Update frequency of BASE open-access repository?

Usually, all sources are updated twice a month. Records that are marked as "updated" in the OAI-PMH interface of the source, will be re-harvested and re-indexed.

Private communication from BASE team


"Editor invited" to "Decision in Process"

It means they're making a decision without peer review. Usually not a good sign; a desk rejection is very likely.

If you're asking why "with editor" didn't show up, there's a good chance it did, but the editor made a decision in a few minutes and you didn't notice it.


Why is the admission process centralized, when the professor who is actually funding may not be in the committee?

I'm a theoretical computer scientist currently serving on the admissions committee of a large top-15 computer science department.

  Some of the things that I heard is that getting admission in TCS in top 15 theory universities is tough. The toughness is obviously due to the large volumes of applications that these universities receive (I don't know how much?).

This year my department received about 50 PhD applications from people whose primary interest is theoretical computer science and probably another 50 with secondary interest in theory, out of 750 PhD applications overall.  We've offered admission to about 10 theory PhD students (out of about 200 PhD offers total).  We realistically expect three or four theory PhD students to accept our offer (out of about 80-100 total).

  However one of the big factors is the limited funding available with professor. So who funds the students? Professors or universities?

It's complicated.  A typical PhD offer from a strong department includes guaranteed funding in some form.  My department promises five years of funding to every incoming PhD student, assuming they make steady progress toward their degree.  (Do not accept a PhD admission offer without funding.  If they really want you, they'll pay for you.)  Most of our students take 6 years to finish, but in practice, (100-ε)% of our students are funded for their entire stay.  A typical theory student in my department is a TA for 2-4 semesters and an RA of fellow for the rest.

When a student is admitted, the department is making a contractual commitment to funding that student, assuming they make adequate progress toward their degree.  In practice, most of that funding comes from individual faculty grants, most of the rest comes from the department's budget for teaching assistantships, and a small fraction comes from fellowships (university, NSF, DOE, NDSEG, Hertz, etc.).

The number of students that each group is allowed to admit depends primarily on three factors:

Advising capacity: How many students can each faculty member in the group reasonably advise?  The limiting resource here is faculty attention, not money.  Theoretical computer science faculty tend to have relatively small groups, compared to some areas in CS.  Steady state in my group seems to be about 3 PhD students per faculty.  This is the most significant factor, in my opinion.
Funding capacity: How many students can each faculty member reasonably expect to fund?  This isn't just a function of the faculty's current grants; a typical grant lasts only 3 years, but each student needs 5-6 years of funding.
Teaching demand: How many TAs does the group need to support its teaching responsibilities?  Conversely, for how many semesters are students in the group expected to be TAs, as part of their PhD training?  The ratio of these two numbers basically determines how many students the department is willing to pay for on its own dime.

  In some cases I heard, that it is the professor who funds the student. Then in that case, why is the admission process centralized (the professor who is actually funding may not be in the committee)?

In US computer science programs, departments offer admission, not individual faculty.    Students are completely free to change advisors or even research areas, even if their existing advisor is funding them.  (Of course, they have to fulfill their funding obligations, but that's an orthogonal issue.)  Formally, students in my department do not even choose their thesis advisors until the end of their first year.  (One of my recent PhDs entered the department as an RA in distributed systems/sensor networks; he switched to algorithms at the end of his first year.)  For that reason, it's crucial that the admissions decision does not rest entirely with a single faculty member.


How can I apologize to my former research professor whom I ghosted?

Often enough in these kinds of interactions, the situation feels much more dire than it really is because you're not in touch with the professor. You are left to your own devices, building scenarios of how much this professor must hate you now and how terrible it is that you left.
You're fine.
Knot theory is knot for everyone (ha ha!), a fact your professor is probably well aware of. Sure, it would have been nice if you had let them know earlier, but I'm quite sure they realized it during your internship.
The best thing to do now is to reach out to them, apologize for not being in touch earlier. Keep the email short and to the point, no need to write a 1000 word essay. You're likely to get a short reply acknowledging your email and that would be that.
The only point that might have genuinely pissed them off is the books you took and didn't return. Offer to return those as soon as you can, at your expense. While I share your opinion about Munkres, an unpleasant read even for seasoned mathematicians, the books belong to someone else and should be returned.


How to handle conflicting instructions when applying for a grant?

When relating to granting agencies, I would say that, as a rule, it is not recommendable to submit more documentation than the one they are expecting.

I would first make sure that the guidelines you are reading are up-to-date; you'd be surprised on how many times they are not. Once you've done that, consider whatever is written as the truth. If it is renewal you are after, restrict yourself to whatever instructions for renewal they have.

Of course, it will depend on the agency, but in my experience if something is missing either the automatic upload service (if that's the case) or someone from the agency will contact you to make sure everything is ok.


Is it a bad idea to mention informal PhD offers in a job application?

tl;dr: No, you should not mention this "offer."

I wouldn't even call this an informal offer. An "informal offer" would be if you applied, and then were told by e.g. email or phone that you are admitted, and that the formal letter of admission will follow shortly. Encouragement to apply, no matter how strong, is not an offer of admission, and doesn't indicate that you would definitely get an offer of admission if you would have applied.

For example, you may sound great according to whatever information you sent to that professor, but your full application may reveal other things that lead the admissions committee to reject your application. Or maybe you really are that great and the professor has funding, but another, better, student applies that year and gets the offer instead of you.

Furthermore, individual professors have varying ability to actually influence the admissions process, depending on how graduate admissions actually works in that department.

Even for a "real" offer of admission, it wouldn't necessarily be a good idea to list it on a résumé. See for example this related question on listing fellowships that are offered, but which you decline. But being encouraged very strongly to apply to something is certainly not a CV-worthy accomplishment.


I recommend that you discuss these issues with an academic mentor who understands your discipline. You may also find it useful to visit the writing/tutoring center at your institution.

That said, I've provided some short answers below. My answers are not intended to be complete because many of the questions that you are asking cannot be answered by people who are not experts in your discipline.

  Should I cite a paper (i.e. give credit) for ideas that are in its literature review, and that are totally not related to the core/added value of the paper?

Generally, no. If you encounter something that you want to cite in a literature review, track down the original source. This should not be difficult, assuming that the paper you are reading cited the original source properly.

  Should I cite every paper related to one field?

No. Unless you are defining "field" extremely narrowly, it will be neither possible nor desirable to cite everything.

  Can I cite only not-that-much-cited source and not classic ones?

There is no universal answer to this question. The answer depends on your purposes for the paper and the disciplinary expectations in your field. Talk to a mentor.

  If I am writing an assertion that is general (e.g. "Polar bears have mostly white fur"), should I justify it?(!)

You do not have to cite things that are considered common knowledge, but the question is this: What exactly gets to be considered common knowledge? There's no universal answer. It depends who you are writing for and what you are writing about. Here are some rules of thumb that should generally serve you well in American academic writing situations:

If you would expect any given high school graduate to know something (like the color of polar bear fur), then you probably don't have to cite it.
If you aren't sure whether you need to cite something, cite it, or at least mark it as a problem. You can always read back through the paper later with a mentor, colleague, or tutor who can help you to identify unnecessary citations.

  Which is the criteria to determine when an assertion need to be proven by a citation, and when it is admited?

Again, there are no universal criteria for this. You'll learn the criteria that writers in your discipline go by as you continue to read and study in your discipline.

  When I define a key term for my paper, should I always rely on past definitions?

In general, you should rely on past definitions if those definitions are (1) technical and specific and (2) an important issue in your paper. If you wish to break away from established definitions, you should explain why and make an argument for the new definition. Finally, a tip: It is practically never necessary to cite a dictionary definition in an academic paper.


Letter of Recommendation/Reference Protocols

Yes. It's quite typical to ask each prof to write a letter for each school you apply to. Indeed, you almost certainly want to do this. Be sure to take care of all the paperwork beforehand, pre-address envelopes if any applications use snail mail, etc. so he/she doesn't have to.
No.
Hard to say. I'd find someone else in your department (who knows the prof in question) to ask. Good luck!


University Test Bank Website- Potential Liability Issues?

Of course, we don't know what your university's academic dishonesty rules say.  But in most cases they are pretty broad, and there is probably a clause that could be interpreted to include your website, if your university's authorities decide to do so.  I think the odds are good that there will be at least one professor who is upset enough to push them to do something about it.  They might just try to get you to take the site down, they might try something harsher.  There's no way to know.

In general, I think most professors are aware that students may be informally sharing their exams with one another.  For that reason, they usually change exams from term to term, and if they reuse questions, do so only after several years.  However, some may be startled to see it done as systematically as you propose, and try to stop it.

I am not a lawyer, nor do I know your local laws, but posting an exam on your website would probably violate the copyright of the professor who wrote it (unless you have his or her permission).  This would be another avenue someone could pursue if they wanted your website gone.

Finally, professors could try to prevent their students from posting their exams on your website.  For example, they might stop letting students keep their graded exams.  Or, they could add a line to their syllabus that "you may not share your graded exams with anyone", on penalty of failing the course or academic dishonesty sanctions.  This could not only deprive your website of material, but also make it so that students can't even share their exams informally anymore, which I assume is contrary to your goals.


The benefits of the social connections made in attending a conference?

Suppose one made connections from a conference, then what are the potential benefits of making those connections? i.e. how to make value out of them?!

For most people, new connections found through conferences at a later stage become either

Potential references
Potential collaborators
Friends or at least acquaintances

(or, in the optimal case, a combination thereof)

For all of those, it is hard to put a numerical "value" on them, but as you progress with your academic career, you will find that it is hard to be successful in academia without a healthy set of all of the three. Without references that vouch for your scientific merit, it is hard to get any advanced academic positions. Without collaborators, it is hard to write strong papers and grant proposals. Without friends in the community, future conferences become a chore and it is very easy to lose track of where the community is heading as a whole (also, the third item quite naturally leads to the former two items).

  Also the majority of the connections would be with researchers and students, not hiring managers so I wonder if there are any value for job search after graduating 4 years from the PhD.

In academia, the notion of "hiring managers" is somewhat suspect. You can definitely meet senior professors at conferences, and those are the ones that decide whether you get a faculty position down the road. Further, never make the mistake of assuming that the "researchers and students" you connect to don't matter, and you shouldn't talk to them - the PhD students from today are the people that review your papers and grant proposals tomorrow (hence the name "peer review").


What questions to ask a famous mathematician

What advice would you give to a youngster interested in math? To a college student?
What do you do to overcome frustration when the going gets hard?
What sort of problems interest you now?
Where should I look for interesting problems?
What was your first interesting encounter with math?

other things like that.

Of course, the talk might cover some of this but might also suggest other questions.

Of course, if the talk is being given to specialists, rather than the public, then questions specific to the talk would be appropriate, but possibly difficult to prepare in advance.


How to survive the remaining 5 months of my postdoc in toxic environment?

Although I may not have stood in your shoes as a post doctoral scholar, however I hope I can give you some insight on the behavior of your PI.

  How do I survive the remaining 5 months of my postdoc with an abusive mentor who has unreasonably high standards?

First and foremost, don't take it personally.

If your PI is for lack of a better word an a**. I doubt there is anything you can do to change that. On the other hand, what you can control is your perception and acceptance of such negative behavior.

Peeling back the emotional layers, is there truth to what is being said? Is there a fundamental misunderstanding on your part of a given subject matter? For example, if your PI berates you in public on not knowing that 1+1=2, you can approach the problem from two (among many) views. One is emotion: your PI just humiliated you in front of your peers. The other is the core issue at hand, knowledge, does 1+1 really equal 2?

With emotion: you can perceive it with the desired emotion or you can dust it off with nonchalance. Reply stoically "I didn't know that, thank you for pointing it out to me". Address the outburst and move on.

If you don't let hate (and in this case, a severe lack of tact on part of your PI) get to you, it robs the abuser of their satisfaction (if it was intentional). If it wasn't intentional, then it is a rather rocky learning process for your PI as one day, when their supervisor (or senior faculty) sees this going on, they will get their a** chewed out for humiliating their people or find themselves without anyone who is willing to work it them, effectively being an academic pariah. (Yeah he/she is smart, but he/she is a pain to work with, let's not).

With knowledge: it will be up to you to determine if you are in fact, in the wrong. If so, adapt your understanding with newfound knowledge and move on. If you are wrong, you are wrong, there isn't much more to discuss. If you are right... well... ask yourself if it is worth the battle to prove to a belligerent PI that they are incorrect.

  I have been so stressed since the past month that I feel unfit for any position. How do I regain my confidence?

Take a moment and look at all of the struggles that you've accomplished and overcome thus far. Your graduate tests, qualification exams, writing a dissertation, defending you thesis, buying your review board's favorite foods, for the last >4 years of your life. Putting up with an a**hole for the next 5 months in comparison is a drop in the bucket.

Keep your eyes forward on the goals you've set for yourself and what kept you going all these years.

  How do I find a position without a reference letter from the current adviser?

My understanding of a reference letter, is to have someone who is knowledgeable of your work ethic, vouch for you. I believe there would be more than your PI whom you've worked closely with this past year. A faculty member perhaps?


How to answer your boss's question about your impression on the progress of a project that you took part in as a newcomer appropriately?

Assuming your professor is a reasonable person, there is nothing wrong with truthfully sharing your view of the progress in the project. They wouldn't be asking if they did not think your opinion matters. Of course, if you are concerned about the project progress, you want to stick to the facts and not over-dramatise the situation of the project. It may also be a good idea to come equipped with at least some ideas how to go forward (since this will likely be the follow-up question if you share that the project currently could be in trouble).
I am sure there are cultural differences related to this, but I don't feel qualified to reason about what the correct way of framing this in an Asian country would be. However, the difference between academia and industry (in Germany) isn't very large - in both cases there is an expectation that you politely raise issues as you see them, rather than pretending everything is great until the car hits the wall.
Edit: one important thing I forgot to mention - this is under the assumption that this is more of an internal meeting. If the meeting also includes external people, most importantly representatives of the funding body behind the project, the only correct answer to "how is this project going?" is "great, we are going to achieve all of our goals." Letting whoever pays the bills know that it may be time to pull the plug on the project is unlikely to go over well.


International standards relating to a professor publishing a student's thesis work without the student as co-author

There is no international standard because authorship practices vary.

COPE is the closest thing to a standards organization, but they do not publish authorship standards, or any other kind of standard.

References:

https://publicationethics.org/files/Recognise_Potential_Authorship_Problems.pdf

https://publicationethics.org/files/u7141/best_practice_for_issues_around_theses_publishing%20(1).pdf

Academia varies more than you think it does – The Movie (why there are no standards)

Publishing a student's thesis without their name is certainly unethical.


Does the managerial title of a LoR writter matter?

I would rather get a letter from a professor, even a lowly assistant professor, who knows you well and can attest to your ability and potential, than I would from a higher level person who may have little experience in what your research area entails. The purpose of such letters is to give the reader an assessment of your likelihood of success. If it can't do that then it will be discounted, no matter the position of the writer.

However, in case the letter is just a general statement of your character and (easily found) accomplishments, then the dean's or superintendent's letter might be useful.


How good are entrepreneurial opportunities for faculty members?

This is quite common in American universities, and there are probably thousands of start-ups that have arisen out of university-based research. The question of financing such a venture is of course a challenging one to answer, but with the right contacts, is usually available.

I can think of at least four or five such start-ups in the department I attended for graduate school, and I imagine there are several more in the planning stages.

As for how enthusiastic industry and VC's are, well, I think it depends entirely on the strength of the idea, and how "market-ready" the concept is. The sooner it's ready to go, the more enthusiastically people will flock to it.


How to correct a fundamental error in a series of papers made by a colleague of your adviser?

Talk to your adviser as soon as possible. I'm a bit surprised that in your previous interactions your adviser did not already tell you whether and how he planned to contact the author(s) of the fallacious papers -- especially given that at least one was your adviser's collaborator.

Here is my advice (it comes from a pure mathematician, if that is relevant to you):

Spend up to one work day writing up a careful description of the error.  If a result is false, give a counterexample.  If you can give one specific, easy to verify counterexample, start with that.  Then if you have a further sense of the "terrain of counterexamples" -- e.g. if you know the result is never true, or you know that it is true precisely under some additional hypothesis, then include that.

The point of this is that in many cases what we perceive to be errors in mathematical work stem from misunderstandings between the reader and the author, including different use of the same terminology.  I would say that approximately half of all the errors I think I see in my colleagues' work turn out to have such innocent explanations.  Another big percentage of suspected errors stem from misunderstandings of the part of the reader: it is one thing if you come across a result that contradicts another result you have already written up.  However, if you are just reading then the odds are fair that the cognitive dissonance in your mind is not actually caused by a mistake in the paper: for instance when I read other people's work, I try to do so with an eye towards its relationships to my own work and my own problems.  As a proud student of the "Richard P. Feynman school of situational genius" I heartily endorse this approach, but sometimes it turns out that what I think is an error is due to an entanglement of "my situation" and the author's.  Finally, when an error has actually been made, there is usually (very understandable) psychological resistance on the part of the author.  This is why it helps to arrive with individual, crisp counterexamples.

If the theorem is correct but the proof is faulty, the situation may be more nebulous.

Everyone has different standards of what constitutes an acceptable proof.  Moreover, mathematicians are still human beings, and the percentage of inessential slipups we make in the course of our written work is non-negligible.  Most people do not appreciate their expository flaws and bone-headed but unimportant mistakes being taken as evidence that their proofs are incorrect.  In fact, where possible, when you claim that someone's proof is faulty it is an honorable thing to give them a chance to correct it.

In this case you speak of a "fundamental error", which I guess means that it is worse than the relatively innocuous mistakes described above.  Do you mean though that the theorems are still true, and you know this because you know how to prove them?  If so:

Spend up to two or three work days writing up as much as possible of what you feel is a correct proof.  If you can only give a sketch, so be it, but try to include all the ideas which convince you that your argument is correct.  Your target audience includes people who are deeply committed to and knowledgeable in this particular area: you can write accordingly.

I would meet with your advisor as soon as you have written each document.  (If you can write both in one day, great.)  Then the question becomes obvious and unavoidable: what should you do with these documents?  If he can vouch for their accuracy, I think you will certainly want to contact the author of the flawed paper, but whether to do this yourself or through your adviser is something you should ask him about.

Why do I place time limitations on these tasks?  It is because of the following important observation, which in my understanding is somewhat peculiar to mathematics:

Even if the author's proof is wrong and yours is right, your corrected proof may or may not be publishable.

There are too many nuances here for me to go over them all, but just one quick thing: you say that you fixed the result using material from old works.  Because of this, it is possible (perhaps; I don't know the situation) that the authors and/or the editors in question will still regard the mistake as a "slip up" (even if you do not).  A math paper which does not contain "new results", "new ideas" or "new techniques" may be very hard to publish...let me readily admit that this practice is not entirely fair or wise, but it most certainly is extant.  So you don't want to spend substantial work time on what may end up being a corrigendum written by the author but identifying you as the provider of both the problem and the solution.

Good luck.


I broadly agree with Davide's answer above, but I would move the list around somewhat:

Tier 1:

Self motivating
Communication, broadly-defined
Ability to stay focused on a single task for multiple months & years

Tier 2:

Work on a team
Creative, curious personality
Strong writing skills

Tier 3:

Learn from criticism
Personable

Tier 1 skills are, in my mind, absolutely required to be a researcher. The inability of any of those will preclude you from doing your work (i.e., unable to communicate means unable to publish; unable to stay focused for long periods of time means unable to complete research projects & grants.)  Tier 2 skills will turn a good researcher into a great researcher. Technically speaking, researchers don't need to be good team members, but having that skill will greatly improve your academic worth and potential. Tier 3 will improve your worth to yourself and others as a researcher. There are probably a bunch here that I missed and should have included.


Should I put a disclaimer on the first page of my thesis after making some corrections which are not allowed by the university?

My university doesn't let me make any corrections to my PhD thesis manuscript after defending it because all the members of the jury signed that no corrections are necessary. Not even typos.

You must follow your university guidelines.

My supervisor is insisting I make the corrections we mentioned during my defense because he finds them necessary and to leave a few copies in the lab's library.

You should explain to your supervisor that the university has forbidden such changes. Presumably they are either unaware of the university's ruling or they know some exception.

However, since this is not technically allowed. I'm thinking of putting a disclaimer on the first page, something like: "This is a private copy".

You are free to make unofficial versions of your thesis available. Suitably marking such variants is advised to avoid confusion and a disclaimer is suitable for this purpose. Rather than This is a private copy, I suggest something more informative, e.g., The official version of this thesis is available from the university's library. This version differs from the original as follows: xxx.


Is it possible to make a decision upon a manuscript just within a month?

I cannot make any statement about this journal and this may depend somewhat on the field, but so far I never spent more than a day’s work on any review. The main problem why reviews take so long is not that the review itself actually takes that long, but that reviewers need to find time for the review given their numerous other duties.

Therefore it’s entirely possible that a referee reviews a paper within a day – maybe somewhat more, depending on the field – if they have time at hand. This needs not have to do anything with the review being sloppy or the paper being bad; it’s just a question of luck. I know of one example where a paper for Physical Review Letters (a high-level physics journal) went from submission to publication in something around ten days. Also, one of my papers once received a positive review within four days.

If the journal expects the review process to take eight to ten weeks, then a month sounds entirely plausible. It’s not even outstandingly short.


Do students needs to be specifically mentioned on grant proposals for projects funded by government agencies in the US?

My experience is that students are not put in NSF proposals by name, but a slot is put in the narrative and budget with the name listed as TBD, "To Be Determined". It's possible that the PI failed to count all the heads correctly and was off by one. I would be surprised for this to happen in a small group, but if there were 10-12 students in the group, it could be easy to miss one.

Edited to add: It's worth noting that a particularly excellent student with lead or primary authorship on the papers that constitute the prior work for the grant might be highlighted in the grant text and budget, especially if the student has won some awards for the work


PhD position interview: How specific should my idea of the topic be?

The way I interpret the topic you were asked to present on is that they want you to present on some work you have complete such as your first paper (or possibly a masters thesis if you have not published anything).

The idea of this is probably to get an idea of how you think/do research and provide a nice introduction into finding out what your interested in.

From your question it sounds like you think they are asking for something else. Now I could be entirely misunderstanding what is asked for (I just have your question), but if you are unsure I would suggest you send a polite email to clarify what the talk should cover.

For what you should say in the talk I would try and answer these questions:

What was the motivation for the research (why is it interesting)?
What did you do?
What are your results/what do they show?
Why are the results significant/interesting?


When do researchers decide to be listed as last author?

This depends a lot on the field, but for many sciences and engineering the following is (at least to some extent) true:

The amount of work invested into the manuscript decreases with position in author list.
The amount of responsibility/funding for the project increases with position in author list.
If a publication has many authors, the ones in the middle are probably the ones with least significance.

The first author usually wrote the most of the manuscript and submitted it. These are PhD students. For some programs, first-authored publications are a requirement, therefore it is desired by many PhD students to get the first place.

The last author(s) are usually the supervisors and professors overseeing the research effort. They probably took part in discussions, maybe even drafted some text. In most cases, they just supervised the process/project. The "big boss" will most probably be the last, though.

For everyone in between, the contribution can be very diverse. It could be someone who did experiments, someone who helped by discussing the matter (mostly these people get an acknowledgement, not authorship) or in some cases even everybody who worked in the building.

Therefore, in an average academic career where somebody progresses from PhD student to professor, they will advance in the author list. This is because they do less practical work and more coordination and organisation. This is some kind of established system that has no written rules to it. I know of professors who demand they be the first author on every publication of their PhD students. While strange, it is not forbidden.


What Types of Content Should Be Included in A Poster Presentation of Unfinished Work?

Rather than 4, you should say something about your hypotheses. You don't have "expected" results. You only have hypotheses and results. The results may support your hypotheses or not.

And rather than 5 you should say something about the potential significance of the study. Why is it worth asking the question and posing the hypotheses?

These two items should be #1 and #2, actually. Your #4 and #5 can only be discussed properly after you know more.

In a poster session for incomplete work, the attitude should be "What do we hope to learn (not show), and how do we go about testing it?"


Both bitbucket and github allow you to publish a static website, which is handled under the same version control policies as everything else that you publish there.

You get no php/database support, but for academic web sites a static website generator such as Jekyll, which they both use, is more than enough.

Note added after reading @RebeccaJ.Stones comment to another answer: github is currently blocked in China, while bitbucket is not, so you may want to go for the latter, to make sure that everyone can access your website.


What is the best way to find plagiarism in a draft research?

It depends what you suspect was plagiarised, how and where from.

If you believe the ideas/structure/references (the latter would apply to a literature review) have been plagiarised, you're only recourse is to use your expertise and knowledge of the field to identify the sources. A literature survey of your own would help this.

If, as I suspect, you mean the text has been plagiarised, you can use services such as Turnitin and iThenticate (as suggested by others). If you work in a university, it is very likely that they already subscribe to one of those services, and you should be able to access it. Very often, universities provide (password-protected) access for students to check their work through such services, prior to submission; usually through their virtual learning environment (VLE, e.g. Moodle, Blackboard). Your librarians would be able to point you in the right direction.

However, there's a much easier way: just Google (and Google Book search aned Google Scholar search) the text you suspect of being copied. Pretty much the only sources Turnitin et al. have access to that Google doesn't is previously submitted student assignments; so (as I read this case) Google is as likely as anywhere to identify the source of any suspect passages.

I just picked a random sentence from a nearby textbook to test this. While "straight" Google didn't pick it up, Google Books did.

When I was a fresher, and we had our "don't plagiarise" lecture, I remember the lecturer telling us that the university subscribed to all these expensive anti-plagiarism services, but the lecturers just used Google instead.


My interpretation of the question is:

  I was told it is unethical to photoshop my data.  Is it ethical to use Photoshop software to make a graph?

The choice of software used is completely irrelevant to the ethics of any scientific image.  You can use python, Photoshop, or crayon.  If the image is drawn correctly, it is okay.

If the contents of the image is false, that is never okay.  It is much worse if it is deliberately false.  When people say it is unethical to photoshop, they mean that it is unethical to lie.  They do not mean you cannot make truthful images using the Photoshop brand software.


How does one keep herself updated with new research without forgetting older results?

Here are a few additions to Suresh's list (converted from a comment at TCSgrad's suggestion):

Don't even try to remember details. Just remember that somebody published something related, and use Google (or Mendeley or Papers) to find the paper again when you need it.
Chase references. Interesting papers tend to cite other interesting papers.  When you read any paper, also look at the papers in its bibliography.
Chase citations.  Interesting papers tend to be cited by other interesting papers.  When you read the paper, find other papers that cite it (via Google Scholar, for example) and look at them, too.
Follow whims.  If you see a paper with an interesting word in the title, or an interesting figure on the first page, at least read the abstract.
Don't try to read everything. That's impossible. Just try to read a little more.
Stop reading.  Eventually you have to do your own research.  Don't worry about reinventing the wheel; sometimes the best (and even fastest) way to understand what someone else did is to ignore them, figure it out yourself, and then read their paper.


How to cite an article from a magazine (no date, published quarterly) in MLA7?

The relevant citation is provided in the site itself.
 My Black Crime Problem, and Ours by John J. DiIulio, Jr.
 City Journal, Spring 1996, pp. 14-28

To cite in MLA7:

DiIulio, John J., Jr. “My Black Crime Problem, and Ours.” City Journal, Spring 1996: 14-28. Print.

Hope this answers your quesion.


Recommendation letter from a research adviser who is expelled from the university

This is a tricky situation, but as long as everyone is careful and honest, you should be fine.

Here's what I would recommend.  Yes, you should ask your former advisor to submit a reference letter on your behalf, from his non-academic email address.  You should mention in your statement that he has left your university, but you should not say anything about why he left.  Any further details are up to your former advisor to reveal, if he wishes to do so.

Your former advisor absolutely should not submit his letter on university letterhead, because he is not affiliated with the university.  He should include a very brief bio describing his former affiliation and listing his departure date.  If possible, he should include some external evidence of his scholarship, like a pointer to his Scopus or Google Scholar profile.  If he wants to describe the circumstances of his departure, he should keep the story very brief; his letter should focus on you, not about him, his former employer, or their political conflicts.


Do it like you would any other web reference with both a link and a date on which the link was accessed by you. This guards against changes that can always occur in any web resource. You can take the title from the page title.

The date is essential.


Reviewing a revision, after the original review did not reach the authors

I cannot say whether the situation is due to sloppiness or due to some technical issue but it seems odd and something that should not happen. I gather that you were in an electronic review system of some sort and then the review should automatically be forwarded. In a journal not working with an electronic system, something like this is more likely to occur but should be a one off mistake in any case. Problems like these, if they recur regularly, will likely sink the journal reputation in the end. you probably have some sense of the standings of the journal.

The lack of response may not mean much and I would not over-interpret it. It is of course not a positive reflection of the journal.

Anyway, I would recommend you to basically re-use your earlier review. Look through it after reading the paper and authors comments to see if anything can be removed. If you catch anything new that needs corrections, of course, add it. You have done the work once and unless the paper is completely rewritten with significant changes to discussion and conclusions, your comments still stand. You can only reiterate your verdict of Major Revisions, which should lead to a third round. I think, under the circumstances that would b fair, unless the authors fully comply with your suggestions, in which case the editors can use his/her discretion (depending on a second reviewers response of course).

So bottom line: your initial review needs to reach the authors but with corrections for whatever has been changed. Unless you receive some explanation for what has happened from the editor, you have to draw your own conclusions about the quality of the journal and particularly the editorship. Try to form a well-founded opinion, whether you think the journal is worth your attention in the future. One mistake is reason for caution, but not reason for judging.


Coming up with a PhD Research Topic after 10 years away from academics

You've been in the corporate world for 10 years. You know better about what is going on 'outside' there, what is current practice, challenges and problems, trends etc. This is a very valuable experience when you delve into your PhD later.

Pair this up with your previous postgraduate experienced (MSc) and I don't think you will have such a big problem to figure out about relevant topic. Approach any potential supervisors (or their postgraduates students) in your field and briefly discuss about topics that relate with your experiences. Really, you've been in corporate world and you must seen much about innovation and management (and problems arise) first hand.


How to effectively evaluate your instructor?

What is the most effective way to communicate with your instructor via evaluation-sheet?

In a word, constructively.

If you are overly negative, there's a good chance you will be viewed as a malcontent with an axe to grind. If you'd like to maximize the chance for real improvement, avoid blanket negative statements. For example, instead of:

  This instructor was never available for consultation.

try:

  This class would be better if the instructor was more available to students.

(You send the same message, but with a more constructive – and therefore more credible – slant.)

Also, you should be realistic in what kinds of improvements you may expect to see. In my experience, some faculty take student evaluations very seriously, some don't. Some probably don't even read them; the forms are only completed because department policy demands it.

There's another important factor, too: the inmates shouldn't run the asylum. Some faculty regard student evaluations with disdain, and there may be legitimate reasons why. Sometimes professors who are easy graders get better evaluations from students, while more demanding professors get poor evaluations from students who are either lazy or else come to class with a sense of entitlement.

Truth is, there are a lot of dynamics that go into this. Just from reading your question, there's no way to tell if you're a good student who unfortunately had a bad professor, or if you're a bad student who got their feathers ruffled by a very good (yet challenging) professor.

A single evaluation won't have a huge effect either way, but, as I said at the beginning of this answer, I think your best chances for a positive impact comes by writing an evaluation with a more positive and constructive slant. In other words, try using the form to suggest improvements, rather than to harshly criticize. Such forms will be harder to dismiss outright.


If I get selected for a diploma in Australia from a recognized University, can I use it to get an education visa?

Visa advise is tricky.  At least in the UK, the recommendation is to leave this to a qualified visa and immigration professional.

Factors might include whether you have paid all or some of your fees, the type and even subject of your course, the level of what you have studied before, whether you are studying full-time or part-time, where you are from etc.  And this will be dependent upon the laws of the region in which you intend to study.

Universities normally provide visa and immigration advice services, so I would suggest you ask the institution to which you have applied to see whether the course will support an education visa.

Needless to say, there is likely to be incomplete advice, at best, available from Stack Exchange.


Permissions to reproduce an image while writing review papers

Usually the journal you are submitting to, will have instructions (even a form with legalese).

If it is just for your thesis, I don't think you need to be hyper legalistic, but ask for permission for the intended use (in your thesis).  Email is sufficient (don't need a signature, but don't rely on word of mouth either.  If part of the thesis ends up becoming an article later, just go back at that time and ask for the fuller permission using the journal's advised form or instructions.


How hard is it to get a good to great grades in undergraduate school?

It is hard to answer this question as the educational systems in the US and the EU are very different at the undergraduate level. A bachelor's degree, say in mathematics, in the US includes many other courses such as writing, history, philosophy, etc. Only about half of the program is mathematics. In the EU the degree is normally much more focused on maths. But for any given course in maths, I'd guess that the level of difficulty is about the same, though this varies widely from place to place.

So, a GPA (overall) in the US means something quite different from one in EU. The GPA in field is a more comparable number.

But, with more focus in the EU, some courses that would be taken in graduate school in the US show up earlier in the EU.

You have to work hard on both sides of the pond to achieve success. Don't expect lower standards in either place.


Recommendation letters choices : is diversity an advantage?

I am currently applying for a PhD and had the same dilemma as you, so maybe I can tell you what reasoning I followed as it might help you as well.

What field are you applying in? If it is a very academic field with few industrial applications, surely recommendations letters from professors or research supervisors rather than previous employers are more adequate.
You should choose recommenders that know different parts of your knowledge or skillset - e.g. if they all say how good you are at one specific software or problem type it will just be repetitive.
In my opinion, recommenders that have worked with you more recently come across more convincingly than older professors or supervisors, as your skill and your interests have developed since they last worked with you.
If you are changing fields, a recommender from that same new field who thinks you are capable of achieving success in the PhD is a big advantage (your 2nd recommender in this case).

If I were you, I would probably go for the "Previous employer in a relevant industry (work with them for a year between masters and Ph.D.)" or "Physics professor for whom I was a TA at B", depending on how academia- or industry-focused you want your application to be. All in all, it has to suit your profile and statement of purpose.

Hope my answer was helpful. Good luck!


What are the differences between a research paper and a patent?

You're asking multiple questions at once, so let's start with:

  What are the differences between a research paper and a patent

There are many, but briefly a research paper has the purpose of communicating research findings to the relevant scientific community and the general public. Patents are legal documents used to prevent other people from commercializing the process or devices they describe. Research papers typically report results of a scientific process, whether experimental or not, while patents describe processes and devices along with their respective intended applications.

Patents are typically very open-ended, not unlike a very long "future works"-section of an academic paper. The strategy is to cover a maximum of possible usages for the technology.

  it is not peer reviewed

That is correct, peer review is a strategy used by researchers to filter, improve, and curate scientific literature. For patents, the review is driven by the legal requirements only. A major point is absence of overlap with existing patents and other publicly available material*. In some regions, a minimal demonstration of how the process/device works is expected by patent offices, but it's not the same as peer review.

  Is it allowed to publish patent and then paper?

Yes, it's the other way that's problematic because as stated above, if you (or someone else) published a paper about your process or device you cannot patent it anymore.

Most journals are interested in novel results and all (legitimate) journals don't want to re-publish existing literature but the fact that the processes are patented is not an issue. As stated in my first paragraph, both documents should have very little overlap.

*On that subject, see the entertaining if not entirely historically accurate
Donald Duck as prior art case


How to come up with research questions that are well-defined and suitable in scope and relatedness for a thesis?

This sort of thing only evolves as the product of your exhaustive reading, and discussions with your supervisors and peers.

After that, at some point, your supervisor will say something like: "before you can really get into your research, just resolve this little thing - it should be fairly trivial."

That's your thesis, right there.


Is it ok to call myself stupid in an email to a professor explaining why I have not completed my project yet?

I would pose two questions:

Is the professor unhappy with you?
Did you really do anything wrong?

If the professor has not said they are unhappy with you, then I see no reason to give an explanation; keep it up-beat.

  Dear Professor, Just a status update on the X project. I've finished X, has taken a little longer than I anticipated, but I think I'll have it wrapped up in the next two weeks. Looking forward to it!

If the professor is unhappy, then the question becomes whether you did anything wrong. If there was no deadline and you're not getting paid, then it's a bit rich of the professor to be angry. You can push back as much as you're comfortable with; here's a reasonably polite version:

  Dear Professor, Sorry for the slow progress on the X project. Given that we had never discussed a deadline (and that I am not getting paid), I hadn't realize you had expected this to be finished by now. Still, I do want to finish the project, and will pick up the pace. I think I can be finished in two weeks; would that be OK? I'll keep you informed on the progress. Thanks,

If the professor is unhappy and you did do something wrong, then a quick apology is in order.

  Dear Professor, Please accept my apology about the slow progress on the X project. I am still interested and definitely want to finish it; I had just [stupidly] been doing the work pretty slowly and hadn't managed to keep the schedule we agreed upon. I think I can finish the project in the next two weeks; would that be OK? Happy to discuss in person if you like, just let me know.

As to whether to include the word "stupidly", I think it depends on your personality a bit -- as stated in the comments, you shouldn't seriously suggest that you are stupid, but I think it's fine as a way to be a bit self-effacing.

(Note, my answer is from a Western/US perspective)


What exactly happens in your arXiv account if you no longer have institutional affiliation?

Log into you arXiv account and change your e-mail address.  You don't need access to your old e-mail to do this, nor will you lose your arXiv account if you don't have an academic e-mail address.  (Having an academic address is not a requirement for arXiv participation, after all.)  Once you have an account, there is nothing (short of administrative action) that would cause you to lose ownership of your papers or your existing endorsements.  It should be no different from changing your e-mail in any other account you have online.


Is it ethical to slightly improve upon someone's unpublished work posted in arxiv and publish before the original work?

I question, as did Dan Romik, your characterization of work posted on arXiv as 'unpublished': it is made available to what amounts to the widest possible public, it is just an un-refereed publication (or perhaps arguably a kind-of very slightly refereed one, if you read the conditions).

I suggest that the ethics of it depend on whether the later-published paper  acknowledged the arXiv paper as earlier work, or not. If it did, I see no problem.

If the later paper made no acknowledgement, then maybe there is a problem if its editor/referee(s) happened not to spot the earlier paper in arXiv and took the whole content of the later author as original.

But what the arXiv author could do in that event I could not begin to suggest. Best response would probably depend highly on the particular circumstances, which would no doubt be awkward to set out in this medium.


Is it recommended not to have a figure on the first page of an IEEE journal article?

To the best of my knowledge, there is no such rule.  It would be problematic to put a figure in the first column (which is tightly compressed between abstract and copyright blurb), but a figure at the top of the second column is fine. However, due to the way that document preparation is done for IEEE publications, it is highly unlikely that an author will end up with a figure on the first page unless they specifically choose to do so.

The reason is that in the IEEE format (both conference and journal), one rarely gets much beyond the introduction in the first page, and certainly never in the first column.  IEEE papers are mostly prepared with LaTeX, and as such, if you use the normal figure placement, your figure will tend to end up at the top of the column after the column in which it is set and referenced in the source.  Since it's quite rare to have a figure at the beginning of a paper's introduction, then it will be correspondingly rare to have a figure on the first page. Complementarily, an author who chooses to have a figure on the first page will typically need to move the figure significantly forward of its reference in the text in order for LaTeX to choose to place it at the top of the 2nd column.  Most IEEE journals work directly from the author-submitted document rather than doing significant layout work by the journal, so if the author didn't put it on page 1, nobody else is likely to either.

Thus, we have the emergent phenomenon you've noticed: because the defaults and tendencies in article production for IEEE make it unlikely that a figure will appear on the first page without author intervention, most papers have no figure on the first page.

Personally, I like to intervene, because a figure on the first page really helps an article pop out to a reader and be more memorable and intelligible.  I suggest that unless you have good reason to do otherwise, you do the same.


Presenting collaborative work in progress

Generally speaking, people should check with their collaborators before presenting joint work, including work in progress that may be controversial.  An exception might be an individual invitation for work that has been published and presented previously.
Certain fields, like particle physics, often have very large collaborations, and they usually implement very formal procedures for deciding who gets to represent the collaboration at what conference, and what official material can be presented.
If you don't have a formal mechanism in place, you're right it's probably good to chat with your colleagues in advance to set the ground rules.


Is it possible to find a PhD without being in the lab all the year in Europe?

There are definitely universities in Europe that allow you to be physically away from university for extended periods of time during a PhD. In fact, I would be surprised if you cannot find one in France.

I think a bigger problem than the actual rules, both for a potential supervisor and for yourself, is that it sounds like you might be too preoccupied with your external situation to do an excellent job as a PhD student.

Have you considered options for resolving your situation before you start your PhD? Maybe work in a temporary research position while you are trying to resolve it?


How do you refer to someone whose title has changed?

The person is now a professor, so refer to them primarily as that.  If you are concerned about confusion, you can add the additional information in the sub-clause, where it reads more smoothly:

  I took course Y from Prof. X, while he was a [lecturer, postdoc, whatever] at [instutition]"


Using the author's reasoning of experimental observations in literature review

When writing either a review section of a paper or an entire review paper, it is extremely important to be clear about which contributions came from which paper, and which form of evidence they are: does that paper have direct evidence on that point, rely on other papers/rely on an assumption, or develop the point as speculation/theory/explanation?
Obviously, you should cite any of these that you use, but you should cite them differently. For instance, if you have an article by author X, X might condense the results of previous literature (possibly citing authors Y and Z), present their own experiment, and discuss the theory and possible implications of their own experiment and interpret it in light of the literature. You would want to distinguish the three.

X emphasizes that the previous literature finds a strong relationship between concept 1 and concept 2, and considers the work of Y and Z to be "extremely strong evidence that causality runs both ways" (X, p. 876).
X finds [shows, provides evidence] that [experiment results] [in context].
X argues [concludes, suggests, wonders, hypothesizes...] that [explanation put forth].

I'm guessing you were already thinking about a certain hypothesis, and then you saw X's paper and realized that they had thrown in that hypothesis at the end. Definitely cite them. Even if you had been looking at X's paper for the experimental results, you should also re-read what their discussion/conclusion says, and if those are relevant to the discussion, you should acknowledge the ideas in some way. (When would their discussion or conclusions not be relevant? Perhaps if you're interested in something that they had to account for on the way to their focus.) It could even be a simple mention just to acknowledge that they said it, too.

Many scholars consider concept 1 to be a likely explanation (cf. X, Y and Z, Q).

It's OK if you conclude your review with an interpretation that's similar to what X suggested, as long as you have reviewed articles suggesting other possibilities and you reference as you're concluding that it's similar to X.

Overall, there is mounting evidence that, as X suggested, [explanation].

Your contribution is a consideration of additional material, synthesis of ideas, and your own opinion/emphasis on what's important. For the purposes of publishing, if X has already covered similar area, your review paper may not be extremely interesting or important unless you can show why the overall question/field matters or that people are still working under alternative assumptions or not yet convinced.


Is a student with weak written examination skills also a weak candidate for PhD?

Let's map what you've written about your friend, onto the sort of things we might look for in a promising PhD candidate, to see why, although exams and PhD research are very different beasts, we might learn about one thing from another.

Meticulous? No.
Demonstrates good grasp of the substance and relevance of theory? No.
Can perform under pressure? No.
Can follow protocols? No.

As you can see, although you say the grade point average is only just below what is needed to convert to a PhD, there are a few warning signs that this student might not be appropriate PhD material; both the student and the decision-making body should pay heed.

I appreciate that this may not be easy for you to hear, as they are your friend. But really, PhDs aren't for everybody: there are lots of domain experts who are not PhD candidates; and there wil be lots of successful Computer Science PhDs who will never be such good programmers as your friend. A PhD is a measure of academic research skills, not of industrial skills or life skills.

Computer science and software engineering are two different disciplines, though they are related. Different institutions will teach them with varying degrees of overlap. But they are distinct. Maybe your friend is a talented software engineer who needs to specialise there, rather than in computer science.


Dealing with the psychological stress of faculty applications

I'm in a field where some positions get close to 1000 applications.  Here are the two pieces of advice I have for everyone on the job market.

Probability does work.  If you're a slightly above average applicant, the odds of getting any job from your point of view (in other words, not having any insider information) are at most 5%.  For most jobs, it's considerably lower.  However, if you send out 100 applications, all those 2-3% chances, plus all those 0.5% chances, actually do add up to something approximating a pretty good chance for a job.  (In particular, they are actually pretty close to probabilistically independent.)  This means you really should not think about any particular job; your chances of that job are tiny.  It's the mass of applications that gives you a chance.

Before the whole process even starts, you should have some idea what you will do if you don't get an academic job.  Having a plan is more reassuring than having no plan.  Also, having a plan gives you some baseline to compare any prospective job against, so that you don't end up in an unsuitable job.

As a professor at a university with a low-ranked PhD program, I make sure students understand how bad the job market is before agreeing to advise them.  I will only agree to advise a student after I've made sure they understand they most likely will not find an academic job after their PhD.


What is the industry equivalent of a post doc?

I am not sure how much sense this question makes, given that no position in a research lab is really comparable to a postdoc position.

That being said, I have seen the term "research staff member", or just "researcher" or "scientist" being used a lot as an entry-level, permanent position in a research lab which requires a PhD. "Senior scientist" or "senior researcher" is typically a bit more advanced ("researchers" become "senior researchers" through regular career progression). However, concrete names of course vary between companies, so you should never assume much of anything about a position purely based on its name.

  "Senior Scientist" seems to be the closest match, because the salary is slightly higher than a junior post-doc.

That's a very bad heuristic. Too many other factors influence salary for it to be of any worth for judging the level of a position.


How much time should I spend on reviewing a paper?

You should do slightly more reviewing work for the community than the community does for you.  So, as a rough estimate, assuming every paper you write and submit needs three reviews and your average paper has three authors, you should review slightly more papers than you submit.

There is no way to predict in the abstract how long a paper takes to review; that varies from field to field, subfield to subfield, and even paper to paper.  Answering a similar question in Theoretical Computer Science Stack Exchange, I wrote:

  Expect to spend about an hour per page, mostly on internalizing the paper's results and techniques. Be pleasantly surprised when it doesn't actually take that long. (If it takes significantly less time than that, either the paper is either exceedingly elegant and well-written, you know the area extremely well, or the paper is technically shallow. Don't confuse these three possibilities.)

No, the answer does not depend on whether you get credit for the review.  If you're not going to write a thorough, professional review, just say no.


Where can I borrow books that my own university's library doesn't have?

Ask your university librarian.
Usually universities libraries collaborate with each other. They can look whether the other universities have the book (I know this happens within Canadian universities)..


University providing CGPA but not grading on a curve

If you believe the CGPA data your university provides does not make your performance clearin your application package, it is your responsibility to clarify in your personal statement or try to achieve this through reference letters.

"My academic performance places me in the top 10% of my class."


Previous publication of my supervisor and a post-doc is a lie

There are lots of ways to go about this.
Since your advisor is a co-author on the previous paper, this may be difficult, since they are invested in the existing paper and have some credibility at stake. Theoretically, they should be happy to retract/rewrite the older paper, but we are human.  You are probably correct that they feel guilty- everyone with their name on the paper is ultimately responsible for all of the content.
At the same time, this can make some things easier for you. Finding an error in previously published work opens some new avenues for publication. Now, instead of a simple sentence, you can issuing a comment or a correction on a previous paper - many journals will allow you to publish a correction or remark on their previous articles, particularly if you can demonstrate a major problem or flaw.
Critically, do not be a jerk about this process. Simply state that there has been an oversight or error in the work by XYZ. Do not speculate as to why it went wrong or how. Even with evidence that their results do not match their data, there could be numerous reasons for it.   Journals don't want to be told they did a bad job, neither does your advisor- but everyone would prefer you correct an error softly and with tact rather than letting someone else do it loudly and disruptively.
Edit:  I am not sure your evidence is legally obtained, nor am I fully confident from this post that the evidence is conclusive that they were fraudulent.  Until both of those conditions are met, I wouldn't recommend making accusations of data fabrication - publicly or privately.  You will have, in all likelihood, a legal battle - for which I am not a lawyer. But you can conclusively say, as another commenter mentioned: "We were not able to reproduce the results."


How to give feedback to students after bad grades

From my perspective as a PHD student (the other side of the spectrum) I feel that there are some crucial aspects to giving helpful and encouraging feedback:

Give the student constructive criticism. Give them the feeling that you are supportive of what they did (regardless of quality) and that you are giving feedback to improve their work in the future. Make them feel safe. Speak about what could be done better in the future and not about what went wrong or what they "should have done".
Emphasize both the good and the suboptimal parts of their work. It is important to balance both positive and negative feedback.
Avoid words like "however" and "but". It is almost always discouraging to hear positive feedback followed by a "however". It (in my opinion) completely devalues what was said beforehand.
Check in if they understood your criticisms correctly to avoid misunderstandings.

I hope my answer is at least somewhat helpful to you, if not, you now have the possibility to practice and give me your feedback! :)


How to the enlarge the font size of a journal paper

If the paper is in PDF (the standard) you can print using the Poster option. You will need to print the page in a bigger size, to make it fit in multiple pages.

https://helpx.adobe.com/acrobat/using/basic-pdf-printing-tasks.html

You can try to convert the PDF to word and enlarge the font before printing, but many don't convert well.

https://smallpdf.com/pt/pdf-para-word


Is it fine to send a message to the author of a paper if I don't understand something and want to clarify it?

By all means ask. A person who goes through the trouble of writing up lecture notes, is almost certainly a person who would be happy to answer.

As someone who receives a lot of questions from PhD students myself, here are a couple of pointers for how to phrase your question. This could be obvious to you, but I know for sure that it is not obvious for everybody.

If you have a local supervisor, it makes sense to ask them first - maybe it is a trivial question.
Read the paper first, and use the notation from that paper when you can.
Cut to the chase as quickly as possible. Don't explain their paper back to them in the mail, they know what they wrote.


Getting article type information [New Result / Confirmatory Result / Contradictory Result] from bioRxiv

Looking at the few XML in bioRxiv's RSS feeds, it looks like the information that you are looking for simply is not included in their schema at present.  Thus, I would say that your only options are:

Screen-scraping
Asking for them to upgrade their feeds


The situation you described is very unfortunate, and, if your description of your advisor's behavior is accurate, not entirely your fault. It is true that sometimes projects don't work out and students need to learn to take responsibility for their own projects, it is also the responsibility of an advisor to guide the project to fruition, one way or another. Most good ideas will not result in a paper without at least one to two years of work, and you end up in a futile cycle if you are constantly changing directions at the first sight of any trouble.

Your current situation is untenable. If you continue with it you will graduate with very little to show for and a difficult time finding a good post-doc or industrial position. If you want to stick with your advisor, you need to have a difficult conversation with her, in a non-confrontational manner, to lay out your concerns and the pattern of inconsistency that resulted in low productivity. Ideally the meeting will produce a plan to make better use of the remaining time you have to maximize your research output and prepare for your next job. But behavior change is hard, and if your advisor is as short-tempered as you say, negotiating a different relationship with her may be next to impossible, and any behavior change may be only temporary. Alternatively you should consider switching to a different lab, which will result in delay to your graduation and people may be hesitant to take you in at this stage of your PhD. Lastly there is always the option of dropping out. It is a difficult decision given what you've already invested. But if it becomes clear that the past time investment can no longer be salvaged the smart thing is to move on; maybe use the time instead to gain some industrial experience that will serve you better down the road?

Ultimately it is a hard decision that strangers on the internet cannot make for you. Nevertheless you should explore these options, perhaps simultaneously, and think through and prepare for the possible outcomes. Good luck.


GitHub repository ownership as a PhD student in a lab

It's fairly common for labs to have GitHub organizations. There are multiple reasons for this.

First of all, it doesn't prevent the authors from getting credit. The commits will be shown as commits of the individual, not as commits of the organization.
Labs often have a scientific "brand" in terms of what they research. If the GitHub repository is completely personal, then your work does not fully contribute towards this brand. But contributing towards the joint scientific output of the groups is a major reason why you may get funding from the group's third party funding.
Perhaps most importantly, PhD students eventually leave the lab. They can continue maintaining their projects if they want to - there is no necessity to be an administrator of a GitHub organization to continue maintaining existing repositories. But what if the leaving PhD students choose not to maintain the code? If the repository is personal, then other people in the lab then cannot commit bugfixes to the repository. They could fork it, but once the repository link is in a scientific paper, the original repository is the official one. And this is problematic if the group's brand depends on the repository because it's a central part of their overall story.


Hiring an academic researcher to implement an algorithm in a paper they wrote

It is definitely appropriate to ask.  University policies on outside work for employees vary.  But typically it is allowed.  There are at least three possible approaches to this.

You hire the academic directly, and it is a side job for them.
You provide the university with research funding, which is then used to pay to make the implementation.  This might have tax benefits, it will make the academic look good, and will allow the university to take a cut of the money.
You partner with the university to obtain funding from a third party (probably a government program).  Your company pays for the commercial part of the project and the third party provides pure research funds the academics want.  This makes everyone look good but can be slow.

The key thing here is that you need to convince the academics that there is a benefit for them to participating.  This is a matter of their personal preferences.


Significance of American Mathematical Monthly Problems in Math Grad School Admissions

It probably depends on the committee members, but I wouldn't expect it to help much.

If you get a really clever solution published, or they publish a problem you submit, that could make a difference.  It certainly wouldn't mean as much as a research paper, but it could be viewed as the same sort of thing on a smaller scale.

Otherwise, the potential impact is not large.  Solving Monthly problems would be viewed favorably, as evidence of talent and effort, but it's not likely to mean the difference between admission and rejection.  (Still, it's worth listing on your CV.)


Redoing my bachelor’s degree for general specialisation and better GPA

If you were living in the same circumstances, what would you do?

If I were you, I would do a part-time Master's degree in Computer Science while working on a not-so-high salary job.

You will waste your money and time by doing another Bachelor's degree in Computer Science. You won't gain too much. The courses are about the same except a few theory courses (depending on the program and school). At the end you still only have a Bachelor's degree.

If you do a Master's degree in Computer Science, the school will teach you more theories, more skills and you get a Master's degree at the end which can earn you more respect that you need when you look for a high-salary job.


How to ask for employment help or referral from someone you don't know?

The typical approach is to send an email saying something like:

  Dear Dr. M.,

  My name is ... and I am applying for the position of ... in your department.  (Brief summary of your professional background and research interests.)  I am particularly interested in the position because I would look forward to the opportunity to collaborate with you.  Please let me know if there's anything you want to discuss.  My CV is attached (maybe also a preprint).

This alerts Dr. M to the fact you are applying, so that he can get in touch with the search committee if he wants to support your application.

However, normally you would do this at roughly the same time as you submit the application.  You say you applied three months ago, but when is the application deadline?  If it hasn't passed yet, or if it was just a few days ago, then there might still be time for an email to Dr. M to have some effect.

But if it passed some time ago, then the search committee has probably already finished one or more rounds of screening.  If that's the case, and you haven't been invited to interview or otherwise contacted, then unfortunately, you probably didn't make the initial cut.  In that case there is very little that Dr. M can do, so not much point in contacting him.

(By the way, it's pretty much irrelevant that your advisor went to the same university as Dr. M, if they haven't otherwise been in contact.  That kind of relationship is roughly comparable to this one.  So I'd leave it out of any message.)


When quoting books, ought pages be separated as they are on paper?

No. Unless the presentation of the text is particularly important for some reason (maybe the author is drawing pictures with the way words are arranged), you can assume that the actual content is more important than the choices of font size, margin widths, inter-paragraph separations, title font size... that lead to the exact page breaks that occur in the particular edition you are reading. I don't really see anything "authentic" about reproducing page breaks. The authors was probably not even involved in the choices that lead to these particular page breaks.


Short summary of other works that cite/build upon your publication

The practice you describe is actually quite common in the slightly different form of a research statement. See my comment above.

  Would it be an acceptable practice?

This seems to be a common question around Academia.SE and comes up in many different contexts. My opinion on such things is that this is usually not a helpful question to ask. For a practice that is not common (say, reciting Shakespeare in a calculus class), there will likely always be at least one person who finds it objectionable or "unacceptable". So rather than worry if it is unacceptable, I suggest focusing on the separate question of whether it is a good idea. If it is, go ahead and do it. If it's not, don't do it, regardless of whether it would be acceptable or not.

  Would it be an advisable practice?

Well, as you yourself say, it could turn out to be awfully time-consuming. However, I can definitely think of situations when it would be advisable. If your result was applied in a key way in Prof. Humperdink's recent proof of the famous Griemann Hypothesis, absolutely find a way to tell the world about that. More seriously, as you create a body of work and your work is applied by others in various ways, there can definitely be a lot of value in creating a short summary that allows people interested in you and your work (e.g. colleagues and prospective and current employers) to get a quick overview of your work and its importance. The precise title of the document ("Research statement", "Research summary", etc.) and how is it formatted (PDF vs HTML, etc.) are not so important as long as it's presented clearly and easy to access. Similarly, whether the document summarizes your own papers or whether it summarizes the use others have made of your results (the former practice being more common than the latter, as you observe) does not make a huge difference in my opinion; you can have two separate documents to discuss those two things, or cover both of them with a single document, which could make a lot sense since in many cases they would logically fit together very well. Or you could just cover one of those two aspects if that makes the most sense to you.

The important thing is that any survey that you prepare of your own work be written in good taste and not in an excessively pompous or self-aggrandizing way. If you make wildly exaggerated claims about why your result is revolutionary, groundbreaking, deserves to win some major award, etc., this will leave people with a bad taste and they will quickly develop a discounting factor that they will apply to any future statement they hear from you. (As an example, a friend I had in grad school used to make wildly exaggerated claims in a humorous fashion, leading to some of his other friends inventing the "log" rule, which was that you had to take the logarithm of anything he says...)

  Should only the works that build directly upon the cited paper be
  included in the list (or should one be more flexible and include also
  papers that are less strictly related)?

It's hard to say. My inclination is to say that you should generally focus on the papers that build more or less directly on your work. In certain cases, say if a paper you wrote was used by someone to invent a whole new theory, which now generates hundreds of new papers every year, it may be reasonable to say that your paper played a key role in the creation of the theory and led to the later wave of publications, even though its contribution was of an indirect kind. Again, the key rule of thumb is that your claims should be seen as reasonable and presented in good taste, with the goal of genuinely helping the reader to understand the development of the subjects you have worked on, rather than to make yourself seem important by claiming credit for anything under the sun that your work has touched on in any way.


Is there any institution or report tracking academic fields in terms of funding (today and historically)?

Two platforms come to my mind.
First, Dimensions offers detailed data about grants and research funding - however, only the paid version would allow users to delve deeper into these data so as to treck trends over time (including at the level of countries, disciplines, topics, institutions or individual researchers).
Second, wizdom.ai seems to allow you to track funding allocations by research topics for free, including a list of "top funders", a "funders analysis" containing the amount of money allocated, a topic wordcloud, and a timeline.
Here is an example for Robotics: https://www.wizdom.ai/topic/robotics/funders/20903754, and a screenshot of how it looks like:


Should I leave my "first" job for a PhD student position?

You did not mention how do you feel in your current job. Do you feel that you are learning a lot, are you enjoying it? If the answer to this is yes, and seeing as it is a private research institute, then maybe consider staying there. There has been a lot of articles around about how you do not need to have a PhD to be successful and satisfied in your career.

Another point to consider is, why did you get this offer despite your GPA being so low? And maybe your GPA being low is an indication to you being able to grow more in a job at a research institute, as the environment, different from academics, may suit you better and you would end up learning more here. Or maybe your GPA is low for other reasons, and it does not always reflect how you strive in a PhD program anyway.


Is "Advances in Engineering" a predatory platform?

A human writing to you about your research would say something about your research and say how it contributes to research excellence. Spam bots tend to use a general template and refer to your research in a way that is easy to automate, for example, copy your title in verbatim.

  We are pleased to inform you that Advances in Engineering selection committee identified your paper “Another XYZ” as a key scientific article contributing to research excellence. We would like to write a feature about your paper and highlight it in our next edition of Advances in engineering news series.

This clearly falls to the spam category.


Feasibility of enrollments in a Masters program at one university and a PhD program in another university

Maybe, but why? Different topics?

In any case, you'd have to check the rules of both universities.

As a supervisor/employer of PhD students, I would not want my student doing this. A PhD is a full-time job, requiring full-time commitment. Financing is scarce and I wouldn't want to waste it on someone who is not fully committed.


What does "30 pp" mean for manuscript submissions?

Some journals restrict by word count, others by page count, yet others by odd hybrids such as counting each figure as a certain numbers of words.  In the case of the journal you mention, it sounds like it is, in fact, page count, with a limit of 30.

Usually, if there is a page-count restriction, the journal also prescribes submission format more precisely, so you may want to look into that as well...


How do I ensure I'll be able to claim authorship over a math proof, as an amateur math student?

Moreover, it would be really embarrassing to me to talk about this with people I know, especially if they rapidly find a mistake in the proof. I fear they'd think I'm silly for even considering the possibility I may have proven something no mathematician has been able to prove before

My advice for this concern is to propose your work as an attempt rather than conclusive. It is normal and okay for attempts to fail: most do. If you reduce your expectations publicly to those that you hold privately, there is little cost to failure and substantial benefit to success. Ask others to find errors in your work, and be humble.
If they can find no errors, they will be sufficiently impressed. If they do find errors, you can be appreciative and they will feel useful for having found and taught you something and you need not be embarrassed, only thankful.


Apply to PhD after expulsion from another

I would strongly recommend mentioning it briefly somewhere in your application, with a very short explanation of why it is irrelevant (for example: you were less mature and motivated, so you procrastinated and your grades suffered, but your performance over the last few years proves that these issues are no longer a problem).  Don't emphasize it too much, but your best strategy is not to hide anything.

You are right that it might hurt your chances, but I do not think it will hurt them much.  If it came up in a committee I was on, I would argue against worrying about it, if the rest of your application was compelling.  If you do not mention it, then you'll have an unexplained gap of a year in your CV, and that will also raise suspicions, since such a gap is usually a sign of something that did not work well.  If you don't want to mention it or have a gap, then the alternative is lying.

You should definitely not lie, by giving an incomplete list of previous schools attended if asked for a complete list, or by giving a different explanation of what you were doing during that year.  You might get away with the lie, since it can be difficult to detect missing information or disprove vague excuses, but if the lie is detected then it will ruin your chances of admission.  (And committee members might even mention it to friends at other schools, if they are irritated enough about the lie.)  Even if you get admitted, the lie may also come up again to haunt you in the future.  For example, a faculty member from your old school may someday visit to give a talk, recognize you, and mention the connection to your advisor.  Or you and your advisor may someday end up attending a conference at that university.  You probably won't get kicked out of grad school if the lie is discovered later, but it's technically possible (at least at some universities), and in any case you do not want to be known among the faculty as someone who lied about his/her past.

You've already done the hard part of moving beyond this issue and demonstrating that it is no longer a problem, and that will minimize the risks of honesty.  By contrast, the risks of dishonesty may follow you for years.


Should I ask for a recommendation letter from a professor who has a bad non-academic reputation?

To me, the key question seems to be whether the type of misbehavior is something that is likely to be seen as impinging on their judgement as an academic.

For example, if the person was known to have been prosecuted for fraud in a company they ran, that would be quite likely to affect perception of their honesty and judgement in recommendation letters.  In the example you give, however, I think that an impaired driving conviction is likely to be viewed as a form of misbehavior largely orthogonal to conduct and judgement as an academic, and therefore not likely to be any problem for you.


First of all, not all research labs are like that. You can find better work environment elsewhere, perhaps even have luck in the same University.

The academic world, however, is extremely small, and people will talk behind your back. You can't fight that. One way to minimize this is to minimize amount of time you spend in the current group.

Hence, one of few options is update your resume and start looking for another job. Your current situation will not become better. One of the reasons is that you have no political capital (friends) to change it, and filing complaint will definitely make your life worse in the group forever.

While searching for new job, try to connect with local chapter of Women in Science or similar unofficial group. Major universities have those these days. Ask them for help and advice. Another contact is something like Office of Equity and Diversity. These people have seen your situation before and will give guidance.

When you get a new job offer, you might want to consider filing complaint with HR specifically naming your current group leader. Hopefully, university will pay attention and investigate.


Accreditation as a whole is a huge and complex topic. Universities are accredited at the university level. Specific departments and programs within an accredited university may or may not be accredited.

Also, different accrediting bodies have different standards and mean different things- one form of accreditation might simply mean "This department has a full set of course catalog descriptions and all the polices and procedures we expect an academic department to have" while another form of accreditation might mean "This department provides an outstanding education and future employers will value the degree".

My feeling is this:

Do a Lot of Looking

A two or four year degree program is a huge investment of time and thousands of dollars. Most people wouldn't buy a car on a whim, would they? The most important thing you can do is to look at enough different programs that you develop a feeling for which programs are serious and which are not.

Institutional Reputation and Word of Mouth

Some schools are known to be good schools. If a reputable 4-year university is offering an online program then they have a strong incentive to make sure their online program is also reputable, or else the university's reputation will suffer. Also, you might know (or find someone) who has gone to a particular school. Ask them what their experience is. They can tell you details like how engaged they felt and whether employers seemed to care about their degree.

Look up Rankings

Many of the organizations that performed traditional college rankings are now starting to rank online and distance learning programs. As above, these organizations have an incentive to provide high quality information or else their reputation will suffer. Reputable rankings organizations will provide their methodology, which is the process they use to determine the rankings.

College rankings are never perfect. That's why it's important to read the methodology that a ranker uses. Does the ranking reflect values that are important to you? Is the ranking based on student surveys, on empirical data like faculty to student ratio, or a combination of both?

I won't recommend a specific rankings set, especially for online programs because I have zero experience here. The US News and World Report is one organization well known for ranking brick and mortar institutions, and they are now branching out into online degree programs.

http://www.usnews.com/education/online-education/articles/us-news-ranks-best-online-programs

Contact the Programs You're Interested In

Reputable schools will usually provide you with data on student outcomes. Ask for alumni references. Ask for accrediting bodies and then follow up on those organizations and see who else they have accredited.

Statistics

Some financial metrics can indicate that a degree program might not be all that great. You can look up student loan default rates for a school, which might indicate that alumni are not able to well-paying jobs. You might also be able to find the ratio of federally-backed student loans to private non-federal loans. The amount of private lending in the student loan market has grown significantly in the last 20 years though, so I don't know how useful this would be.


Being a co-supervisior of a branch proposed for Master thesis from my PhD thesis

I'd consider that an excellent opportunity to get further into research, and gaining a pair of hands in your job (even more, as the advisor will also chip in). As long as everybody is happy with this, particularly the master's student (who clearly is on board, as you were approached in the first place), I don't see any possible ethical problems.

But you'd have to check carefully that this doesn't run against any local regulations.


Top tier publications for job application in the Czech Republic

I finally got a response from them.

They asked me to provide the publication counts according to the journal impact factors or actually ranges of impact factors [1:5[, [5:10[ etc. One of the options I guessed anyway.

Maybe this still helps somebody in the future.


In Politecnico di Milano, Does the university wait until the end of the deadline to review all the documents?

Yes, in Italy all the applications, for whatever position (PhD student, postdoc, professor) and regardless of the university, are reviewed after the deadline.

No, none of the applications that arrive on time can be ignored.


I believe a portion of a paper I am coauthoring is false

You seem to be giving two stories: you note that you 'still believe the conclusion of the paper is true' but you then note that 'it is dishonest to publish something which I believe is not true'.  If the issue is simply the handling of the data analysis (with alternative paths leading to the same conclusions through more or less fancy approaches), I might suggest a compromise. Add a footnote at the presentation of that analysis indicating that conclusions remain even under a more conservative statistical analysis.  If the journal allows, you can elaborate a bit there.  That way, you've solidified that you understand there are multiple approaches, but the conclusion is robust to that. This might be even more convincing.


Fellow graduate student discusses problems but gives no credit afterwards

What you describe doesn't sound particularly unreasonable or problematic to me.  Researchers discuss things with each other all the time, and of course the results of such discussions often show up in published research.  That's what you ought to expect when you have a technical discussion with someone.  In fact it's the best case - your contribution was useful and advanced science.

You ought to have been acknowledged in the paper, but the standard thing would be to have a brief section at the end, with something like "The author would like to thank House Ninja for helpful discussions."  If this was omitted, I would guess it's most likely due to C's unfamiliarity with publishing practice - he is a grad student after all.  You could have a brief word with him about this, or ask his supervisor to mention it to him.  But it isn't reasonable to expect that the paper will contain a detailed catalog of which specific idea was due to whom.  People don't keep track of things like that.  And you shouldn't expect this sort of credit to advance your career in any tangible way - it's a mere courtesy.  Such an acknowledgement wouldn't make your interaction any more or less "exploitative".

If you were expecting to become a co-author on the paper, then you should have said so explicitly at the time of the conversation: "This is really interesting to me.  Would you like to work on a paper together?"  Of course, in that case, you should expect to contribute a dramatically greater amount of work than just sharing ideas.

So I think what you gained from the discussion was about the most that you could expect - you made a contribution that helped to advance the state of the art.  You can decide if that feels like a sufficient reward for the time you spent.  If not, then maybe in future you want to spend less of your time having such discussions.

But I wouldn't see this as exploitation.  Researchers talk to each other to get ideas.  That's the point of research.  Maybe someday C will be able to share some interesting ideas with you.

  While the other students would talk about everyday life topics, current events, family, etc., C would only ask us questions about his own research.

So, C happens to be more interested in his work than in mundane topics.  I don't think that's a problem.  You'll meet a lot more such people if you stay in science.  Maybe he wouldn't be an interesting guest at a party, but it doesn't mean he's exploiting you.


Are there available corpora of academic works?

Yes, JSTOR provides a corpus for linguistic (and other) analyses of academic literature, at JSTOR Data for Research

See this Language Log discussion of one such analysis done on that corpus.