How to contact a foreign professor and ask him to cooperate in a research work?

Can I apply to the same professor for a Ph.D. position who I am going to work with him on this project?

Yes, at least at US institutions this would not be a problem. I don't know of any reason why it might be problematic anywhere else.

Is it constructive and has a positive effect on my application process? If yes, could you please tell me how can I explain the situation to a professor to persuade him to work with me. I mean let me know how can I take the advantage of this project on my application process.

As I mentioned in my comment above, it's often an advantage to have previously contacted a potential advisor and discussed working with them. Many prospective graduate students "cold email" professors to express interest in working with them, discuss potential research projects and--usually the primary reason for emailing--to make sure the professor recognizes their name and remembers them when actually reviewing applications.
Having a particular topic or project in mind tends to be a positive--as long as it's something the department or professor you're applying to work with is interested in. The only downside to having a specific project in mind is that it might be limiting if the professor isn't interested in it and you haven't expressed any interest in things they DO want a student to work on. That seems unlikely if you're selecting them as a potential collaborator because their work aligns with your project, but I'd make sure to explicitly state that while you want to work on this project, you are also interested in ___ (things that they study that you would be interested in doing for your PhD--read their webpage to get an idea of their broader research interests and ongoing projects).
In general, when emailing potential advisors/collaborators, keep the following rules in mind:

Be polite and respectful! Don't ever come off as arrogant/demanding/expectant.
Mention who you've worked with--you'll gain credibility if they know your advisor, respect your institution, etc..
Demonstrate that you've done some background research into what they do--mention work they've done that interests you, papers you particularly liked, etc.
What can you offer to them or their lab? Describe your background, strengths, interests, etc... show them (without being arrogant!) why you think working with you/taking you on as a student would be worth their time.
Show your enthusiasm!
Try to keep it as brief as possible while still including all relevant information--be succinct. Professor are extremely busy and get about a zillion emails a day. He/she will probably not bother reading your email if it's super long. Also on this note, make sure you include enough info to snag their attention in the first few lines, since that may be all they read if they aren't hooked by then.

An example email would be something like the following (reorganized/worded as needed):

Hi Professor ___,
I'm currently finishing my Msc. degree at [institution] with [your current Professor], and am planning to pursue a PhD in [field] this coming [whenever you'll be applying]. My thesis work has been on [describe your research].
I'm contacting you for two reasons: first, I'm considering applying to [institution], and was wondering if you are currently accepting new PhD students. I'm especially excited about your work in [topics], and [describe any particular topics where your interests intersect with his/her research, strengths you have that would be particularly helpful in pursuing this/these avenues of research, etc.--e.g., I think my background/experience in __ would be an asset in studying __].
Second, one of the outcomes of my thesis work is [describe your ongoing project], which I would like to work on as a [side project/chapter/Phd project/etc. depending on the scope of what you have in mind]. We have 1 year of funding to complete this [maybe include more details--mentioning the funding is very important since it means you come with support!], and are currently looking for collaborators to [describe what you need them to help with]. [Explain why you think he/she would be the perfect collaborator].
I'd love to discuss potential PhD research topics and collaborating on our __ work if you have time in the next [give them a reasonable but discrete timeframe--few weeks is usually good].
Thank you for your time,
Arash


Referee reports I have written in tenure packet?

Absolutely not.  Referee reports are confidential, especially for papers that were rejected.  Including them in your tenure packet would violate that confidentiality.


Author order - seniority vs contribution

Assuming you are a junior researcher like a PhD student, I would defer to the professors to sort this issue out themselves. Voicing any opinions about this matter could have a non-zero probability of stepping on someone's toes.

Given that, there is essentially no perceived difference between second and third author. And in the two possibilities you just described, all authors 'get their due', so there is no issue about fairness here either.


Is it a terrible idea to aim for a lower journal for a paper?

From my point of view, there is nothing wrong per se with submitting to a low-tier, non-spam journal. I have always maintained the position that if you find out mid-way that your work isn't what you want / should be doing, it's better to submit what you have to whatever is achievable at this point than to either stick it out or throw the work away entirely.

However, in your case it actually sounds like you may want to go for another iteration at the mid-tier anyway, because you don't think your work is that bad, it's just the write-up - and this can be fixed with a modicum of effort, in the worst case re-writing the paper. Also, assuming you are an early-stage researcher, getting more writing practice is basically never wasted effort. In the end, we are not talking about investing a year more into this project - it's a few more weeks for re-writing, and then some on-and-off effort for revisions. Finally, would it not be annoying to you to "waste" your work to a low-class venue just because you did not want to write it down properly?


A current PhD applicant in a dilemma between current lab and other programs

I would suggest that you be as open and honest with your current supervisor as you can. No surprises, no evasion. Tell him your list of schools. Tell him you want to aim as high as you possibly can. From your current A+ school, possibly to an A++ school.
I have known some students in your position. A student who excels under a professor makes the prof look very good. If that student goes on to one of the very tip-top schools after working with the prof, the prof's reputation grows. Maybe he is sad to see you go, but he should also be glad to see somebody he taught go on to Big Things.


The PURL service (https://archive.org/services/purl/) allows you to create a persistent URL (e.g., "http://purl.org/my-thing") that redirects to a specified target URL.
You have the flexibility of changing the target URL at any time (e.g., when the target website undergoes a content reorganization or web host migration, breaking the previous URLs).
Also, partial PURL redirections are supported, for which you can use one PURL record to handle all resources that share a common location prefix (e.g., "http://purl.org/my-doc/A" redirects to "http://example.com/doc/A").
If the target website is yours, then you may need to shop around for a suitable web host;
free web hosting services may or may not be sufficient or appropriate, depending on the size and complexity of your website (dependencies on frameworks, databases, etc.), expected traffic, whether you mind serving ads, etc.
If the target website is third party, then you may need to monitor it over time to ensure that your PURL remains valid and accurate.
The PURL service is hosted by the Internet Archive, which IMHO will be around for a long time.

Wayback Machine (https://archive.org/web/), also hosted by the Internet Archive, is another option, especially if the webpage contents are relatively stable (or immutable).
This service allows you to "capture a web page as it appears now for use as a trusted citation in the future".
Other similar webpage archival services include
Perma.cc (https://perma.cc/) and
archive.is (https://archive.is/).
These options work best for simple static webpages (text and images);
I recommend testing them carefully to ensure that the archived version of the website is sufficiently accurate and that you do not lose too much functionality.

figshare (https://figshare.com/) is yet another approach along the lines of open research.
This is a "repository where users can make all of their research outputs available in a citable, shareable and discoverable manner".
figshare issues a DOI for your uploaded content.
This could work if you can package the website contents suitably for viewing through figshare.

Finally, you can also directly create a new DOI for your website through a suitable DataCite (https://www.datacite.org/) member (see list of current members).

Assuming a simple static website, I would suggest the following steps:

Host your website on a free web hosting service (e.g., GitHub Pages, Neocities), create a PURL to point to it, and include the PURL in your paper and the website itself (use partial PURL redirects to handle individual pages that share a common location prefix);
Archive a simplified snapshot of your website (perhaps on a single page) on the Wayback Machine, and include the resulting link on your website too; and
After the paper is published, add the complete paper citation with DOI to your website, and archive it again on the Wayback Machine.

I believe this should help readers of your paper find your website and/or its contents long after the paper is published, using the published links or general search engines.


You have a lot of questions all interspersed within your question block so I will try my best to answer. Here is a disclaimer:

Disclaimer: I am a past graduate student of the Indian Statistical Institute

Mathematics research, especially in theory, is pretty good in India. The top institutions (in no order of ranking) are:

Indian Institute of Science, Bangalore
Indian Statistical Institute (Kolkata, Delhi, Bangalore, Chennai)
Tata Institute of Fundamental Research (Mumbai, Bangalore)
Indian Institute of Technology (KGP, Kanpur, Delhi, Mumbai, Chennai)
Institute of Mathematical Sciences, Chennai
Chennai Mathematical Institute, Chennai

All of these are quite good internationally and attract the best Indian students. The entrance exams are quite tough and many of the BS, MS students go on to do PhDs in top world institutions. Those who stay, are also quite good and publish papers in the usual top journals. The problem is neither funding nor red tape in my opinion.

The problem is that compared to most "top" mathematics departments, these institutes are rather small (i.e. ISI Bangalore had ~only 20 full time faculty in my time and of those, 10 published regularly). You see, its only in recent years, that regular publications have become quite the norm and its usually being driven by younger faculty (usually those who have done their PhDs from US or Europe).

Please see him, him and him for reference in theory and on the applied, computing side, him [He is my MS thesis adviser] This is one small example from one school. I can assure you that the situation is similar in the other schools that I mentioned.

Most Indian PhDs go on to do postdocs internationally. Why just last year, we had a postdoc (who finished his PhD in ISI Kolkata and was joining IIT Bombay this year) in the ML lab here. He was great and very smart.

In conclusion, if you get a PhD in Mathematics in India and do good research while you are at it, I don't see why you shouldn't get international postdocs. Tenure track job positions will be restricted to the Indian subcontinent and south east Asia because USA and Europe have their own PhD glut problem. But, thats cool because most of these schools I mentioned are hiring very well. In fact, I plan to apply for several tenure track positions in CS departments in India when I graduate.


How to start the Background section of Research Grant application?

Assuming that the funding agency has no guidelines, you can write it so that it makes the most sense to yourselves and, hopefully, for your readers.
The why can go elsewhere, of course, such as in an introduction or abstract (if short). Whether it is a mistake to just avoid the why of it is a judgement call that only you can make. Some problems are well enough known that a reader will understand without any explicit statement. But not everything is like that.
Write it up and then make a judgement about how it fits together. Take the likely knowledge of the readers at the funding agency into account. If they are likely to be generalists, you may need to say more. Less for specialists.


Yes, it makes sense.

Doing so will add value to your thesis, if you do it well, and help the readers. Most people don't do this because they think of it too late or do not have the energy. Start doing it early and do it well, or don't do it at all.


If you make your code public, you need to think about the consequences. If your goal is to contribute toward academic research, the GPL should cover you just fine if someone wants to use your work. Remember, this means people can (and might) use your code for their own work. This doesn't stop someone from taking your incomplete idea and running with it. However, it can ensure that you are credited for your contribution (at least in the codebase) and that your code cannot be monetized for someone else's benefit. But remember, this is the internet we're talking about. Not everyone is conscientious.

I generally go by the belief that an idea is worthless without execution. Thus, if someone beats you to the punch, it sucks but that's life. Nevertheless, the best way to curate a good idea is to get input from others, hopefully some of whom may be more knowledgeable about the topic than you or have different takes on it than you. Therefore, it's a cost-benefit trade-off. You should decide whether the risk of someone completing your idea outweighs the potential improvements you may make from sharing your work and receiving feedback. If so, don't make it public. If not, share it with the world and seek informed feedback.

I am personally inclined to go with the latter case. There's a lot of stuff out there. The chances someone steals your ideas are often pretty slim.

To answer why people are often so afraid: I think most people have tunnel vision about their work. Because everyone is an expert on their own work, it seems pretty easy to them. They've also put so much time in to it that even the most minute chance of someone taking their idea frightens them. Having read plenty of OPC (other people's code), it's usually a pretty high bar for entry in order to actually try to steal someone's ideas.


Following up on a postdoc application at an academic conference in person

You could try to reach out by email and tell them that you've applied for a postdoc position in their lab, and that you are going to be at the conference where you'd love a chance to discuss your research contributions and qualifications as well as the opportunities that they may have. If they have an interest and tell you as much, by the time you two meet you both know why you're talking to each other.


You want to ask some trusted people in your department whether such a grant would qualify as grounds to renegotiate your contract, as standards for this matter differ widely between universities and departments. Further, what exact grant you won matters much more than the sum - it's ultimately more about the reputation than about the money.

That said, my suspicion is that a 200k grant will not be a reasonable token for any serious renegotiation. While a very nice boost for a young lecturer, such grants are ultimately bread-and-butter for the university, not something that would trigger them to radically rethink your position and rank in the university. Usually, the only grants I see people occasionally use to renegotiate immediately are the top-level personal grants (ERC, or the respective national equivalents) - the type of grants that very few individuals in the entire university get, and which make a dean nervous that you might also get wooed by some other universities to leave and take your grant with you.


I feel that I have a weak application. Should I take a gap year before applying to grad school?

I think you are overemphasizing the importance of the GRE. Consider it as a box you need to check, rather than "the most important factors in admission". Still, you should get started on that process only because opportunities to take the test are few and far between, and if you are ill the day you intend to take the test or otherwise do poorly, you might want a second chance.

I think you still have time to get some research experience. I don't know what is available in your field of study and at your institution, but in my field I would recommend you find a lab that would possibly be interested in hiring you on in the spring after you graduate, assuming things go well in the fall. Although applications will be due before that spring semester, at least you will be demonstrating your interest in research, and hopefully you can get a decent letter of recommendation from your research advisor.

I would also suggest finding a faculty mentor: not an administrative academic advisor, yes, those people are mostly interested in your undergraduate progress, you need to talk to professors who have gone through the grad school experience, who are involved in admissions for graduate school, etc (of course one of the disadvantages of a smaller state school is that no one there may have experience with graduate admissions, except as a student).

I don't think there is an either/or question here. If you are set on doing graduate school, you should apply and plan for what you might do to make your application better next year if you don't get into a program you like this time.


Wondering Wether to tell the Truth to another PhD program that I have resigned from the first one

How I should answer about my experience at ex-group and how I can call it in a way that didn't leave a bad impression?.

In these situations the more neutral you are the better. However, you should never lie on these matters. As you said, the group is well known, and the world can be very little sometime. On top of that, it is not very ethical.

I do not know what happened with your previous group, but try not to blame them too much. Again try to be neutral without going too much into details. I would put something like "My team and I did not make a perfect match" or "The topic I choose was not a good match for me". Keep in mind that they may contact your previous group to ask their opinion on you. Moreover, every person is different, maybe for some people it is ok that PhD students do not always end up with the perfect mentor for them, for other people this is not acceptable. For this reason, there is no perfect way to answer them, but for sure, I would avoid omitting important information.


google scholar citation for github repository

No, your name is not on the paper so you should not include it on a list of your publications. You can, of course, list it as an achievement/project/experience on your CV/Website/ORCID/whatever.

If you think your name should have been on the paper and you were not consulted prior to submission, you can inform the journal. This will be a quick way to make enemies of your not-quite-co-authors, however.

You can make your code "citable" (scare quotes because "citable" is being used to mean creating a version of record and a DOI for it, rather than merely being allowed to cite it). There are various repositories which will allow you to get a DOI for non-publication work, here are some examples:

GitHub/Zenodo - integrates directly with GitHub
Figshare - not just for figures, despite the name
Mendeley data - owned by Elsevier, so perhaps can have reasonable confidence in its staying power

Another option is the MethodsX journal, although you'd have to check that your work is suitable for the journal and not going to constitute double-publication. As this is a peer-reviewed journal, it gives you a higher level of "credit" than the other options above. Note, there is a mandatory open-access charge with this journal. (Or, even, if your code is distinct enough from the paper, you could look at publishing a full paper of your own in an appropriate journal; there are lots of software/code papers, even in non-CS fields.)

As you wish for the code to appear on your Google Scholar profile, you will probably need to choose MethodsX (or another Journal) as Google Scholar only indexes article-type documents. You could manually add the others to your publication list as an "other" type publication, but you won't the full suite of scholar features (citation monitoring etc.) that way.

Finally, unless the code is entirely your own work, any of the above will require communication with, consent from and credit to your collaborators (presumably those who published the paper you weren't on).


What if your reviewer told you need to cite author A and Author A is you?

If it's a wide practice in your field to remove self-citations at the submission stage, and a well-known practice, then reviewers should be aware that the conscious omission of author A should be a sign that author A might be an author of the work under consideration. This suggests that the reviewer may not be aware of the convention—perhaps it was written by someone relatively new to your field.

I would just proceed by incorporating the comments, and explaining to the editor why you broke with convention.


Can you increase your undergrad gpa after graduating?

Yes, it is possible.

Faculty at my university have the right to change their course grades up to five years after the course ends.  I have a standing offer that if any student publishes a research paper as a result of work in my class, I will retroactively change their grade in that class to an A+.  I have actually done this a few times, in one case two full years after the course ended.

(All the students involved in those changes already had A's, and my university counts both A and A+ as 4.0 in its GPA calculations, so the change did not actually change their GPA.  But in principle, it could have.)

But this is the only way I can imagine a student at my university changing their GPA after graduating.  In particular, I believe the university maintains separate GPAs for different degree programs, so taking any post-bacc or graduate courses would not effect their bachelor GPA.


PhD requires technology - is this something I will have to fund?

As a student, you should not be required to fund equipment purchases yourself.  Rather, it is your supervisor's responsibility to work with you to scope a project that is within the funding that they wish to allocate to it.  So if your supervisor wants to do a study with 15 people, your supervisor needs to have a sufficient budget to support it.  Otherwise, you might end up, say, doing your work in simulation instead, which is much cheaper but less convincing in its results.

Now, some students do buy small things themselves, especially if it is a low-cost "toy" that they want to play with themselves (e.g., a Raspberry Pi or a phone sensor pack) and they don't want to go through the delay and hassle of university purchasing.  That's an exception, however, and certainly not to be expected for a multi-user study.


Are official transcripts required for faculty appointment?

In the United States, at least, the norm is that you send official transcripts once you are offered the job.  At my university (and I believe by SACS regulation) the transcript(s)/degree(s) must be on file with the university for all faculty members, thus it is a requirement to be able to get the job.

During the application process, though, unofficial transcripts are generally sufficient, if they even ask for it.  Sending official transcripts to 100 different places in the application process would get very expensive, very quickly. For example, if they wanted from every post-secondary school I had attended, I would need to request transcripts from no less than 8 different universities, some of which would just have a course or two I took in summer programs abroad or were unrelated to my field. Even if they only needed my terminal degree, at $10/transcript, it adds up fast in addition to being a gigantic hassle for everyone involved.


How to efficiently (and aesthetically) display an evolving publications list on your webpage?

(this is close to a shopping question, so I see some danger of this being closed - however, I think the question comes up for enough people in academia that it warrants an answer here)

What I have found most efficient is to indeed generate the publication list from a hosted bibtex file. The solution that I went for is to have a repository at Github Sites where I can commit my bibtex file (and any other static resources I want in my web page, including pictures and preprints), and then I generate the actual publication list using JavaScript code I extracted from the bibtexify project.

The result looks like that, which I find visually quite pleasing:

A live version is available on my website. To get access to the code you can clone my public GitHub repo. Then the actual publication list can be rendered on any website using some JS/CSS code. This should work either in a stand-alone Web site, integrated into whatever your university uses for hosting (as long as JavaScript / CSS code is allowed), or a CMS such as Wordpress.

Advantages of this approach:

Easy to update (just update the bibtex file and commit it)
Responsive (also works nice on mobile etc.)
Very few assumptions on the hosting environment - it just needs to support JavaScript and CSS.

Disadvantages of this approach:

Setting everything up is a bit hacky as you need to plumb together some JS/CSS code (but once it works I found the solution to be quite stable)

If there is interest I can try to find some time to write more detailed instructions on how to set everything up.


How to supervise an undergraduate reading a paper for the first time?

I would ask the student for a written summary of the paper as they understand it along with a list of questions they have about the parts they don't understand. This can give you an idea of whether they are on the right track or not.

Make sure that they understand that it is just a summary (main points) not just a restatement of the whole paper, which might be able to be done with little real understanding. What is important about the paper.

The questions are also helpful for your guidance. But you don't necessarily need to answer the questions. If the student is diligent, then you can help them by pointing to how they can answer the questions themselves: a book or some computation, whatever.

A couple of cycles of this and they might even have an outline of their final report.

There is another benefit to the student, actually. They not only get to practice writing, but they get to plan what they say and the questions they ask. This is probably more comfortable to many students than facing a professor who asks them questions that they need to quickly come up with a response for. Some students will freeze up and seem to know less than they really do.


Simply state the honest reasons to your supervisor why you are quitting, in a respectable way since you might want to hear his/her point of view also. That will give you complete closure, and it will be satisfying for the future you.
There are three possibilities:

If he is not interested in guiding you, he will not even try to understand your situation. It is a win situation for you since you made the right choice.

He might have other reasons for not supporting you. Probably he does not want to spoon-feed you. Or maybe he going through something much worse than you. It is easy to judge another person.

You are simply not interested in the subject. The opinion of the supervisor might not move you.

After the conversation, think about it for one day or two. And, email him about your final decision.

Note: There is no need to feel sad about it. You should be happy that you figured it out early. I wish more people could be like you.


Remote PhD Using My MSc University's Lab

It depends on the country and the PhD program.

In the UK, you could look for a relevant supervisor in nearby universities (e.g. a couple of hours drive away) who might be interested in your proposed project and might be able to fund it (even if you don't need lab space, you'd pay fees etc). You would probably need to meet with them (and other academic supervisors / trainers) every quarter, with more frequent email / phone / video contact - depending on the particular universities rules & regulations. I've seen lots of people do these sort of multi-site projects.


Can my supervisor use my code in his paper without acknowledging me?

A lot of questions here are left unanswered.

Are you a student?  A staff programmer?  Do you have a work-for-hire agreement with the university?  Is it just your implementation, or is it your original synthesis of several algorithms?  Is the synthesis something that is novel & not obvious and do you think it constitutes a significant intellectual contribution?  Have you previously published about this synthesis and if so is that cited?  How core is the use of these algorithms to the main results of the paper?

It might be reasonable to point out to your advisor how it would be helpful to your career (ability to get a great job after leaving, etc.) if your contributions are recognized in the papers that use them, at least in the acknowledgements section.  It may be that for whatever reason the supervisor hasn't thought of this (or doesn't remember when writing it up close to the deadline) but may be very willing to do so.

If you are a student and the supervisor is your academic advisor, you may also ask questions/have a conversation about what authorship means in your field and what the expectations are for what contributions warrant authorship in your collaborations.  Part of an academic advisor's role is to teach their students about these sorts of things.

If you don't feel comfortable with a direct conversation or with the results of one, go to your program director and see what their perspective might be.


Is academia right approach in order to implement an idea presented in my MSc Thesis?

I think the very first thing you have to do is outline what time, skills, personnel and money is necessary to realize your idea. What is the technology readiness level you have achieved so far? At which point would you need industry help to develop the product? High-technology product development can easily take 5-10 years from lab idea to a certified product. A university/PhD is not a money source for a undefined part of a bigger project in its self-understanding.

For a PhD you have to publish and technical optimizations are not the scope of most journals. Could you publish single development steps? This is something you have to ask and plan with a possible supervisor.

Sometimes this is a good idea, especially as there are many funding sources for academia to develop and realize ideas together with industry and industry often has not the time/skills to write proposals. But also then, the PhD students often have to submit a project plan of their future PhD work, they get paid for working on working packages of the industry project and have to find and outline work separated (best case related to reduce work load) from these working packages to write a PhD thesis with scientific results rather than technical optimizations.

I just got funded such a project based on results of my master and PhD work and a following idea, identified possible university and industry partners, wrote proposal etc, got funded (overall 6-12 months minimum till money is available/project start)


Why is novelty mandatory for a Ph.D. degree?

Novelty is a basic requirement in research because without novel results, the work is of at best limited usefulness. It's not useless - review papers are useful - but it's less interesting to the people at the frontier. In the case of a PhD, it is supposed to signify a student is now capable of doing research. Research (as opposed to literature review) necessarily involves new and novel results. Therefore novelty is a requirement.

If I understand your last paragraph right, you're wondering about open problems which might be too complex to solve in one go. But in that case, you still get new and novel results - they might be partial results, but they're still results. The same goes for research using new methods that turn out not to work: knowing where not to look is not as useful as knowing where to look, but by narrowing the parameter space, it's still useful.


How can I tell if an honor society is legitimate?

In all of my experience: no one within academia cares about honor societies whatsoever.  To expand on that: in academia we routinely (closer to constantly) evaluate people based on their academic qualifications, in a very serious way: i.e., the "winners" get offered substantial scholarships and/or jobs.  Not once have I ever heard anyone mention membership in an honor society in any of these decisions.  Not for faculty hiring, not for graduate admissions, not for picking TA's...never.

When I was an undergraduate I did join Phi Beta Kappa (junior year: whoop de frickin' doo) and Sigma Xi.  The way I recall it, I was moderately encouraged to do so by my undergraduate program.  And I must say that the amount of money that I gave to these people -- if any; maybe my school paid it themselves? -- was truly negligible: at most $40, or something like that.  Based on this money, for many years afterwards I got:

Regular newsletters from the organizations that made what looked like reasonable attempts at giving me some kind of scientific / academic contacts.  (Not that I read them...)
Semi-regular very strange calls offering to sell me gold-laminated books and other such frippery.  Often these were done with enough of a "hard-sell" solicitation to get me a little steamed: one caller spoke breathlessly about the gold-laminated books and at the end asked me how many additional copies I wanted to order at a discounted price.  I mentioned that she skipped an important step, and she asked what that was.  I revealed that at no point in the conversation had she asked me whether I was even the slightest bit interested in buying anything from her.  The rest of the conversation was brief but tense.

Based on these experiences, whenever any student asks me whether they should join an honor society -- the ones which are not supposed to be scams, like Phi Beta Kappa -- I say "I do not advise you to do it if you have to pay more than the most negligible amount of money."

However, I have occasionally talked to other faculty and university personnel about this issue, and their experiences are not always as negative as mine.  What I suspect may be true (but I have unfortunately never had the occasion to find out!) is that: academic honors societies may be useful for people who are leaving academia, by providing some kind of modest continuing contact with the academic world.  I mean, the idea that I need to open up a bi-annual newsletter and read about what other academics are doing makes no sense for me: I learn about what other academics are doing by going to work.  But for people who go off into industry -- or something else -- maybe it is valuable.  On the other hand, I have to imagine that, as with so many things, the internet makes this kind of thing largely obsolete: the amount of access that any citizen of the world with an internet connection has to current academic activity is greater now than what any professor had twenty years ago.

One final question: does anyone care if your CV says you are a Phi Beta Kappa (junior year!)?  I suspect not -- as someone else mentioned, these awards are given for your GPA, and you put your GPA on your CV anyway.  But I would, as ever, be interested to hear other perspectives.


PhD dissertation burnout duing pandemic (COVID-19)

From what you've said you have already slipped into depression precipitated by external factors associated with the COVID pandemic. You could screen for this by taking a PHQ-9 questionnaire which is probably what a GP would do (https://www.mdcalc.com/phq-9-patient-health-questionnaire-9) but if you are crying daily and cannot concentrate then it probably isn't necessary.

If you have had thoughts of suicide or self harm you need to seek urgent medical help. If not, you still need to seek professional help on a semi-urgent basis. You should apply to your university's disability services or whatever it is called at your university for special circumstances and adjustments for which you will need a letter from your health provider and you should do this early rather than at the last minute.

In the meantime, you should try online cognitive behavioural therapy websites such as Headspace (https://headspace.org.au/) or Unmind (https://home.unmind.com/) or whichever equivalent your institution may have access to.  Some have made their platforms available for free during the COVID pandemic to certain groups and this may be worth a look. You need to tell your supervisor and consider pausing the PhD or going part time if you can.

Most importantly, you are not alone and you can find many people who have written about how the COVID crisis has negatively impacted their mental health (https://www.theguardian.com/news/audio/2020/apr/24/what-is-the-covid-19-crisis-doing-to-our-mental-health-podcast) or (https://www.theguardian.com/world/2020/mar/22/think-about-the-best-case-scenario-how-to-manage-coronavirus-anxiety).

Don't suffer alone, get help early, know there are many people who empathise with you.


Reapplying to a PhD program while attending another one

I was able to transfer from Georgia Tech to MIT after a year. I initially went to GA Tech to study with a famous professor, who, once I got there, said that she was slated to move to Carnegie Mellon in 2 months. Nobody else at GA Tech was doing what I was interested in at the time, so I decided to go through the application process again. I re-used one of my rec writers from my app to GA Tech, and got 2 new rec letters from GA Tech profs I had worked with. I was able to do this because of a great program GA Tech had at the time (I hope they still do), wherein first-years do 3 mini-projects with 3 profs in their first semester. 2 of those profs provided recs, one of which had come from the MIT department I ultimately got accepted to.

To do something like this, you'll want to do the same and hit the ground running at University Y, starting research projects immediately despite your first-year courses. This will give you recs, and also give the admissions committee at X something new to consider.

One tricky thing is if/how to present your intentions to the profs you work with at X. If they know you're planning to jump ship, they'll be less invested in you. It's probably best if you don't come in saying that you'd like to leave for X ASAP.


Contacting via email or Linkedin (or similar sites) to help land a faculty appointment

As a general point, email and linked in are very different tools. Personally, I find linkedin doesn't have much weight in academia. I realise people use it, particularly in business areas, but I don't think many academics use it much for social networking with other researchers. Social networking tools for academics is an emerging area. Researchgate has improved a lot in recent years and is starting to get more popular as a place to share research and connect with other researchers. So in general, being on sites like this may help a little with connecting with other scholars.

That said, publishing good work in good journals, going to conferences, forming meaningful collaborations and so on are going to do more to improve your social networks.

If you are going to contact someone by email, you don't want to waste their time.

So, if you are legitimately wanting to connect and form a collaboration with an academic and you think that they might be legitimately interested, then by all means send them an email. This site has various tips for writing such emails.

More generally, there is the question of when you should contact people who work in a department when you are applying for a job in that department. I think this can be a good strategy but it depends a lot on how it is done. And it's definitely easier if you know someone in the department or you know someone who knows someone. If you can have an informal chat with a contact in the department, you might learn something more about the school to help you decide whether you want to apply, determine how competitive you are, or help you to frame your application. They may also be able to assist you in meeting others.

That said, you don't want to waste people's time, and you don't want to come across as someone who wastes people's time. I'm also mindful that for some positions there are hundreds of applicants for one position, and if every one of them contacted people in a department, it could be a huge issue.

Also, remember that some employers (universities included) wont let you know that you did not get the job. Or if they do, they may take a long time to let you know.


Can I use examples of others' research in my presentation on scientific conference?

Yes, it's fine to do that. If you do an introduction on the topic or you are comparing your results/methods to others you can talk about/show their work and you even should do that.

Just be careful that you talk enough about your own research and you always make it very clear if something was done by someone else.


Unfortunately, your institution is the most likely avenue for recourse in these situations. I believe most journals leave it up the authors to sort this out and direct you to your university or institution for adjudication, despite spelling out the various and detailed criteria for authorship. Even if the editor agrees with you, any authorship changes after publication must be approved by all the current authors. I don't mean to be overly cynical but getting your name on that paper would require an exceptionally ethical and proactive worker/administrator at your institution. Seems like quite the uphill battle to me...  Here are the relevant links to Nature and Science:

https://www.nature.com/nature-research/editorial-policies/authorship

https://www.sciencemag.org/authors/science-journals-editorial-policies


Disagreement with supervisor regarding sending an erratum

You said the error is small.  Therefore the need for an erratum is small as well.  Ideally you would publish the erratum, but if you have more important things to do, that is understandable.


Finding and requesting research funds from private sponsors for basic research with low short term marketability value

Step in their shoes and figure out what they would be gaining from giving money to you. The question is not only about the benefits as such, but who will benefit. 'One day you may tax it' may be actually reasonable to a large government, but it is absolute nonsense to a private company, who will NOT be able to tax it when other companies use it. "What's the use of a newborn baby" also implies that the adult will be useful - but it will NOT be useful to the company unless they can own & control that long-future result.

In general, if you want to get industry funding for research where the results cannot be commercialized in the short term, then anyway your results have to be valuable from them in particular, rather than the whole industry including their competitors. So if it's too early to produce a commercial product/process, at the very least the end result should be some protected IP - usually patents - that would be a property of the funding organization.

If it's an investment, then take a look at how large the return benefit would be, when would that be, and how likely it is that it will/won't work out.  If it's a 'sponsorship', well, sponsorships generally are a PR/marketing issue - in order for that to work out, the company needs your research and/or your name to be visible and known (not to academia but to their customers), so that they'd get some marketing benefit by their customers seeing (a lot of) their association with you and/or your research topic. It sometimes happens (for example, with high-end audio products; or IBM's Watson project is a case of such PR), but it's clearly not an option for most researchers.

An alternative might be private philantrophists - but that is based on individual relations, connections to very rich individuals, and your PR ability to convinve them that your research is so valuable to the world. Looking at how some other researchers have achieved such funding, it generally requires writing a popular book or a few of them, and years of public promotion of your research direction and ideas; that seed tends to grow into an ability to fundraise for continuing such research.


Half points and IELTS overall band score categories

Be as specific as you can. When asked for IELTS results, specify a decimal result of 8.5 wherever possible. If specifically asked for text description instead of a decimal result, be on the safe side and call it "very good user". For all my experience with IELTS, a result above band 7 is considered a pass for all purposes.


Is it a faux pas to ask for a colleague's figure in a separate but related publication?

You can always ask, then it is the choice of the author to accept or not. As for the citation, if the paper is accepted but not published, you can have a note in the citation "to appear". For instance, your text could like:

Following [Alice12], we describe ... as illustrated in Fig.1.
[Alice12] Alice, paper, journal, accepted, to appear.


A student forgot to answer an exam question

You should give zero for the answers in question. You are grading what the student handed in, not what s/he potentially could have handed in. The logistics are just as much part of fulfilling an assignment as the knowledge. It would be unfair to the other students to be more lenient on this particular student than others.

If you wish, you may give the student another chance to answer these questions, but then you should do the same for all students.

(I once failed to notice in an exam that the question sheet was printed front and back, and only answered the questions on the front. I duly accepted my C+, along with the two others who had made the same mistake...)


I am an engineer by qualification. But want to do a PhD in marketing. Is it possible? Or am I day dreaming?

It will depend on where you apply. One question an admission committee would have is your academic preparation. If your transcripts show marketing prerequisites it will help tremendously.

Practical experience is valuable but a PhD requires basic knowledge in the common theories of the field.


Outsourcing your research to Kaggle for co-authorship or other non monetary options

It's true that fitting the Kaggle competition framework is a bit of a constraint, but if you understand that framework and see how your problem fits into it, I'd suggest you e-mail quote@kaggle.com with a description of the data & problem (and ideally sample data), even if you don't have funding. We can see what comes of it!

(Disclaimer: I work for Kaggle.)


The differences between AMS research journals

If a mathematician wants to submit a paper to an AMS journal is the decision process for which one really as simple as "If my paper isn't good enough for JAMS I'll check its length and ship it off to the appropriate one of the other 3?"

Yes, more or less.  Journal of the AMS is a special case (as you observed) because of its extremely high level, and Memoirs of the AMS because it will consider incredibly long papers.  In both cases, there are only a small number of competing journals with these properties.  On the other hand, Transactions and Proceedings have substantially more competitors.  The primary distinction between them is length, but from my perspective there's also a difference in prestige.  Proceedings of the AMS gets some great submissions, but the length cut-off is pretty short for mathematics papers and this means it gets fewer great submissions than Transactions does, so the prestige level is a little lower.  Other than length and prestige, they are pretty much identical, for example in topics covered (a broad spectrum of pure mathematics, but limited coverage of applied mathematics).

So for Proceedings/Transactions papers, there's a four step decision procedure:

Is your paper on an appropriate topic?  (To a first approximation: is it pure mathematics?)
How long is your paper?
Do you have a realistic shot at acceptance?
Is the journal prestigious enough that you would be happy publishing your paper there?


Should I cite a source for a direct quotation separately if it is inside a paragraph with the same source?

The objective of citation is to provide clarity in attribution.  In the case where something might be unclear, it is generally better to err on the side of over-citation rather than under-citation.

In this case, I would judge the direct quote to definitely need a citation, because the source of a direct quotation should always be crystal clear.

It is the second part of the paragraph that might go without a citation. If it was short and you began it with a connector like "Adam further reports..." then it might be clearly enough linked with the quote citation to not need a separate citations. In this case, however, where it appears there is quite a bit of additional material, a second citation is likely to provide more clarity.


How to leave a collaborator after being offered to join a new group?

First make sure that this is what you want. This is a very important thing to do. Being in a better team is a chance, but also a burden. They will expect you to cooperate at a certain level, which means: stress, lots of work and being on time. If you think that's worth the result and that you are willing to dive into that, then do it.

If your friend is a good friend he/she will understand. I'd suggest to invite your friend for an activity that both of you enjoy a lot, then bring up the topic. Make it clear to your friend that you value the relationship and how difficult it is for you to take that decision, but also can't put down the chance. Ask him/her what he/she would do in your position to get your friend to see it with your eyes.

True friendship will survive that. And if not, then knowing that you took the right decision will help you getting over it.


Requesting raw data from previously published research

This will, as it seems nearly all questions on this site, vary based on field. My answer applies to Epidemiology and medical research only. Your mileage may vary.

It is very common for this to happen in my field. There has been an increasing emphasis on using meta-analysis and systematic reviews to summarize bodies of work, and with those there is almost always a need for some more information, raw data, etc. to come from study authors. It's fairly routine now. They may not say "yes" for a number of reasons. One may be that they're working on their own projects in a similar direction. But there are others - that privacy laws prohibit releasing data to just anyone or their funding dictates similarly is a fairly common one. So be prepared for "no".
As for the authorship question, it likely depends on the extent of your data request. Generally, if you're just asking for a few numbers that go into a reported value, then in all likelihood, an acknowledgement is more than sufficient. If, on the other hand, you're asking for access to the raw data from their 5 year, many thousands of dollars cohort study? You're likely going to have a member of their study team be an author on your paper, and there will be far more extensive approval processes than just "Sure, .csv file is attached."
"If my model (without fits to specific data) is in a pre-print state then should I send a pre-print to the authors I contact? What if the pre-print points out weaknesses in their approach to modeling similar problems?" For the initial contact, I'd suggest it isn't necessary, because what you're really trying to find out is "Is the release possible". At later stages, I would expect to see what you were doing, either in a full explanation, or as a pre-print. As to your "What if?" question - so what if it does? Science is about improving the methods we use.


Using Google Trends diagram in a scientific paper to show evidence of interest in an area

Yes, you can use it, but treat it like any other source of data.

I have been encouraged to use Google Trends data as supporting evidence by my professors.  You would need to explain the implications of the data, including caveats, just like any other type of data.  In the case of Google Trends, be careful not to overstate what it is saying.  It is only counting searches made on the Google platform, so what does this tell you directly, and what does it imply indirectly?


Should I quit my job and travel the world before applying to PhD programs?

The way PhD admission works is that you usually apply during the fall, receive admission decisions in the following winter/spring, make a decision around April and enroll in the fall. This means that there is usually a four-month(ish) long gap between the admission process and enrollment. Many students fresh out of college will use this period to relax, maybe even travel around the world. So if you can afford to quit your job or make certain arrangement with your employer, this time window could be a compromise between your need to enjoy life and appear productive, since people don't usually expect you to work hard just before you formally enroll in the program. On the other hand, if you urgently need to travel well before application and still want to impress the admission committee, my general advice is that a generic travel plan will not achieve the goal here. For your travelling to be viewed positively, it should yield concrete outcomes demonstrating excellence in whatever skills valued in your field of study.

I should also say that this is based on my experience with Ph.D. programs in science. A political science Ph.D. may have difference culture/expectations.


Incompatibility between job and field of study

As a graduate PhD your options are staying in academia and moving to industry, as you correctly point out. If you stay in academia, be it as research staff or as postdoc, it is generally because there is a interest in your field of study. In industry however, especially with rather specialized studies, you are not hired for your research to this point. With a PhD you have proven you are capable of independently solving challenging problems. And math/physics PhDs are generally considered as being good at working with numbers and abstract concepts. This is why they end up in the banking sector or working for insurance companies. It doesn't matter if your PhD is from a high ranking university or not, once you move past a certain point of specialization there is simply no demand for the research you are working on, you are hired for the skills you developed during your PhD


Conflicting views with my supervisor on how a thesis should be written

Would you rather pass your thesis, get a degree, and start to get control of your career or get blocked? It seems to be an easy choice.

Don't lose track of the fact that this work isn't, hopefully, going to be the best work you ever do in your life, only the first (or an early one).

Fighting with a supervisor who can be a block is seldom (never?) a good path to success.

Take her advice on this. Get finished. Get a good letter of recommendation. Move on. Make you own choices then, when it doesn't have negative consequences.

Think of "getting done" as the big win, not winning an argument.


Delayed manuscript publication by publishers

Unless your paper was intended as part of a special issue, you absolutely should contact the journal to inquire about why the publication has not yet been published. In this digital age, three months is more than enough time to get a paper through the post-acceptance pipeline.

In your first email, I would just ask about the delay in publication. If you do not get a satisfactory response, then I would escalate and mention the need for the paper to be published to graduate.

Also, I would check with your school about the need for formal publication to occur. In many instances, an acceptance memo is sufficient.


I can only speak to common practice in the US. Other places may differ.

That is something to be negotiated as part of the process of accepting the new position. I doubt that many universities have fixed rules, other than being open to considering it.

For some people it is an advantage to get "credit", shortening the probationary period. This would be someone with a strong record; research and/or teaching as appropriate to the position.

For some people it would be a disadvantage. It might be useful to have a longer probationary period if your record is relatively weak and you need the time to build up that record of accomplishment.

I was once able to get a 2 year probationary period as I was moving into a senior position. Yes, even a Full Professor might need a probationary period and a tenure decision. Obtaining tenure-at-hire can happen, but I doubt that it is the norm.


Can I challenge a paper already published in a peer reviewed conference/journal?

I think you have to further examine your motivation for wanting to “challenge” these substandard papers.  All of the following are reasons which are suggested in your question.

You feel that contentless or decisively problematic publications bring down the quality of the academic community as a whole.
You feel that the people who are publishing these works get too much credit.
In particular, they are holding themselves up as superior to you.
Specific people – e.g. you – suffer when you try to rely on publications which do not do what they promise.

This is a lot to answer, but I’ll take a stab at it:

This is a disturbing trend in the world of academic publication.  I now get more “journal spam” emails than all other spam put together (well, counting only what makes it into my inbox).  One can no longer assume that an academic publication is reputable, legitimate, or sincere in any way without having prior specific knowledge of the people and institutions involved.  I think this is a terrible problem, but it's well beyond my pay grade.  I do not have a solution in mind.

The best revenge is living well. In line with point 1, there is an increasing segment of the worldwide academic community in which people, in order to maintain their very low-paying academic jobs, simply must meet a certain quota of authorship.  No one cares about the content or quality; in many cases there is no infrastructure there for them to evaluate the content if they did care.  This is very sad.  At an individual level, what seems best to me is just to get out of this part of the academic community.  In many cases this is best accomplished by relocating to a different part of the world where the academic infrastructure exists.  You are not going to get a job at a research university in the United States by having 50 bullshit papers: that's just not the way things work here.  However, if you are a scholar in India, you can get offered a job in the United States (or Europe or Japan or...) on the basis of your work: it just has to actually be very good.

The person who tells you that he’s right and you’re wrong because he has twice as many papers as you is on the one hand an asshole.  On the other hand, he’s splashing around in a pond that you want to get out of: I can assure you that there are many academic environments in which who's right is not decided by counting publications.  You sound like a serious person: get yourself into one of these environments.

This seems to open up another can of worms, but relative to point 1 above: you simply cannot uncritically take publications at face value.  To be honest about it, you can do this to a greater or lesser degree according to the level of trust and esteem you place in the author, the journal, the institution...but doing this at all is a compromise we make only because we are finite beings living in an imperfect world.  Learn to develop a “nose” for what is correct and what is problematic.  Definitely do not accept a work-for-pay situation which is predicated on the assumption that an unvetted academic work does everything that it promises!
In general, I would say that point 4 is a good reason to challenge papers: if you sstumbled by relying on a paper or can imagine another serious, reputable person doing the same, then you owe it to the community to try to get the word out about the defects of the work.  But as above you should also understand that part of being a good academic is knowing what looks good and what looks bad.  There is an ever-expanding sewage sea of worse-than-useless academic papers.  You can't take responsibility for getting rid of all of them.  But you can teach yourself to avoid the unpleasant experience of being submerged in this sewage sea, and you can teach your colleagues – and, as you get older, your mentees – how to do the same.

Good luck.


Is it possible to get a PhD through government/industry/military lab, and if it is, what is the process?

In the US, you cannot have your PhD degree awarded by a government or military  laboratory, and similarly industrial labs generally cannot award degrees, either.

However, having worked at several government labs, I can confirm that it is possible to be a grad student and do your thesis research at a government lab. Usually this is done under a co-advising arrangement within an existing collaboration (Prof. X at university A works with Dr. Y at lab B), or under a cross-affiliation (Prof. X has a joint appointment at both university A and lab B).

More specific details differ too much depending on the university and department's regulations, as well as those of the lab in which you're interested in working, so you'd need to ask them specifically. However, it is also worth noting that many graduate departments still have a "residency requirement" on the books—which states that you must spend some number of semesters actually registered as a student at the university before receiving a PhD.


How far in advance of applying to grad school can I ask for a reference letter?

I think if you're seven years out, the reference letters won't be as relevant. I would check with the master's program, but sometimes if you've worked for a certain amount of time you can provide one academic reference and one work related reference. I would try to keep a relationship with at least one professor - keep them updated, visit for coffee, etc. but wouldn't use a letter from seven years ago to apply for a Masters program. Maybe through your diplomas which will be more recent, you will find a more recent reference.


How acceptable is it to ask a professor a question such as "so you think it's justifiable to take points off my proof for this?"?

It's quite difficult to catch the tone of what you said from a written recollection, but:

  So you think it's justifiable to take points of my proof for this?

(emphasis how I imagine the professor perceived it) is indeed not very respectful. Next time, try something like this:

  I'm sorry, I understand that I should have given a more detailed reasoning about why [...] but it's just such a small and obvious part of the proof -- isn't it a bit harsh to take off Y points for this, what do you think?

Keep in mind that if you do this often you might still get a reputation as "that kid who tries to argue every tiny point even when they already have a pretty good grade" but if you are reasonable about getting told "no" it shouldn't be much of a problem. Still, you have to weigh your chances of getting an increased grade against the chances of being perceived as annoying or needy.

However, the professor's response in this case is completely unacceptable. Giving you full marks based not on your performance on the test but based on you getting out of their office is a gross violation of academic standards (even if they later rescinded this "offer"). Honestly, the whole thing that transpired here sounds like both sides messed up. It sounds like the professor (rightfully) immediately regretted "offering" you full marks.

So many people getting their grades increased sounds like the professor should invest a bit more time in designing a clear grading model and then consistently apply it. The way they currently have it set up pretty much guarantees having to argue every little point with every student. Even if what you said is inconsiderate and perhaps rude, they had themselves set up for it.


Is it okay to submit manuscript to arXiv after "revise and resubmit"?

The version you mention is called a postprint. Publishers have various policies about them. You can use the SHERPA/RoMEO service to get a summary of the policy in place for a particular journal.

Here is an example of what you get for Lecture Notes in Computer Science, edited by Springer:

As noted in the comments, you do not necessarily need to abide by these policies, for instance if your funder has set up an open access policy.


Recalling standard results in a master's thesis appendix for reader's convenience and/or self-containedness

My answer is very similar to the one I gave to the question I linked to in a comment:  There is usually no reason not to include something in a thesis.  Your thesis is a place for you to give a coherent account related to your work on a topic.  There are (usually) no page restrictions, and it should serve as a reference document for future readers.

Many theses include a lot of review material, beyond just what might be contained in a literature survey. A thesis has to contain new material, of course, but it does not all need to be novel, and there can be a lot of merit in giving detailed explanations of known results, if the readers are not necessarily going to be familiar with them in detail.


Can my supervisor adjust and publish my bachelor's thesis without mentioning me as a co-author?

Your question is: Can they do this without mentioning me as a co-author?

The answer is unambiguously: No.


What if the production editor does not respond to important email after a few days?

It's been four days, and that might also include a weekend day depending on where in the world the production editor is. Have patience, and let the process work itself out :-)


Is it better to have done a Masters Thesis before applying for a PhD? Or are shorter semester projects sufficient?

It is a general piece of advice that for a successful PhD application one must demonstrate sufficient aptitude for and experience of doing research, and an ideal way for an applicant to do this is by participating in research projects as an undergraduate and/ or during a Master's degree.

PhD admissions committees will also be aware that many applicants are applying before finishing their Master's degree (if we are talking about UK PhDs here, where candidates are generally expected to have a Master's degree by the time they start- unlike the US, where someone going from Bachelors direct to a PhD is more common). This means that having a research project or thesis still in progress when you apply is not going to count against you.

  "In the first university, and I will have done more semester projects throughout the year, but the Masters thesis is only at the very end of the degree, hence after PhD applications."

While you may be writing the thesis itself after the applications are finished, I think you will be aware of who your supervisor is going to be and what topic you will be working on well beforehand. If you choose this option, you will be able to discuss the future project in your research statement and interviews.

  "The second option would consist of a Masters project in either the second or third semesters (thus, either before or during applications), although likely not in the areas I'm interested in."

This option doesn't sound so good to me. I made a point of finding a topic for my Master's thesis that I was very interested in, and it led almost directly to me getting a PhD place (even though I was barely halfway through the project when applying for the PhD). Admissions committees want to see motivation for your studies, and if you're not keen on your thesis topic this might be difficult to convey.

  "...how many solid research experiences (equivalent to a Masters
  thesis-level) would be needed for admissions into the top 10-20 US
  schools?"

From what I have learned by participating in this site, many US PhDs don't even require one Master's thesis- and I think, unless you're changing field significantly, it would be unreasonable to expect applicants to have any more than one Master's degree.

Finally, you mentioned in a comment that EPFL (I think) offer some neuroscience courses during the physics MSc. Given your goal of a neuroscience PhD, the opportunity to gain some experience in neuroscience before you apply can only be a bonus- one, because it will help you justify your motivation for applying; two, because you will be able to confirm for yourself that you really are interested in the field; and three, it may give you some ideas of topics you could focus on in your PhD.

The bottom line

Find a topic you are really interested in for your Master's thesis, regardless of when you will be working on it. If you know the topic beforehand you can at least read up on it and discuss preliminary aspects of the project in your PhD applications.

Admissions committees want to see research experience (which in university number 1 you will get from the semester projects) and enthusiasm/ motivation for the topic, which you can demonstrate by talking about the ongoing thesis work.


How to professionally handle sexist remarks by a student?

This is similar to the person of color getting stopped by the police. Is it just a random stop, or is it racism? Very hard to tell without statistics on large sample sizes, or direct evidence of racism. Would the student have made the same accusations if you were male? Possibly, but very hard to tell without direct evidence of sexism.

The student could be complaining just because he got a bad grade. The backing off after you told him the syllabus was from another professor could be because that professor was male. But it could also be because that professor was as you said, very senior. Or because you showed him that indeed more people used that same syllabus.

My advice in general would be to fight sexism when you have clear evidence that gender played a role. In other cases: address accusations like this on their merits or lack thereof. If people find that their accusations towards women are unfounded, that also combats sexist views.

Hopefully this post helped a bit.

Regarding your edit and how to deal with explicit sexism: I would call them out on it. However exactly how to deal with it and whether appearing as a bully is a concern is difficult to say without an explicit case. Is falls in the general case of students making inappropriate/unacceptable comments or actions. Maybe a guideline could be: is it severe enough to contact other people in the university? If not, you might admonish it more lightly if concerns about being a bully are top of your mind. If it is severe enough to contact the administration or the person at your institution to contact out of line students, let it be their decision. You can never be accused of being a bully if the punishment came for an independent third party. Especially if you presented the case to that third party plain and factually, with the question being: what should we do now?

Again it is hard to talk in general about these things. That is why I focused on the more specific case, because I could be more specific about it.


Am I allowed to use published research in building an industry project?

In general, research that has been published openly in the scientific literature is freely available for anybody to use and build upon.  As such, there is no requirement, either legal or ethical, to involve or notify the authors of the use to which you are putting their work.

The exceptions to this are:

If there have been patents filed (which should be stated in a conflict of interest statement in a journal paper, but may not appear in a conference paper) you may be constrained by patent licensing if the patent actually gets granted (though that typically takes a number of years).
If you publish a paper yourself, then you are ethically required to cite their work.
If you think the users of the system would find it interesting/useful to know about its origins, you can include it in appropriate parts of the documentation.

Beyond this, of course, most people would be happy to learn that their work is being put to good use: if you decide to contact the authors at some point and tell them what you're doing, they'll probably be glad to hear it.


Infrastructure Expectation of University

It is common practice in the US for grants to be managed by the university itself, usually through a special "Grants Office". The grant is charged a fraction of the grant, sometimes quite substantial, for something called "overhead". This is about keeping the lights on and providing space and maybe general clerical assistance. But it is unlikely that you would see "light bulbs" as a listed expense unless the grant accounting is extremely detailed.

But, you can normally expect that if you are awarded a billion dollars (we wish) that you will only, really, have any control over a part of that. Your own such office can probably provide guidance on their expectations and what they provide for the "charge" against the grant.

And, the funding agencies have something to say about the amount of the charge and have their own expectations. See, for example, https://www.nsf.gov/bfa/dias/caar/indirect.jsp


Should computer science indexing sites be considered in rating research?

Computer science is typically badly under-represented in the "traditional" citation indices, which do not consider conferences to be peer-reviewed publications.  As any computer scientist knows, that is a bad joke: many computer science conferences are much more stiffly reviewed and difficult to enter than most journals.

It is for this reason that DBLP was created, to actually index relevant and reputable computer science publications.  I believe that DBLP should cover everything in ACM DL and IEEE Xplore, so getting just that accepted by the university should be sufficient.

Unfortunately, what you are seeing is another instance of a long-running and frequently waged fight.  Take heart, however, that this fight has already been won at most top institutions, and can be won at yours as well.


Would 3 years of master's in Computer Science look bad in PhD applications?

I think in the current circumstances, taking a few months extra to finish your Master's will not be looked on negatively. It will be easy to explain in your applications (exactly as you have done here) the reason for the extra time taken. Overall, a thesis-based Master's will probably be better for PhD applications than a coursework-based one, as you will have more demonstrable research experience.


Female students coming to office hours in overly revealing clothing

Does your institution have a student dress code?
Does your location have public indecency laws?

If their clothing violates either, refuse meetings until the problem is corrected.

Otherwise, ignore their appearance and carry on as usual.

Their sense of appropriate dress is clearly different from yours, but like political or religious opinions, such senses are often personal and cultural.  For all you know, a bikini is her preferred set of comfortable clothing.  Without a clear agreed-upon set of rules to defer to, such opinions are unproductive to dispute.  Let it be.


If the poster gets a prize, who gets it, the person presenting it or the first author?

A prize is typically given for both content and presentation of a work, so a typical fair way to handle prize money, whether for poster or paper, is to offer to split it evenly amongst all of the co-authors.  Co-authors who feel they have not offered a full share of work might choose to decline their share, but the basic assumption should be an even split.  To do otherwise just opens the opportunity for much interpersonal conflict over a generally quite small amount of money.

Remember also that the most significant value of a poster or paper prize is not typically any money that happens to be associated with the prize, but rather the increase in your personal credibility and future prospects that comes from the recognition.


My University's communications office reserves "Dr" for MDs only - is this common?

The AP style guide does say that "Dr." is used to indicate medical doctor, and that academic degree (Jane Doe, Ph.D.) is used to indicate doctorates. That said, if you don't like that policy, you can point out:

1) It is standard etiquette to use the title a person prefers, and rude to do otherwise.

2) The AP style guide is just one convention among many. Lots of institutions have their own policies (e.g. NASA's communication office has the exact opposite convention, referring to Ph.D.'s as "Dr." and referring to medical doctors as "Jane Doe, M.D."). Several high-profile press institutions (including the New York Times and Wall Street Journal) do not follow the AP style guide in this regard as well.

https://en.wikipedia.org/wiki/Doctor_(title)#United_States


I usually see acknowledgements in papers with just the full name of the person, regardless of their degrees or academic status.  No "Prof." or other honorific would be used at all.  "We would like to thank Jane Doe for helpful advice regarding our data analysis."


Name and cite specific figures/results of related work

It's quite normal to site specific parts of a reference. Pointing at a figure is very much like citing a large block of text. It is legitimate.


Yes they are interested otherwise you won’t be invited. The is fairly normal procedure; some institutes interview candidates in person. I believe the goal for such visit is to set your expectations clear, meet with advisor before official acceptance, and to see where you would live in the next couple of years.

The best thing is to ask them what they expect from you during the visit.


help needed for contacting a supervisor for PhD

If you have funding, you might email him:

  Hello Professor X,

  I am interested in researching stem cells, and see you are an expert
  at researching stem cells. I am wondering if you are accepting new
  graduate student this application cycle?

  My background is QRS and also have some interests in TRV. Your paper
  on "MMMMM" is interesting, and wonder if your group is going to expand
  on that paper and if there are any opportunities in this field for
  graduate students if you are accepting students?

  It is also important to note that I have a scholarship that will fully
  fund my education, and thus, am looking for a place to spend this
  scholarship money.

  Thank you for your time,

  Marviii

Your actual email should probably be more specific and formal, but keep it brief. You are essentially a free graduate student (except time), so potential supervisors should be interested in you. Don't be modest about mentioning it.


How to design an undergraduate internship project?

The number one thing that I would advise you to expect is the unexpected.  The skills and performance of undergraduates is almost impossible to predict, because their work with you is likely to be one of their first deep technical experiences.  Among the key implications of this:

their true skills and background vary greatly and are often not well indicated by transcripts (and they often have little ability to self-evaluate)
their motivation and ability to act professionally varies wildly and is very difficult to judge before they are actually working on a project (they often do not really know themselves)
there is often little possibility of obtaining a meaningful reference for them

Given this, I have found that the following are very useful to do when designing a project for an undergraduate:

Do not put them on anything critical path.  Choose an interesting side project that you've wanted to get around to, but won't be sad if nothing happens on.
Create a set of milestones that starts with simple "warm-up" work, and then builds sequentially.  Make sure they will see a concrete result that they can feel proud of at each milestone.
A good rule of thumb is to plan assuming that 1 week of work for you will be 1 month of work for the undergraduate.  A really good one, though, may progress much, much faster, though, so...
Also add a set of "stretch goals" that will give a really good undergraduate a chance to do some really cool things, rather than running out of work after the first few weeks.

Every undergraduate is a roll of the dice.  Many will simply waste your time.  Many will be marginal in value at best.  But the good ones really make up for all the rest, and may become your future colleagues.


May authors opt-out of the proceedings of a conference?

I don't know if there would be any negative consequences from the conference from refusing to include your paper in the proceedings, but there are several positive reasons to do so. I don't know about theoretical CS, but I understand that for many sub-disciplines of CS, the conference publication is more imporant for your career than any journal publication. So, if yours in one where the conference article is more important than the journal article, you may have already accomplished the most important part for you already by the time you give the talk. That being said however, you might still prefer to put the paper into the proceedings volume since:

it should be easier to find and refer to for future researchers and yourself than if it is on your website or the arXiv
a journal special issue is probably considered more archival than arXiv.org by some
if your discipline is other than I mentioned, you now might be considered to have a more prestigious journal article as well (depending, often, on whether others understand the level of peer review associated with that conference).

If this printing is a free service of the conference and goes in the publisher's digital archive, I'd be inclined to take the opportunity over trying to host it myself or arXiv it, and I have done so, even though CS is not my primary discipline. I'm not a big fan of the copyright transfer that is basically required to allow the big publisher or the professional societies to publish a copy of your work that they did not author (at least in the US and Europe).

I'd say that it's unlikely to be a big problem with the conference for you not to publish in the proceedings, though you might get some pressure from them to include your article. Some of the organizers, if they are common one year to the next, might remember your refusal and hold that against you the next year, but that would be unethical in my view, so they might also just let it go. As long as the paperwork to submit the article to the proceedings comes after the conference, there's not much they can do to you before the conference (like pull your talk), so I wouldn't worry too much about that. Finally, before you sign the copyright transfer with the publisher, you have an opportunity to read the publishing agreement and decide if it currently or ever will meet your standards for openness. If it doesn't or never will, then you can make that call as late as possible if you want to.


What is the best way to schedule an office hour appointment with big name professor?

By all means, contact the admin assistant and be extra super nice and polite because they have more power than you might think. Even if they don't schedule appointments, they'll know the best way to reach him.


This answer assumes that the course you are teaching is not about note-taking itself.

Make sure there really is a problem to address

Are the students who you think take bad notes also performing badly in the course? Different students have different ways of taking notes, or even different purposes (for example, I used to write down as much as I could because that would help me learn the content afterwards through "muscle memory").

There is not an unique "correct" way of taking notes. If you know exactly what notes the students are supposed to take, then probably they do not know, so why not provide those notes to them? That would help them much more, and the goal of your course is to transfer knowledge about a specific topic.

If, after considering this, you still want to get the students to learn these note-taking skills, you will probably have to dedicate some lecture time to explain how they should be taking notes. Having them submit some of their notes as an assignment will also help. After all, if it is not part of the course, many students will not be motivated to do it. Keep in mind that students have developed their own learning methods for many years, and changing to a new note-taking method might actually make some students perform worse while they get used to it.


Should you recuse yourself from the hiring committee if you have had a past romantic relationship with an applicant?

I will almost guarantee that your university has a Compliance office. Here's the one for my university; you'll notice that it has both a number of links to written guidelines, as well as phone numbers for an Ethics hotline. Your university may not have the exact same thing, but there are people there whose job is to answer these types of questions. Make use of them.

That said, from my completely uninformed standpoint, your situation sounds like a conflict of interest. If I was in a similar situation I would definitely recuse myself.


How can I ask to not be assigned a seat near a particular person during exams?

Yes, I think you can ask. You don't need to give a reason if things are handled justly. "Personal reasons" should be enough. If the person has harassed you in the past or is known to you to cheat you have adequate reason.
And, it might be important to do so if you think that it would affect your performance.
You will need to decide whether to give a reason if asked. But be honest without revealing more than necessary. You might not achieve your objective, of course. Be ready for that.


Applying to US Phd Programs while doing a UK Master's

I'll speculate that most places wouldn't find it to be much of a problem, but it is up to the accepting institution, certainly.

However, you will need to get accepted based on your current record without the MSc and will need to present sufficient evidence of success in the doctoral program. Since most US doctoral programs in the US don't require completion of a master's first it wouldn't seem to be an impediment to be doing both. But you will need to be sure that the required work on either of them doesn't impede the necessary work on the other. It would be sad to fail at either because of overload.


How many years of industrial experience needed for a Mechatronics Professor?

Your answer seems to confuse teaching with being a professor. One can teach without being a professor. Furthermore, and although this may be controversial, I think the quintessential characteristic of a professor is a scholar who can carry on substantial independent research.

Neither teaching skill nor experience in industry counterbalance the lack of that.


Publishing a creative, important result – does it create any real finance opportunities (jobs, etc.)

Sadly, there is not a strict correlation between doing good science and being financially successful. It is entirely possible to do "creative, important work" and still not be well rewarded for it. For instance, one could have published these results in an obscure journal that very few people will read. Or, as another example, the researcher might be a poor "salesman," unable to convince readers and fellow scientists of the merit of his work.

In general, you need a combination of both networking and technical skills to forge a successful career as a researcher: the contacts will help you get interviews for jobs; your technical knowledge will get you the job.


Is it appropriate to put a scientific/technical document about code developed by our group on arXiv?

If your manual is specific to your group's environment (software, lab, equipment, protocols, etc.), then I would consider posting such document on arXiv as not appropriate. A better place for such documents IMHO would be figshare or Zenodo. Both services allow artifacts to be not only citable, but also discoverable (via DOI assignment). Version control is supported as well, but the advantage of Zenodo in this regard in comparison with figshare is Git and GitHub integration.

If, on the other hand, the document is not specific to your group's or other particular environment (or, perhaps, you want to share this document as a model of how such documents should be structured, presented and what content should they contain), then I agree with other answers in that it is totally appropriate to post such document on arXiv.


I included some results in my thesis that some other PhD students included in theirs. Is this plagiarism?

You should cite the other publications, your authorship involvement and your noted contribution status.

You should also note that you are presenting the complete result set while the cited publications each contain a part thereof. You should informally notify the other authors of your intentions - this may not change your course of action but it would be useful to know that they don't intend to contest any of your work.


Is it wise to target three different proposals for three different fellowships with three different supervisors/hosts?

No, it isn't unethical. You aren't expected to be exclusive at this stage. Later on, however, if you get more than one offer, you may need to dance about a bit to stay honest with everyone.

Seems like a lot of work, though. Maybe overkill. Would you really be happy with any of them?


How to cite a dataset, when my calculations relied on the data?

If you are computing something from a dataset, then you need to explain what you have computed and how.  This should resolve the question of citation fairly naturally.
For example, with the example you have given, you might say something like:

  Using the Spanish-language corpus in (Brown, E. K., 2014), n-gram frequency
  computation indicates that
  'E' is the most frequently occurring vowel in the Spanish language and
  appears most often after the letter 's'.

Because the computation is yours, you need to explain and attribute it correctly, as you may have made a mistake in your interpretation, or the dataset itself may be biased.  Thus, it is best to use a few more words and given the reader a clear explanation of the relationships.


In my experience, if you're interested in joining a PhD program, as long as you're above the minimum required GPA they weigh your research experience, publications (if any) and recommendation letters much higher than your scores. If you want to find out whether you like academia and academia likes you back, find a professor willing to work with you on a research project or ask if one of their graduate students needs help with something. There are people who are great at both research and exams, but they are two very different skills IMO.

  Whenever I talk to graduate or PhD students or even professors, they
  always tell me that they have been straight A+ students.

Depending on the school, country and program, graduate courses are almost always straightforward to get very good grades in since they are largely literature and/or project based. Undergraduate programs tend to be harsher with grading and exams. I would wager that at least some of these academics you've spoken to don't remember their undergraduate scores exactly. :)


What is the proper way to judge the quality of education of a university?

The best metric is comparing the quality of current and recent graduate students, in various research outlets. If students from institute X stumble more over questions at conferences compared to those from institute Y, or if they publish in lesser venues, or produce less-solid papers (more errors, more failures to think a problem through), then you can conclude either that Y attracts better students or that Y does a better job of training students than X (I don't think it would matter, for your purposes, which it is). But this is a very labor-intensive evaluation. A second runner-up method would be to look at the job-placement histories of institutions, though getting hired often reflects politics (who your adviser knows, who hates your adviser) as much as student quality.


Is it immoral to expect uncompensated contribution to the university from doctorate students?

In universities in the USA, the type of work that you describe is typically paid for, with the student being employed as a Teaching Assistant (TA).  In some cases, this is an hourly job; in other cases it comes with a stipend and tuition support. The time a student spends per week varies, but in my experience is most typically averages to 10-20 hours/week (typically lower for hourly wage, higher for stipend).

Many departments do require students to spend time as a teaching assistant, under the theory that the work of instruction is an important part of one's education.  It sounds like the universities that you describe are using this theory, but then not compensating the students.

To my mind, whether this is moral or not depends on the nature of the work and the amount of time that is required.

At one end of the spectrum, if a student is asked to give a couple of guest lectures over the course of a semester, then the experience of preparation and explanation seems like a reasonable inclusion in their educational experience, especially if coached by the professor.
At the other end of the spectrum, if a student is asked to do 20 hours of grading and other "scut work" that has little educational value, then it is clearly a job for which they should be paid.

Somewhere in between there is some grey area, but in general my feeling is that the more routine and less educational aspects of teaching are work for which whoever conducts it should be definitely be compensated.


If my papers are always accepted, should I submit future papers to journals more diffficult to get published in?

"Then you are aiming too low" - this may or may not be true. That you are not asked for major changes doesn't necessarily mean that your papers would have been accepted, maybe after major changes, in higher rated journals. The "secret" to get into higher rated journals is not to write papers that don't require much revision. It's rather about originality, having done the right thing at the right time, potential more general interest, impact, and influence, and difficulty. These things don't play a role for a reviewer who thinks about whether to accept with minor or major revisions. So whether your papers would be fit for higher rated journals cannot be said based on what is in your question.
That said, chances are (obviously depending on your career aims) that papers in top journals would improve your standing, CV, chances for grant success, so surely it makes sense to try to get into better journals if you have work that you feel is up for that (and maybe even with the best you have without that feeling, because maybe you're underestimating yourself). But read some stuff in top journals related to your work and try to learn about how these authors managed to get there (maybe you find out that this stuff doesn't look very different from yours, in which case go for it!).


Applying for a new doctoral program after expulsion

I don't think your goal is impossible, but it will be difficult to achieve. I assume that your past infraction was serious or you wouldn't be in the state you are in. You can do one thing now, and you must do another thing later, however.

Now, you can find ways to behave in a way that shows you learned from your experience, have paid for your sins, recognize them for what they are, ameliorate the bad effects they caused, and that it can never happen again. This is harder (even) than it sounds, as some acts might not be repeated, but an underlying attitude might lead a person to do other things, not exactly the same, but also quite bad. Narcissism, for example, can often lead to a lot of bad behavior of various kinds. Also, thing things you do should leave some visible record that clearly shows a change. Even better if other people can attest to your good character now and in the future.

The thing you must do later is to be completely honest with any institution that you apply to. It won't be enough for you to promise to behave better. But the things you have done in the interim should speak for your change without your comment.

Even then, of course, there are many who won't believe in your change. You need to make it real change, both for your future chances and for yourself generally.

Good luck.

Note that I mention narcissism as an example only. Lack of empathy is another. But I'm not trying to attribute either to you.


What should I do if I am asked to review a paper that should have been reviewed by an ethics committee, but was not?

I think it's quite a leap to jump from the fact that there is no such statement to the conclusion that it has not been reviewed. You should ask for clarification on that point in your review, rather than outright rejecting it.

Also, there are different rules in different countries, and the notion of an IRB might not exist, or the procedure may go by a different name. In our department, for instance, a formal process of ethical approval was only implemented a couple of years ago.

So, short answer: ask what ethical procedure was followed, and how that relates to the obligations in the country and/or university the researchers and the participants are based.