fast on the text editor. The text editor on your laptop is very efficient when the lecturer refuses to hand out the notes. I'm still using my small netbook to take notes during seminars.
If it's a CS class focusing on the codes/syntax, you should bring your laptop and have all the tools installed before the class. You should always type in the commands as the lecturer does and save all the commands together with comments which include your own notes. Those are very precious materials to your own benefit.
Learn to use the short forms of words when typing:
with as w/
without as w/o
experiment as exp.
statistically significant as stat. sig.
Practice the ability to type without looking at the keyboard.
Always have a good sleep.

Hope these help you


In the U.S., most academic fields are not like medicine: there is no licensing and for most purposes there are not strict legal requirements for what constitutes a degree.  In particular, there is nothing that needs to or can be done to accredit a foreign Ph.D.  (Other countries may differ.  For example, Germany used to treat non-EU Ph.D.'s differently; see http://www.zeit.de/2008/12/C-Seitenhieb-12.)

Regarding more specific issues:

Employers sometimes verify CVs, but that is not your responsibility.  If they need to check that you have a legitimate Ph.D. from Cairo University, then they will get in touch with the university directly to verify this.  You do not need to help (and in fact they won't allow you to help, to make sure the verification is unbiased), so all you need to do is to make sure everything on your CV is true.

You may run into people who acknowledge that you have a legitimate Ph.D. but have no idea what the standards of Cairo University are.  That will give you a modest disadvantage compared with students from, say, Stanford, but there's nothing you can do about it.  Ultimately, if you publish strong papers in prestigious venues, then that will matter much more than where your Ph.D. is from.  If you don't, then you will not get a research job anyway, wherever you studied.

If you are talking about upgrading the degree somehow - perhaps getting additional certification or even another degree from a particularly prestigious school - then it basically can't be done.  It's not truly impossible, and I know of a couple of cases in which people with Ph.D.s from other countries enrolled as students in the U.S. in order to improve their job chances.  However, most U.S. universities strongly discourage this, on the grounds that it's a waste of time and resources to devote a space in a graduate program to someone who already has a Ph.D. in the same field (or a closely related one).


Citing another author’s summary of other works in a journal article

What you need to do is write it so that the author of article is clearly identified as the compiler, rather than the originator, of the idea. For example:

  Lukas Blinka notes that some critics have “compared the player and avatar’s relationship to a transmission field” (##).

You would only include Blinka's article in your bibliography. If I cared to know who those critics were, I'd go to his article to find them.


How do you "grow your own" post doc opportunity?

From what I've seen, you've just described perfectly what many professors would view as the "ideal postdoc". As one of the main goals of your postdoctoral training is to gain experience writing your own grant proposals, your four steps are very close to what you should be doing.

The most crucial part for you will be finding a postdoctoral advisor with whom you get along. As is typical in research settings, look for someone with significant research experience who has a successful record of getting proposals funded. Given that this is your goal, this is possibly more important now than their publication record. You should be able to find this out by asking around the department and speaking to graduate students, and even just asking the advisor directly about their recently funded grant applications. Once you find someone, everything else should go fairly smoothly.

  1) Come up with feasible research idea and approach advisor.

  2) Discuss idea and possible collaborations.

You should do this both on your own and through talking to your advisor. Remember that one of the main factors driving whether a postdoctoral grant is accepted is previous experience of both the postdoctoral fellow himself and the advisor; consider ideas in areas where you have experience doing research and your advisor has experience mentoring.

While you can consider collaborations, my postdoc advisor told me that at most I should consider one other collaborator, other my advisor himself, as collaborative proposals are more complicated, both from a submission and administrative standpoint.

  3) Try to categorize it into NSF's or any other funding agencies categories.

Your advisor should already be aware of relevant funding opportunities.

  4) Write a proposal in the summer and submit it during the next window of opportunity.

I assume you wrote "summer" because you were thinking of a particular grant, but different opportunities have different grant submission deadlines. Again, talk to your advisor to see which grants the thinks would be a good fit for you, and check out their respective deadlines.


How can I ask a professor for time-sensitive information when they are out for a family emergency?

I'm an academic who has had to cancel class and office hours due to emergencies myself. We are all pretty tied to email these days wherever we happen to be, and regardless of what is going on in our personal lives, our professional responsibilities to continue to limp along. Depending on the specific nature of the emergency and the demands on their time, the professor may actually be able to help you nevertheless, but i) may well need reminding, and ii) may have higher priorities at this time.

I would send an email like the following (and if I received it, would respond as positively as I am able if the tone does not rub me the wrong way.)

  Dear Professor X:

  I understand you have had a family emergency. Sorry to bother you at
  such a time, and I fully understand if you are therefore unable to
  respond to this email. However, in case you happen to be working
  remotely, I would much appreciate your comments on the below, since I
  need to ... by .....  Or is there someone else you would recommend I
  contact instead given the timeline?

  Thanks and apologies, ...


is a 6 years Biology Degree comparable to a Master's Degree?

You are in a slightly tight but not an impossible to overcome situation.

What you describe relates very closely to the pre-Bologna_Process situation in Europe. People especially in Science- and Engineering-related disciplines had 5 to 6 years Bachelors (usually called Diplomas). When these graduates applied for graduate studies, especially in UK where the BSc in usually 3 years, they found themselves massively downplaying their qualifications. (The situation is somewhat sorted now.) Currently the old diplomas are almost universally accepted as Masters degrees because the retroactively calculation of ECTS points puts them nearly always in the same range as a Masters degree.

When you say abroad you do not specify where.

If abroad translates to Europe then things are quite straightforward. You say you have a Masters and leave things be. Departments are quite used to the phenomenon of "5/6 years of studies". Most of admissions committees will not blink an eye. It would almost certainty good to present it in your CV as "Integrated BSc and MSc studies" or something equivalent, so one can immediately spot it. Your programme of studies is far from unheard in Europe.

If abroad translates to US/Canada I do not have personal experiences; I think it will greatly dependent to the particular university's guideline. (I will be happy to be corrected at this point from a North American native if there is some standardised framework I do not know of). I can tell you for sure that 4-year BSc are not counted as Masters. I know very few people who applied for PhD straight out of a 5-year Engineering degrees from Greece; both them were accepted but they were very strong students anyway so I would not extrapolate based on them. Some others went for Masters (and continued to PhD eventually).

In general, a 6-years degree puts you in a very strong position if you are to be compared with simple BSc holder for PhD admission, probably your compare favourably to most MSci programmes as well. I would not worry much in that aspect. Having strong grades in those six years will be more important than what one equates your certificate to. (Assuming your references, cover letter, etc. are the same.)


Is the arXiv a good way to get feedback on one's work?

There is not much of a "formal feedback" system associated with the arxiv.  I say "not much" instead of "none" because the arxiv apparently does do some degree of automatic tracking of citations to its papers.  For instance this arxiv submission contains a link to a MO post in which my paper is (briefly) mentioned.  I had not seen that post before, so that was somewhat interesting.  However, I don't know how this system works and it seems to be much less systematic than, say, what google scholar does.  In particular, I have 25 arxiv preprints and the arxiv itself lists this kind of citation for very few of them, whereas google scholar lists much more.

In terms of an informal feedback system: yes, the arxiv works very well for that, in the following organic way: for many academic fields and subfields it is by far the one place to put your preprint in order to get the most (and the most interested) people to read it.  This includes publication in most journals and the implications this has had on some academic fields are immense.  E.g. I hear that in theoretical physics -- a fast-moving field in which it is apparently rare to look up a paper written much more than ten years ago -- pretty much everyone who is anyone uploads their preprints to the arxiv, and as a result theoretical physicists almost never go to the library anymore or look through actual journal papers: they don't need to.  My field -- mathematics -- seems to be converging to this kind of phenomenon rather more slowly.

On the other hand, to expect feedback may be putting it a bit strongly.  The volume of papers uploaded to the arxiv is fast and rapidly increasing.  I just looked at the math.NT arxiv submissions, and last night 15 papers were uploaded.  I am a number theorist with broad interests, and if these papers came at a rate of one a day or less, I would probably peruse about half of them.  But the current volume forces me to be much more selective.  The arxiv is great advertising, but all the advertising in the world doesn't guarantee that people will engage with your product rather than the sea of competing products (competing for their attention, anyway; they need not be competing with you in the academic sense).

In my experience, I most definitely get enough feedback from my arxiv submissions in order to justify uploading them (although there are arguments to be made for doing so even if you never hear directly from anyone about them).  It happens that in the last three weeks or so I have uploaded four arxiv submissions.  (Since I have 25 altogether, this is obviously a spike in the upload rate.  Some other people do this too.  Now that I think about it, from an advertising perspective it would probably be better not to do this.)  Since then I have received comments on two of the four papers.  The two papers that I haven't heard from yet are I think perfectly solid and interesting -- in fact, one of the two concerns the Combinatorial Nullstellensatz so probably has broader appeal than most papers I have written, and the other is a really substantial project that I did jointly with my PhD student -- so the fact that I've gotten no feedback about them seems to be mostly random.

In summary: yes, posting your papers on the arxiv is a great way to get feedback.  Will it guarantee feedback?  No, guaranteed feedback is exactly what you're buying (so to speak) when you submit to a journal.  Other than that it seems impossible to guarantee. I would definitely submit to the arxiv and see what happens.  If you hear nothing, then you might try sending a few emails to suspected experts which just point to your arxiv preprint.  Having an arxiv preprint versus just enclosing a file adds a certain veneer of legitimacy.


Doing good translational research is hard because it requires a good understanding of clinical issues (both from the patient and carer sides) and a strong research background. In order to obtain those skills you need to spend time in the clinic and time in the lab. An MD-PhD program guarantees that you will have the opportunity to spend time in both environments. It is worth noting that having that opportunity doesn't mean you will capitalize on it. Further, you don't need to do an MD-PhD to have that opportunity.

Another advantage of some MD-PhD programs is that you can get funding for the MD side. If it is what you want to do, saving 100k USD isn't a bad thing. If it isn't what you want, trading a few years of an MD salary for 100k is a bad investment.


Should I include PhD experience in MSc application?

You joined a PhD program without a master's degree?

Well... a master of science is about doing an small version of a PhD. In that sense, it could be beneficial to show that you do have some experience in research.

On the other hand, the fact that you left, probably without results or something to prove how well did you do it so far, might not be so positive.

But anyway, honesty should be the most important thing, and you shouldn't hide what you have done before. Also, it is definitely more beneficial to fill those gaps on your CV with the PhD time, instead of letting them think that you were just lounging around...


Well, you let him copy. What else can you say?
Bear in mind that lecturers hate hunting down plagiarism/collusion. In one course, hunting the offences and collecting proof cost me more time than marking all submissions (and these were a lot).
You just created a bunch of pointless extra work for them. Don't increase it, you have already been caught. This is not a court lawyer cat and mouse game. You are not going to get out of it free by technical tricks and it's insulting to your lecturer's intelligence to try, trust me on that.
Put the cards on the table and promise with contriteness never to do it again (and, of course, adhere to this). That's your best bet.


Where is Harvard referencing style most commonly used?

The distribution is not so much geographic as field-dependent. For instance, most of the papers I see that use the Harvard style come from the areas of geology, hydrology, and geochemistry, while most of the remainder use various numbered citation styles (RevTeX, AIP, ACS, etc.). This is true regardless of the geographic location of the authors, because the decision regarding citation style is generally made by the publisher, not the author.


Should request payment details for a project I am to do?

Compensation is an integral part of the decision to take on any job. Not only should you know the amount ahead of time, but also the mode of compensation: is it 1k up front? Is it $10/hour? Is it $500 now and $500 at the end of the project? This is information that you are owed as a prospective employee.

You should just be straightforward about this. There’s no decorum that you need to follow outside of whatever is usual in your relationship. I would write something along these lines:

  Hi James,

  I’m excited about the research opportunity that you mentioned after class last week. I was hoping you could fill me in on some concrete details such as when and how much I will be paid, the expected project timeline, the scope of my part of the project, and who else would be involved.

  If you don’t have these details set yet, I totally understand. In that case, do you have an idea of when you will have them?

  Thanks,
  Stella

I’ve sent some variant of this email tons of times. I’m somewhat making up the details, as I don’t know what you have or have no discusses with this professor, but I would strongly recommend that you ask about any of the things that I have listed that you don’t know already. If this is a project that is part of publishable research, you should also ask about authorship and (if applicable to your field) authorship order.


Definitely yes: if in the future you're looking for a teaching (or part-time teaching) position, having less experience than other candidates will be a really bad experience.

Yes to some extent: even for non-teaching research-only positions, teaching experience can be seen as a positive for the applicant. Some of the qualities required for teaching are necessary for other aspects of the job (handling a team, tutoring interns or PhD students, communication with non-scientists, etc.).

So, I would advise you to continue having some teaching duties during your PhD, even if you have to take those outside of your own institution or do some of it pro bono (or for not-so-great pay).


Is international Ph.D. student's stipend enough to support a partner in the U.S.?

I am hoping to start a grad program in one of those medium cost-of-living cities, and have been doing lots of research. Since it sounds like I'm more familiar with the US than you, I'll give you what I've learned.

This will of course depend on your standard of living. I assume because you are married, you would like to live in your own apartment/house and not live in one bedroom in a four-bedroom house. This answer is based on that.

As another caveat, I would say I'm moving from a very expensive area, so it's possible I'm overestimating other expenses based on my experience here.

At more than $30k (the value of some awards), I feel like I could minimally support myself and my wife (who is also going back to school). We also have a nice chunk of savings that we've been accruing for two years that helps me feel better about living on the stipend.

At less than that, around $25k, we would plan on my wife working 8-12 hours a week to supplement my income.

Those numbers are totally unlivable in high cost-of-living areas, like where I live now. I couldn't imagine trying to live here on less than $50k combined; and that's a totally unachievable PhD stipend.

Tl;dr:

< $20k - Not a chance, would expect my partner to work at least part
time
$20-25k - Doable, with decent savings and a few hours of work on your partner's side.
$25-32k - Much more doable, but still tight living
>$35k - As comfortable as you can be on a PhD stipend.


What can I do if my advisor wants me to keep working, even while I'm on medical leave for severe depression?

There is only one suitable course of action I recommend, as an advisor and a physician. Stop with anything that has a potentially detrimentally effect on your health and focus on your treatment (thus if you believe so also your MSc commitments).

Indeed, your work is likely contributing to your depressive symptoms (irrespective of the differential diagnosis between burnout and depression; e.g. Bianchi et al, Soc Psych Psych Epidemiol 2015).

Much more importantly, if you do not treat yourself now in the best possible fashion you might fail the treatment and even face substantial complications early or later, even life-threatening ones (e.g. Mann, New Engl J Med 2005).

I would definitely inform your physician that your advisor's attitude is likely a contributory factor to your condition.

Finally, notify any oversight committee at your institution, as individual or organizational issues impacting on your depressive symptoms could and probably should be addressed thoroughly (e.g. Theorell et al, BMC Public Health 2015).


Name of a fictional scientist with fictional publications invented and ‘working’ at an existing British university

Are you thinking of Professor Moriarty (he's from a fictional book series, but he did author two works that have been cited in the literature), or one of the three fictional winners of the first Ig Nobel Prize, Josiah S. Carberry, Paul DeFanti, and Thomas Kyle?


Paper is based completely on my thesis, but I'm mentioned in the acknowledgements only, not as a co-author, what should I do?

I will try to give my perspective, on both sides if possible. In many countries, most incentive professors have for supervising undergraduate or MSc theses, is that some of them (or all if possible) may actually lead to a publication. There is a problem though: Most of the time undergraduate or MSc students leave the university and the paper usually can only be prepared after the student graduates. Unfortunately, at that time the student has already left academia and has really no interest in publishing, since he has more important things to do (like finding a job). This is quite the setting that the OP describes.

Still in your case, your supervisor of the thesis has started writing the paper himself and he needs your help. Initially you provided the help needed but you became frustrated because it was more work than you wanted / expected to do, because (let's face it) the paper really does not make a huge difference to you. On the other hand, you want to stop him from publishing it solo. So, both parties are partially right to be angry at each other. You do not want to take orders from him and he does not want to be treated like an idiot (who calls his questions silly) from his former student.

So, how can you fix this? For me, writing emails back and forth is not the way to discuss details for a paper. Why don't you use a better mean of communication such as skype, face-to-face meeting, phone call etc. You can there discuss all the details and your problem will be resolved. Of course he writes the paper and he will be the first author. But you get a publication and everyone is happy. And who knows? In the future you may collaborate further.


How to change author profile name in Google Scholar?

While signed in, visit My Citations in Google Scholar.

Click on the "Edit" button next to your name to change the name in your author profile.

Click "Save" after you have made your changes.


Comparing a career in medicine vs. medical research?

As a person who faced a similar dilemma a few years ago, I think there are major practical differences:

The working environment. Every doctor will spend his early career in a hospital, whether he plans on practising in the community later or not. A hospital environment is really different than the research one. In the former you are constantly on your feet, working long hours, nights, etc. However, you are constantly working with the people to whom you're helping. In a "lucky" week (depends on the POV), you might save a life every day.
Taking work home. While a M.D works long and hard hours at his/er practice, when she goes home - she can rest. Her patients doesn't follow her home. As a researcher I can tell you that I'm even dreaming on my research.
Independence. The medical environment is a very hierarchical one. Starting out as a M.D, you can't even sign off your own orders (in first world countries, at least :) ), contrary to a graduate student who might be given an independent project very early in his or her study course.
Goals. As a researcher, you end up working for the sake of science. You might find yourself pursuing a direction which might take decades before it translates into helping people. As a practitioner - you're working for the people in front of you.
Demand for your skills. In general - there are hardly any M.Ds who go unemployed. Most healthcare systems are understaffed and there is always a demand for M.Ds. I wish we could say the same about positions in the academy, and the industry is never as stable (and here it's field specific and I can't say much about the specific field in question).


How to organize lots of assumptions/equations in a math paper? (I need to refer to them in my main theorem)

Possibly you could lessen the problem by also mentioning this in your introductory paragraphs, such as saying something along the lines of "Our main result, Theorem 6, will follow from (1), (5), (21), (24), and (45)." If the following applies, even better would be "... and (45), which have independent interest" (or "which are of", or "which we believe have", etc.).


Can someone really be assigned to review in the APS’s editorial system for over a month without reacting at all and if yes, why?

Yes it really works like this, except that:
(a) the editor selects 1-2 reviewers, not a single reviewer (see http://journals.aps.org/authors/web-submission-guidelines-physical-review). In my experience / field, it's usually two.
(b) I'm not sure which APS journal you are submitting to, but for Physical Review B, the median time with referees is be about 30 days (Rapid Communications) or 40-50 days (regular) in 2013--see https://journals.aps.org/prb/rapids. This is roughly consistent with my experience.
Some journals are much faster.  In my experience in refereeing manuscripts, I'm usually given only 1-2 weeks to respond with "Yes I will review" / "No I will not review".  However, I'm usually allowed to request for an extension of the deadline (and there's usually a box where I'll need to give a justification for the extension).

A 1+ month wait may be a little bit longer than normal--you may wish to consider writing directly to the editor (and if the editor feels there is a need to do so, the editor may choose send an reminder email to the referee). Note that the referee could already be receiving reminder emails (auto-generated by the system)--I have received such emails as the deadline for review approaches.


How to reply to students' emails that show anger about their mark?

When dealing with angry students, your number one priority should be to de-escalate the situation and bring it back to a more factual ground. That means you want to:

Stay calm. Even if you are getting agitated yourself, you should never let it show through in your answer (easier via email than personally, but the same principle applies independently of the medium). I tend to opt for a more formal tone than what I usually use, mostly because I have found more formal phrasing harder to be misunderstood as dismissive (your milage may vary).
Provide short, to the point, answers. Answer the student's query or complaint politely, but don't get pre-emptively defensive and don't overly detailedly explain your reasoning. The more you write or say, the more an unhappy student will find to be upset about. There is a time and place to give a student detailed feedback, but when they are currently raging isn't it.
Stay with the facts. Scrub all subjectivity from your own answer. You want to bring the conversation to a place where you are talking about specific assessment results (exam questions, assignment tasks, etc.) rather than "I felt I did better", and the more you are using subjective statements in your own answer the more the student will feel validated that his own subjective understanding of the situation is as valid as yours.
Require the student to provide concrete, factual arguments. Once you bring the discussion to a more factual level, you should ask the student why, specifically, they disagree with their grade. Are there specific assessment results they feel were wrongly graded? Are they unhappy with how you aggregated the assessments? Once you are discussing on this level, it becomes easier to both, convince a student that their grade is correct according to the framework, and see cases where your framework is indeed unfair (or can at least be perceived as such).
Answer, but don't answer too quickly. Especially when receiving complaints via email: avoid the temptation to immediately answer questions by upset students. Give it a day, this will allow both you and the student a chance to calm down. A little delay in your interaction will also motivate the student to think more carefully about what they are actually writing, since a non-question like "How could I get this mark, when my colleague got higher" just means longer delay for them.
Remember that student's don't have to agree with their grade. At the end of the day, not all students will be happy with their grade, and even after you have explained your reasoning not all students will be convinced. That's ok. You and the student don't have to agree on the final grade. There is a process in place what, if anything, students can do to further escalate a grade dispute (I don't know if that includes sending a mail to the dean at your department, in mine emailing the dean about a grade dispute would mostly result in a confused dean).


Why would a university restrict publication of work due to plagiarism fears if TurnItIn was used?

Those plagiarism checkers can only detect certain kinds of plagiarism. They will detect for example if text parts are the same. They won't detect missing references or plagiarized ideas.

So if you host your assignment there then others can be "inspired" by that, and if they rewrite everything in their own words and change the code in certain ways but don't cite your GitHub project then it would be a plagiat. But Turnitin might not recognize it as such. Especially since I guess you would need to set the detection level quite low, because for such assignments there will always be a certain overlap in the results if everyone solves the same problem.


Contacting a Potential Supervisor about Funding (after agreeing on project)

I wouldn't push unless I had another option to consider and might need to back out of acceptance for another position. Ten days isn't a lot of time to move a bureaucracy.

However, if you need to write to him on another legitimate matter you could add a note at the end whether anything has developed about funding. If your acceptance is contingent on funding he should know that.


Qualifying exams are never to be taken lightly. Even when they prove to be a surreal experience, they need to be given the attention appropriate to their seriousness. These are exams that you typically only have one or at most two chances to pass. As a result, you want to get through them on the first try, so that you don't have to worry about them again.

How hard you have to work does depend a lot on the structure of the exam, and based on your previous preparation. If there are a lot of subjects to be tested with which you are not familiar, you may have to work harder than if you're getting A's in all of the classes that will be tested on the exam. (Even then, you'll still want to work through some practice problems to get a feel for the kinds of questions that are asked.)

As the original questioner mentions, in many cases the oral exam can be a "sanity check"—in more ways than one. If the decision has been largely made on the basis of the previous coursework and written quals, then the oral exam can act either to confirm the decisions of the panel, or as an effective psychological exam. One of my panels turned things into what amounted to a carnival side-show, with everybody acting completely out of character, and in a manner I found entirely unbefitting an oral qualifying exam. However, it made sense to see if there was any way to make me "snap" and lose my cool. (I was too busy trying to figure out why everybody was acting so oddly to really snap.)


What is expected from a post-doc application?

Is it possible to apply with a proposal like "I want to make international publications based on my PhD Thesis during my post-doc"

This is appropriate if you want to pursue a post-doc with your PhD advisor, or you want to pursue a post-doc with an advisor that will allow you to do whatever you want. It is inappropriate if the advisor has their own research agenda.

  Does someone have to formulate an entirely new research question/proposal in the application?

This is appropriate if the advisor doesn't have their own agenda.


What determines how many master/PhD students a given professor can take (STEM)?

At American universities, each department is allowed to accept a certain number of PhD students each year.  This number is determined annually by a dean or provost's office, primarily based on funding and student retention.  It could also be limited by the supervisory capacity of the faculty, but funding is usually more important.  Each department has its own procedure for matching students with supervisors.  Often the procedure is for students to go and ask faculty to supervise them.  In principal, there is nothing stopping a single faculty member from taking all the graduate students.  This probably happens from time to time in small departments.

In the case of the rumour you mention, we can guess that this professor does not have access to additional TA/RA funding at this time, and is currently only taking students with external funding.  Typically TA funding is linked to the department, while RA funding is linked to a particular faculty member's grant.


In the US as a grad student, is it normal to ask a professor for "extra" grant money for doing more research?

Whether this is acceptable or not will generally depend on whether the TA and RA are set up as "salaried" positions or as hourly positions, which can vary from institution to institution.

When set up as a salaried position, a TA or RA generally covers tuition and "living expenses," where that living expenses is a stipend intended to be sufficient to enable you to live somewhere nearby in a fairly sparse and monastic manner.  In this case, you are expected to be acting as a full-time student, a significant part of whose time is spoken for by the TA or RA duties.  In this case, it would not be appropriate to ask for a second TA or RA, because you are already being paid for your full expected working time.
When set up as an hourly position, on the other hand, the TA or RA is more of a "piecework" employment, where the school is only paying you for the particular hours you work, and taking no responsibility for ensuring that your pay can cover tuition and living expenses.  In this case, it would be perfectly acceptable to combine this with another job, including another TA or RA.

If you are in the first case and you aren't being able to make ends meet, then you may need to adjust your lifestyle to meet the level of poverty that your institution expects of its students---or else find outside consulting work (if permitted) or organize for better wages.


Second undergraduate versus masters with qualifying year

If possible, avoid the 2nd undergrad. To see if possible, pick an online copy of a typical textbook, level advanced undergraduate/graduate, and browse it for fun, and do some of the early exercises. Examples: Artin: Algebra; Munkres: Topology; Spivak: Calculus on Manifolds (or more advanced; Guillemin & Pollack;: Differential Topology); or better yet, browse whatever the curriculum of your chosen university indicated for this fall semester as text books. It doesn't have to appear easy, as you are supposed to learn it; and learning math is hard, no matter what your future classmates will falsely claim: most of them struggle too. But it shouldn't terrify you either.


Self studying and letters of recommendations

How best to organise your self-study? Pick your 10 favourite PhD programmes and look at their admissions requirements. Those are the courses you need to cover in your self study.

Then read the email you received carefully. Notice that it's not the letter that needs to be special-- it's you. You've already hinted at your drive and motivation to continue studying your subject at graduate level; why else would you devote so much of your (presumably) otherwise free time to studying it outside of classes? This effort may carry some weight with the admissions committee. Think of it as your unique selling point.

Now the tricky part: really making sure that the admissions people understand your USP before they meet you. This is your referees' job, and to help them do it successfully, it's your job to make sure they know and understand you as a student, as a mathematician and as a person.

In this task, I think communication is the key. Talk to your instructor; tell her your plans for self-study, discuss what topics interest you the most, ask for feedback on your work, chat about relevant literature, where you want to go for your PhD, whether the moon really is made of cheese-- you name it.

What I'm getting at is that for your letter to stand out from the no doubt tens or hundreds of other generic letters the admissions committee read, you need to come across as a real person with a genuine interest in your subject and the requisite skills and knowledge to back it up. And the only way that will happen is if your referee knows you as such.

(Disclaimer: I've never written or read a reference letter, but I've had some small recent successes in the hunt for a PhD place, largely (I think) due to my reference letters.)


What does archival contribution in journals mean?

Presumably, he simply meant that your paper does not have enough long-lasting contribution to your field of study. That is, there either is too little contribution at all, or the editor assumed that your paper only has a very temporary contribution which will be outdated soon.


I want to completely redo my thesis without repeating the research course. Has anyone had a similar experience?

In all of the Masters programs that I have encountered, the specifics of one's thesis are largely unrelated to the classroom courses that you have taken. As such, changing thesis topics would not be any problem as long as you have (or can find) and advisor who approves of the new topic.


Journal requires permission to acknowledge people: person not replying

I would submit the paper to get the process started, but send a note to the editor that Prof. X has not yet given permission to be named, though you have tried to contact him. The editor will make a decision. Perhaps the paper will be returned to you. Perhaps the decision to publish will be deferred, but review begun. Perhaps the editor will ask the person if they will permit. There are a lot of possibilities.

But in April 2020 the world of academia is in chaos due to a worldwide pandemic. Lots of things that used to take a while, now take a very long time. And some people are dealing with illness, their own or that of family members. Don't expect communication to be quick at the present time.

You could also explain this to the professor yourself, that you have submitted, provisionally, but will respect his decision. You can always modify the ack later if needed. The review process will take plenty of time.


Assuming that the documentation does not explicitly tell you not to email the maintainers about bugs, and assuming that there's not a forum, bug-tracker, etc. for the package, then I think it would be perfectly reasonable to contact one of them via the email address they provide in the documentation.

If they provide no other means of reporting bugs in the package, then I don't think they'd have any justification for taking offence at being contacted at an address they provide alongside the package.


Should I reply to Travel Grant Award Notification?

I don't think it's necessary, but my inclination is to just write a one or two sentence response, just saying "Thanks for the wonderful news.  I'm looking forward to the conference." This way they know you got the email and are still planning on attending.


Should I retake the general GRE or focus on subject test?

Other commentators have suggested that little notice is taken of GRE in graduate admissions, but I am a bit more reticent about this.  I think some faculty will give little weight to it, but others will use it as an estimation of your abilities (in conjunction with other evidence such as your undergraduate grades)  In any case, if you are going to submit these results as evidence of your abilities, you should make sure they put you above other applicants, instead of below them.

With that in mind, you are right to worry about your quant score - it is a bad score (relative to the program you are applying for).  The distributions of GRE general scores by intended major can be found here, and as you can see, for students intending to pursue "Applied Mathematics", the average GRE Quantitative score is 164 (SD 6).  Your score puts you above 78% of general test-takers, but it puts you in the bottom half of those applying for postgraduate maths.  Students who make it into postgraduate maths generally have very high levels of quantitative ability.  Around 20% of them get a perfect quant score in this test.

Based on this, I would suggest you retake the general test and try to at least beat the average Quantitative level for postgraduate maths applicants (GRE Quant 164+).  Your verbal and written work is well above the mean, so just try to hold your scores here, but really, you need to improve your Quantitative score.


Is it ok to include references to a book in a report even if I have not quoted the book in the text?

Felix, the short answer is no. Though you can reference a book from which you did not include a verbatim quote, but you must not ref a book you have not read and used.

Books have a legitimate role even in the life of a webmaster. I am sure the information you looked up on Stackoverflow is also covered in books like, for example Red_Hat_Enterprise_Linux-7-System_Administrators_Guide, Modern PHP: New Features and Good Practices or Hacking: Beginner to Expert Guide to Computer Hacking. Have half a dozen of these substantial reference volumes at hand and use them. Your teachers aim to build a practice they you will follow later on, the practice of using several reliable sources for the information and knowledge you gather.


What is the value of journal publications outside academia?

If you are planning to work outside academia as a specialist in your field, then you need to have academic knowledge. I don't see any value of having PhD papers publication while you are seeking non-research job positions; but, a wise employer will decide upon your CV.

As far as most of your time as a PhD student has been spent on research, so the employer is probably seeking the out put of the years you spent in university. These are the years you did not have enough freedom to work in industry, so the question here is what this candidate did at the university.

Nobody wants to hire a tired and depressed candidate who did not do well in his studies as a student and it may come to mind that he will be as tired as the years he was student, why to have him in company?!

So by having publications in your CV, you not make your CV comparative and comparable to the other candidates registering for the job; but also you will show that you are an ideal person in every situation. When you attend university, you did your best, finished your degree and have some publications; and the employer becomes more sure about choosing you. Percents bellow is my approximation of the need of publications in job market.

If I want to generally answer your question:

If you are going to be hired somewhere:

100% If it is a research job and related to your studies; then you absolutely need to show your research capabilities. So you need to prove that can do the research chores and then having paper publications is good idea.
80% If it is a research job and not so related to your field, then the title of your papers may have no significant value but you need to show your ability to conduct research and having publications shows that you have the ability and the knowledge to do research.
50% If it is a non-research job and related to your field, it seems that having publications does not make any sense but you have to show what you did in your education years, so if you don't have work experience in your CV, show that you have published something, show that you are expert in your field, have something in your CV!
10% If it is a non-research job and not so related to your fields of study; then you may not need that much publications (see my answer above).

0% to 100% If you are going to work on your own and do not have any plans to be hired somewhere, do some business, be an entrepreneur, etc., you are the one who wants to hire you, so having publications isn't significant. But keep in mind that having research publications gives you ideas to work with, opens your eyes as a specialist and opens many more job opportunities than a person who has not any insight to research. So having publications may give you many more opportunities than having no publications.

In my opinion, be firm in every step of your life, finish your PhD with most output and publications; and enter a job which is so related to your field and make use of the things you learn during your studies at the university. If you do not gain much from your education, then it seems that you have lost your time for a PhD. So what was the use to get a PhD?

By the way, I think that your question highly depends on answering to this question: What are you going to do after graduation? And, What the consequences of not having publications would be in your future careers and jobs. You are the only one who can answer these questions precisely.


How to automatically add articles in Google Scholar profile for journal?

In the comments, you list two examples:

Robotics (by MDPI), and
JEEECCS

Interestingly, Google Scholar (GS) profiles are meant to showcase authors' research, and not journals' research. (Cf. GS' self-description.)
Consequently, GS contains a function that can algorithmically add new publications to your profile based on author names. But it does not provide such an automatic function based on journal names.
Thus, if you maintain a Google Scholar profile for a journal, then you need to add all publications manually.


How can a phd student lobby against university wide publication restrictions?

Plan S is explicitly meant to change the publishing practices of researchers, and the business model of publishers. This comes after decades of half-measures that did relatively little towards open access, and nothing to prevent subscription costs from increasing. Therefore, it will be difficult to convince your university and/or Coalition S to accommodate the existing practices in your field.

Some large American universities are committed to open access, irrespective of the field: for example Harvard, or the University of California. And the situation is evolving relatively fast. In this context, it may actually not be impossible to convince conferences to offer Plan S-compliant options. Lobbying for that would still be quite an effort: the first thing to do might be to contact well-known open access advocates in the field.


Is passion a must-have for a Master's student?

Passion is not necessary for a master’s degree.

You’re still at the stage of your career where you’re getting your feet wet with research. The important thing right now is to separate your feelings about research in general from your feelings about the specific research topic you’re exploring. You can always move to another topic for your PhD, and nowadays, you’ll almost certainly have to change focus areas multiple times in your career.

At this point in your career, being able to determine that:

You love research and your focus area;
You love research but not your focus area;
You love your focus area, but not doing research in it; or even
You don’t love research

are all perfectly valid outcomes because they will help you to decide on a long-term path.


Prizes and awards: what about travel grants?

Yes, travel grants belong there, in particular if there is no other field like "personal scholarships/stipendia" or similar.
Also, you are probably overthinking this, as even if you find another more or less appropriate section and put your travel grant in both of them, it won't hurt you application chances in any way.


How can I identify research opportunities I am qualified for, and position myself as a competitive candidate, in a different field from my degree?

Frankly, most undergraduate students (and new graduates) are under-qualified to do research in any field, including their own. For various altruistic and non-altruistic reasons, we're often willing to take them on anyways.

When I hire an undergraduate or M.S. student to work in my research group, I look for qualities that tell me they'll be train-able, and also a good investment for me. Things like:

motivation (as demonstrated by showing that they actually know what we are currently working on, have looked at our publications before asking for a job, etc.)
interest in pursuing graduate studies related to my field of research
soft skills (oral and written communication, organization, note-taking, etc.)
ability to learn new concepts and skills quickly and somewhat independently
basic quantitative and technical ability

I don't expect anybody I hire at this level to have relevant experience or experimental skills specific to my lab, whether they have a degree in the field or not.

So, keep pursuing opportunities like these, be honest about your lack of a biology degree, but highlight your eagerness to learn and your "transferable" abilities.

You might also look for research opportunities in cross-disciplinary labs that combine your new interest (biology) with your previous degree (environmental science). For these opportunities, your degree might actually give you a competitive advantage over biology students.


Speaking as a researcher working in industry, I have seen no particular pattern in the citation style used by people working in corporations.  It tends to default into whatever they are used to, whatever comes most easily to them, whatever their citation manager happens to be set on, whatever arbitrary thing corporate policy has settled upon, or whatever arbitrary thing is being required by the external organization they are interacting with (just like inside of academia).


Is it normal that the PhD research proposal of a candidate be completely written by his/her supervisor without them being involved?

This is a regional practice more than a field-specific practice in my experience. It seemed to me that countries like France that are very strict on the 3-year limit for PhD students tend to have the advisor work out the research topic in advance so as not to waste valuable research time, whereas in countries like the US or Germany, where there are only practical/financial limits on the time you are allowed to be a PhD student, the advisor will more often let the candidate look around a bit at the beginning and formulate the topic themselves.

Another aspect is grant money: if your position is part of a specific project (especially if funded on one of the big EU grants), you are bound to work on a specific question anyway, so there is not really a point in letting you paraphrase a topic that was already fixed well in advance of looking for a candidate.


It is fine as long as the reference is clear. Use the language to express your ideas as best you can. But if there is any doubt, make it explicit. A friendly reader might give you some advice on clarity.
You can also use "therein" for a more remote reference.


What is the difference between a "electronic preprint server" and a "subject repository"?

I do not know of any agreed-upon definition of these terms that would clearly distinguish one from the other.

It would be appropriate to ask the publisher to clarify.  You may wish to ask specifically about the sites where you would like to upload your work.


Is it wrong to impose a challenging time constraint on exams?

The objective of an assessment can vary from one lecture to another. Quite often, the point is simply to validate whether the expected learning outcomes of the lecture have been met. For instance, if an expected outcome is to know almost by heart how to write an array sorting program, then it's quite reasonable to ask to write a small amount of lines of code in a fixed amount of time.

If, on the other hand, the expected outcome is at a higher level of understanding (in the sense of Bloom's taxonomy), for instance by asking to design and assess a new data structure to handle a new problem, then it could be more reasonable to expect more time.

The problem you are referring to by "would never have such extreme time constraints in real life" is addressed with the notion of authentic learning (Rule, 2006), which identifies the four following themes for a learning to be authentic:

  1) the activity involves real-world problems that mimic the work of professionals in the discipline with presentation of findings to audiences beyond the classroom;

  2) open-ended inquiry, thinking skills, and metacognition are addressed;

  3) students engage in discourse and social learning in a community of learners; and

  4) students are empowered through choice to direct their own learning in relevant project work.

Authentic learning comes with its upsides and downsides (the reference linked acts as a survey paper, if you are interested), so it's not necessarily the best approach. In particular, (Lombardi, 2007) note that the reliance on traditional instruction is not simply a choice made by individual faculty—students often prefer it. For instance, not everybody wants to be tested on writing code in a highly complex environment, using bugged code written by other people, implementing specifications that are sub-optimal, but the client want them in this way, which could be a typical real world situation.

I don't think you should complain about time constraints, but if you believe that authentic learning would be more beneficial to you and your fellow students, you should probably discuss with the professor about the objective of the assessment.

Lombardi, M. M. (2007). Authentic learning for the 21st century: An overview. Educause learning initiative, 1(2007), 1-12.

Rule, Audrey C. (2006). The Components of Authentic Learning. Journal of Authentic Learning, Volume 3, Number 1, Pages 1-10, August 2006


Assuming it isn't formally published, then the citation would probably include the university instead of the publisher. Otherwise the same.
Links are always a problem since they are subject to disappearance. It is good to also include the date that you last referenced it there with any link(s).
And yes, you need to cite it to avoid various plagiarism issues.


Based on your description I suspect an appeal will not work. That's because you are not disputing the reasons that went into their decision, you are only disputing the decision. But they have already made the decision. Saying "your reviewers were right, but your decision was wrong" is not likely to change their minds.
To have a real chance at changing their minds, you need to argue that their reasons for rejection were wrong, e.g.:

Reviewer said X, but X is provably incorrect, because [reasons].
Reviewer said this topic isn't worth spending time on, but your journal published [these papers] on that very topic.
Reviewer said your manuscript doesn't explain Y, but it does, and here is the paragraph.

That's not to say you can't appeal - you can if you want to - it's just that it probably won't work.
I think, based on your description, the best course of action is to rewrite the paper such that it's clearer, then submit to another journal. See also this question about the same situation where the reviewers didn't understand the paper. You can also ask the two co-authors, they should be experienced enough to offer suggestions on what to do next.


Will it improve my PhD applications if I take a gap year to work on research?

Your situation sounds similar to mine. After finishing my undergrad and not getting a PhD position, and since it was too late to apply for a full MSc, I moved to another country, enrolled just in the thesis and I worked on it for a year. After that, I got a lot of experience, a good recommendation, and a position. Now, I was lucky I could move and found a university that the only requirement for registering was finding a willing supervisor. So, I won't say necessarily that everything is lost, but it may be difficult depending on your situation.

I would advise against being fully independent researcher. You are fresh from undergrad, and with not so much experience in the field. If you work without adequate supervision chances are you will be reinventing the wheel, walking down paths that lead nowhere, or creating a beautiful yet useless theory. Your priority should be finding a professor that can guide you and provide some interesting problems to work on and feedback.

You should also keep an eye to applications in Europe: positions are opening and rolling all year round.


What are the consequences to the researcher in cases of academic fraud?

As I posted in answer to another comment, more often than not, schools want to avoid the dramas associated with plagiarism scandals. That is why schools like Harvard will prompt researchers accused of fraudulent behavior, such as Marc Hauser, to resign, rather than go through tenure revocation procedures.

But losing one's job is fairly likely, and an unofficial blacklisting is almost certain to result.

One other consequence, though, is often forgotten: the peripheral damage of academic fraud cases. Sensationalized results, such as those in the Jan Hendrik Schön and Hwang Woo-Suk cases, led many graduate students to embark on projects in those disciplines trying to reproduce and expand upon the promises implied by those projects. When those projects collapsed, a lot of graduate students were left in the lurch.


What should be included as part of a comment paper?

should [I] just list the facts with proper citation OR also justify that by some experimentation?

You should give some intuition behind facts. You needn't justify established facts with experimentation, but doing so may provide useful knowledge. If facts aren't established/accepted, then experimentation should be provided.

  I have an alternative justification which could explain the results. Should I perform experiments and prove correctness of justification that I propose?

For a comment paper, you surely need only provide facts that show the "basic assumption" made for justifying the result is wrong.

For a research paper, you could provide an alternative justification which could explain the results, along with experiments that prove correctness of justification that [you] propose.


Are pure mathematicians at U.S. universities expected to win research grants?

At my large R1 state university in the U.S., it might be impossible to get tenure without having an active grant at the time, even with an otherwise excellent record, since mathematics faculty disinterested (or hostile to whatever the specialty or person in question might be) would use this as grounds for doubting the quality. After all, supposedly, all the best people are funded. Supposedly, endorsement by the NSF (or NSA) is an external, objective test of quality. This is certainly a convenient assumption for arguments in certain directions. EDIT: and since a strong super-majority is needed for a "positive" tenure vote, even irrational ranting can sway otherwise uninformed or disinterested people to scuttle the vote.

Issues of external funding are apparently even more identified with research activity by engineers (and experimental scientists), who often dominate the college-wide tenure (and promotion) committees. That is, it is sometimes apparently unimaginable that a person would be doing research without a grant.

Further, at my university, in other hard-science departments, often large grants are allowed to "buy out" faculty from any teaching at all. This is rare in my math department. EDIT: thus, in the minds of some engineers, "teaching" is stigmatized, since in their own depts it's only the disenfranchised who have to do any of it. And then there're the wildly different paper-count standards for experimental science/engineering versus mathematics.

The literal "funding of research" usually is less critical, apart from the expense of travelling to conferences, and extra summer salary.


Emailing a professor for points on an exam when you want a recommendation from the professor

Let it go.

You discussed this before, he made his arguments and it is unlikely that he will change his mind. It isn't only up to you to make a good argument for the points, but the professor himself will have judged the points again when you discussed them and will now be convinced that the points are fair.

Begging even more for the points will probably not get you any more points, but may annoy the professor, e.g, because you already discussed it and you are still not satisfied after he told you the final outcome. He has neither the time to discuss this again and again, nor he will consider that he was wrong the first two times (the first assignment, then your previous discussion).


Frame of reference: I am a mathematician with disabilities that impair my focus and my ability to do mathematics, but not tinnitus.

Disabilities and chronic illnesses suck. Very often, there is no easy way around them. But that doesn’t mean that you should give up on mathematics, not remotely. Giving up means that you don’t even have a chance of living the life you want to live, whereas not giving up means you have that chance. Go and try. If it doesn’t work out it doesn’t work out. But don’t decide it’s not going to work out ahead of time.

It may be the case that your condition prevents you from pursuing a career in mathematics. If that happens, it happens. In a year or two you’ll be in the same position you are now, and not much will have been lost. But I promise you that if you give up on it without trying you will wonder for the rest of your life what would have happened if you had tried.

Every school in the US has an office dedicated to helping students with disabilities, and I can only assume it’s the same in Europe. I’ve taken exams in silent, distraction-free environments, gotten large extensions on assignments, and extra time on exams. The process of obtaining those accommodations can be frustrating, but they’re totally worth it. Since healthcare in most European countries is so cheap, it shouldn’t be that expensive. In the US, the required tests can run you several thousand dollars. The disabilities office might not advertise themselves particularly well, but any academic advisor and many deans or other figures of authority should be able to point you in the right direction.

Again, I cannot speak specifically to your condition, but I and many people I know have similar conditions it seems. Here are some suggestions for coping techniques:

Buy the best noise cancelling headphones you can afford and wear them all the time, even when not listening to music. These changed one of my classmate’s life and enabled them to do homework again.
Find the quietest places on campus and spend your working time there. Many universities have some libraries or reading rooms dedicated as silent zones.
Seek out locations where you’re unlikely to be interrupted. My concentration comes and goes, and the worst thing for my productivity is interruptions. If you’re working near/with friends, tell them how it’s really important that they try to not interrupt you or distract you. I had a habit of working in the astronomy tower, which was not only out of the way but had a locked room that only about 20 other students had access to.
Seek out others with similar conditions, and see if there are any disability advocacy groups near your university. The moral boost you get from being around other people with the same or similar struggles is incredible, and they might have location-specific coping suggestions.
If you feel comfortable doing so, tell all your professors. In my experience professors tend to be extremely accommodating, and will often go above and beyond what the law or university policy dictates. I understand if you don’t feel comfortable doing this, but it was a huge boon for me to out myself to my professors.
Be kind to yourself. It’s really hard on your psyche to struggle with things that used to come more naturally, and it’s extremely common for people with disabilities to become depressed. It’s okay. It’s not your fault. You’re not worth less (or worthless) because of it. Anecdotally, severe depression as a result of disability tends to cause more people to drop out of school than disabilities do. Keep an eye on your mental health and focus on healthy behaviors.


Should I participate in non-funded bioinformatics research?

The fact that work was funded says almost nothing to me as a reviewer of a paper about that work nor about the odds that such a paper is good. I think funded work is more likely to lead to papers, because the researchers have been paid directly to work on it and have better odds of making progress. That being said, funding is not a guarantee of goodness.

Your assertion that unfunded work is normally weaker and unreviewed is not well founded. Unfunded work is often preliminary work designed to prove the feasibility of an idea and lead towards some sort of publication (poster, presentation, or article) to bolster the case for later funding. This is very important work and is often done by researchers (establish and new) who are moving into a new area or working on a new direction or idea. To attribute lack of funding to weakness is fallacious.

Also, many, many good ideas go unfunded. The rejection of a grant application is not necessarily a reflection that the idea is bad, wrong, unsound or otherwise unworthy of funding. Sometimes, many times, it represents the fact that grant programs are highly selective and very competitive. Some have a less than ten percent funding rate. This means that many good applications will be turned away.

I would suggest that you soften your judgement about projects based on their funding or lack thereof and focus on which you think is a better idea for purely scientific reasons. If you truly get to pick, then I would suggest that you work on the one that's more interesting to you, will better promote your career, or may lead to the biggest breakthrough.


Can I withdraw my accepted journal paper due to data confidentiality issues?

The basic problem here is communication. You failed to do the necessary communication up-front. Now you are going to have to do it, and do it much better than your first attempt.

Firstly, you need to talk with your coauthor and your supervisor. Expect them to be unhappy that you are only now reaching out to them, and that the proprietary nature of the data wasn't fully explained.

Secondly, you need to talk with your school's research administrators. What is their policy on externally sourced data?  Is there a common form of agreement?  Is there a term sheet listing what are acceptable and unacceptable terms?  What are the ethical expectations for dealing with commercial and with third-party data? It's very unusual for a student to negotiate directly with a company about the provision of data without some formality being required by the university. The aim being to avoid your current predicament. As a result the administrators may not be best pleased that whatever process exists wasn't followed.

Thirdly, you need to have a formal meeting with the company. Do some homework to ensure that you are speaking with the right people. Take copies of your paper -- I am assuming they have seen it, but maybe they haven't looked into it. Explore with the company what the cause of their objection to publication is. Maybe you implied a confidentiality they now feel you have betrayed, so you may need to make some deep apologies. Once you know the cause of their concern you can both explore if there are ways which meet both your wishes. It may not be possible to do all of this in one meeting. A negotiated agreement will almost certainly mean a rewrite a substantial portion of the paper.

Since you have already displayed poor communication, negotiation and business skills I strongly suggest you engage with the university and see if they can provide a senior person to do most of the heavy lifting with the company.


Submitting very quickly a revised version of a paper

As long as you don't exceed the deadline, I don't think it really matters - it won't get "more accepted" for being resubmitted quickly. Of course, sometimes it can help getting it into production faster.

However, if you have spare time I'd suggest not rushing the resubmission. While you could get away with taking a day, consider taking closer to a week. Forget about the paper for a couple of days, and carefully proofread it again - both the revisions, and the unchanged parts.


How can a PhD in Machine Learning and AI help you in a life out of Academia?

Working at your startup

One thing for sure is that, if you want to start a company (a startup), you should not be afraid of being overqualified, since you will be "the boss" and there is no one to classify you as such.

Working in the industry

While being overqualified sometimes (perhaps, even, often) applies to positions in the industry, a Ph.D. graduate is highly unlikely to be considered as such in ML/AI domain, where it is often a requirement for most positions.

Working for other people's startup

Even though most startups generally don't care about degrees, those, working in ML/AI-related domains, will be happy to consider and hire a good Ph.D. graduate for the obvious reason: due to relatively high complexity of the required ML/AI-related subject domain expertise.

P.S. Please note that my answer addresses only your concern of being overqualified, but does not touch a larger question of feasibility of your plan, factors to consider in decision making and so on. However, it implicitly suggests that this one of possible routes to achieve your goal (whether it's the best or the optimal one, depends on a lot of factors, including your personal circumstances).


Can I show my long-term research interests on SOP, which are very important topics but aren't constantly researched yet

Only put something in your SOP as a research goal (short- or long-term) if you can make a credible case that (a) you understand broadly what it's about, and how it fits into your field as a whole, (b) you're capable of achieving it, and (c) the department you're applying to is a good place to do it, or start to do it. As an extreme example, saying you want to cure cancer is a bad idea because it's not realistic. But even saying you want to get into cancer research needs to be supported by evidence that you know something about it, and about the cancer group at the department you're applying to.

If you can't satisfy conditions (a), (b), and (c), it's not necessarily a bad thing, it just means you should be less specific about your goals. You could say, for example, that your end goal is to do research in applied CS, including bioinformatics. Then talk about what you've done already in that area, the skills you want to learn, and why department X is a good place to learn them. Make sure to keep it as focused on CS as possible. The last thing you want the committee to think is "why is this person applying to our department and not stats/applied math/biology?"


Is there any free alternative to Mendeley desktop app on Windows?

Zotero is a free (and open source!) alternative: https://www.zotero.org/
There is a plenty of other tools (just google 'citation managers'), but I believe that Zotero's open source nature renders it preferable to all alternatives - including Mendeley, which belongs to the large commercial publisher Elsevier.


What's the best way to share my presentation slides online?

I typically post my slides on my website as pdfs.  On the title page of my slides, I have started adding a line that says something like "slides available on my preprint page", and sometimes I'll mention this at the start of my talk.  On my website, I have a page for all my slides and I also link to the relevant slides on my preprints page.  Personally, I prefer when speakers make their slides available as pdfs, because I like being able to download them and file them away, rather than needing to bookmark a website.  Similar to my preprints, I'm excited to have folks download my slides (so I don't see any reason to control their distribution).


One of the key questions for any piece of scientific work is this: how does this work contribute to human knowledge?
If a work fails to even discuss its relationship to prior work, then it is entirely appropriate to reject it. Likewise, if the authors mention algorithms that are directly comparable but fail to actually make a comparison with any of those algorithms. When I am given a paper that is entirely isolated in this way, I will not even bother to check the details of the algorithm's soundness, since the work already has a major disqualifying failure.
For many algorithms, however, the differences are qualitative and not quantitative, and thus a direct comparison would be unenlightening or pointless.  For example, if algorithm X tolerates a class of failures that prior algorithms do not, then it is enough to show that algorithm X tolerates those failures.  One does not necessarily need to re-prove or empirically demonstrate that the others do not.
Likewise, the number of potentially related prior works is often vast and complicated. No algorithm paper will ever compare to all of the other related algorithms, because "related" is a broad and fuzzy concept. You and the authors will generally not make the same judgements about which algorithms might be interesting to discuss in related work or to directly compare against.  Thus, the standard to which you should hold related work is not "Do I want to see comparison against Algorithm Y?" (that's Evil Reviewer #2 behavior) but rather "Does the comparison provided sufficiently support the author's assertions?"
Bottom line: be generous in your judgement of comparison to prior work, but papers with no meaningful comparison should be rejected.


Getting into a doctorate program with B-

Since I am frequently a member on the PhD student admission committee in our math department, I can tell that B- in one class does not really affect the chances. What affects it are recommendation letters and  Summer projects (REUs).
If the letters are not very strong and there was no (Summer) research done, the chances at my department are very small.


How can I cite an company website using IEEE style?

Software available online should be cited as a website, following the description given in the various IEEE style guides.  The easiest way to do this is typically with a citation management system like BibTeX.


Panic Attacks during an exam - Can the student be re-tested?

If you are in the US, your school is required by law (the Americans with Disabilities Act, often abbreviated ADA) to make reasonable academic accommodations for students with disabilities. This includes mental illness.

In the US, schools have a formal ADA policy that describes the procedure for requesting accommodations. This includes a description of who to contact to make these arrangements. This person is trained in dealing with these issues.

Your next step should be to contact this person, find out what can be done about this exam, and find out what accommodations they can offer for future exams. (For example, they may help you arrange to take future exams in a separate room with no other students and/or with extended time, which may help you stay calm.)


What is a good length for the statement of purpose in a U.S. PhD application?

Depending on the program I would keep it between 1.5 to 2 pages.  I framed mine to answer the following questions:

Why am I applying to this school.
What are my research interests.
Previous academic accomplishments.
Previous professional accomplishments.
Personal story of triumph (optional, I talk about having to drop out of high school to support my family)
What is your goal after graduation.

Addition:

I would also target schools that are pumping out the research that matches with your interests... this will help when you are stating why you are applying like:

  A major factor in helping me choose Awesome University was Professor Awesome's research on being awesome.  I feel that this aligns well with my research interests, and would make for a great fit between me and the department.

Also, if you talk about any abstract ideas be sure to elaborate on them to give a level of specificity.  They want to see you be able to translate abstract ideas into specific thoughts.


Ordering of co-primary authors on website

In Can co-first authors’ positions be swapped in a CV?, the answer with the most upvotes says

  No. The reference is the reference, changing it to move yourself higher could be misinterpreted as willful deceit.

I believe the same logic applies to a website.

However, in a website, you do have more freedom in style and formatting than you would in a CV (although you still don't have the freedom to change author order...) For example, if you want to call attention to first authorship, you could list first authors and co-first authors in a slightly different weight or different color than the other authors.


Asking a professor if you would be able to manage the material in their graduate course given lack of background

I get multiple emails about this every year, so I certainly consider it normal.  It's my impression that most faculty will.
Before you do that, see if the syllabus is available to you somewhere.  That will show the professor that you did some due diligence on your own, and may even answer your questions.  Also note whether or not the class has a firm prerequisite listed - if it does that may make this more challenging.  If it does not then that suggests to me that you've got a better chance at success.
If you're still not comfortable asking, or the professor doesn't reply, you should be able to get help with this from your academic advisor.  They may be able to secure the past syllabus for you also, so if you prefer that route it might suffice.
Another suggestion is to consider asking about auditing the class - if it's outside your department and isn't necessary for your degree, maybe that would be enough to help you with your research.  A related element would be asking to take the class pass/fail, depending on your university's restrictions on such a practice.  That would allow you to take the class and, even if it's a struggle, all you need to do is pass in order to come away with what you need from it.


I don't feel confident about my place in research. I am objectively less equipped for this career. How to move forward after a PhD?

While I'm not convinced it isn't just imposter syndrome, I'll also assume that you know something about it already.
However, you sound as if you know how to get the job done in research, focusing on what is needed to perform well. It isn't necessary, of course, to know everything before you start a project. Little would get done if that were true.
However, note that the situation has changed. In grad school and maybe in the post doc you were surrounded by a support system of people that you could bounce ideas off of and get feedback. The more independent you become the less automatic that is. So, I suggest that you try to reproduce that environment virtually by forming (or joining) a circle of collaboration.
A lot of very productive people maintain relationships with their former advisors and become part of that person's network. They invite others to come and speak or they go elsewhere to speak (and meet and collaborate).
It is very difficult for most people to do serious research in a vacuum. A few can manage it, but the collaborative network is a much richer environment for the generation and testing of ideas.
It doesn't have to be a classroom. You can take a much more active role.


Is a combined BS/MS in math a good idea for pursuit of PhD?

I finished my undergraduate degree at 20, and I know a number of others who have finished undergraduate considerably younger than I did. So, no, 20/21 is definitely not too young to apply for and begin a graduate degree program.

Since you list yourself as a US college student, here are a few questions to ask yourself before embarking on a dual-degree program:

Who is going to pay for the MS part of the program? You may not want to have to pay out of pocket the extra costs of the master's, when it would normally be covered if you picked it up "on the way" in the PhD program.
Are you happy with your choices for a research advisor for your master's thesis? (No point in being miserable by working for the wrong advisor—even if it is a semester or two, a miserable time is not what you want.
Where do graduates of your school's master's program end up for PhD programs? Are these schools you'd want to go to? (You can ask the same question of the bachelor's program, of course.)
Who will write your letters of recommendation? Do you have people who know your work beyond the classroom well enough to recommend you for external graduate programs? If not, this may vote in favor of staying for the master's program.
Do you have to make a decision about which program to do before you apply for external programs? No point in making a tough choice if you can keep it as a "fallback" option.

As for topics and coursework, I will leave those answers to the mathematicians.


If it is stated that two authors have contributed the same on a research paper, are both authors co-first authors?

There is only one first author. But the 'prestige' associated with the first author, in certain fields, could be extended to a second author.

An example:

  The two authors contributed equally to this work

(source: https://arxiv.org/pdf/1404.7748.pdf)

When cited, this work would be "Najman and Cousty" ("Najman"/"Najman et al" in some contexts, if more than 2 authors), but it is clearly stated that both authors contributed equally, so they both share the 'main author' credit.

(this is the only example I know of this approach, they were my phd advisors - yes, both of them)