Is it good style to create http links in a B.Sc. project?

I would say that at least a footnote, preferably a reference. The rules how it must be vary between universities, but the rules are old, and generally there may be a rule that some physical copies must exist and such, so I would play safe and do it always as if it would be printed.


How to set bibliographic entry to display author only when applicable?

Okay, apparently you can get the [1] style in Zotero, but it's not installed by default.

Also, there's a "protect from manual changes" checkbox which can be unchecked in Writer. This way you can edit the entries in pretty much any way. It's far from ideal though, as manual changes are overwritten every time you update the bibliography.


Would a (temporary) industry position before starting a tenure-track position have a negative effect on academic career?

Note:  I'm not addressing the ethics of taking the industry job in bad faith.  That's addressed above.

Regarding future negative impact on tenure:

No, it shouldn't have negative impact.  At least, not at a reasonable school.  But I don't know if the school you will be working at is reasonable.  I wouldn't expect this to be a negative at Georgia Tech.

The only reason it could possibly hurt is if you had zero publications during that time, and even then that shouldn't matter if it's a non-research industry job.  But even then, if you are getting interesting experience you can talk about later, that might help your research or make connections for future collaboration or funding, it's still good.

Remember, when you come up for tenure, you write your research and teaching statements, do you can contextualize this year any way you want!

Regardless, I would hope it's viewed positively. When you come up for mid-tenure review and tenure review, the committee should look at your impact (in all ways), your publications, teaching evaluations, and so on.  Generally, they want to look at the trajectory of your work since you started as a professor at this job.  Will you appear to be someone who will continue to be successful?

What you do during this gap year shouldn't impact that.  So, I would expect it wouldn't hurt in any way.

That said, I would ask the opinion of a few senior faculty at the school, and I would explain to them that you think the experience would be a good one (perhaps for informing your future work, and teaching).  That will both give you a chance to find out how senior faculty feel about this (they are the ones judging your tenure case later on) and put into their minds a positive reason for you doing this.  Looking deliberate and thoughtful about your career choices is a good thing.


Biotech: Competing Interest Statement after leaving academia

This would seem to me to be somewhat in the same class of things as citation. If you fail to cite or fail to disclose when you should, then you have problems. In the current situation, possibly legal problems. If you over cite or over liberally interpret the requirement to disclose possible conflicts, then there is little chance of problems. Consumers of research, whether readers or patients, have a right to know that the best judgement was used in such areas. Failure to disclose is a problem as it calls the honesty and motives of the researcher into question.
As you note in a comment, a conflict in itself doesn't invalidate results, but simply warns others that they need to be certain of results, a bit more than if no conflict exists.
Quite a lot of "research" was published in the climate change (global warming) area where no disclosures were made and the "research" turned out to be propaganda. The tobacco industry was accused of the same thing. But, a lot, likely most, of sponsored research is completely valid. Someone has a "need" to know and is happy to pay for the knowledge.
So, the advice I have, though it isn't my field, is "when in doubt, disclose". I am, of course, someone who could benefit or suffer from research done well or badly, so I have a vested interest in things being done right. In the pandemic situation at the moment, we all seem to be experimental subjects of one sort or another.


Is there anywhere I can find reliable reviews of popular textbooks?

I am not aware of any specific aggregator of textbooks review. But... reading reviews on Amazon may help. (By reading I mean actually reading, not just comparing average scores;  especially reviews with non-extreme grades. Usually they also gives some context the reader's position and motivation.)

Also:

some journals have a section with book reviews,
some researchers and lectures write blog posts, reviews or suggested readings,

however, each single review is only a single data point.

But once you focused on a few books, there is no shortcut to actually looking at their content and deciding whether it fits your course, approach, taste, etc.


Best Paper Awards — especially at top conferences — count for a lot in computer science and can certainly help you stand out on the job market. I've seen people introduced multiple times in computer science venues as having won "many best papers awards" or "multiple best paper awards." People notice and people care.

Lots of other things matter as well and will matter more. A best paper awards at a conference nobody has heard of is unlikely to help much. In that sense, I don't think that hiring committees are "watching out for" best paper awards in any systematic ways. But I think it's absolutely normal to note your award winning papers as such in your CV and I think you definitely should. Having your work recognized as among the best at a conference will only help so there's no reason not to mention it.


Why do some authors seem to ignore reviewer comments?

Personally I would do things the other way round fix 1 and 2, and not ignore 3 but maybe push back in what's asked.

Anyway back to the question, I expect it's a either an expectation that the journal will correct spelling/formatting issues (depends on the journal) or a gamble that you wouldn't reject a paper just because of a spelling mistake.


Does a letter of recommendation from a postdoc who's been my instructor carry much weight?

The issue with getting a letter from a post-doc is not their job title; it's the degree of experience they have with different students, and the authority with which they can judge their preparedness for a graduate program.  So, it's not that a letter from a postdoc is unacceptable and as soon as they have an assistant professorship everything is great.  There's a subtle continuum where the more experience someone has, the more weight their letter has, because they have known so many more students.

Also, this is a bit more cynical, but humans are social creatures.  It's well-nigh unavoidable that they give more weight to a letter from someone they know personally.  A postdoc is much less likely to be well-connected and thus able to leverage this for you.


Is it advisable to mention rejected publications in resume?

You can certainly list them as manuscripts. I'm not sure what you are asking exactly: it would be a poor idea to list them as "Rejected from Prestigious conference A", or even "Submitted to Prestigious conference A" if Prestigious conference A has already made its decisions, and it is clear from the non-appearance of your paper that it was rejected.


Submit an academic paper to arXiv built over a patented idea

To the best of my knowledge, arXiv has no rules against posting preprints that discuss patented material.  The only requirement is that you grant them a license in the copyright of the text you posted, so that they can distribute the article without having you sue them.  They have no such strict "open publishing" rules as you suggest.

However, in many jurisdictions, if you publish your invention (i.e. make it public in any way) before applying for the patent (or maybe before having it granted?), your patent can be invalidated.  Thus, you should consult with your patent attorney before publishing anything.


Let me clarify some terms:

Despite the language,  Visiting Faculty are not usually faculty who are gainfully employed at one university who are just staying at another university during their research leave.
Most visiting faculty are "Visiting Assistant Professors" who are (usually recently graduated) scholars who do not yet have full-time employment and are hired as one-year (or two-year) replacements for professors who have gone on sabbaticals. This is different from an adjunct as the recipient university is hiring you full-time (not per course) for a term of one or two years.
Visiting (Full or Associate) Professors: Only rarely would a tenured, senior faculty use their sabbatical year to go to another university solely to teach. Exceptions would be: 1) they aren't being paid during their sabbatical year and need the money; 2) the recipient university has resources that they would like access to (archives, etc.); 3) they  want to live in the recipient city for a year, etc. This last one is the most common -- especially with American faculty visiting European capitals (sigh... Paris...).  Some faculty are contractually forbidden to use their paid sabbaticals in outside teaching -- at my university, a sabbatical is a leave from teaching responsibilities but it is ultimately a time when I am supposed to be doing research.
There is also the category of Visiting Researcher - this is the category which most visiting full faculty would use on sabbatical at another institution if they had no teaching responsibilities. It would not normally come with pay or any benefits except library/archive/gallery access, e-mail, and an office.

Thus if Prof. Smith@UniX goes on sabbatical, then Visiting Asst. Professor Jones@Unemployed is hired by UniX to replace Professor Smith.

To answer your specific questions, UniX is entirely responsible for Prof. Jones' salary and benefits.

Hiring is usually done by the department who needs a replacement. Often a full search is not run and sometimes the hiring is done on the Chair's prerogative. While HR of course handles the details after the department makes their choice, it is rarely HR that runs the search from the very beginning.
Credentials may not be checked as thoroughly since it is a temporary hire.
Visiting Faculty have appointments in their recipient universities and can serve as the instructors on record for courses. Depending on their term (and the rules of the institution) they can also serve as readers for senior essays, but usually they do not serve on doctoral dissertation committees. They are also usually exempt from most service work.

Biographical note: After I received my PhD, I taught for a year as a visiting assistant professor, as a sabbatical replacement. This was before I received my first tenure-track job. [note: simplified version of a complex reality]


Should you include uncited papers in your CV?

Convenient? No.  Appropriate?  Yes.

Unless you are at a point in your career where you can release an impressive "selected publications" CV, your CV is expected to contain everything that you have ever published.  That includes publications that nobody has cited and even ones that you are embarrassed by in retrospect.  I've certainly got some of those in my CV (we were all grad students once), and I simply trust that they will be drowned out by all of the good work that has been done since.


How do grad schools look upon students with chronic illnesses?

Do any of your letter writers know about your illness and can speak to your strength in spite of it? If your application on its face is strong (ignoring the withdrawn course and year gap), a mention of your illness and overcoming it in your personal statement (not your statement of purpose!) might be a good thing to do. I do not think they will look down upon you for this, quite the opposite. From what I have read, they cannot discriminate against you simply based upon your illness so that shouldn't be a problem (see ADA). If it's clear that you're dedicated, I think you'll be okay.


Postdoctoral applications - informal enquires

Introduce yourself (briefly), ask for more details of the project, perhaps ask for recommendations for background reading. Other things you might enquire about include the level of support for conferences, opportunities to teach/help supervise students, and the likelihood of follow-on funding (if the advertised position is relatively short). Note that you don't have to ask everything in your first email, and save yourself some questions in case you get called for interview. Attaching a brief CV can't hurt - but don't make me open an attachment to find out where you've studied and who you're currently working with.

Also, remember: writing this email seems important from your perspective. However, the PI probably gets dozens of emails daily, and will barely notice the precise words you use. Don't get too hung up on the content of your message!

I would always direct my letter towards the PI, even if it is to be sent to an HR contact for initial processing.


Good practices for skipping chapters when reading

I'm usually backtracking, i.e., I try to read a subsequent chapter, then I usually discover that there are some definitions/concepts that I do not understand, so I go backwards to look these up, and, once I've understood these notions I can resume the reading of the subsequent chapter.


How can you tell if a faculty or group is on decline? Am I being used?

In the final year of my PhD, I made a tour of several places in the USA to try to establish contacts in the hope of finding hidden postdoc opportunities.  I knew of those places because I frequently saw their papers.  In some places, I have seen signs of decline:

In one place, the main senior scientist had moved away some years ago.  Since then, one by one, others had left.  It appears nobody was replacing them.  The people who were still there appeared to be the ones who were less successful at getting grants and writing papers, than the ones who had left.
In another place, I didn't see any PhD students in a group, and only a handful of postdocs.  Most people were above 50, with the head of the group being well above 70.  Although certainly a great name to have as a support, I wouldn't recommend anyone starting a PhD project with someone who will turn 80 before the candidate is expected to get their PhD.
I also overheard conversations from which it was clear that people were not very ambitious.  I almost literally heard someone say, that they now had a permanent position so they didn't need to write a lot of papers anymore.

Those are some signs that a place might be in decline: Have more than two senior scientists left the place in the past five years?  Is the median age above 60?  Are some people happier to stay on their desk than to attract great PhD students and postdocs to produce some great science?


Read both revised and original version to cite paper?

I believe that you are somewhat misinterpreting the advice given in the questions that you link: the general consensus seems to be to cite the most recent version (as being the most current state of knowledge), unless you have specific reason to cite an older version.

As such, I do not believe that you generally need to read or cite prior versions.


How to handle Supplementary Instruction of Subject-Deficient Students with language difficulties

assuming that this student met the English proficiency requirements of your school it is still common for esl students to fail courses due to language issues. this is due to the fact that they have to acquire the language of the course in addition to everyday English.

if you are willing you can try to accommodate this student through providing additional teaching and or additional time for assignments and assessments.

from personal experience for a hard working esl student the second time through id always a charm. as their language skills improve the chances of repeating are drastically reduced.


Should I "offer" something when asking for a letter of recommendation?

Just straight up ask for the letter.  There is no need to "pay back" with some favor.  Writing letters of recommendation is part of a supervisor's job.  However, it would be wise to include in your email:

Position description so they can describe the most applicable aspects of your prior work in their letter
Ask if they would be willing to write a "positive letter of recommendation" because if it is not positive, they should not write it
Information about: where to send the letter, to whom it should be addressed, and the date when the letter is due
Ask if they would like you to send a reminder email 2 weeks and also 2 days prior to the letter of recommendation due date

Additionally, if it has been some time since you spoke to this person or you do not know if they remember you, include your latest CV or Resume with your email. You should never have to draft your own letter of recommendation.  I highly look down on this practice, though you may encounter it.


Can I accept two funded offers from universities and decide later after April 15?

No, you cannot do this.

According to the April 15 Resolution of the Council of Graduate Schools, you cannot accept multiple award offers simultaneously. You are not committed to any offer signed before April 15, in that you can submit a written statement declining a previously accepted offer. But you cannot accept multiple offers before or on April 15, and changing offers after that date requires a written release from the school with whom the offer that was “in force” on April 15.


My potential advisor is suggesting a project that I don't think I have the knowledge to take on?

First thing, in a master or in a PhD, you are a student and it's normal to learn new things. If your potential advisor wanted someone for this project that already knew how to do it, he/she would hire a postdoc. Actually, learning new techniques, in statistic or other, is what every scientist do, during their entire career.

Second, you are already planning on taking additional statistical courses and your potential advisor knows your background. It seems to me that you will be fine and that you can do this. This sounds a lot like impostor syndrom and you should read on that. In that case, I wouldn't talk about that to a potential advisor. Do talk about it if you need to, but preferably to professional help or people who know you. For the record, I wouldn't hesitate in talking about impostor syndrom with my advisor, but I know him, he knows me and we have an healthy mentor-mentee relationship...

If you still want to touch the subject with your potentiel advisor, do it simply:

  I'm very interested in this project, but I'm worried I don't currently have to knowledge to do it. Are those courses sufficent to help me with the project? Will there be additional help available ?

This is the good moment to enquire about lab resource, which can be professional statistical help or colleagues. Good luck.


Which is more beneficial prior to PhD: research experience or a second Masters degree?

The question is framed oddly.  A master's degree without research experience will probably kill your chances for PhD admission, at least into the top programs.

Here's a better framing: Is a second master's degree the best way to get more research experience?  Unfortunately, the answer depends on your personal situation.  If you're already doing active research with a strong possibility of formal publication, with well-known faculty collaborators who will write you strong letters of recommendation, then a second MS is probably not necessary.  If that doesn't describe your current research environment, a second MS might be the best way to find such an environment.


How to know one's way around for PhD in Covid times

I'd like to continue my formation with a PhD after my thesis.
You should have told us why. Think over it. Be ready to answer that question. Only go for a PhD if you can tell why. If you find your own answer convincing.
consider the idea of going someplace...
Excellent. Go to some place where research is decently funded, and where corruption is low. An easy measure for corruption is in the faculty's CVs: did they come from outside, or have they been promoted in-house?
even in the subfield of high energy theoretical physics
Don't choose the prefered subfield of some of the brightest minds, except if you are so brilliant that you can reasonably hope to make some difference in that field. Rather be the clever guy in a down-to-earth subfield. There are fascinating research questions everywhere. Lots of engineering is built on wild heuristics that is waiting for solid physical foundations. In condensed-matter physics, given the incredible variety of material structures, there are much more challenging questions than in theoretical HEP, and much less theoretists per question.
How should one approach this problem in Covid times?
Yes, times are hard. But I see there also a little advantage for your remote applications: as these days everybody has to use electronic means of communication, this brings you in one line with local candidates.
Is it common to ask "what are your researchers doing" in an email?
To whom would you write that mail? Wouldn't they get the impression that you haven't done your homework?
Is there an online list of who is doing what
Of course you can start from faculty lists, then proceed to their CVs and publication lists. But as you are not yet decided geographically, it's better you scan recent editions of high-level research journals, and look for work that is really impressing you. Then contact the authors.
in what university?
In many places, universities are second-tier. Don't overlook the well funded national laboratories and other research institutes outside the university system.


Should you let the editor of a paper under review know when you post preprints of additional papers that build on the paper under review?

No, there is no need to do this.

If you submit a work to a journal you submit it as is and related to the current state of the art at time of submission. Things that happen after submission should in general not interfere with the current submission. While it could be in some exceptional cases that events after submission may influence the perception of the article, in general the article should be processed with respect to the date of submission.

If I imagine that people would start sending any kind of "additional information" after an article has been submitted, I would expect that this could lead to a great mess (articles submitted which are in fact only preliminary, additional appendices added at a later stage, corrections/amendments…). So I would guess that an editor would generally ignore the additional information and even may find this a bit strange.

However, you may add additional information in case of a revision/resubmission and this is the right time to add anything that could be relevant (with the only exception of severe error in your work - if you find one inform the editor immediately).


How to find published article from arxiv preprint

No, this is impossible to determine definitively because there is no complete list of publications.
The correct solution is for the author to update their ArXiv submission with a citation.
The practical solution is to use Google Scholar to search for an article with the same text.
You can also ask the author, who will know if there is an authorized publication.


Is it legal / ethical for a professor to monetize course content videos?

Legal? Probably yes, depending on university policy.

Ethical? Universities and politics nowadays encourage academics to be business-savvy and profit-oriented (I guess, as long as the uni gets a cut). So, while the described constellation indeed carries a "smell", it may be perfectly in line what society wants academics to do.


What are the ways a professor in top R1 public universities can increase their salaries (through research)?

Although the NSF won't generally allow you to receive more than 2/9 of your 9 month salary from NSF grants, other federal agencies (ED, DOE, ARO, NRL, USDA, etc.) don't have such a rule, so it is possible to get +3/9 summer salary from such grants.
It's also possible to use a "buy out" to pay part of the 9-month salary out of grants in exchange for a reduction in teaching load.
Beyond that, the regulations forbid taking more than 12 months salary from federal grants.  Of course, the institution can give a very successful researcher a pay raise so that they can take more salary from their grants.
Here are some other ways to earn additional income:
Consulting.  There are usually restrictions on how much consulting you're allowed to do during the academic year but no such restrictions over the summer.  You can charge what the market will pay (e.g. I charge for consulting at an hourly rate that is more than twice the hourly rate that my institution pays me.)  However, you'll also be responsible for all of the legal and tax complications that arise (you may need professional liability insurance, you'll have to pay self-employment tax, etc.)
Royalties.  If you write a best selling textbook for a lower level service course, the royalties paid to you can be a substantial addition to your faculty salary.  However, there's a lot of work in writing a textbook and in most cases, the royalties won't amount to much.
Patents.  At most institutions in the US, faculty work under intellectual property agreements that lay out how the profits from a patented invention will be shared.  Depending on how generous your institution is, you might be able to earn income from patents.
Start your own business. In some fields, it's possible for faculty to spin their research off into a start-up company.  There are usually intellectual property agreements with the university that require ownership and/or profits to be shared with the institution.


Where to put a cited paper: introduction or discussion?

Some very general guidelines from my own expertise; kept rather simple to be a starting point for first-timers in article writing:

In the Introduction one mentions/describes the papers most relevant to the research conducted. E.g., if one analyses the volume of wolves' howling, there should appear sentences like "in [1], Smith et al. measured the howling loudness of 12 wolves in the Carpathians, and found they are quite loud"
In the Methods section, one cites papers that are relevant to the methodology of the work/its analysis, e.g. something along the lines "following [2], we set up 18 automatic sound recorders [3] in the Beskids. These recorders were triggered according to the Wolf-Howler criterion [4], i.e..." blah-blah-blah "we performed standard statistical tests [5] to verify..."
In the Analysis/Results section, one usually mostly emphasizes what is new in the presented paper. Some immediate comparisons are very helpful, e.g. "the howling that we recorded is statistically louder than what was presented in [6]; this discrepancy may be due to the fact that most of the wolves that we recorded were males, while 17 out of 24 individuals measured by Hound & Forest in [6] were females"...
The Discussion is the part where one discusses the importance of the presented research. One compares, emphasizing and discussing in more detail, similarities/differences of the newest results with previous findings. If a new method is applied, one discusses its strength and weaknesses in the context of the present and possible future research. Phase like this can also occur: "We showed that the automatic recording of wolves howling is efficient, and so can be applied in the field of raccoon noises [7]...".

I think that in my papers, papers that were not mentioned earlier rarely appear in the Discussion. Although there are exceptions, e.g. when some comment from a paper from a different field seems to be adequate in the light of the discussed results.

Overall, I think that most (and all relevant) papers should be cited as early in the manuscript as possible. There are no general rules of thumb whether it's fine to introduce a paper in the Discussion or not. It's mostly about the gut feeling and personal writing style. I can imagine people justifying that one should absolutely not cite in the Discussion/Conslusion/Summary papers that weren't cited earlier in the text. They may have good arguments, certainly, and if one tends to agree, it's completely fine. There might be exceptions, though, that are subject to personal judgment and one's preferences, so I'll stop here.


Find articles that share datasets and code

paperswithcode.com.
It contains publications and the corresponding code.

Most top computer science conferences ask for relevant supplementary material, which includes code. Many papers (atleast in Computer Vision/Machine Learning) which are published in top venues contain links to the code as well.

Many professors also maintain public git repos, which contains the code for their publications. You can search on Github or go to the homepage of the professor to find the link.


Do professors in the STEM fields at U.S. universities get summers off?

While no one is technically forcing you to do work over the summer, you'd be foolish to take extended breaks.

One of the benefits of a tenured faculty position at a research university is that you get great flexibility in your schedule. Today, I left work early (e.g., 4pm) to pick up my kids at summer camp and go to the park. I have no (or almost no) formal obligations over the summer.

That said, this evening, I was doing data processing and reading through papers. It's now 1 AM.

My long answer to your question is that it's certainly possible for a research active faculty member to take a whole summer off, collect summer salary, and pick up in the fall with research and teaching.

This sounds like a very bad idea.

Right now, funding levels are so competitive, that everyone I know with research funding is trying to be as productive as possible throughout the year. The summer might be a bit more laid-back, and I bet most research faculty spend less time in the office or lab. Most will probably travel to at least one conference or workshop, and I bet most also take a week or two of "real vacation" with family or friends.

But, if you're not working on papers or grants year-round, you're probably falling behind and will likely have difficulty getting that grant (and summer salary) renewed.

This summer, I helped submit a major center grant, I'm drafting another grant for my group's research, and I'm trying to finish up ~3 papers. Add in some papers and grant proposals to review as service. I'm not trying to boast - I suspect this isn't an unusual summer work load for research-active faculty.


Importance of having a "connection" while applying to PhD

At least for schools in the US, it is not necessary for you to have a direct "connection" or contact at a department to be admitted.

In general, where contacts can be useful is if one of the people who writes your letters of recommendations for you knows a particular person in the given department. If that "connection" is good, and you get a good letter of recommendation, that will carry more weight than a typical letter of the same quality, since you will be better "known" than someone who the department doesn't know at all.

That said, though, there is no expectation that you would directly know someone already at the school—although your research interests should align with the department as a whole.


Does the year of publishing for corrected proofs change in the final version?

Re. 1 - Yes. I have a paper that was published "epub ahead of print" in one year, and later published normally the next year. Both versions have different year numbers when cited.

Re. 2 - I would expect they do it in chronological order normally, but sometimes journals publish "special issues" on a specific topic that result in postponed or quicker printed versions. Also comments/replies to specific papers often get published in the same issue, suggesting that those ended up in print version quicker.


how do you verify your knowledge in a subject area for grad school admission while you have not been enrolled in regular class?

What you want to do will limit your choices among schools.  Where I teach, we do allow provisional admission for people without the requisite undergraduate degree.*  Those students are required to take a series of foundation courses before beginning the "real" master's courses.  It is possible, although not easy, to test out of the foundation courses.  The provisional admission is revoked for the student who earns unsatisfactory grades (C or below) in the foundation courses.

So, you will need to look for institutions that allow provisional admission, and then check the details of the provisions.

* Students must have some accredited undergraduate degree to be admitted; but it need not be in computing.


Phd Thesis vs 5 years publications documentation

You should check with your university. Some universities allow an "alternate thesis format", in which some or all chapters are just reprints of published papers.


Postdoc interview presentation "of yourself and your research"

I can only guess, but from my own experience I think the phrasing "present yourself and your research" is an informal way of saying:

Briefly introduce yourself, including your career/professional development and your research interests,
thereafter devote the major part of your short talk to explaining the research that you want to pursue at the institution at which you are applying.

Good luck. The hearing for my current postdoc job was also via Skype, but it was much longer.


How to cite sources written in a different language than English?

You cite the original title, for the very reason you gave: to enable readers to find the original title. If your work is subject to guidelines, you should also check those.

Usually, there is no point in giving a translation of the title as it does not contain any relevant information for the reader. Many citation styles do not mention the title of papers at all. I see two exceptions though:

If a translation of the cited work into English exists (but you worked with the French original), you can mention it in addition to the French title, e.g. with:

  [actual citation] (translated into English under the title [translated title])

If the title allows the reader to estimate what the source contains and whether they want to read it at all. In this case, you should arguably change your text such that it states in what way the citation is relevant for your work.


This sounds like "I want to punish them but not really". Fact is that these students have cheated even after multiple warnings. You are not teaching little children. Responsibility and accountability are important and adult students should have both.

If you are sure they plagiarized the only correct course of action here is to report them. It is then up to whoever handles such issues to assess the severity and appropriate punishment.

The students knew the risks of plagiarizing and decided to do it anyway. Giving them a milder treatment now will encourage other students to behave similarly since the consequences become less severe.

Note: are you sure the students copied from each other or is it possible that they are using the same source?


University's motivation for having tenure-track positions

In most jobs in industry, new employees go through a probationary period during which they can be let go (fired) for poor performance without the protections and benefits that more experienced employees might get.  If a new employee isn't working out, then they'll be let go during this probationary period.

In higher education in the US, the (customarily at most 7 years long) tenure track is an extremely long probationary period tied with policies that (in the name of academic freedom) give tenured faculty very strong protection against being fired or laid off.

When a tenure-track professor is denied tenure, the university has decided that they're not doing well enough in the job to justify a lifetime commitment from the institution.  There are significant costs associated with recruiting a replacement, as well as significant consequences for the morale of other junior faculty,  so these decisions aren't made lightly.

Allowing a tenure track faculty member to continue as non-tenured faculty member after you've denied them tenure has problems.  In addition to lowering the morale of other tenured and tenure-track faculty, it runs afoul of the guidelines for tenure promulgated by the American Association of Union Professors (AAUP) that say that tenure must be granted after seven years of service.

It should be noted that the tenure system is in a significant decline in the US.  More and more, teaching and research work is being done by people in non-tenure-track positions and the number of tenured faculty is declining.


Can I get a university teaching job with only a bachelors degree?

(U.S. answer follows)

It is virtually impossible to get a teaching job at the college or university level without an advanced degree at the Master's or PhD (or terminal professional degree) level.  Most faculty have a terminal degree.  The opportunities for teaching with a Master's are limited, especially because competition is high and even collegiate level positions that are open to Master's holders still attract PhDs.  Master's degree holders are normally limited to non-tenure track teaching positions and adjunct teaching positions.

If you really do want to be a teacher without an advanced degree, there are opportunities at secondary schools, although most public schools will expect you to start working toward your Master's degree in either Education or your specific field within a few years after you begin.  Private secondary schools are less strict in this regard, but these days you'll find that most teachers will work towards their Master's even in private schools.  With a computer science / engineering degree, you should be competitive for teaching positions in mathematics, physics, computer science/technology, and possibly other sciences.  When I started teaching high school physics, my undergraduate degree was in electrical engineering (but I also finished a Master's in education).

There are obviously exceptions to the above -- Bill Gates could get a job teaching at virtually any school in the country, and he doesn't even have a bachelor's degree.  But, unless you are in a unique category like that, you should be prepared to get an advanced degree of some sort if you want to teach at the college or university level.


How can I cite interviews for radio and TV on CV?

"Media Appearances" sounds better to me. Then I think I'd cite each appearance as if it were a conference talk:

  "How to Solve the Problem of Evil," WFUV Radio, 29 February 1904.

or

  "Why I am So Clever," The Today Show, National Broadcasting Corporation, 9 August 1999.

Maybe insert some descriptive language if the citation is unclear.


Should I hold back some ideas for after my PhD?

I don't see a point in holding back ideas on purpose, at least not for a longer time.
If you are doing well in research, you will generally have more interesting ideas than you have time to pursue.  And you will keep having new ideas all the time. So there won't be a time when you will have ample of time, but be in desperate need of a great project.
So you should work now on the best ideas you have now: First, people will judge you by your best work and best ideas. If you work on more exciting ideas now, you will be more likely to secure good postdoc positions later. And if you have a fair advisor, they will clearly credit you with those ideas (e.g. in recommendation letters).  So you win by working on your best ideas now.  Second, your best ideas now might be outdated in a few years time, or your interests might shift, or you might have even better and more timely ideas at that time, so there is not much point in saving those ideas.  Third, someone else might have the same idea and publish a result on it in the meantime, making your ideas not new any more.  And finally, even if you don't have the time to work out all ideas fully yourself, it can make sense to share them with colleagues: Maybe they get excited by the ideas and collaborate with you on them, increasing your scientific output.
Finally, what if you will not have good ideas any more in the future? Well, then very likely your chances to secure a permanent position in research are slim, and having kept your old ideas will not save you.


Should I refuse the invitation to review a paper which I recommended for rejection? What should I do if I suspected who wrote this paper?

It's fine to review a paper that you have previously recommended for rejection (assuming you gave reasons rather than just dismissed it). The editor took your comments into consideration when deciding to seek a revision and I would expect the authors to respond to your concerns in their revision.

However, the second question is definitely grounds for refusing. The editor may wish to include you because you raised concerns and are in the best position to assess the extent to which those concerns have been addressed, and you may be incorrect in your authorship guess.

What you could do is an email to the editor along the lines of "Since providing the previous review, I have come to believe that PERSON X is one of the authors and I have a conflict of interest if that is true. Unfortunately, I must therefore decline to review unless you can assure me that PERSON X is not one of the authors."


I take it that the position you are applying for don't specifically ask for such samples. In some cases, hiring committees will look at only what is asked for, nothing more. This is to protect the commitee's time and to ensure that each candidate is considered in equal light. While you likely won't be penalized for offering more, don't be surprised if the extra pages end up in the trash can before the committee sees them.


How should be your relationship with your PhD advisor

This depends on personalities. For some it is perfectly acceptable to be very informal. For others, such as mine, a more formal relationship was needed. But, even in a formal relationship, you need to have your questions answered and concerns addressed. But it is really a matter of "style" how you go about that.
So, the first thing to do is ask the advisor what they prefer and how frequently it is "good" to touch base. Even with a formal relationship, an advisor might want a progress report every couple of weeks (or more, or less).
But work it out initially. And, you want to have a good relationship so that they will be willing to support you after you finish, as well as during your degree years.
Of course everything was, and we hope will be, in the absence of a pandemic.

Note that different advisors rank different parts of their job differently. Some value their own research very highly, which can be a problem if they aren't as helpful as they should be. I often worry about untenured advisors for this reason (and once suffered because of it until I switched). But, I'd just guess that phone conversations with advisors are pretty rare (though mumble mumble pandemic).

And you might also want to look at my earlier question and its answers on this site: How do you build a healthy and productive relationship with your supervisor?


Spousal-hire arrangements at a postdoc level

I do not think that any of these are realistic strategies.  Sorry.

If you are in a field where there are many jobs, you may be able so separately obtain positions which are in the same city.

Spousal hire arrangements are used to recruit highly prestigious candidates to permanent faculty positions.  It would be unusual to have the resources to use that hiring strategy for a temporary postdoc position.


How common are self-funded PhDs in the STEM fields in U.S. universities?

From the Survey of Earned Doctorates, a large-scale survey of students who earn doctoral degrees from U.S. institutions,

In the life sciences, 9% report "own resources" as primary source of support.
In the physical sciences, 3.8% report "own resources" as primary source of support.
In the social sciences, 25.3% report "own resources" as primary source of support.
In engineering, 3.8% report "own resources" as primary source of support.

See TABLE 35. Doctorate recipients' primary source of financial support, by broad field of study, sex, citizenship status, ethnicity, and race: 2014.


Low undergrad GPA, how should I inform a tenure track faculty job search committee?

Don't mention anything about your undergrad GPA in your application if it is not mandatory. During interview, if they get to know and ask, you can tell every problem you faced during undergraduate career and show up your proof such as medical certificate. They will consider it.

If it is a mandatory option, then write it down. However, in such mandatory situation, be straightforward (as said by @AlexandersWilliam below) and mention about your poor performance in undergrad period somewhere in your CV or resume, but not necessary always. Because selection committee care less about undergrad GPA, they mostly see your recent records. Hope this will work.


Is repeating a mathematical formula or equation in a scientific paper considered bad writing?

I'd suggest just referencing the previous entry. People reading technical articles are pretty used to skipping back if necessary. It might be confusing to repeat it with a new number, especially.
An alternative would be to repeat it along with the original number, making a note of what you are doing:

...repeating equation (42) x = y + z...

But the reference to the equation is likely enough.


Undergraduate and Masters degrees in the UK before PhD. Why do they last so little time?

I can only speak for my area, mathematics. In the UK, there is a very clear division between which degrees include coursework and which are strictly research. A Masters degree in math consists of approximately 10 (very intense) months of course work, and only on extremely rare occasions research. A PhD consists of 3 years of very intense research, and only very rarely coursework. This allows students to focus on one specific task and complete it faster. Here in the US, Masters and PhDs include both coursework and research. The research for the Masters degree means that it takes more time, and the coursework included in the PhD means that it takes more time.

In theory, these two systems are supposed to be equivalent, and both countries produce excellent mathematicians (we currently have two postdocs who were educated in the UK who are both quite brilliant). In practise, I would theorize that more years working on essentially the same level (an advanced grad student and a postdoc are both expected to be independent researchers) would of course give someone more knowledge. However, the PhD is supposed to be evidence that a person is a capable independent researcher, not that they are familiar with X number of the main methods in the field. As long as UK PhDs satisfy that requirement, I believe they have earned the degree.


There are several reasons why a field might not use arXiv, or another pre-print service. Whether or not these are correct is left as an exercise to the reader:

It will interfere with publication. This is a little circular, but if a field doesn't use pre-prints, journals might not recognize a pre-print being put in a depository as not prior publication. Whatever merits there are in putting something in a pre-print repository are offset if you can't get it into a journal.
Pre-prints create version sprawl. If there's significant revision of pre-prints, there's now sort of two versions hanging out, the one on the pre-print server and the one that sees publication.
Priority is not necessarily as important (not that it isn't important). In biomedicine, the ideal is for multiple studies to all independently estimate an effect, so being first isn't as critical.
Pre-prints are not peer reviewed, but a pre-print of an RCT or something may still be used to influence medical decision-making etc.
Pre-prints and double-blind peer review are basically mutually exclusive. This one is, in my mind, the biggest downside of pre-prints.

When it comes down to it though, much of it is just field convention - if preprints aren't used, there's very little utility to being a "pioneer" in that regard - it's work, and explaining, and some risk for very little benefit.


Is it appropriate to use acronyms when citing a source in MLA?

From the 7th edition of the MLA handbook.

  Abbreviations are used regularly in the list of works cited and in
  tables but rarely in the text of a research paper (except within
  parentheses). In choosing abbreviations, keep your audience in mind.
  While economy of space is important, clarity is more so. Spell out a
  term if the abbreviation may puzzle your readers.... The trend in
  abbreviation is to use neither periods after letters nor spaces between
  letters, especially for abbreviations made up of all capital letters.

The following points are from a MLA style guide on the doc scribe site.

If an acronym is commonly used as a word, it does not require explanation (IQ, LSD, FBI, ESP).
A term must be fully written the first time it is used, thereafter just the acronym is used.
If an acronym is not familiar use an expanded abbreviation; for MLA write Mod. Lang. Assn

Also from the same source (Page 8)

  The common practice in research writing to spell out the name or
  phrase to be abbreviated followed by the acronym in parentheses.
  Thereafter, just the acronym is used. For example, the Modern Language
  Association (MLA) publishes a journal. The reverse is also works—the
  MLA (Modern Language Association) publishes a journal.

So in your case Centers for Disease Control (CDC) or CDC (Centers for Disease Control) for your first citation and CDC afterwards should be fine.


How to get second chance at pursuing honours/PhD if your undergraduate grades are poor in Australia?

Regarding your hypothetical argument about getting accepted to honours and good grades there not mattering: if you did get accepted and get great grades in the so-called honours program, It would almost certainly help you far more than by just averaging up your GPA. Universities will notice the upward trend and some will be willing to believe you have turned things around.

More generally, no matter what you do next, poor grades say two things, both of which you need to overcome:

You have poor study habits, hence you'd probably fail out of grad school by doing more of the same, because a "C" average isn't acceptable in grad school.
You didn't learn as much of the material as you should have, and are now behind everyone else who got better grades. And now you will be in over your head in graduate courses which build on those undergraduate courses.

You can address #1 by showing a pattern of improvement in taking new classes and doing well. For #2 you will need to basically learn the material in a second try. If you had non-existant study habits in school with all the support and pressure on you, I don't have too much hope for self-study. I'd suggest finding a way to retake some key classes.

I'd also note that machine learning may be very different than what you expect coming from a computer science background. It is a heavily mathematical subject, where the programming is the easy part. So you may be gaining some edge by focusing on a topic that is more interesting, but you're also doubling-down on what is likely the hardest component of your studies.


Is there any evidence that double blind peer review systems are beneficial?

Yes, there is scientific research on this topic.

Using data from ACM WSDM'17, A. Tomkins et al. showed that double blind reviewers are less likely than single blind reviewers to accept papers from famous authors, top universities, and top companies.

See: http://www.pnas.org/content/pnas/114/48/12708.full.pdf

Update: As mentioned by @thomas-supports-monica in the comments, there is some evidence that the article linked above may have some issues. See https://papers.nips.cc/paper/8770-on-testing-for-biases-in-peer-review.pdf .


Reviewer asked to move every mathematical proof to appendices for an engineering journal

In all cases I have been involved, together with the revised manuscript a response letter to the editor is submitted, re-iterating the specific comments/issues of the reviewers and explaining the changes made in the manuscript to address these issues.

What you are describing is typically one of those things that can be explained in the response letter. You can formulate a nice response where you can explain to the editor (who essentially has the last word on whether or not the manuscript will be accepted) that ...

"while we believe that moving some of the mathematical formulas and derivations to the supplementary will improve the readability and flow article, some are indeed essential in order to give the reader a fair chance to understand the assumptions/model/results/..."

There are two major benefits of addressing the situation in this way:

You show that you do not disagree with the reviewer(s). People tend not to complain much when you agree with them.
You show the editor that you take the matter seriously, have put effort into amending the manuscript in order to improve the situation and also put thought into making the paper easier for the reader, while not losing the important bits.

I would discourage you to use formulations where you decide what does and does not count as long, or what does and does not impair readability. I say this mainly because you are not in an objective position to judge these things. You have written the manuscript and to you, at the time of submission, the manuscript (hopefully) is informative and has a good flow. You have been working on the project for months, maybe even years. At the time you pick it up, you have all the necessary background to understand the paper. The reader is far away from that position.

Instead consider picking out things that you feel are absolutely critical, in order to understand the essential bits of the work; that is the motivation, the goals, and the conclusions. Everything else could go into the supplementary...

Lastly, does the journal not have any information on how to handle mathematical calculations/proofs etc, on their guidelines for authors?

Likewise, if you have co-authors what do they think? Your supervisor has some opinions on the matter surely?


If you change your name while doing research, can you list both names on a publication?

This is indeed a weird question, though not an uninteresting one.

Fundamentally a name is a pointer to a person, of a formalized and official sort, but of course for every person there are multiple phrases that point to them.  Any article byline gives a mapping to the set of objects named, and the idea that perhaps this function need not or should not be one-to-one is a very curious one.  I don't know a general principle to invoke from which to deduce the "injectivity of authorial bylines", but multiple names pointing to the same person would be highly nonstandard and powerfully confusing to many.

I'm not sure what to make of the fact that your example of a name change is motivated by a sex change.  Name changes are common occurrences for people of all genders, and the percentage of name changes which are motivated by issues of gender identity and/or sex changes is very small.  The largest percentage is surely when people (not just women, though still more women than men) get married, and then comes people who have moved from one part of the world to another where their name is difficult to pronounce, written in a different alphabet, sounds like something undesirable in the language of their new home, and so forth.  Also papers published in one language are often translated into another, with the effect that e.g. many Russian authors are known by several moderately different names in the anglophone academic community.  Adding a clarifying note that say that multiple spellings point to the same person could be helpful.  In this recent preprint the byline is "Yuri G. Zarhin (Zarkhin)", which is perhaps the closest thing I've seen to the practice you're asking about.

However, there are nuances in your question that suggest the sex change example is not accidental: you actually mean to consider deeper issues of personal identity.  In other words, what if beyond changing their name, someone considers themself to actually be a different person? I get this for instance from

  What happens if Jane never worked on the project, can she be the author or does it have to be John?

The obvious answer is "What are you talking about? Jane Doe and John Doe are the same person.  So of course Jane worked on the project.  The fact that the name 'Jane' was not applied to this person while she was working on the project is totally irrelevant."  However, it could be that Jane feels that she is really a different person from John.  Maybe she arranges [illegally, perhaps; I don't know how this works] to get a new social security number and otherwise systematically denies and delinks her new identity from her old one.  In that case it could be meaningful -- even critical -- to her that Jane didn't work on the project, rather John did.  However, though Jane's perspective is a highly interesting one, it is not going to hold up in the practicalities of an academic career, as she presumably wants to regard John's training and credentials as her own.  If she tries to make a CV of Jane Doe's work only, she is going to at best confuse everyone and more likely shoot herself in the foot.

It would be worth hearing from a transgendered academic [I am not one] for more nuances about this.  My understanding is that the above exigencies essentially require them to explain carefully in their CV that they have changed their name from John Doe to Jane Doe and thus cannot professionally behave like they are two different people.  If you are including the identity "John Doe = Jane Doe" anyway, then if it has deep personal significance to you to list yourself as John Doe on a paper that you worked on while you were John Doe even though you now sign all your papers Jane Doe, you can make that choice (and certainly it is your choice: the idea of anyone else telling you what to do here is somewhere between cruel and absurd).  What you cannot do is list both John Doe and Jane Doe as authors.  Well, not unless you wish to be truly transgressive: perhaps there are some areas of academia in which the jarring, confusing nature of such a byline would be viewed positively.


Resources on how to overcome writer's block, especially for non-native English speakers?

Of course there are plenty of resources about how to overcome writer's block, however for different people different techniques work. The advices I always found very useful as a PhD student (although I cannot find the original sources, it's been years) were these:

do not aim high at the beginning. Crappy and hasty first draft is perfectly fine, iterative improvement will come later: as the author here points out, inexperienced writers tend to have too high standard on themselves. Since I am in a formal field, I therefore refrained to start with the paper's motivation, but rather tried to work out the mathematical flesh first. That one is easier in terms of language since the form can be copied/learned from good papers of others. But this differs across disciplines.
block time every day for writing and do nothing else at that time, even if you should stare at a blank wall: this is my way to kill the procrastinator in me. Simply three hours every day a week for writing. Even if during that time one would really just stare at a wall and write nothing, it's better than procrastinating. Eventually the boredom is so high that writing becomes welcomed activity. It is imperative not to do anything else, especially not to study, read or otherwise consult any literature, also get disconnected from Internet and colleagues, etc. The best for me was to go for this to the department's library where was no wifi connection. I read somewhere that this technique is used by some novel writers, but can't find any source of this advice.
Another powerful technique is use public commitment wisely: that is, publicly commit to delivering an artifact at a precisely specified deadline. E.g., first draft of the paper next Friday. Tell to your boss, tell to your office-mate, whatever. The higher the authority you tell, the better. For many people this has a magic effect, because we tend to value our commitments, however painful it sometimes is to stand up to them.

But again, different techniques work for different people.


How to tell my supervisor I won't use the data that a colleague prepared?

You have come across an important lesson in research: if the person or organization providing your data is not responsible somehow for that data being correct, it won't be. Collecting and preprocessing new data is an iterative process with lots of restarts as you discover that common techniques need to be adapted to the particular dataset. If someone just hands you data they didn't have to test or validate anywhere, what you get is their first failed result. If they touch the data to do anything to it at all, they almost certainly did so incorrectly; if there is a sign, they probably created sign errors; if they did any sorting, they probably did not sort the labels and values consistently, etc.

As for how to proceed, there's another unfortunate lesson here for anyone in a mentored research position: you should generally do whatever your supervisor wants. I don't mean behave unethically if they push you to. But to change your focus to doing the best with what you have rather than letting the perfect be the enemy of the "at-least-you-did-something". Honestly your supervisor probably has a better grasp of the big picture. I.e. getting a result out to show the funding agency you were productive, getting a notch on your CV, and such outcomes, are the critical ones. While a wonderful research result that drives the science world vertically is probably out of reach already. You can however adjust how you present the data in your paper, e.g., focus on the methods not the results, or put some mixed validation results and note not all of them worked properly, caution that your data may be flawed as one possible cause, and so forth.


Is it possible for MPP students to apply for an econ PhD position?

As you might guess, it is more common for a MPP student to apply to a Public Policy PhD vs a Econ PhD. However, you may be a candidate for the Econ PhD if you work the opportunities at Harris.

Like other PhD programs, Econ programs are looking for students who will be successful Economics researchers. You should try to get research experience at Harris and take the most quantitative classes possible. You may also need to take some advanced Math or Econ courses.

The best way to prepare is to talk to faculty at Harris. You will especially want to discuss the situation with faculty who have PhDs in Economics.


What kind of index of papers is behind the search functionality of web applications and services related to the scientific literature?

There are various APIs that other services can use to search assorted indices from other sites

For example, according to the about page of ShortScience.org:

  The search can access all papers in the DOI, arχiv, dblp, and Bibsonomy databases

Some of those (e.g. DBLP) only host bibliographic data; others (e.g. arXiv) host the full text of articles or preprints. Some allow access to their data by API, others make their complete database available for download.

SciRate uses arXiv. Brevy does not seem to have an index; it's just a wiki, and the search function just searches user-submitted content.


A minor gives a grad student the option of diversifying his/her learning experience. Much research is interdisciplinary (like stats and CS), so taking a few classes in another department can be very beneficial. It also gives a grad student an excuse to take courses in something that isn't directly related to their research. (Minoring in a foreign language or business can be generally useful, for example.) In my own experience, most grads minor in something closely related to their research.

As far as I know, very few people look at a graduate student's minor. The biggest reason I can see for having a minor outside one's home department is to diversify one's educational background.

I looked around to see what universities said about this. Georgia Tech states that "The purpose of the minor is to encourage a wider interest on the part of the student and to provide a broader basis for the evaluation of the student's capabilities." (source) Stanford requires a minor for its Education grads (source).


In applications for academic jobs that ask for a "copy of transcript", is a "copy of transcript" an unofficial or official copy?

To know for sure, the easiest thing is to email the application contact person for a given job and ask.

My impression is that in many cases, the committee reviewing the transcripts does not really care whether they are official or unofficial, photocopied or not, whatever.  All contain the same information.  If you reach a later stage of the application process, they may require an official transcript to satisfy bureaucratic requirements.

As W88's answer says, every printed version of your transcript is "a copy of your transcript".  "A copy of your transcript" doesn't necessarily mean a photocopy, it just means "a piece of paper with your transcript printed on it".  If you receive a sealed transcript from your school, that is "a copy of your transcript" and you can send it in as-is.


Could I work as a Professor in Europe if I only speak English?

You can certainly do with just English in most countries.
This is true even for countries like Spain or Italy where English is not that widespread.
Personally, I've worked on a few Spanish universities and some of my colleagues didn't know any Spanish at all when they first arrived.


Is it proper to ask an editor for clarification

There is certainly no problem contacting an editor to enquire about a manuscript and review responses. It is difficult to assess the issue in your particular case but I do agree that adding new data can be a significant endeavour indeed. Shorting the paper may be a relevant point in any case but I do not see, in general how, shortening a paper would improve any lack of data although it may be obvious in the individual case.

So, if you feel the advise you have received is difficult to follow or is unclear (and that seems to be the primary point), then asking for a clarification is in place. You can be constructive and also suggest some plan of action for the parts you see more clearly and then focus on the ambiguous parts in your request to the editor.


Is there a valid way to put up a paper on arXiv or GitHub and make it private just before a conference?

would uploading the paper to GitHub in a private repository serve as proof if I ever need to prove that I came up with the idea first, if I've been scooped?

You can prove you came up with the idea first, but you can still be scooped, since credit will be given to the first public work.


US graduate school: expected proficiency and competency in the area of specialization at the beginning of the program

This will vary widely from program to program (so much so that this question is borderline "off topic" in this forum), so your best bet would be to discuss this with members of the department where you are thinking of applying (even/especially students). Still, some thoughts...

I feel that I may lack some of the more general knowledge that would normally be expected from a computer science graduate

My biggest concern is your skills in analytical math (i.e., writing proofs). If you are starting from zero and expected to take difficult classes in theoretical computer science, this could be difficult. If your gaps are elsewhere (or such courses are not required by your program), it may be easier to fill these gaps through self-study.

Is it socially acceptable to be spending a significant amount of time during the first 1-2 years of the Ph.D. doing courses and, generally, exploring the subject widely?

In my experience, these classes are very difficult, so it is socially acceptable to spend every waking moment trying desperately to pass. Research is for later years. Of course, this will vary school to school.

Should I make it reasonably apparent in my applications (in the personal statement) that "I am interested in studying such and such subjects in-depth and I am pleased that the department XYZ provides a unique opportunity to do so".

Well, your application to a CS PhD program makes it reasonably apparent that you want to study the subjects in detail, and your application to department XYZ makes it clear that you approve of XYZ's program. So, I'm not sure what this sentence buys you. It's also unclear what you find to be "unique" (i.e., one-of-a-kind) about this particular program; offering courses in CS does not make a CS department unique.

The reasoning behind it is that I do not wish to be perceived more competent than I am in the broad area of computer science.

I didn't get this at all from your quote. If this is what you want to communicate, I would phrase it as: "I do not wish to be perceived more competent than I am in the broad area of computer science."
Snarking about the language aside, I would suggest that you omit this from your application. Attempting to give a balanced picture of your strengths and weaknesses is perhaps a good idea, but recall that your goal during the application is to sell the program on you. If you yourself have doubts about your ability to be successful in the program, it is better to resolve these outside of the application process (i.e., either before applying, or after being admitted).

I am interested in what are the general expectations from the Ph.D. students with regard to the ratio of the time spent doing coursework/teaching/research

Again, this will vary from program to program, but as a general guideline, I would say 80% courses, 20% teaching, 0% research for the first year, leading to 100% research by the end.


How should I deal with critical comment that may affect on my research path?

"Insulated" is a strange word to use there, but that reads for all the world like "This was a one-off project for me I don't really work on anymore".

Many academics end up having those. It doesn't mean anything about your research, and definitely isn't "shocking".

To respond to your edit, one-off or isolated projects aren't inherently better or worse science than any other project, so there's no reason a top tier journal wouldn't publish someone's side study. Indeed one of my best publications is from a one-off project.


Publishing a high-quality indexed book retaining copyright

One outside possibility is self publishing, though (a) it is a lot of work and (b) unless you are well connected to potential readers it will have little impact. There will be no marketing effort other than what you do, though there is little such for a lot of publishers in any case. Amazon, for example, has a subsidiary that helps with this, as do some other sellers.

Some publishers will let you keep copyright (perhaps jointly) but normally only for the superstars in the field with a long publishing history. At a minimum you would need to give them a license that satisfies them. Probably an exclusive license for some things. They want to cover their risk, as is natural if unsatisfying for authors.

But many more publishers, taking your copyrights, will give you back a license to your work that, if carefully worked out, will let you do pretty much what you want other than take it to another publisher. That may be your best bet. Think hard about what you might want to do in the future and get those things enshrined in a license.

But some of what you want is normal. New editions are actually expected for some work (textbooks especially). And cover art and such reflects on the publisher as well as the authors so may not be a big problem.

And while you say you will produce LaTex or such, you really want a copy editor to go over your book. That is one of the hardest things to arrange in self publishing. You need at least some independent readers of the book to give you feedback. Publishers normally pass this task to seasoned reviewers even before copy editors get a look.


Scooped and left alone by PhD advisors. What are my options?

Non-responsive/bad advisors seem to be the rule rather than the exception in acadamia.

Switching programs will probably only result in switching to other bad advisors and cost you enormous amounts of time for little effect on the results. Dropping out because a handful of people aren't as helpful as they once were would be foolish as well.

Finish your PhD and move on.

Lastly: Keep working with mental health professionals. You said you're depressed and seeking treatment. I'm glad you're getting that medical condition checked out. Sometimes that treatment can take time to take effect and get some relief from it. You might also want to interview some other professionals to see if they might have a better diagnosis or treatment plan for you.


How much do soft skills matter for admission decision?

I don't really know for PhD, but for Postdocs, from what I've seen and heard, these skills count a lot, especially when the recruitment process is well structured, as I experienced it in the UK and in Germany. Basically, the recruitment process consists of three steps:

Sending the CV, application, reference letters, etc. At this point, soft-skill do not really count, although knowing how to write a good cover letter can help.
Seminar/Public talk: the applicant is invited to give a presentation of his research work to a public audience (usually including the committee, and the staff from the department).
Interview: the recruitment committee interviews the applicant.

In the steps 2 and 3, the soft-skills are very important. Basically, all applicants reaching step 2 have good credentials, so it's somehow already established that they can write papers and solve research problems, so the quality of the talk and the attitude during the interview are crucial.


Justification that 'good exposition' is uniquely defined

This is a false dilemma. Good exposition is not uniquely defined.
Yet, if a referee claims they don't understand what you write, chances are that they are right. Add some clarifications. This doesn't mean necessarily rewriting everything with the referee's favorite approach: maybe just a remark tailored to people with their background. ("If you're used to seeing concept X defined in this other way, note that this is equivalent because...") If there is a wrong approach that you wish to refute, do it, in the paper or in the response letter.

Good exposition doesn't mean the referee's preferred viewpoint, but it doesn't mean your preferred viewpoint either.


Writing letters of recommendation for more than one student to the same department

Since each individual student is asking for a letter of recommendation it would be appropriate to approach each letter as an individual task and not implicitly cross-reference between the letters by making comparisons. Direct comparisons between the specific students should not be made. It is after all the person or committee admitting the students to the program that will make decisions who may fit the best and their criteria may not be the same as yours. It is, however, reasonable to make implicit comparisons such as ranking each in relative terms to, say, all students you have encountered or some other frame of reference. This way each student is compared to a group and not each other. This is what one commonly does anyway.

I can imagine that you may get a request for more details by the person/committee if there is a difficulty in separating students. You could if you are willing, add a comment to the fact that you are willing to answer any questions that may arise during the process regarding the student in question.


Is it inappropriate to email a senior academic with whom I have no pre-existing relationship, asking to check/inform my work?

Inappropriate or not, you aren't likely to get a response. Professors tend to receive a lot of email. If they don't have a compelling reason to respond, they might not.

You're asking them to put time and thought into a response to a stranger. The best course would be to talk in person to a professor whose class you've taken. Ask if they would mind looking over your work, and get feedback in person.


Is copying standard definitions from e.g. ICD without quotes considered verbatim plagiarism

Definitions straddle a line between things that clearly require attribution and things that are "common knowledge" and do not require attribution.  For example, if I write on my own that:

  influenza is a viral disease of the respiratory system that causes fever, aches, and other symptoms

then I need not attribute any source, because this is common knowledge.  On the other hand, if I copy verbatim the Merriam-Webster definition:

  a common illness that is caused by a virus and that causes fever, weakness, severe aches and pains, and breathing problems

then even though it's almost identical, I need to attribute the source because they aren't my own words.  For such simple and widely accepted information, that attribution might not need a formal reference or even quotes, e.g.,

  The Merriam-Webster dictionary defines influenza as a common illness that is caused by a virus and that causes fever, weakness, severe aches and pains, and breathing problems.

Quotes would be better, but the attribution is still clear, so it's a minor problem at worst.

Now, how does this apply to the situations that you have described?

First and foremost, if the definitions are being taken from standard references, the link to standard references is valuable for students to know, so from a pedagogical point of view they should be included even if it weren't strictly necessary.
If a large number of definitions are being presented specifically as the professor's own work, when they are not, then it is clearly a case of plagiarism (albeit a particularly banal and pointless one).
If, on the other hand, they are being presented more generally as "information about the subject", then it is more of a grey area.  They should be attributed, but informal material like course notes is often treated quite sloppily in practice, and it is likely to be perceived as a shortcoming to be corrected rather than a serious issue of plagiarism.


Invitation to anti-plagiarism service Turnitin

by Turnitin xxx Administrator.

Ask xxx if they created an account for you. If they have no idea what you are talking about, or xxx is not in your organisation, mark as spam and move on. That Turnitin is a paid service matters little, as many universities pay for it on organisational level.


Will PhD rejection return to haunt later?

What was written down on an application years ago will generally not come back to haunt a faculty candidate later. However, actions that might have been taken on a faculty visit—or in later interactions with faculty members at a department—could have repercussions.

If the reputation that someone builds is being a person who "doesn't play well with others," that will be a tag that follows that individual for the rest of the career. It can make life a lot more difficult, because that person will have to work a lot harder and be a lot more successful than someone who is able to interact with current and potential future departmental colleagues in a civil and cordial manner.

But what's written in an application? Unless it's fraudulent, it shouldn't have a bearing on future ability to get hired somewhere.


Bachelor thesis without a research question

I can't be sure, but from your description it seems like this thesis does not include original research, and that is what troubles you. Instead of original research, it sounds like your friend may have produced a survey or review of a particular area, which informs the reader about the body of work in that area. (See this answer to Difference between research paper and scientific paper).

A bachelors thesis may or may not be expected to include original research. Your friend should ask his or her thesis advisor to clarify the expectations in their department.


Acknowledgement of submission to the Annals of Mathematics

A week is not so different from three days, especially if that week includes the July 4th holiday in the U.S.  If several weeks pass and you still have been given no indication that the paper was received, then it would be worth asking if they got it, but in the meantime I don't think you need to worry.


Unequal pay between grad students, enforcing a more egalitarian policy

The more competitive and prestigious the school, the easier it is to be egalitarian, because you can always get students to enroll there. When you have trouble attracting students, incentives that may lead to an unequal playing field may be needed to get better students.

For instance, when I was applying, there was about a 50% spread between my lowest and highest offers. However, some of this was handled not by awarding an RA on top of an external fellowship but a “merit prize” of several thousand dollars as a reward for bringing in the fellowship. That might be a way to offer something substantial for people who have their own money without making things too far out of balance.


Two applications to different departments at same uni. But: One professor is affiliated with both departments

If you've submitted two different applications and they each specify what you're interested in working on, this shouldn't be an issue.


How badly does failing a core class and retaking it hurt your chances at grad school programs?

At any stage in your career, people who will evaluate whether to give you an opportunity will (or at least should) be looking at multiple aspects of your CV. For each "weak" aspect there should be a "strong" aspect that offsets it. Provided this is true, you should become eligible for consideration. After that, it is often a matter of luck and the competitive nature of the opportunity.
Having said, that, there are places and systems which I personally know of that will automatically reject applications that have a single blemish. These places and systems are making a mistake (in my opinion). In any case, perhaps you would not want to be in a place that does not believe in giving people a second chance.
In summary, I think there are a number of good places which would give you the opportunity if you can counter this particular failure by something---which could even be a good grade in the same course on your second attempt.


What to include in Abbreviations and symbols?

My supervisor asked me to make an Abbreviations and Symbols part to my thesis

This is a reasonable request: when there are many symbols, a list can be definitely helpful to the reader.

  Now, obviously I won't put every variable (and abbreviation) into this list.

You won't put every variable, but you surely want to put any abbreviation.

  What should the criteria be for putting an entry to the list?

I suggest you to put: special quantities which are defined in your work; special operators and functions; mathematical spaces; and all the abbreviations, even those you think are well known in your field.

  I also have tried to explain the variables where I'm using them, is this now redundant when done in conjunction with the list?

No, it's not redundant because a list of symbols does not typically give the complete definition, but just a short one. Actually, it would be also useful to list the page number where a certain symbol has been defined for the first time.

  Additionally, should the symbols and abbreviations appear in the list
  in alphabetical or appearance order?

If you can define an alphabetical order, go for it. Unfortunately, this is not always possible (in a universally recognized way) with symbols. In any case, I'd separate symbols and abbreviations.


Multiple paper submission deadline extension (three times in few days)

Typically, I have seen two cases of deadline extension:

Some venues have a "customary" extension, which always happens, and thus all regulars know that the de facto deadline is slightly later than the initially stated deadline.
The other main case of extension is when a venue wants a few more submissions and is hoping an extension can drum them up.

Multiple deadline extensions sounds to me like desperation, and you might well be looking at an event that will either be cancelled or accept a lot of trash.  Unfortunately, there's not much you can do about it right other than withdraw your paper if you are nervous, which might not help you much either.


Changing fields after PhD, master or post-doc?

I don't expect this to be the best answer (I am not from these fields), however what I'd do in your place would be researching websites of environmental science departments and research groups in order to find some topics/projects for which your qualification up to now makes some sense or adds some relevant competence. There even may be postdoc positions, however maybe you can ask for some project or internship work. Maybe also there are some biologically oriented temporary teaching jobs in such departments, which could enable you to get into the community.
In the meantime try to read and learn, and try to get into contact with people. I can't guarantee it of course but sometimes opportunities open up when looking for them in a determined way. And surely try to make use of your already achieved qualifications, try to connect things somehow.


Dealing with someone who asks many questions during presentations

You are not obligated to accept somebody disrupting your talks, particularly when the questions are off-topic and when much of the audience appears to be disapproving.  The basic solution is to act as a moderator for your own talk.

For questions during your talk that you find disruptive, a simple solution is simply to say, in a calm and gentle voice, something like:

  I'm going to defer that question for now.  We can come back to it at the end.

During a question period, if a person is dominating the discussion, you can say something like:

  I think some other people may want to ask questions as well, so I'm going to ask you to hold your questions for a bit while we hear from others.

The key here is to be firm, gentle, and impartial.  Your voice should make it clear that it's not about this particular questioner or about you being defensive, just about keeping on topic.

After you say something like this, most people will leave the question and let you come back to it later.  If the questioner does not, simply repeat yourself, remaining as calm and unruffled as you can, and then move on.  If the person continues to be disruptive after that point, it will be clear that they are making an unusually large problem, and others are likely to help intervene.


When and why did conferences pick up the habit of giving out conference bags to attendees?

For the why part: One reason is to make registration at the conference as smooth as possible. Imagine the first morning of a conference and all the attendees at the registration desk lining up and for each and every participant the guy at the desk hands over the program, the book of abstracts, the badge, the ticket for the conference dinner, the ticket for the prebooked tour (if there is any), the receipt of attendance, the receipt of payment, the complimentary notebook and pen and, of course, the stuff from sponsors. Takes much longer than pre-packed bags. (And even with all things pre-packed, there are always queues during the rush hour.

As for the when part, I have no idea. But if you have ever sat at  a conference desk you'll agree that it must have been no later than the first time one guy organized a conference with more than 100 people for the second time.


Is there a template for academic paper changes report?

At jakebeal's suggestion, I'm converting my comment from Jan. 12 to an answer:

Some people just use the referee's report and insert the information about what they did with each comment. So a minor comment (about fixing a typo for example) might be followed by just "Done." A comment about adding some more information might be followed by "Done; see page x, lines y to z." A comment that one didn't comply with might be followed by a careful explanation of the reasons for not complying. On the other hand, I've sometimes just written "I've complied with all the referee's comments except x. The reason for the exception is that ...."


Portal for sharing a research manuscript with supervisors/advisors

If your use case is really only about sharing a document, then it does not get much easier than Dropbox. If you are actually collaborating (more than one person is writing stuff at the same time), I would not recommend Dropbox, as it is much to easy to overwrite changes of other people. For such collaborations, I would recommend a collaborative writing platform (Overleaf if you use Latex, Windows Live if you use Microsoft Word), or a private version control repository such as Github if you feel confident using Git.


Making corrections to PhD application after submitting it

This is not a material error. I wouldn't worry about it. We get much more egregious errors such as uploading the wrong statement (such as for another school) or misspelling the name of the core faculty member you wanted to work with, etc.

You'd think those types of mistakes would be killer, but they really aren't. We realize students are under stress and that application management systems are cumbersome. We're all human in the end.

What's most important is the qualifications of the applicant as a whole.


You would typically mention this type of help in the acknowledgements section, if at all. It is well understood that developing tooling requires manpower and that there are others on the team aside from the researchers, and it is up to the authors how to acknowledge that assistance. For what its worth, if their contribution was so significant to warrant authorship, that should be a discussion among the research team.

You mention "cite" in your question; this sort of mention would not go in your references, in case that was your thought.


how to share to mention/publish large datasets?

Take a look at http://thedata.org/, which provides free, permanent hosting of data allowing you to cite a specific iteration of a dataset in your printed work.


When is it acceptable to write a bad letter of recommendation?

Never write a bad recommendation letter. If you can't say anything nice, say nothing at all (and tell the student you can't write the letter).

As for warning other. Leaving aside the law for a moment, the only time I can see it being appropriate to warn others about a student is if you believed them to be dangerous. Examples of this might be a history of sexual harassment/assault, bullying or other abusive behaviour.


Which section of a research paper is best to state that results also depend on equipment used?

I think it depends. In my opinion, it makes most sense to address equipment limitations (e.g. instrument resolution, reachable temperatures, etc.) in the method(ology) section, as was suggested by astronat. Limitations on your results, however, are more naturally addressed in the discussion (e.g. since we are resolution limited, we cannot definitively rule out alternative interpretations X, or Y, but our results are consistent with prevailing theory Z). If it is a particularly important qualifier that's central to your work, it can make sense to repeat it in the conclusion and possibly elsewhere.


Can a former employer provide a useful recommendation for graduate admission to a science program?

The important thing to keep in mind is that the goal isn't this specific letter, but composing the best possible application for, in this case, Stanford. So the primary question is: would a letter from your supervisor at Apple improve your set of recommendation letters? If you already have 6 letters from very qualified people that know your work well and can comment on your ability to perform at the Stanford program, a letter from your former boss might not add much. However if you only have 3 people at the moment who can really say something about you, adding your former boss couldn't really hurt. A few things in mind are:

How long, how long ago and how closely did you work with your former boss compared to the other people writing you letter of recommendation?
Was there a (strict) selection process to get into Apple? If so, the selection people at Stanford might be interested why the selection people at Apple chose you out of all possible candidates.
Did you do any research at Apple, or answer any research questions? Even when not doing theoretical physics, your attitude towards discovery and finding new knowledge might be relevant.


Why do some fellowships require "leadership experience"?

Precisely because we cooperate a lot, we need good leadership. A good leader is someone who can bring the best of everyone in the group. For example, encouraging everyone to voice their ideas, assessing which ones have actual value, but without making the group pursue all the wild geese. A good leader should also be able to recognise the strong points in the members of the team and assign tasks accordingly.

I accept that everyone here should be motivated, but it is important for the group to keep it up. No matter how eager I am, if my professor were to start giving me contradictory orders, unreasonable workloads, or dismissing my ideas without explaining why, I can tell you, I would not remain that motivated after four years. After all, I can be motivated to work "in the grand scheme of sciency things", but not necessarily in the particular group I am in.


What is the expected level of commitment for postdoc positions?

Every position is different. Every PI is different. Every field is different. In math you can probably set your schedule to suit yourself. In some lab sciences with demanding PIs it isn't so easy. But a few points to consider:
First it is fair to explore your working conditions before you start, though it may be a bit risky. If you can manage a visit, you may be able to get a sense of it from other post docs at the institution. But you can also just ask for expectations. You aren't required to damage your health, but some PIs don't know where to draw the line.
Next, you may find that the burnout you experienced and your need for a reduced schedule doesn't continue into the future and it might just go away. Lots of people have such a period, some in the middle of their studies and some shortly after. But a change of scenery, literally, might have a positive effect.
Don't worry about the future too much. Your situation, health, and attitudes may change. But a positive post doc experience could go a long way to helping. Many professors work long hours, but it is because they truly love to do the work. It ceases to be a job and becomes an avocation. What could be better than to be paid to think?
If you take time off, make sure you can explain it as something other than recovery. Have a flexible plan for your return if you decide to do that, and find something to do that keeps you from getting rusty. If you come back, you want to seem enthusiastic about it to anyone who reviews your CV and SoP.


What is the meaning of the various postdoctoral job descriptions in the US?

As Jon Custer mentioned in the comments, there are no standards whatsoever, however generally speaking:

"Visiting" is a short-term position (I've never seen a post-doc with this title), probably even shorter than a usual postdoc, probably 9 or 12 months.

A "fellow" is usually a prestigious assignment, it may be a  university, college, or departmental soft-money position. For example, my university has "President's Fellows" although I'm not sure if they are funded specially or if that's just an award. However, nothing stops anyone from calling anything a "fellow."

An "associate" professor outranks an "assistant." However, I do not think there is any meaningful difference between "postdoctoral research assistants" and "postdoctoral research associates." One doesn't outrank the other. Probably, people just try to avoid using "research assistant," since that somewhat connotes an junior position.


Physics masters and PhD degrees in England/UK

I'm not sure how much this question strongly depends on Physics/UK, so let me detail how it is done for Computer Science in France (as far as I know, the French and British systems are quite close on this, and hard sciences tend to have a common academic process).

The PhD thesis is indeed a novel contribution to the state of the art, and demonstrates the ability of the candidate to be an autonomous full-time researcher. In many fields, it's usually required to have several publications before submitting the PhD thesis.

On the other hand, the Master thesis corresponds to an research internship done in a lab (usually the one in which the candidate will pursue her PhD). The role of the Master thesis is two-fold:

First, it demonstrates that the candidate has acquired some techniques taught during the Master, and that she was able to use them to solve a particular research problem.
Second, it's a first step for the candidate into the world of research. Often, the Master thesis constitutes the first chapter of the thesis.

(note that I'm talking here only about research-focused Masters, as there are also industry focused Masters, for which the thesis has a different role).

As such, the topic of the thesis is usually a "simple" research problem, defined by the advisor based on the interests of the student. By simple, I mean that even though the exact solution might not be known, the advisor is usually confident that the solution can be found in a reasonable amount of time.

Note that in France, the time constraint is quite strong, and the thesis must be written in 6 months maximum, otherwise the Master is not validated at all, and therefore the topic of the thesis is usually not an open and complex research problem.