How to deliver thank you letter and gift to the professor who wrote letter of recommendation for me

Another important point to mention is that you should make sure that your gift is not too generous. Some universities have rules in place against personal gifts that exceed a certain monetary value (I think that in my university it's $100 or so). Anything more than that, and the professor will have to (a) report the gift to HR and (b) most likely won't get to keep it. These rules are in place to prevent academic misconduct, so I would really make sure that your idea of small fits university guidelines on what small means.


I don't think that any style guide or policy (besides maybe some journal about aesthetics in writing) will force you to an odd or even number of sections or chapters. A scientific text should get the number of chapters it needs and not a number that fits aesthetic principles–basically you write it to tell the scientific community about your findings and not to please them.

If you manage to write a scientific paper in Haiku form, this will be nice but it may also make some referee think you don't take your research serious enough. More or less the same holds for odd or even chapters. If you force the text to fit a certain number of chapters by dividing a chapter into two pieces, the reviewers might also consider that bad style.


Few Months Left to Prepare for Pure Math PhD Application

It is hard to do much in a few months and have anything to show for it but effort. But having said that, showing effort may help you a bit. If you have a research opportunity available that will, among other things, let you work closely with a professor or two, it can solve a few of your issues. If you make a strong effort you will not only learn something about research, but have a better chance for good recommendations.

You don't have to finish the project you start for this to have an effect, but it would be good if it is a project that you are invested in enough that you would want to finish it. It might give you some research direction for the future.

Beyond that, and even as part of it, ask a lot of questions. Funny thing, but you actually show some intelligence by asking good questions. More so than you would by not asking any and seeming passive around professors.

I don't think blogs and such will help you much. What you need is effort that will give you some feedback from those who might help you later.


The only thing I can think of given the lack of other details is this They claim to be "the world's most comprehensive collection of dissertations and theses." While that is not "ALL", it certainly is "MOST"?


What motivates scientists to fabricate results in prestigious journal articles?

Only if you're either really (really) stupid or desperate, or naive enough to think that you'll never be found out.

The person in question here seems to have been a serial offender. And I'd be very surprised if anyone who offends so blatantly has no previous history. Fraudsters always start out small and relatively inconspicuous, but confidence and brashness grows until they're caught.

Yes, fraudsters seem attracted by the prospect of fame – but I can't grok why you'd submit a fraudulent paper to Nature. Seriously!? Of course you'll be found out! But no, it's not worth it. Ever.


Using harry potter in my Statement of Purpose

Can you use it? Absolutely—you have the freedom to write whatever you choose in a statement of purpose.

Should you use it? Almost certainly not, unless your research topic has something to do with literature. Otherwise, you run the risk of confusing the reader (who may have no knowledge of the books or movies), unless the reference is extremely obvious, in which case it will probably come across as clichéd and stilted.


Asking to reattempt research after having a hard time initially

This is somewhat field-dependent, but a lot of undergraduate research is not really for the professor's benefit. If they needed help, they'd enlist graduate students or postdocs. Working with undergrads is more about giving the student a learning experience.

You don't say anything about feedback from your professor, but in any case, I see nothing wrong with asking to work under him again. As for your idea, it's definitely a good idea to run it by your professor before investing much more effort, as he is in a better position to judge whether it's feasible, whether it's been done before, etc.


Why do people sometimes put authors with equal contribution in non-alphabetical order?

There are some requirements for funding¹², a degree³, tenure and similar for which literal first authorship counts. If one of the equally contributing authors gains an advantage from being the first author due to this while the other one doesn’t or has a smaller advantage, it can make sense to have the order deviate from the alphabetic one.

Another conceivable scenario would be that the first authors is well-known in the respective field and was made first author to attract a little bit more attention to the paper.

¹ For example several faculties in Germany have schemes for evaluation and publication-based funding that assign special value to first-author publications. Some of those do not mention joined first authorships and do not make sense with multiple first authors, which indicates that first authorship is meant literal (example in German, search for Erstautor).

² This journal, e.g., lists a handful of funding organisations that will pay the publication costs, if the first author is funded by the respective organisation. Joined first authorship is not mentioned. Even if this may be dealt with on a per-case basis, just flipping the first authors may be easier.

³ For example, for a publication-based PhD thesis, it may required that the included publications be first-author publications (example, again in German) without the case of joined first authors being considered. While the latter may be allowed on a per-case basis, flipping the authors may be much easier and avoid a lot of bureaucracy.


Coauthorship across communities with differing standards

You say the work is done in their community, and two people in that community (including a professor) agree you meet their standards for authorship.

I see no reason to apply authorship criteria from your field to theirs.


What is the meaning of "review is overdue"?

This means a review is overdue: the editor invited a reviewer with a given deadline, which has passed. It seems the editor's deadline was only ~20 days. That's pretty fast, but since the website is claiming that review takes one month, it might be necessary.

The good news is the journal treats its authors well; many journals simply report your paper is "under review" and leave it at that until the decision is made. The bad news is, if the reviewer doesn't submit a review, your paper might take another month (or more) to process if the editor elects to invite more reviewers.

In any case there's nothing to do except wait.


Should a PhD thesis reflect the state of research at the time of writing?

Some options:

Explanatory footnotes often work well and can be used to 'talk across time' so to speak;
Appendices can also be used for covering material that may be out of sink, if you think you need to go into more detail;
An afterword can also be an appropriate way of accounting for developments between the time of writing and the time of publication. This is fairly common practice.

Basically most examiners will view the dissertation as YOUR journey through the research, rather than as an exact snapshot of the state of play in your area.
HOWEVER - they will be looking for (and be impressed by) you demonstrating that you know what good practice looks like in your field of research, and this extends to how you handle (and acknowledge) circumstances of this kind.


Should I cite all the open source python packages I used like numpy in my paper?

Presumably your research uses your software, which in turn uses and acknowledges open-source packages. Your papers need only cite the software used directly, which is perhaps just your software. You could also mention your software is built from open-source packages, but I don't think that's strictly necessary, since acknowledgements appear in your software.


How to respond to exploding PhD job offer in Europe

Unfortunately, this is a fact of life in academic applications.  Offers come with deadlines, and often you will have to make a decision on one offer before hearing back about the others.

There are two things you can do:

Contact the departments where you still have applications outstanding.  Let them know that you have another offer, and ask them when they expect to have made a decision regarding your application, or if they are able to tell you anything about your current status (for instance, there may already be a short list of preferred candidates, and they might tell you whether you are on it or not).
Contact the department that has made you an offer, and ask if they can wait for your decision until date X, where X is late enough that you expect to have heard  back from all or most of the other departments, based on what they told you in step 1.  But be prepared to get the answer "no, we need your decision by date Y << X".  Keep in mind that if you turn down the offer, the department likely needs to move on to another candidate, and they would like to be able to do that before the next candidate accepts an offer somewhere else.

But it is quite possible that you will not have the opportunity to make an "educated decision", as you put it.  You will have to judge for yourself whether you want to accept the current offer, or take a chance on a future offer that may not materialize.


PhD application asking what other insitution I am applying to, how to answer?

Repeat after me:

“I'd rather not tell you.”


Citing a paper whose title has received errata

In this case I'd use the corrected title, and add make sure to note that the paper is corrected, e.g.

Van Breukelen, G.J.P. (2006). ANCOVA versus change from baseline: more power in randomized studies, more bias in nonrandomized studies [corrected]. Journal of Clinical Epidemiology, 59(9): 920-925

Note that this is also how the paper is listed in Pubmed. I also recommend citing the erratum next to the paper.


Will a MS with ~3.7GPA with good research experience and strong recommendations offset my horrible U-GPA to get into PhD?

It is good to aim high. It is also good to have broad target. If you apply to only a few schools with very similar profiles then being rejected by one will probably have a similar outcome at the others. So, I recommend a range of schools if you really want a degree and not just bragging rights about a top 50 school.

But, about your GPA. It isn't a plus, of course, but most (not all) people who evaluate your application will weight the more recent work as more important than the earlier work. Therefore, if your recent work is good and you have letters that attest to the quality of your work and your dedication, then the older numbers will be discounted by most.

But, the competition is still very strong and the slots are few. If someone has to make a choice between two candidates, the choice has to be made and lower priority things may bear some weight.

However, the only way to know whether you have a problem is to actually make application to some places and then evaluate the feedback. There are some questions, like this one, that can only be answered by actually trying. But, you will be more likely to get accepted somewhere if you don't target too narrowly.


How to cite different chapters of a book in the same paragraph?

If the chapters are part of a unified work (e.g., a textbook or monograph), then it's appropriate to use one citation, and to say the chapter in the text:

  Here's what I'm doing. Chapter 2 of (Trout, 1946) presents an interesting fact. I
  then fit the interesting model, described in Chapter 8 of (Trout, 1946).

  References: Trout, Kilgore. (1946). Ice-9 and its Applications. Ilium,
  NY: Slaughterhouse Press.

I'm not quite sure of where APA puts the parentheses; my point is about handling chapters as prose.

On the other hand, if the chapters are separate pieces of a collection (e.g., contributed texts in a "recent results in..." book), then each should have an independent entry in the bibliography.


Can I do a PhD in Mechanical Engineering without experimental work?

I'm an expirmentalist, and I have worked with FE modeling for a long time now. I have many publications based on tests, validated models and purely numerical "without validation". I can tell you this much, the ones that keeps me awake at night and the hardest ones to publish are those with "numerical models without any experimental tests" to back the numerical predictions up or at the least include some sort of validation.

My MSc (structural engineering) was all numerical (but based on full scale tests done by others), so I did not have to test my own specimens (validated my models against experiments that were already published). I can tell this much, without a validation, your model is just a model! As you know FEA is just an approximation with multiple simplistic assumptions of a real phenomenon.

However, I tend to agree that whether needing to validate your model against measured data (solely by doing your own experiment or simply against other published work) is case specific. I do not know your "thesis problem" and the fact that you have published a good number of articles (if published in high quality journals) and your advisor was fine with that "until now!" leads me to think that you may be able to get away to a "numerical" thesis.

Perhaps you can discuss the following ideas with your advisor/committee;

If they insist on an experiment (although they are tight on funding as you have mentioned [not a very good sign in your case since you are trying to avoid that!]), try to find a somehow similar published work, use your model to validate it. I understand that this may not be a "direct validation" but at least your advisor/committee can be assured that your model is capable of simulating a real problem. In other words, your model is "not-directly" more than an FE model.
Ask if you can validate your model with some other ways i.e., analytically, hand calculations, published methods etc. (I hope you have done this by now!). You can always do a parametric study (I assume you did already), pick parameters that can relate to an actual problem (either from literature or industry) and see how your model performs. If possible/applicable, contact an industry firm (that is willing to share) and see if they have anything on hand that you can use to validate the model.
Discuss with your advisor why did not he ask you to do this long time ago ("usually" one will do an experiment and then develop a model! [that's what I always do, keep in mind this is different that finding a problem and trying to get some funding for in which you will develop a model first to show the feasibility of your problem rather than spending money on an experiment that turns out to be "worthless"]). I understand this is too late to ask now, but if you know the "inside" of whats going on "with your committee (perhaps?)", you will know how to tackle this issue more specifically.

Remember this, you do not have to prepare a 6 months, $ 100k experiment to validate your model. Sometimes, all what you need is a well organized set-up, few strain gauges, loading-inducing actuators and a specimen (of course this is a simplification - but you get my point).


How do you self-teach yourself about a field you don't know about, specifically for STEM?

Would they read a review from major peer-reviewed journals, such as Science or Nature, and then dig deeper from there?

Yes.

  How would they get teach themselves techniques, and knowledge?

Techniques can also be learned from journal articles, but it's also typical to defer to or collaborate with other researchers who are more familiar with those techniques, or to travel and visit labs. In my personal experience, several times contacts at conferences etc led to communication between labs. The lab I worked in during grad school a few times hosted grad students from other labs both inside and outside our institution that spent a few days or hours here to see how we did a particular thing, and similarly people from our lab would travel around.

When academics travel to give talks at other universities, one of the key parts of their visit is to tour other labs, which can include observing techniques used by those labs.

I'd add that this doesn't just apply to new or unfamiliar techniques, either: it's part of the normal art of improving research methodology.

More broadly, though, mid- and later-career academics don't tend to move from field to field arbitrarily (whereas it's not uncommon to make a big jump between undergrad and grad school: you simply aren't that committed to a field at that point): they usually have some adjacent knowledge that's taking them into that area, so they aren't starting completely from scratch.


Do I have any legal right to fair grading by my university? (UK)

The procedure for complaints and appeals against  the decisions of UK Universities is managed by the Office of the Independent Adjudicator for Higher Education (known as the OIA).
They will only consider your case when you have completed any formal internal processes of the institution and the institution is required to issue you with a "completion of process" letter confirming your complaint or appeal is at an end.
To make a formal complaint or appeal within your institution you will certainly be able to get advice, help, support and representation from the Students Union and their respective Education or Welfare officer. It is highly likely that there are also University staff who can assist students with this process, perhaps called Senior Tutors, or some such title.
Before going to the formal process you should also see if an informal resolution can be made, as is often the case when it is a simple error or system fault. You might need to contact the departmental Director of Studies, Programme Director or Head of Department. You are also likely to have your own "student reps" within your class or programme that also can raise a case for you within the department. They often raise such matters of quality within a framework of a "staff student committee". The UK Office for students would  likely expect such student representation to be present within a UK institution.
There will  be information about this on the web page of the university and the web pages of your students union or student association.


Why does arXiv not allow numbered lines in submissions?

In my experience, it is much more useful to give some context (a few words, name of the theorem, ...) to any editorial suggestions than line numbers. My documents exist as LaTeX source, so line numbers in some printed version don't correlate at all with line numbers in the text I currently work on. A few words of context are easy to search for in a text editor, line numbers would require referring to the printout to find same first. Besides, text changes (paragraphs get rewritten, shuffled around, new chapters are added, a new example appears, ...).


Is it plagiarism to use an online tutorial as the basis for completing a programming assignment?

Using online material to learn is not plagiarism.

This is a great way to learn (e.g, worked examples and subgoal labeling) and is a common way for instructors to try to teach something. Am I plagiarizing every time I use a common design pattern? No.

However, copying and pasting code from online is. It gets a little fuzzy when working on simple assignments that can be found easily online because it could be weakly argued that you are recalling it from memory. I would definitely not be concerned about this, especially if you think you understand the code and were not trying to cheat.

If you're genuinely concerned, you could even discuss it with your instructor and they might realize that they are not spending enough time discussing a certain process or giving you enough practice material.

EDIT: Based on your clarification in the comments, if this is something more specific/arcane and not a tutorial on something general, then just cite it. I have done this in my programming courses before. I added a comment at the top of my code linking to the material I referenced and gave a very brief description of what it is and how I used it.


How do so many people here on Academia.SE, and in general, afford lavish higher education programs?

Bachelor and Master degrees are a lot cheaper in Germany. In fact, they are mostly free (you need to organize and pay for your housing and living). For a PhD you don't pay but get paid, often with employee status, but sometimes with a stipend instead. So financial issue pose significantly less of a constraint compared to the USA.


Forcing to list a co-author that did not contribute after publishing

You might take a look here; and as for a more detailed response, let me focus on this one question:

Would you do some "preparing steps" from my side if not willing to give in?

You could ask everyone to tell you which contributions they offered based on the Contributor Roles Taxonomy (CRediT). And make sure that the CRediTs are visible in the publication as well.
On the one hand, it is possible that they will hesitate to point out their contribution in case they do not find anything worthwhile to pick from CRediT. On the other hand, you might actually end up finding one minuscule contribution of that co-author that does merit a mention according to CRediT. The "objectified" nature of CRediT might help to resolve such conflicts.
And if you have the CRediTs published as well, then the readership will at least know the variation in efforts of each co-author.


Consecutive holidays for faculty in the US

I can't really make much sense of the question, but I can explain how time off usually works in the US, though of course there are variations.
Professors aren't really typical employees. They likely technically have a set number of days they can take off and need to register them in some HR system, but usually no one is watching closely to make sure they are working on a work day (unless they don't show up for class), and even being absent from an office is not a very good sign a professor isn't working. Taking an extended vacation (a month or more) might be more noticeable, but even then, no one outside their lab is likely to even notice unless they are missing committee meetings or other responsibilities. Professors tend to be pretty self-motivated to work on their own research, and they won't be able to keep up with expectations for funding and publication if they take too much time off. Smart professors will still take some time off, though: however much they need to keep some balance in their life and remain productive during their working time.
Some days of the year are "days off" for everyone working for an employer (for employees in the entertainment/hospitality/retail sector this doesn't apply to them). These typically occur around secular or Christian holidays, and are usually just a single day or sometimes two consecutive days (for example, December 31st and January 1st). In practice, professors may work on these days anyways.
Academic calendars have some other breaks, most often a week in the spring for "spring break" and some time between semesters (often much of either December or January). However, these are mainly breaks for students, not employees. Professors could take this time off, but in practice those with teaching responsibilities often use that time to get caught up on grading and prep or focus on research.
The rest of time off is covered by "vacation days" allocated to individual employees (perhaps this is most similar to "casual leave" that you mention?). In principle these can be taken whenever an employee wants, but in practice their employer may designate days they can't be used. For someone teaching a course, it would be expected that no vacation days would be taken that conflict with being present to teach the course, except under exceptional circumstances (during which a professor would be expected to find their own substitute and communicate with their students unless they are physically incapacitated).
Some faculty under teaching contracts are only employed for 9 months of the year, during the typical fall/spring semesters, and are either not paid for the summer or have their 9-month salary prorated to give an income over the whole year. They don't have summer responsibilities directly, but this is the time they would have to devote to their own research, side projects like authoring books, and towards preparing courses for the next semester. Most will try to get these months covered by another salary source, however, and then do not have the time off.
If it was important to a professor on a 12-month contract to take a month-long vacation in some summer month, they can almost certainly do so assuming no conflicting responsibilities, but that would use up most/all of their annual leave. For an assistant professor on the tenure-track, there might be strong personal pressure to not take this sort of break as it might make it harder to achieve tenure, but that's really up to the individual. Longer leave in the form of "sabbatical" may be arranged, but typically professors on sabbatical still use this time to be productive in some way (for example, writing a book, travel related to their area of research, visiting collaborators at other institutions).


While answer to your question needs more detail, but in general the answer looks like this:

Starting PhD in different universities is different. In many universities , faculty member receive application from the PhD applicant and evaluate individually. However, in other universities mostly in US, the application is evaluated by the committee.

In the first case, certainly, the best way to start is to initiate a communication with potential PhD supervisors by sending an Email -as you said- along with your CV, academic history, SoP, and research proposal (proposal is not needed in US, but should not be a problem if you send). However, I think it may not really work if you ask them for assignment (maybe it works in some universities that I don't know).

One thing I noticed when I was searching for my PhD is that many supervisor write some notes on their pages and provide some instruction for potential students to follow. If you don't simply follow them you won't be able to get position from them. Try to read their pages as carefully as you can.

I admit that there are tension in getting PhD position. But it is all right and should be okay. Some guidelines may help you figure it our.

In general, to successfully secure a PhD position, you need certain qualifications and certificates listed as following:

Bachelor degree in relevant course with high GPA/CGPA (this is must)
Master degree in relevant course with high GPA/CPGA (This is not really a MUST-have requirement, since many universities offer PhD without having Master).
English Proficiency certificate (for English speaking countries) if you English is not your native language.
2/3 reference letters in your favor (no wonder).
GRE for US-based universities.
Money to pay tuition fee (supervisors consider this as well. If you need financial assistance you should be really good compare to others).

Thats all REQUIREMENTS. But, they are not sufficient to convince a potential academician to offer you position, especially paid positions which are very competitive. If you want to enhance your chance, I think in CS you need the following qualifications:

Good quality publication(s) in good publishing venues (top ranked conference and journals)
Research experience (It may be true that Master by research graduates have better chance here).
Working experience in relevant areas
Teaching experience
Professional certificates from well-known organizations like Microsoft, and Oracle.
Volunteer jobs in the society (I heard a lot about it)
Academic or professional Awards like best student, best thesis, and best paper award.
GRE and SAT certificates
Intellectual properties (patents)

But, I think the most important thing is the first impression that you make using your first Email, CV, SoP, statement of research and so on. If they look professional and neat, it attracts potential supervisor's attention and will evaluate your application optimistically.

Don't give up. You have to find the RIGHT supervisor, in the RIGHT university, at the RIGHT time, using the RIGHT channel. Keep trying and you will succeed.


How to minimise student's discomfort when suggesting they need to improve his/her English?

One way to approach this is from the perspective of why the quality of prose matters in the first place.  After all, why should we bother with spelling, grammar, etc?
Having good spelling, grammar, etc. is important because not having them puts roadblocks in the way of communicating with the reader.

You can minimize a student's embarrassment by emphasizing this aspect.  Assuming that student is otherwise doing well, you might can bring up grammar by approaching it from this angle.  You can emphasize the pragmatic aspect that, in pretty much any career they choose, written communication will be important, and that it's important to not have others' appreciation of their good work be impeded by problems with grammar and spelling.  It's really the linguistic equivalent of keeping yourself clean and well-groomed.

If a student is not doing well with the core material... well, then grammar's not really the key problem to talk to them about anyway...


Strategically, it gives better chances to aim for journal that are recognized by your peers. This need not be related to openness of the journal, but it is true that there are fewer well-recognized OA journals than subscription journals. Ask around (to several peoples, taste can vary in a field).

Do not forget that you can in many cases publish green Open-Access (self-deposit into an Open repository) your manuscript even if you publish at a paywalled journal. This gives a good compromise between openness and strategy for beginning careers. Information about what you can do publisher by publisher and journal by journal is available at Sherpa/Romeo.

Last remark: judging a paper by the journal it is published in is quite bold, but judging it by the publisher of said journal is far worse. Elsevier has crappy journals in its portfolio, as most publishers do.


Should I talk about a unpublished paper in my SOP?

Talking about an unpublished article that has inspired you is certainly fair game for a SOP essay in a graduate application.

Certainly the inspiration, and the differences between your approach and different, existing methods would be highly interesting to me.

I love to see undergrads who take initiative in research - they tend to make good Ph.D. students. Taking ownership and initiative in your project is a key step of maturity in grad school. So if you have already done so, that's a great sign.

And yes, if it's only in Arxiv and you haven't mentioned it to your letter-writers, I'm not likely to read the paper if it's not otherwise mentioned in your SOP.


If because of some recent mental health situation you cannot perform as good as before, should you mention it when applying for a position?

I don't think you are obligated to discuss health conditions with a potential
employer. Your references discuss your prior work and the importance of your research program. (To the extent they speculate about future performance is irrelevant.)

Go for your dream job and work as hard as you can. Allow your career to evolve as it will.  You shouldn't undermine previous effort by speculating about things that have not happened yet.


Is it appropriate to ask a professor for publication opportunities?

There is nothing wrong with asking about the contribution to a publication. This shows your interest and that you will work for it. Also, you have nothing to lose. Think what's the worst that can happen if you ask! They'll say no, right? So, what happens if you don't? You still won't get the experience you want and the publication! So, your best bet always is to discuss your interest.

How to ask? Just show your interest in the project and that you are willing to work for it. Since you are an undergraduate student, you may face some skepticism at first, but if you show dedication, that'll prove your sincerity.


Reapply to a postdoc position that I rejected before?

What do you have to lose? Worst case scenario is that you are rejected. I don't see any possible downside here.

Anecdote: This was not for a postdoc position, but for a research internship: I contacted the researcher who I wanted to work for not just once, but three years in a row. All three times they expressed interest. The first time, it was too late so they said to apply next year. The second time, they were going to give an offer, which I turned down. The third time, I felt mildly awkward, but I knew that this was a position I still really wanted -- so I simply explained as much, and thanked them a lot for their interest in previous years. It worked and I got the position again.


How to explain why I want to go to a summer school?

To answer both questions of "what to write" and "why they ask for this," I will quote an answer from @badroit to a related question (which deals with writing a research statement):

  You're trying to demonstrate why you and your background are a good fit for a summer school and that you will benefit greatly from that school.

The general idea is the same for writing a "why I want to attend" statement: you want to show the organizers of the summer school that they won't be wasting their time and other resources on you.

So, the two things you'll want to make sure your answer conveys are:

That you are genuinely enthusiastic about the topic. Explaining (as you suggest) that the relationship between biology and mathematics is something you are very curious about/interested in is a perfectly reasonable thing to write. You could also mention related coursework or projects you have undertaken, to further demonstrate your interest in this area.
That you will benefit from the summer school. Discuss relevant goals that you think this school will help you achieve; for example, your intent to take graduate-level courses in the subject as a senior, to pursue independent study/research in this area, to go on to graduate studies in biomathematics, etc.

Finally, if there is a professor in a related area with whom you have some relationship (e.g., you took his/her class), you can ask them to review your summer school application before you send it in. This has the double benefit of (1) getting expert help with your application, and (2) cultivating a relationship with faculty in your field of interest.


File / Data / Script management as a PhD

In general I would distinguish between two approaches or a combination of both before ending in a very time consuming categorization of all your files

top-down
This means you use intelligent software to find again files you are looking for and don't worry too much about where it is stored. For example reference manager (Mendeley, Zotero,...), a Desktop search engine (Copernic). In the desktop search engine or with windows search (indexing turned on) you should see which file was changed at the latest. Most of your ideas and sketches you save in Onenote or something else that can link to files and www links.

bottom-up
This means you come up your self with a distinct structure like you did with a rough categorization (raw data, devices, projects). But don't complexify this, when most of the files can be identified by the file type/ending, then it may be more convenient to order it by projects and keep all file types within such subfolders.

Additionally, one trick I use is tagging files in their filename like "#phdthesis" or "#interesting" or "#cite" or "#collaboration".
Sample files (data, images of samples) always get a date ProjectnameDayMonthYear independent of their file type.
Don't make your system too complex or too time consuming. For instance most of PDFs I read and download end in one folder. No point in categorizing them, this will not work/help over years and decades. Defining content-relative filenames takes too much time, most of them I find again over my desktop search engine months or years later if they were memorizable with keywords and search operators or self-created #tags.
For files which the PI or teammembers have to have the possibility to retrace them you anyway have to arrange a common plan how to structure and save the files everyone understands and can contribute. I would either suggest cloud storage or a local wiki here (moinmoinwiki for instance).
The most productive system is probably the one "invented" by Stephen Wolfram, but it took probably even more time to set it up than writing his article. But you get a lot of ideas, so I'm not sure it is future-proof to organize yourself with a propertiary software.
A personal opensource free wiki like moinmoinwiki or tiddlywiki is also an alternative and combination of bottom-up top-down and file system. So my experience is a wiki is only worth the additional time and effort at least with 2 or more team members, otherwise your personal choice and mixture of bottom-up and top-down is more time-efficient and humanities/experimental research/programming single reaserchers will end up with very different management system due to available time, number of files, work-flow and necessity to document and retrace everything.
File systems and desktop search engines will never die out, so my general tip is not to rely too much on fancy software like onenote, mathematica or alternatives to have a future-proof system.


Definitively identifying spam is next-to-impossible because:

Spammers can change their email addresses with trivial effort.
Spammers work hard to mimic legitimate content.
Any spam detection method that becomes popular will be analysed and actively subverted by spammers.

All of the above are true of predatory journal spam. So I don't think there is anything like the resource you suggested (I did do a bit of searching).


All his past students without exception say bad things about him: he writes negative letters of recommendation to his students even after agreeing to write strong letters and in some cases, he did send negative letters un-invited to schools that accepted some of his M.Sc. students.

Short of a serious, substantiated allegation of research misconduct, we would take a letter like this to be weird and immediately disregard it (with a few choice comments about the professor involved --- in a small field I suspect we might already know that this professor has some issues).

If an offer had already been sent out, it wouldn't be rescindable based on this. I'd wager to say that this is probably the same case across all public North American institutions.


What are some career options for Math PhDs who want to work in non-Western countries (e.g. Southeast Asia, Central Asia, Africa)?

This answer is mostly for Asia.
Yes, there are programs in at least Japan and Korea (that I am aware of) for American Ph.D to find a job, including professorship.

I think the largest difference/challenge you will face is that many times, being a student and working in Asian countries such as China, Japan, Korea, is very different.  In general, the faculty, students, local businesses, etc. are happy to accommodate students spending some time in their region, learning their language, and living.  Systems are in place for this and the universities most often actively encourage it.

Meetings

As a professor it can be (but not always) different.  Unless you learn the language fluently before you go, think about your new colleagues and how they will feel, being required to speak to you in a language other than their own.  Not necessarily about the weather, but more importantly (what I noticed) is in faculty meetings, budget decisions, etc.  In this case, you can easily be the only person not able to understand, which leaves two options: you are left out of the meetings or everyone else is forced to speak your language (if they can).

You mention not caring about prestige, but I would caution you that many 'bad' universities have a lower chance of faculty being comfortable in English.

Administration

Beyond faculty, which may or may not speak English, you still will have administration to deal with.  Do you assume your contract will be in English? While some online university systems are in English, I have seen many parts that are not, such as the email system in English, but the login systems or vacation registration is not.

Culture

Of course, you need to think about culture.  The idea of Asian culture may allure you, but remember it is not always what it seems (just as people going to America find out).  In at least Japan and Korea, Impact Factor is the largest measure of performance, and you must follow it.  Be ready to change your work style if it does not fit into the way you are evaluated.

Resources

You can check https://www.higheredjobs.com/international/  for international job postings.


I don't think applicants in the US are ever required to prove that they taught particular courses on particular dates, so no system like official academic transcripts certified by the university has arisen. However, if there were some doubt that courses listed on a CV were not taught, it would be a simple matter of contacting the department to verify.


I work at a major Flemish institution (but am not local). Here there are different salary scales, depending on your rank.

You start as faculty as a "ZAP" (tenure track Assistant Professor). It is true that your salary increases every year. But that is normal I guess. To keep track of inflation I guess.

In order to have a more significant pay rise you need to advance through the ranks, get tenure, become associate, become full professor, etc.


Why are (university-) teachers also examiners at the same time?

At least at the university level, I think the biggest issue is practicality: who is going to write and grade the exams, if not the professor in charge of the course?

I think this is especially true in things like humanities courses, where the content is so often individualized according to the professor's interests and preferences. (The same thing also happens in STEM courses, but there's often much less freedom in what can be covered, often for "continuity" within a larger degree program.)

For example, say I'm teaching a French literature course with a specific set of goals (at least in my mind). How much information do I have to communicate to someone else, so that this other individual can write an exam that fairly assesses what the students have actually studied, as opposed to what the examiner thinks they should have studied?


I think that @ndpl hit the nail on the head when he commented that what's most important is that your message to the professor be clear and concise.

During an academic semester I, like most academics, get a crazy number of emails. (I'm an assistant professor of mathematics at a college in the US.) If your email is short and to the point then chances are I'll be able to read it right away, decide what action on my part needs to be taken (if any), and move on to the next email. Empty statements like "I'm sorry to bother you." are polite, but just make my goal of getting through all the unread messages in my inbox that much harder to achieve.

So if your email was written in a professional manner, but was just terse, that's absolutely fine.


You're still a high-school student and you may find that your interests change in university or later.  Mine did, at least twice.

In any case, one's graduate research is often in a quite different area than one's undergraduate research (if any).  (And then one's post PhD research may go far afield of one's thesis.)  Neither school should limit your graduate options significantly.  So go to the school you're most excited about.


For a first printing of an edition, should the Print year or the Copyright year be cited as the publication date?

Whenever you have tricky issues like this, go back to the basics of why we reference works at all.

The aim of a reference is to help the reader locate a copy of the work, so that they can replicate or investigate your results or argument.

So ignore the publisher's gaming of the copyright year — which suggests to the reader that book is an advance copy, and thus not available from the publisher, but only from the paper's author and other 'insider' sources — and use the date the work was actually available to the reader from the publisher.


In-text citation: what is the correct way of using both last name (i.e., \citeauthor ) and typical citation (i.e., \cite)

I don't think there is something like a general convention for this, aside from the usual rule of being consistent. So follow your personal/conference/journal/university/whatever style.

If that style dictates to use numbered references such as [1], always include this. Even if, like in your example, you start one of your sentences with the author name (and year). Note that (as @Ian_Fin mentions in the comments) the year is usually omitted when using an author name with number styled references.


Is it inappropriate to apply to a long list of PhD programs?

There is no such thing as "too many places", except if it is compromising the quality of your applications (or your other life activities). Start applying at your most wanted places, making sure to polish your application to your best effort, and keep going until you run out of time, energy, or programs you would actually want to attend.


US university scholarship for international students

The very top (mostly private) universities will decide which students to admit without considering the financial circumstances of the students or their families.  Then they will look at the student's family's financial situation and cover whatever the student's family is unable to pay.

Slightly less top universities will consider your financial circumstances in making admission decisions, but will admit you (and provide a combination of scholarships and loans sufficient to pay for your education) if you are sufficiently better than their average student.  (How much better is sufficient depends on the financial circumstances of the university, and in particular whether they really need tuition to cover their expenses or cover much of their expenses using interest from prior very large donations.)

The universities that are well off enough to subsidize their international students in this manner almost all do admissions holistically.  That means, for a competitive candidate, someone will take some time to get a complete picture of you as a person from all your application materials and decide on your application on that basis.  They are interested not only in your academic abilities, but also want to consider how much you will contribute to the university community (both academically and socially) as well as how much you are likely to make a contribution to society (and hence to the fame of the university) after your studies.  Note your likely contribution to the university community may depend on who else is already on campus and who else is applying that year.  If you are a good bassoon player, this will help you more in a year when a bassoon player is graduating and only one other bassoon player is applying than in a year when two bassoon players enrolled the previous year and three others are applying.  (It is quite common at top US universities for people to participate in activities unrelated to their studies, so students may continue to play the bassoon in the university orchestra even if they are not interested in further musical studies.)

To make such a judgement, a university will look not only at your standardized test scores, but also at your complete school records, recommendations from your teachers, your activities outside of school, and your responses to the (longer or shorter) essay questions on their application.  If your country regularly sends students to the university in question, someone at the university will be familiar enough with cultural norms in your country to interpret these other parts of your application appropriately.  If not, they will try to learn what they can.

Doing admissions in this way is time consuming and expensive, but if a university is using substantial resources to subsidize its students' education, then it will find it worthwhile to spend some extra resources in trying to get the students it wants.


Where do research labs get their funding?

Most labs get funding from granting agencies, governments, industry agreements, or private foundations. Some universities also provide funding in other forms.

Now, what they can do with the money depends on the conditions of the grant. Some, are attached to a specific project. They may also include a breakdown of the expenses: this much to hire two PhD students, this block to hire a posdoc, publications, experiments, computers... Some other grants are more open, and may give the PI more freedom to allocate the resources, or to work on sub-projects.

Some areas of research have economical interest, and may lead to patents and industrial agreements, that could help the lab to be less dependent on grants.

Lastly, some students may get their own funding, that may be attached or not to a specific project.

Universities do support labs, mostly by paying salaries of the staff and infrastructures.

Regarding the times, most labs apply to any grant in reach: you can never know if the grant you are hoping for will be renewed; and there is never too much money.


Mentioning that my paper extends my project X: compatible with double-blind review?

Yes, refer to Project X without stating that it is yours.

In my field, instructions to authors for conferences that are double-blind reviewed often say:

  Do not omit references to provide anonymity, as this leaves the reviewer unable to grasp the context. Instead, a good solution is to reference your past work in the third person, just as you would any other piece of related work.

In reality, of course it is often obvious that the paper under review is likely to be an extension of the cited work by the same author. However, as an author, it is not your responsibility to make sure that the reviewers can never identify you. It is only your responsibility to

  make a good-faith effort to preserve the anonymity of your submission, while at the same time allowing the reader to fully grasp the context of related past work, including your own.

Citing your own previous work in the third person is a good faith effort to preserve anonymity, and (at least in my field) that's all that's required.


Can I submit published articles to arXiv as well?

I suggest you first of all check

the copyright transfers you signed
the publisher's FAQ on rights you retain as author
Many publishers nowadays allow you to self-archive the version of the manuscript that passed the review. Some do not allow self-archiving on public repositories (but e.g. Elsevier makes an exception explicitly for arXiv). For a quick overview have a look at the SHERPA/RoMEO site.
and your local copyright legislation.
E.g. the German UrhG now allows secondary publication (e.g. to arXiv) of your manuscript (including the version with exactly the content of the published paper) for journal contributions that were financed mainly by public grants.


How often do universities in General have admissions for graduate programs?

In the US there is no general system. Most universities will have deadlines for admission once or twice a year with a few having more. They are matched to the normal Fall and Spring semester system used in most (not all) universities. However, most students enter in the Fall with deadlines for application likely sometime in the Summer or possibly the Spring.

But each university will operate on its own schedule so you need to check.

Another consideration is when you need to apply for positions like Teaching or Research Assistant. Those might possibly be once a year even if the admission deadlines are twice. So, check about that also. Likewise scholarship and grant funding can have separate schedules.

Narrow down your search to a few universities and look at the details for those.


Computer Science Publications: conference vs journal on application form

Discuss this with the contact person for the fellowship.

Pretty much every job posting and funding call has a contact person listed, who you can call or email to actually discuss what they are looking for. This is an underutilised resource.

If you talk to this person you can find out the best way to fill out the form, and it is also a great way to alert them to this issue, put you on the map as a candidate, and find out anything else about what they are looking for in this fellowship.


How can writing a Review Paper possibly help in the CV of a undergraduate student?

Any work of quality adds value to your profile. If I refer to your question, even the act of writing a review paper, if performed by the rules of the art, is something that you can show and discuss about.

Addtionnaly, if the work has received some sound academic validation (published in a reputed journal) of course this adds to your resume. It adds sometimes more if the topic of your work is close to your background, which seems to be the case here.

Beware though: it is not common for an undergraduate to be able to write correctly a review paper, esp. on a well-paved topic such as Fibonacci numbers. So, to be blunt, if your paper was accepted almost without review in a local university journal, it might weight less. Or even negatively.

This really depends on who reads your CV: some will be impressed by the: "published in the Mathematical Journal of Mathematics". Some others may have a look at your paper precisely. If they find that the content is of low level, they might have a more negative opinion than if they were not aware of your paper.


How to tell speakers that their English is terrible?

I think that your plan is based on number of possibly wrong premises. And even if they were mostly right, I doubt such a plan could have any reasonable success. Let's see my reasons.

  I just had a lecture from someone who has been a senior scientist (and has completed a PhD, post-doc) at a hospital for already 15 years.So I'm assuming this person is experienced in giving talks in English.

I've met along the years many senior researchers, even native English speakers, who where definitely not experienced in giving talks, at all. If academic researchers are frequently experienced speakers because, at least, they have teaching duties, some researchers from research institutes are really "lab rats" who rarely deliver talks. To give you an example, a few years ago I was attending a poster session in a conference and I told one of the presenters (a native English speaker) that I was surprised that his work had been accepted as poster presentation and not as an oral one. He told me that it was actually accepted as oral presentation, but he asked for a poster one because he doesn't like to deliver talks.

  My impression is that the talk was a waste of time for the two dozen people present.

Talks can be a waste of time for other reasons than terrible language: slides with unreadable results, talk targeted to the wrong audience etc. I certainly attended many talks that could be considered a waste of time for almost anyone in the rooms, and a large fraction of these talks were delivered by allegedly experienced speakers.

  Now I wonder if the speaker is aware of this problem, my guess is no

In my experience among non-native speakers of English, most of the people is well aware of their level of English and of their pronunciation: your guess is likely wrong.

  I feel the need to bring this to the speaker's attention.

Would you feel the same need if the talk were a waste of time for any other reason? And note that preparing readable slides is usually much easier than fixing pronunciation. And are you planning to do such an action for all the useless talks you will attend in your life?

  I feel the need to bring this to the speaker's attention.

As I said, the speaker is probably well aware of this issue, but can you offer any solution that the speaker is not already aware of?

Improving pronunciation is not something that can be done easily, especially if one is not keen on languages. The speaker might have had good reasons for not having been able to improve pronunciation more than that. Time and money can be two of them. I don't know how many languages you speak -- you speak more than one, right? I speak Italian, my native language, English and French. My level of English is decent, but my level of French is basic. I cannot make great conversations in French, just short sentences, and sometimes I've been misunderstood (e.g., I once asked for a book called Rue des Maléfices and the clerk searched for Roue des Maléfices). I'd love to improve my French pronunciation because I spend most of my vacations there but, guess what, I really cannot find the time to do this. Or I'd like to learn German, because I have many German colleagues and I also found some nice physics book in German that I'd like to read without Google translator. Again, I cannot find enough time to learn German even at a basic level.

To conclude, don't.


Is there some generally academic accepted categorization of subject areas and subject categories?

Australia and New Zealand rely upon the Australian and New Zealand Standard Research Classification (ANZSRC).  This standard comprises of Type of Activity (TOA); Fields of Research (FOR); and Socio-economic Objective (SEO).

You would be most interested in the Fields of Research code specifications.  In the FOR code, Division 08 Information and Computing Sciences includes group 0806 Information Systems which is specified here: http://www.abs.gov.au/Ausstats/abs@.nsf/Latestproducts/21AF3378B57615E7CA25741800047563?opendocument

Sources:

http://www.arc.gov.au/applicants/codes.htm#ANZSRC
Industry experience


Where to put the citation for a review article

In general, citations should be placed at the point where you actually use the information, not in acknowledgements.

For a case like this, then, you might say something like:

  A useful review of this area may be found in [citation], which suggests viewing the field as follows: [paraphrased review material].


Guidelines for changing terminology introduced by self?

I also admit to doing this. The reason was twofold. Firstly, the old terminology clashed with existing terminology for concepts that I also needed, and secondly, the new terminology better reflected the concept that I was studying. It is also difficult coming up with a name for something when you invent it. But concepts need names.

There are obvious pitfalls to this approach, such as making papers harder to read. It is beneficial in the long run, because the accepted terminology (assuming that the newer terminology becomes the accepted terminology) does not clash with other terminology I need to use.


How much does the choice of professors on my thesis committee matter?

For academic positions, what is relevant for your application is your letter of recommendations.  Who is on your committee does not matter (except the head).   Your job applications will not even list the members of your committee---this will only be seen by someone who looks at your thesis.

In academia, it's common that non-tenured (sometimes even non-tenure-track) faculty are on PhD committees.  This is not viewed in any negative light.  You want the most relevant people on your committee, so they can give you the best feedback, and will have a better sense of what you are doing to be able to write you recommendation letters.  Often your supervisor can suggest who to put on your committee.

I imagine that non-academic employers will care even less, as they are (typically) not interested in your research.


Is it acceptable for the secretary to have full access to our entire Outlook agenda?

My own perspective on this from the UK is that it is completely normal outside universities that outlook calendars are made fully accessible by anyone in the org. Many of my non-academic friends continually express surprise that I am allowed to keep my calendar private (I just share busy/free information). Even within universities, all of my professional service colleagues are expected to make their schedules accessible. On the other hand, this would seem to be a place where in general academics tend to be privileged, and I've not heard of faculty colleagues who have been forced to make their calendar public.


What are the Pros and Cons of Pursuing a PhD after 5+ years in the Industry?

As with most people asking such questions, your approach is exactly backwards.  You shouldn't be thinking about the pros and cons of going for a PhD -- you should be thinking about what your career goals and long term goals are, and whether you need a PhD to reach them or not.

Once you understand the answer to that, all your other questions will then be in context.  For example, If you long term goals are to retire at age 55 with $2M US in a retirement account, now you can actually do the math based on current salaries, starting salaries in a new position, living on a stipend, ....

Without us knowing your goals, because you haven't told them to us, there is zero context for answering this question.  Unless YOU know these goals, you can ask about pros and cons all you like, and not really understand the answers you get.


How to verify a proof prior to peer review in mathematics

Ask your teachers. They know you well, probably know math better than you, and are your closest connection to the academic world. That means they're the most likely to be willing to look through your proof, capable of finding an error you didn't spot, and if they can't find anything wrong, they'll know who to approach next (e.g. their professors from when they did their degrees).

You could conceivably approach math professors at your local university directly, but you risk coming across as a crank and being ignored. If you're able to get your math teacher to vouch for your proof, that would lend strength to your claim.


What exactly does an "unstructured research problem" mean?

An unstructured problem is one that does not have a direct solution already established: that is, it's not immediately obvious how one gets from the problem statement to a working solution, or even if there is a solution.

This is the standard for most doctoral-level research problems in STEM fields: if the problem is so well-defined that the strategy for solving it is immediately obvious, it is likely unsuitable for doctoral work, and a new (usually more challenging) problem should be selected.


Is it ethical that the PhD student is not offered a chance to become the communicating/ corresponding author?

Things might vary across fields, but I think that you might be overestimating the impact of being the corresponding author.

In my experience the corresponding author handles the communication with the journal (hands in the article and revisions, copyright form, etc). Furthermore, you might get a question every once in a while from a fellow researcher, but they are mostly like: "can you send me the article", or "may I use your figure".

Reasons for your PI to insist on being the corresponding author might be that articles may get questions long after you left the institution, and in some fields the corresponding author indicates who is the PI.

I would not worry too much about this. When your publication list is assessed, people will look how often you are the first author (when that is applicable for your field, some fields put the authors in alphabetical order). And when somebody has a question about the content of the article (which happens less frequently than you might expect) they either write you directly, or your PI might forward you the question.


Your sense of things seems to be correct, but you can't control others. It would be "nice" if they shared more, but it may not happen. So, you need to assure that you aren't exploited, but, beyond that, your example might even serve, over time, to change things.
However, as you build a career and build a circle of collaborators, you can, then, have discussions among yourselves about sharing. Being the sponsor/leader of a research group, for example, gives you some "standing" to influence the rules. Those rules should revolve around authorship among other things.
Generosity is a good thing, but not everyone will contribute. This is especially true in high risk high reward situations, which can, unfortunately be the case in academia.
You are responsible for your own behavior. You have some, but limited, influence over that of others. Setting a good example helps as long as you don't get exploited.


How competitive are places for PhD positions in mathematics?

I don't know if my opinion is representative of a general consensus, but I would look for candidates who fit well for the program, in particular those who fit well with the area(s) I'd like to supervise and work on. Research is so broad, that a candidate can not be "best of the best" in all areas simultaneously. If you are trying to impress people and present yourself as the best of the best candidate, you end up writing a generic and vague statement, full of unjustified self-praise with a little evidence. Some of applications I deal with don't even have the University name in their statements (e.g. I apply to your University because...) - guess what happens with them?

I suggest you to really do your homework, research a few Departments you are really interested in, choose the place (or two or three) which suits you and then write your application very specifically for each place, to demonstrate how well your interests and skill set match their interests and research programs. It's all about the right match, not being a jack of all trades.


Can I write I worked as a referee in a journal in my CV?

Yes, you can do that, but it won't mean a tremendous amount in any evaluation. But probably better to list it than not. And the section you suggest is the correct place for it.
It is immaterial whether you have published there or not, assuming, only, that the journal is reputable.


solution to questions of lab equipments and funding search during faculty interview

Fortunately, as a post-doc you should have access to two people to discuss this with. The first would be your PhD advisor, and the second your post-doc advisor. In most cases (yes, this SE gets many bad stories, but there are many more good endings), these people will want to help you continue in your career.

You PhD advisor is a professor, so went through this exact kind of interview at some point, and has likely seen it from the hiring side as well. If your post-doc is at a university, well, you get a second view of that process. If your post-doc is in industry or a national lab, it is highly likely that they either applied for tenure track positions at some point, have friends who did so, or have had other post-docs do so. Further, to get their positions they went through a slightly different interview process, but that still sheds light on how to approach an interview in general.

I have always been interested in helping anyone who worked for me to fulfill their goals. Perhaps they don't work for me anymore, but they are 'my' people forever.


How to email current students in graduate programs you're considering?

My email has been posted at both my MSc and PhD department's website. I do not mind cold emails, even before applications are submitted. I answer this question maybe 3-4 times a year before applications are even due: "If you could go back in time and start over, would you still come back?". Applications cost money, I don't mind spending an hour or two every year helping people whose shoes I was once in.

Most people are the same I'd think.

Edit:

I'll read anything with my advisor's name in the email, so, if you title the email "Prospective student for Advisor" or something like that, then It will probably at least get read.


By and large, taught students (ie, ones who are not paid a stipend or salary) by default retain the copyright to their own work (in contrast to employees, who generally agree to assign it to whoever they are working for). Therefore, you should probably have then sign an agreement to assign the copyright to the lab or university, and you should certainly do this before they do any work. This will ensure you can continue to do what you want with the source code without having to ask permission from the students in question.

For research students, it varies from country to country, so the copyright on their work may be assigned to them, or it may be assigned to the university. If it is already assigned to the university, you don't need to do anything else.

You should probably speak to your university's legal department about this and especially if you do need to write up a contract to assign the university copyright. You may also find this question on programmers.se useful.


Why isn't it the norm to have research repeated immediately by other academics?

Researchers make or break their reputation on ground-breaking, innovative, and high-impact work. Reproducing the results of another group provides essentially no benefit to any individual group (even if a culture of replication could arguably benefit the field).
More often than not, in my experience (in physics), reproduction of results is done as a first step in a new research project. The point of this is usually to check one's code/understanding before building up to something new. But it is not unusual for errors to be found and corrected this way. If a result is important enough to serve as a stepping stone for another research work, usually the key aspects of it are reproduced and it's not common for a visible, erroneous result to survive very long.


What is the circumstances will the Editor consider rearrangement of authors after the manuscript has been accepted?

I do not think that the editor will have an issue as long as all other authors (or even corresponding author) have approved the change. To be honest, it is not up to him who to include, omit or lay the order of authors. After all, he is an editor who (most likely) does not know who contributed the most and who did not! To be honest, I have been in a similar situation, and there was not an problem at all.

Ethically speaking, why does the dept. head want to make this change now (giving that the 1st author has done most of the work)? And why he agreed to be the last author at the first place?  Why is he changing the order after the paper has been accepted?

I understand that a lot of politics take place in determining authorship order. Unfortunately, in most cases, the person with the most influence tend to get stuff his/her way! But, I do not think that this is ethically right.


Should I mention in my thesis that a live demonstration motivated me to implement an algorithm instead of others?

Yeah, definitely.

Comments on the reason you started work are totally appropriate in the introduction of a thesis and even make it a little less dry.  It makes it a little more of a narrative.  You still have to show all the dry results and analysis and all that.  But some minicum of storyline is actually a positive.

Actually even in a paper (where you are limited in format and space to concentrate more on results), some motivational comments in the intro are still totally in place in the introduction.  They set context, they help people.  In a thesis, even more scope is available and desired for explaining motivation (which gives contextual insights).  In science talks it is also very important (not just allowed) to show motivation (personal, economic, or social) in the intro.

I'm sure it is possible to overdo it, but in general, the issue is more the opposite (people not explaining personal motivation, inspiration from other researchers, economic motivations, etc. sufficiently).


What to do about academics who fail to fulfill their collaborative responsibilities?

As  zibadawa timmy mentions in his comment, something smells fishy here. I really see only two possibilities how the scenario you describe can transpire:

Your collaborator did  in fact provide input to "your" papers to the extent expected for "second authors" in your discipline. In this case, you are really not supposed to expect anything more from him, and writing a snotty email will reflect only badly on you.
Your collaborator did  in fact not provide input to "your" papers to the extent expected for "second authors" in your discipline. Rather, you expected that the "value" for you will come in the form of later papers for you, to which you would have contributed equally little. This is called a publication ring, and it is considered highly unethical. Writing a snotty email calling out the fact that your collaborator did not do his part in a more than shady deal sounds like a terrible idea.

Of course there is some amount of grey area between those two possibilities, but at the end of the day, you should never "pay forward" an authorship on a paper that the other person doesn't really deserve with any sort of expected or promised future benefits.

And if the other person has in fact contributed sufficiently, then what is there to complain about? Sure, one can be disappointed if the other person promised to lead a different research project and never gets to it, but that's a different story altogether.


Common practice for references to articles with different spellings of author's names

I suspect there is no single practice, for the simple reason that our society is very bad at dealing with the massive degree of variation found in names.

As a matter of principle, however, I would tend to approach transliterated names in the same way that one approaches name differences within a single language (e.g., complete formal name on a dissertation vs. "preferred name" on articles; post-marriage vs. pre-marriage name; name change following change in gender identity).  Here, I see two general use cases, which fortunately correspond with the two options you identified, and it's just a matter of selecting which is most important for a particular usage.

Name as an identifier for a person: This is the use for references, either in the citations/bibliography or in prose (e.g., "As Chebyshev writes in [5]...").  In this case, you should use the same single name for the person, ignoring different historical versions, because the most important thing to communicate is the shared identity.  Since people generally are allowed to choose their own names, you should typically choose the most current accepted name, as the best reflection of the person's current identity (though there are some exceptions).
Name as a historical record: In this case, the thing to be identified is  the artifact, not the person, and any issues in the rendering of the person's name are secondary (e.g., "Festschrift for Tschebyscheff" would not be modified).

Something that I see as a somewhat problematic boundary case is when there is an "live" artifact named after a person, e.g., Chebyshev's inequality.  Here, I would recommend simply going with a recognizable version of current consensus in the community where the publication is being sent.


Willingness to share ideas that could turn into a paper

I don't think that somebody should expect people here on Acedemia.SE to perform literature search for them (regardless of their motivation for a question), hence the feedback you've received so far. Having said that, I have briefly looked at the topic and have selected the following references that might be of your interest. The caveats are as follows: 1) the references below are intended to be used mainly not as primary sources, but as containers of more relevant references; 2) scope of the studies referenced below ranges from some specific context to more general knowledge sharing;

Keyes, Jessica. Identifying the Barriers to Knowledge Sharing in Knowledge Intensive Organizations. ProQuest, 2008.
Wang, Sheng, and Raymond A. Noe. "To Share or Not to Share: Is That the Question?" Human Resource Management Review 20.2 (2010): 115-131.
Pilerot, Ola. "A practice theoretical exploration of information sharing and trust in a dispersed community of design scholars" Information Research 18.4 (2013): 18-4.
Wang, Sheng, and Raymond A. Noe. "Knowledge sharing: A review and directions for future research" Human Resource Management Review 20.2 (2010): 115-131.


Can an academic paper be published about vulnerabilities found in a bug bounty?

I would say Yes, depending;

Is it an interesting new type of vulnerability?
Did you use an interesting new method to find it?
Do you have interesting new insights about this kind of (already known) vulnerability, perhaps linking it to a different concept?
Can you take the actions you took to find specific vulnerabilities in specific cases,  and generalize them to a broader methodology?
Can you compare the effectiveness of two different methods to detect a particular vulnerability?
Do you have a testbench of vulnerable setups that can be used to evaluate new detection tools?

Or similar things. The key aspect is novelty. What are you telling experts that they don't already know?

Apart from wholly original ideas, there's also the class of papers known as Survey Papers. These collect a range of existing studies and give an overview and analysis of the state of the field of research. In this case, you could do a survey of what the current state is of research into particular types of vulnerabilities.


Some specifics about research and teaching statements

I can tell you about what's normal in math.

It's uncommon to depict your research areas in the form of a diagram.  However, if you are studying interconnections between different kinds of objects, say, a diagram may be appropriate.  Of course figures/tables/graphs can be very useful in illustrating your research.  If you include a diagram, it should be worth more than filling the same amount of space with text.
References to the literature are standard, and makes your research statement look more professional.  I don't think people actually go look up these references, but if they know the area, they may check to see what papers you refer to.
One or two quotes is fine, if they truly express a key point better than you can yourself, but more is not a good idea.  The more quotes you have means the less you personally have to say, and this is supposed to be a personal statement on teaching.  (Quotes from student evaluations etc are a different matter.)

In any case, it's a good idea to have colleagues/mentors that you trust take a look over your application material for feedback.  This way they can let you know if you've done something crazy, or if things are just unclear.


How many recommendation letters are enough?

In the US in math my understanding is:

For the NSF fellowship follows the rules to a T.
For other postdocs there's probably no harm in submitting an extra letter, but there's also rarely a compelling reason to do so.
For tenure track positions it is common, and not frowned upon, to submit 4 or 5 research letters instead of the requested 3 research letters.  If you have a compelling reason to submit more (for example, you work between two adjacent fields) then go ahead, but if you don't have a compelling reason you're also not going to be penalized for sticking with 3 research letters.  It's better to have all the letters be great than to have more letters.

There's a lot of discussion about this in the comments on this thread.


Preparing an IEEE conference accepted manuscript for arxiving

Here the relevant bits of a correspondence with copyrights@ieee.org.

Question:

  I am having trouble understanding the policies on what exact
  information needs to be included in an accepted manuscript before
  posting it to arxiv.

  Given an accepted manuscript at an IEEE conference, am I right in
  assuming that I need to include the following?
  (a) the full reference of the published version,
  (b) the doi linking to ieeeXplore,
  (c) the copyright notice as shown in 8.1.9.B, http://www.ieee.org/publications_standards/publications/rights/rights_policies.html

  If yes, is there a standard procedure how to include those in a
  standard IEEEtran tex or does one just add them in any way convenient?
  If no, could you please clarify?

  Note, however, that the accepted manuscript of a conference paper
  sometimes already contains a copyright notice of the following form
  "123-1-1234-5678-0/12/$31.00 c 2015 IEEE" i.e. the accepted
  manuscript, the version finally sent to ieee for publication and prior
  to copyediting etc already contains a copyright notice that is
  different from the one mentioned above. Would this one need to be
  replaced by the other one or which exact notice would need to be
  included?

Response:

  Sorry for the delay in response. To the best of my knowledge there is
  no standard format to provide the information. You would need to
  provide the copyright notice as shown in 8.1.9.B from the PSPB
  Operations Manual:

  “© © 20xx IEEE. Personal use of this material is permitted. Permission
  from IEEE must be obtained for all other uses, in any current or
  future media, including reprinting/republishing this material for
  advertising or promotional purposes, creating new collective works,
  for resale or redistribution to servers or lists, or reuse of any
  copyrighted component of this work in other works.”

Not sure this really clarifies the situation..?


Should I include a grad student who only duplicated my calculations as an author on an article?

There does not seem to be much arguments pro or against including him.

But when in doubt, it's probably better to include the student them not.

I've been in that situation myself and I've decided to include the student. The arguments I used to convince myself to include him were as follows:

I could not really find any argument against including him;
If I include him, he would be much more motivated in future works with me; whereas if I don't, he may get a little frustrated when he realizes that I published a paper exactly on the topic we were discussing without inviting him;
It looks good to whoever is looking at your interaction with students (graduate committee, department, etc) that you are publishing with them;
As the student should be learning to write his own papers, it's probably good that he starts doing this on a paper where he is not the main author.

So for me it was a win-win situation.

Of course, by include him I mean that you should invite him and have him help in writing the paper.


Is it okay to upload slides based on others papers?

It is almost certainly a copyright violation in the US. It's probably also defensible via a fair use argument (in court!). I think that the odds of getting sued or DMCA takedown noticed are pretty low, but I still wouldn't encourage the practice of uploading the property of others to the Internet without their permission. That's a reasonably big ethics issue for me. The easiest thing to do might be to use a placeholder figure "See Figure 2 page 6", or similar, in the uploaded material. You might also try asking the publisher for reproduction permissions. They all have a process, and it ought to be free and easy for purposes of commentary.


How to structure a presentation for a Post Doctoral Research Fellowship

Firstly, your host institution might offer some advice on this, possibly also including the opportunity to practice your interview before a panel of people who have sat on grant assessment boards.

Otherwise, take the hint from the time allocated to you. There is little point in going into any details of your proposed research. When I went through the interview for a similar grant, I posed and answered the following questions:

What?
Very briefly, and for a general audience, describe the proposed research.

Why You?
Express why you are the right person for the job. Your background, skills, networks.

Why Now?
Why should this research be done now?

Why Here?
Why should you be doing the research at insert host institution, in particular?


Should I assume that attendees have read my papers when I give a talk?

This really depends on your audience.

At a department colloquium, I assume very little background, probably an undergrad degree in math, but not even an undergrad class in my research area. Here the audience will often be smart, but ignorant of the relevant background.
At a research seminar with lots of undergrad and/or masters students, I still don't assume much background, maybe an undergrad class in the area, but even then I "remind" the audience of important information they "should" know.
At a research seminar with mainly PhD students and active researchers I assume more, but even here I usually don't assume that they're familiar with the problem or the relevant literature or techniques.
A conference special session (or minisymposium) is similar to a research seminar with mainly PhD students and active researchers.  Here I often expect that much of the audience is familiar with the background and the techniques, but I still usually review them at least briefly.  I've never gotten complaints about giving too much background and context.

I never assume the audience has read any of my papers.
I typically view my talks (at least in part) as advertisements for my papers.  The audience will never want to read my paper if they don't see why it's important (so that's my job during the talk).  For those few that already want to read the paper, I hope they leave my talk with an outline of the paper, which will make it easier to read.  Any time you're talking to an audience with varied background, it's good to briefly describe the key definitions.  If you can do this quickly, perhaps only verbally, you don't bore those who already know, and you give the rest a fighting chance to keep up.


I doubt that it is possible. Getting a PhD is a full time job, and your CV will raise a lot more eyebrows if people see that you were doing two PhD at the same time rather than a 4-year gap.

A 4-year gap on your CV has not "destroyed your academic career". If you manage to complete your PhD, everything will probably be fine. Most "clocks" (e.g. "you can apply for this grant only if your PhD is less than X years old", "you can be a postdoc only if…" are based on when you completed your PhD, not your own age. I've known people who defended very old compared to the norm and they became established professors. Be prepared to explain the gap in interviews, but don't try to hide it with tricks.


find papers that are based on another paper

Google Scholar is a possibility. Another possibility is Web of Science (WoS), if you have access to it. It allows you to access a list of all papers citing the one you are interested in via 'Times Cited' (click on the number). Of course only WoS-indexed sources will be included. On the resulting list you can perform all refinement and sorting actions that WoS allows.


Is it unwise to list coursework on CV for PhD application

In my experience, most applications ask for your coursework separately so it might be a moot point. However, in case it's not:

I wouldn't list everything. I wouldn't even list all of my CS courses. I would only list things that are particularly interesting or unique, such as courses that had relevant projects that you can describe. Seeing a big list of courses without anything to differentiate it will probably do little to improve your chances, but if you have something like

CS 520 - Operating Systems -
Implemented a complete rewrite of the Linux kernel that does computation in negative time.

you might consider including it. I've found that it's more helpful to include projects (things you've done) rather than courses (things you've sat through).


Mathjobs.org cover letter: Address to "Hiring Committee Member" or to faculty member listed on job posting?

No.  Although the person listed for further information might be on the search committee, they certainly won't be the only member of the committee.  Furthermore, the person listed for further information might not even be on the committee.


Alternative title for research assistant

Since you are in the US, I think "Research Assistant" is actually not as inappropriate a title for your position as you suggest. See for example https://en.wikipedia.org/wiki/Research_assistant

"Research Assistant" is typically the job title a PhD student would hold if they are compensated for work on a professor's research, whether or not they have a masters degree. It is differentiated from "Research Associate" which suggests the person has a PhD ('postdocs' often have a job title of Research Associate, though they may also be referred to as Postdoctoral Research Assistants). Your years of experience on the outside aren't particularly relevant to the title.

You write:

  I’ll be doing research and publishing, but in support of someone else’s project

That's roughly the job description of a graduate student with a research assistantship.

Undergraduates may also have a "research assistant" title but in my experience that is not the most common use/connotation of the term, so I disagree with that statement at least within academia. People outside of academia may be misinformed, of course, but it's up to the rest of your resume to inform potential employers of your responsibilities and accomplishments besides your particular job title. You could be an independent consultant and name yourself CEO if you wanted, or Grand Emperor for that matter. It may be harder to change your official job title in a rigid university bureaucracy than you think - I'd concern yourself with other aspects of your resume instead.


Do having 2 masters increase the possibility of acceptance in a joint PhD program?

One of the answers here emphasizes that all else equal, the extra prep is better.  I understand this rationale but think you may actually getting the wrong idea from it.

Of course all else is not equal.  And at the end of the day Ph.D. programs are WAY more interested in talent than experience.  So emphasizing doing extra time in the salt mines to make up for past issues (and we get MANY questions down that line of thinking) is probably not an optimal strategy.

This is a key insight you need to consider.  Given the massive overproduction of advanced degrees (and the miserable job possibilities because of supply and demand), you really should not enter this "tournament" unless you have confidence that you are well above average.  If you need to be doing extra degrees to even get into the tournament?  Bad sign.

I realize this answer is both contrary and discouraging.  But I would at least consider the alternate insight.


Is it ethical to ask the postdoc employer to cover my trips for visa purposes as well as my main travel fees?

In the cases the I have known in the U.S., the relocation allowance is a fixed amount of money, and the university is fine with it being spent on anything reasonably related to relocation.  If this is the case with your university as well, then they'll probably be fine with it being spent on your combination of expenses---but if they combination of flights is expensive, you are likely to hit the cap and have some of the costs become your own responsibility.

The exact rules and regulations, however, can vary highly from place to place, so you really need to ask your university.


Is it common to get a job (industry) after getting a PhD degree in Germany? (engineering field)

Yes, many engineers do this. In fact, industrial partnerships with academia for PhD students are much more frequent in Germany than in the US. Many of these lead to job placements following graduation. So it certainly is a possibility—most of my grad students there decided to go to industry.


Searching for papers on a subject I'm about to start researching myself but nothing comes up. How do I know that I've searched enough?

Literature search is a skill like data analysis or writing. You need to learn the basics from an expert, find a good sample and dissect it, then try it on your own. Simply entering terms into Google is not enough or won't get you very far.

I suggest that you

spend time with an information specialist in the library to learn about constructing answerable questions and learning the basics of searching
learn about the basic databases used in your field and the proper way to search them through your subject librarian also at the library
locate several systematic reviews in your field and dissect their methods. Pay special attention to the databases and search terms they used.
ask your supervisor and peers for advice about the databases that they've used.

I hope that you develop a new-found respect for librarians in the end. They are a godsend.

Good luck!


Is it a bad idea to take a research position unrelated to my desired area of research?

Anyways, how bad of an idea is this if it is a bad idea?

This is a matter of balancing your own intellectual interests with your career goals. In terms of career goals, not only is it probably not so bad, it's actually probably a good thing; it looks great at this stage and later on if you have experience in multiple areas, as this will increase your breadth of expertise and your ability to collaborate with other researchers down the road.

However, in terms of your intellectual interests, you must carefully decide how much you are willing to sacrifice. It may be that you are only passionate about topic X, and working on anything else you would just not be happy. Or it may be that you are flexible, and you would in the long run be just as happy working on topic Y. Also note, that switching to topic Y now is likely (but not guaranteed!) to mean that later on down the road, at least if you are successful in Y, that your research interests evolve and become more related to Y. That could be a good thing or a bad thing, it is up to you to decide. Above all, you should never choose to work on something that you have no passion for.

  Also, is it generally assumed that by accepting an assistanceship in a specific subject that I'm also planning on doing my thesis in this area?

You should check with your program (how many years away is your thesis?), but likely yes. It could also be a flexible blend of topic X and topic Y; have you talked to the professor about your research interests? Are they willing to mentor you even though you want to retain some interests in topic X? Are there possible opportunities in the future to do some research that is "between" X and Y?

  I've never seen a graduate student that did work unrelated to their research

This is very surprising, because in my experience this is extremely common. While you may think that graduate students were always "set" on the topic they work on, in actuality many of them who work in some field actually started out in another field, but then started working with a professor and ended up switching trajectories. Research interests often inevitably evolve. Keeping an open mind with your research interests and directions, if you are willing and happy about it, can be a huge asset in academia as it opens up the number of possible professors that you can work for.

  and that lack of overlap with my own intererests might increase my workload.

Yes, this would be true if you continue research X while working on Y with the professor; that is something you should talk to the professor about.


Is teaching experience of any value in a National Laboratory job?

Preface: I worked at a US national laboratory for five years.

Under most circumstances, I don't see teaching experience being very useful in a national laboratory career. You won't lose anything by having it, but you're not likely to be able to spin it as a true "positive" in an interview. The only exceptions to this would be:

If you're going to be in a "customer service"-type position, where you are going to be working with people who are using the services or tools your team is providing.
You're in a position co-sponsored by a university, in which case you may have to do some teaching anyways.

Also, if you're invited in for a technical interview, you're almost certainly going to be interviewed by multiple technical staff members, so don't try to spin the teaching into something it's not; it won't win you any points with most of the staff members. (All of the staff members I had the fortune to work with had excellent BS detectors.)


Reasons for dramatic differences in pay for adjuncts?

Highest pay is probably very misleading. What's the median? The survey doesn't say, and so isn't really all that helpful..

It's entirely possible that the highest-paid part-time person at Mt. San Antonio is a doctor teaching a health science course or a lawyer teaching a business course which the North Orange County school doesn't offer, and so market forces may have dictated a higher salary to the part-time person who teaches it.

Trying to draw conclusions from the outliers in a data set is very difficult if not impossible and inadvisable at the very least.


Student continues to email me after I told him I would not regrade his paper. Do I need to reply?

No, you don't need to reply, but you should make sure that you retain all evidence for your decisions in the event the student complains to some higher authority. Retain the email thread as well.

You've already said it was closed. Stick with that unless your chair or other such people force it to be reexamined.