What to do when you have two manuscripts under review where one cites the other, but the citing paper gets accepted before the cited paper?

If I understand correctly, this is your situation:

Paper 1 was submitted for review 11 months ago
Paper 2 was submitted for review six months later.
Paper 2 was accepted for publication. Paper 1 is still under review.

Presumably, Paper 2 cites Paper 1 as being "submitted". The present version of Paper 1  does not cite Paper 2 because Paper 2 was not in existence when Paper 1 was submitted.

Are these correct? If so, here are some thoughts about your questions:

Should you continue to cite Paper 1 in Paper 2?

I would. The fact that Paper 1 is still under review is out of your control. In fact, its final disposition is also up in the air. Nevertheless, Paper 2 uses information derived from Paper 1, hence the need to cite it. That Paper 2 was accepted with the citation to Paper 1 is important evidence that the reviewers and the editors thought that it was appropriate, despite the "submitted" tag.

Should you remove the citation of Paper 1 in Paper 2?

I wouldn't do this, unless there was a material change in your manuscript. If the parts of Paper 2 that depend on Paper 1 were lost in revision, then fine. However, it is not a good idea to eliminate references simply because of publication status.

Should you cite Paper 2 in Paper 1?

You should only cite papers that support your statements. Frivolously citing one paper of yours just because it was published is a rather trivial reason. However, if you genuinely feel that Paper 2 has substantial contributions to Paper 1, then this should be fine. You would do this in the revision stage. Be aware, though, that alert editorial staff may review this change with skepticism.

If you retain the citation of Paper 1 in Paper 2 and Paper 1 gets rejected, then what happens?

Generally, there's nothing you can do about this. Journals still operate as if the manuscripts were static entities. That is to say, once a final version has been approved at the galley stage, no changes can be made. Paper 1 will always be cited in Paper 2 as being "submitted" in perpetuity. There are some publishing models now that account for this fluidity in publication status, although there are not widespread, and rather experimental. Say, for example, that you cited the work of Doorman (2014) and your work was published in 2015. In 2016, Doorman was found to have committed research misconduct and his 2014 publication was retracted because all the data were fabricated. Well, your 2015 publication would still cite Doorman 2014. There are no easy solutions to this issue as yet.

Good luck.


My PI publicly humiliated my colleague. I want to report the incident but don't have a recording. What should I do?

We do not know your local laws and culture, so beware that advice here may be inaccurate.

He makes micro-bullying or threatening statements occasionally, but this public humiliation seemed very serious and crossed a red line.

It is the pattern of behavior, not the specific example you gave, that is what you need to report.
A recording is not necessary to make a complaint.
Reports are usually made to a union, ombudsperson, office of civil rights, or diversity office.  It depends on local customs.  Check your university's policies, or possibly local laws.
Usually being rude, offensive, inappropriate, wrong, or stupid is not against the rules, but threats, bullying, and harassment are.  Do not expect all bad behavior to result in punishment.
Do expect to get the same amount of leave that the university policy
says you should get.

making judgemental statements

Keep in mind that judging people is part of the PIs job.  But it should be done in an appropriate manner.


What features should be included in your actual accomplishments and skills to be accepted in a top university like MIT

Although your question doesn't specify it, I assume you're looking for admission to a top-ranked PhD program in electrical engineering.  I'm one step away, in a top-ranked program in computer science, so take my answer with a grain of salt.

  Two ISI papers Including one 'Power systems, IEEE Transactions on' and 'Electric Power Components and Systems'.

Since you already have a master's degree, having a couple of publications is a minimum requirement for admission to a top PhD program.  Where the papers were published is of secondary importance (although your emphasis of "ISI" over "IEEE" is a little worrying).  What really matters are the actual results in the papers.  Are they good results?  Are they well-known to people in your field?  Are your papers likely to be highly cited?

  IELTS and GRE meet the minimum requirements.

"Meet the minimum requirements" is not what top programs are looking for, on any axis.  Fortunately, test scores don't really matter all that much (except, at public universities like mine, the spoken English test).

  Having a very good recommendation letter as my supervisor professor is one of the top guy (top 50) in his field.

The fact that a top guy in your field wrote the letter matters far less than what the letter actually says about you.  A weak letter will kill your chances, especially if it's written by someone well known in your field.

  Two years teaching experience in a small university as a lecturer.

Hmm.  Okay.  can't hurt.

  If not, which points should be added or improved generally?

You really haven't given enough detail to point out anything that needs to be improved.  What matters most is the quality of your actual research contributions, and that's just not deducible from the information you've given.

  3) How much is it matter how old are you for applying for phd at these places?

Not at all.  Age discrimination is illegal in the US.

  4) What does a namely CV should contain when applying to a top university as opposed to one that is an average university (like Calgary Canada).

I assume you mean "What features differentiate the CV of someone admitted to a top school versus someone admitted to an average school?"  (No matter where you apply, your CV should accurately and honestly reflect your accomplishments.  Don't add bloat.  We can tell.)

You may be able to gain admission to a lower-ranked school on the basis of grades and test scores.  But the competition for admission to the very top ranked schools is absolutely fierce.  (My department gets 2000 graduate applicants per year, from which we admit about 100 PhD students and about 50 MS students.)  If you want to be admitted, you really have to manifest like a successful PhD student already.  You don't just want papers.  You need  high-quality, high-visibility, well-written results, ideally which would not have been possible without your contributions.  You need the beginnings of a well-reasoned and compelling research vision.  You need to display intellectual strength, depth, maturity, and taste.  Well-known leaders in your field must sing your praises in technical, personal, and credible detail.

If you have all that, your CV will take care of itself.


Why do some universities not allow dissertations to be publicly available?

As the one whose comment triggered this question, I figure I ought to answer: one of the foundational principles of science is that it should be freely and publicly available.

At the same time, there are a lot of human interests that push in the opposite direction.  Some examples:

A nation may want to restrict high-technology in order to promote its own interests.  For historical examples, consider the British empire's secrecy around timekeeping for navigation, or Bavarian secrecy on methods for making high quality optical glass.
Information may be considered dangerous to release to the general public, such as regarding atomic weapons or the DNA sequences of deadly pathogens.
Commercial companies invest in technology in order to gain advantage over their competitors.
A scientist may want to avoid publishing patentable research until after the patent is filed.

A lot of science that is done is thus never openly published, or openly published only long after it has been completed.  The question then is, how should universities relate to this, particularly regarding dissertations?

To the best of my knowledge, in all of the high-ranked U.S. universities, a Ph.D. dissertation is required to be entirely public, as a matter of scientific principle and integrity.  This wasn't always the case, particularly during the convergence of scientific research and military funding around World War II.  As the country became more uncomfortable with that association, however, the elite universities began to remove classified research from their campuses and require that theses be publishable.  In many cases, classified research still goes on in association, but through a separate entity, such as Lincoln Lab for MIT, SRI for Stanford, and LBNL for Berkeley.  Likewise, sensitivities have developed around commercial research.

The general principle that is followed then, at least for elite U.S. universities, is that the research leading to a dissertation may involve unpublished or restricted information.  The dissertation, however, must be public and substantial enough to stand on its own without depending on other non-public research that may have been done in association.


Supervisor demanding impossible workload at the very end of my PhD. Considering change of supervisor

I agree with user Maarten Buis that this is probably too personal to really give good advice. But let me suggest a few things.

You should probably optimize everything now for quick completion of your degree under a situation over which you have little control.

While you can ask your supervisor for more funding, he has already said no. What has changed to make him say yes?

While you can complain to the institute that would most likely result in animosity from your advisor, not helping your path to completion.

While you can ask for a different supervisor, that would set you back, possibly for years and not necessarily leaving you in a better situation, depending on the local culture generally.

You have been given a steep hill to climb - two papers, etc. Start climbing. Do what you can. That is, in fact, all you can do anyway, but give it a good effort. Everything you do for that will get you closer to completion and will help build a good record of accomplishment for a future position.

I would, myself, try to work on the two papers in tandem. Getting a rough outline of both as quickly as possible and then filling in the details as it becomes possible. I assume that the work behind the dissertation contributes to the papers and is done or nearly so. That might make it possible to work on all three items simultaneously. Then, as the deadlines approach you will have made progress and if you need additional time for completion you have an argument for it and additional funding.

No, it isn't right or fair. But a short term push toward a better future might be better than just fighting it when you have not much chance of winning the fight.


Is it OK to send email to journal asking for extension for a revision?

Ask for an extension. This is quite common in case more extensive changes/analyses need to be done.

Submitting a subpar version would waste their and their reviewers’ time, and may even end in a desk rejection for you.

When asking for an extension, shortly explain why you need more time (ideally, related to the reviews you got – show them you are working on the paper), and make a good estimate on when you will be able to resubmit. You don’t want to ask for several extensions during the same round.


What do I do with my exam tomorrow given that I supplied medical certificates

This isn't an answer, just some points you can consider and some 2 cents:

Given the short time, if I were in your shoes, I'd:

Comb through the student academic handbook about sick leave and how should the makeup examination be scheduled. Look for keywords like "... upon mutual agreement." or "... student and department will decide." etc. and quote that in a written document to urge the committee to honor the wording in student academic handbook.
Identify the chair of the grievance committee. Every department/school should have one, and inform him/her about your situation. Ask for guidance and potential on filing a grievance.
Objectively figure out what are the number of quality days available for a non-sick student to prepare for the tests, and then come up with how many quality days you have been given, minus the ones that you have spent. Ask for the exam to be rescheduled to a reasonable time that would provide a fairground to you. Down play the fact that you "want more time," emphasize on the desire "to be judged fairly." Should the number of days are actually comparable, chance is you really have no ground to delay.
Chat with the admission people and discuss the possibilities on the followings: i) retrospectively request a medical leave (this is more viable if you are on a trimester system or this is a half-credit course, missing 4 weeks might as well mean you have not taken it at all) for this semester, and retake the whole thing again. ii) Negotiate for fee reduction or fee waiving so that you don't have to pay again. iii) Also make sure the half-done course will not end up as F or even appear on your transcript.
If you think you're not being fairly judged, never take the exam. Once a grade is given it's next to impossible to revoke. Inform the school as soon as possible with your reasons (preferably sound and focusing on the lack of fairness), give them a summary of your arguments and what you have talked about with different representatives in the department.

I think, in a sad way, that you only decide to decline one day before the rescheduled date is an extremely bad move. If indeed everyone also had one week to prepare, then it is pretty much done for. When the decision was just made, you can still negotiate for 2-4 more days to collect lecture slides, notes, and meet with the lecturers. Now, it's a bit too late to do that.

In a nut shell, set your worst scenario and figure out what are the things that you cannot afford to mess up. If your first thing is GPA, then strive to make this trimester/semester not counted. The cons: you may need to retake, but given your circumstance, retaking seems a lot more viable than taking an exam. Also, don't position yourself as a victim. It's unfortunate but you're not asking for leniency or special treatment. Show them that you're very conscious about the grade situation and your determination to work through this glitch with the department, and hopefully they will reopen the case.

I wish you best of luck, and if you have time, come back to update us by revising your question.


The editor cannot find a referee to my paper after one year

As you pointed out you have several options:

Do nothing and wait for the editor to find a referee.
Withdraw and submit elsewhere.
Send the editor a list of people who might be able to review your paper.

Nobody, including the editor, can predict what will happen if you do any of these things. Doing nothing and waiting is probably the least likely to result in a good outcome quickly, because the editor's already shown they are not able to find reviewers quickly (although there's always the chance a reviewer's time frees up and they can review). Withdrawing and submitting elsewhere would mean starting over, and there's no guarantee the editor of the new journal will be able to find reviewers either. The third option is effectively a better (for you) version of the first option, but it's still not ideal, because you can't guarantee the reviewers you suggest will agree to review either. You can only tell who might be interested in your paper.
Because there's no ideal option, you will have to make your own decision. How badly do you want to publish in this journal? If the answer is "very", do #3. Otherwise consider (but not necessarily take) #2.


Register as a listener to access course materials with no intent to attend lectures

First, the usual term in the US is not "listener" but "auditor"; you are said to be "auditing" the course.

People generally don't care too much what you do or don't do when you register as an auditor, so most likely this would be fine.  But I think that, as a matter of courtesy, whenever you are considering signing up to audit a course, it is good to contact the instructor, let them know what level of involvement you have in mind, and check that this is okay with them.  In some cases there may be certain things that they ask you to do or not do.

In this case, when you ask, the instructor might just offer to share the course materials with you directly, without you having to sign up to audit the class at all.


How often do publishers sue researchers for copyright infringement for putting their articles on a personal website?

I have never heard of an individual scientist being sued for posting a few articles online (large-scale systematic activity is a different story).  So far, unlike the music and movie industries, scientific publishers appear to have simply not found it worth the cost in resources and community relations to do so (though they've been quite comfortable suing organizations on occasion).

If a scientist decided to resist a takedown order, however, it seems possible that a journal might feel forced to make an example of them.


List unpublished masters thesis in preprints section on CV?

This question addresses how to list a thesis on your CV, but generally is speaking about dissertations that have already been completed.  The basic conclusion is to list theses in their own separate section.

For your situation, with a nearly complete dissertation, it would be appropriate to list it the same way, but for its date list the future date when it is anticipated to be finalized.  This would look something like:

  Master's Dissertation: thesis title, September 2016 (anticipated).


How to Ask via email for supervision of professor for Japan Graduate program admission

It needs to be much snappier. Consider something like this:

Dear Professor Name,
Do you have any positions available for graduate students in the Fall? I have a lot of experience with CAD, control systems, and signal processing (i.e., my autonomous underwater robot won the 2018 Singapore competition), and have published a few well-received papers [1,2]. This seems well aligned with your past work on similar topics [3,4], so I would be pleased to discuss opportunities working for you (or your colleagues) as a PhD student. Please let me know.
Name
[1] https://arxiv.org:blah.pdf
[2] etc.

where [1] and [2] are references to papers, links, codebases -- anything they can dive into to understand you more, and [3] and [4] are references to their work, so they see that you took the time to research them.
For me personally, I almost never respond to generic e-mails.
Note, I know nothing about the Japanese system; I'm only commenting on how your e-mail could be generally improved. (In particular, I'm wondering if this mail should be written in Japanese -- I know a lot of science is done in English, but if you speak Japanese, and the language of the university is Japanese, it might be better to write in Japanese or at least provide a translation).


Someone cited citations I used without citing my work and effort in finding the references

No, this is not plagiarism, unless the authors specifically used the same wording as you. Citing the same sources as another paper is not plagiarism, otherwise anyone who cites an influential paper would be guilty of plagiarism unless they also cited the hundreds of other papers who also cited that influential paper.

In your specific case, you say

  Out of the 6 examples 4 are exactly the same in my publication with 3
  of them using the same exact citations I used. Which made me believe
  with zero doubt that the one of the conference paper authors read my
  workshop paper and found those applications and citations useful and
  decided to reuse them in their publication without giving my work
  proper citation for finding those references.

This is speculation, and you can not know that this is indeed what happened. It is also quite likely that the authors did a literature review or simply knew parts of the literature, and found examples of applications that were relevant for their paper. Using the "exact same citations" is what is supposed to happen when you cite the same work.

Unless your paper is relevant and related to the work done in their paper, there is no reason for them to cite your paper, and citing work that is related to both your papers can not be considered plagiarism. At worst, you could argue that the authors should have included your paper in their related work.

Remember, people cite your papers for the work that you describe in that paper, not for the citations you give.


What is the explicit meaning of “corresponding author”?

IEEE distinguishes between contact author and corresponding author:

Contact Author: This is the person who is contacted in regards to the submission during the peer-review and production processes.
Corresponding Author: This is the person who is listed as the author to be contacted in the printed publication.

PLoS states two types of corresponding authors:

Please note that the corresponding author for the online submission process can be different from the corresponding author of your published manuscript.

Copernicus uses the terms contact author and corresponding author:

From submission to publication, the authors of a manuscript are formally represented by the registered contact author(s). After publication, the authors of a manuscript are formally represented by the corresponding author(s) specified in the published paper.

Personally, I've seen this differentiation several times. Sometimes the corresponding author is simply a role in the journal system that the submitting author/person can assign to one of the authors during the submission process. The corresponding author might also change during the process.
Conclusion:
Some publishers make a difference between the author corresponding with the journal (submitting/contact author) and the author corresponding with potential readers of the article (corresponding author). Some publishers don't. It's absolutely inhomogeneous and seems also to vary by journal not only by publisher. And it varies over time.

Side note:
And yes, these publishers are indexed in SCOPUS and Web of Science (Science Citation Index, Thomson Reuters Master Journal List).
Search for the publishers in SCOPUS (select checkbox "publisher") or the Thomson Reuters Master Journal List (TRMJL). The latter includes all journals indexed in Web of Science. Unfortunately, the search in TRMJL is only based on journals and not on publishers. Search for "plos" to see PLOS journals, "ieee" for IEEE journals and e.g. "geoscientific" to see two Copernicus journals. See also IEEE indexing agreements, Visibility of PLoS and Copernicus metrics.


Postdoc application: professor verbally committed to hire me, but now says that regulations have changed and keeps delaying the process

Is this normal in post doc recruitment?

No, this is obviously not normal. There is something going on, and your guess is as good as mine as to what that is exactly. Maybe there is indeed some sort of administrative chaos due to changing regulations. Maybe the professor hired somebody else and is trying to weasel out of his earlier commitment to you. Maybe the position just got cancelled, and the prof is trying to find funding to hire you anyway (and failing). Maybe it's something completely different. There is just no way to tell from the outside.

  How long does it take to process post doc applications?

That really depends. However, "a few months" certainly sounds like the upper bound for how long selecting a postdoc should take.

  Should I start looking for other positions?

Yes, independently of what is really going on, I would not get my hopes up that there is indeed a position for you in this department in the future. Maybe you get lucky and it works out after all, but at this point relying on this post seems to be very optimistic.


What is the process for retroactively (post completion) reviewing plagiarism on a dissertation?

The scenario of an investigation for suspected plagiarism in a PhD thesis is so rare and unusual that I'm pretty sure there is no "typical" recipe for how it would unfold. However, I'm familiar with one such case that happened some years ago at my institution, and I'll take that case as my definition of what "typically" happens.

  (1) Would such a review process be limited to the dissertation itself or would all the work of the student be reviewed?

It might, if the student's other work was available to be inspected (which I think is doubtful since the student will have already graduated), and if there was some concrete basis for suspecting plagiarism in that work, and (which IMO is the least likely condition to be satisfied) if the people involved in the investiation had enough time on their hands and were energetic enough to pursue such secondary investigation leads.

  (2) Would such a review involve questioning the academic advisor/research supervisor? What about the thesis committee?

This would be highly embarrassing to the people you are mentioning, so I expect they would only be questioned if there was a strong basis for believing that the information they could provide would materially affect the outcome of the investigation. Thus, the advisor might be questioned to get some background information on what took place when the student was writing the dissertation; the thesis committee members, almost certainly not.

  (2a) On a sidenote: Would the thesis committee for a doctorate degree be obligated to check the research in detail or are they allowed to rely on the research supervisor for that task?

See the comment by BrianDHall. The thesis committee never "checks the research in detail", and in all except a rare handful of cases, neither does the research supervisor.

  (3) Would such a review look at the theses of other PhD graduates who were under the same supervisor?

This question suggests to me that you have watched one too many episodes of late-night TV crime shows. Unlike such shows, universities aren't populated by dogged investigators (with checkered pasts and colorful personalities, usually divorced and heavy drinkers) who work day and night, dedicating their lives to exposing all instances of wrongdoing and then bringing the perpetrators to justice.

In other words, the answer is no.

  (4) What happens if such a review finds a doctorate is academically or ethically flawed? What, if any, penalties can be invoked against the student?

Given that the student has already graduated and is no longer a member of the campus community, the only punishment the university can actually impose is to revoke the degree. The only real question to debate would be whether the student would be allowed to come back and rewrite the dissertation if they wished to. Moreover, given the severity of the offense, and the risk posed to the university's reputation and credibility by PhD degrees it grants that are based on plagiarism, revoking the degree seems like a completely appopriate and logical response.

  (5) If the outcome is to void the degree would the student be offered a chance to comment/defend or would the degree be revoked without warning?

Undoubtedly the student would be given a chance to defend themselves against such an accusation before any action such as revoking the degree is taken. They would likely be entitled to ask for the case to be reviewed by a committee, and to have a panel convened where they could present evidence in their defense. Given the high stakes involved, if they wished to contest the accusation they would likely hire an attorney.

  (6) How long would such a review typically take to complete?

Probably a few months, but I assume it can vary a lot and take longer in some cases or be completed quite quickly in other cases.


Do notifications of conference papers' acceptance/rejection sent to all the papers' authors at the same time?

In my field (software engineering):

Suppose that authors X, Y, and Z submit 3 different papers to the same conference. Will they all get notifications of acceptance/rejection at the same time (or a short period of time) or not necessarily?

By and large, for most conferences, yes. But there are exceptions: For a conference with separate thematic tracks, it might happen that the tracks send the notifications at separate times. I have also seen very few individual cases of conferences where individual notifications were sent late, which made a poor impression on me (something that very good conferences want to avoid).

2- Is it possible to get a notification of paper acceptance/rejection before the notification deadline?

Absolutely, yes. From my experience, this is actually more common for top conferences than for other conferences.


I am lost with my career path. I am questioning my ability to be in research field, academia or otherwise. What to do?

Academia has convinced you of things that are not true.
Your post has a strong air of imposter syndrome about it, but let's assume that you are largely correct.  You managed to get into a PhD program with an undergrad record that was not truly excellent, but you still managed to get into a PhD program.  Most undergrad records are not sufficient to do that.  GPA of 3.4 isn't "mediocre student" unless your school goes in for some severe grade inflation.  You stumbled through your PhD in 6 years - longer than you would have liked - but you still managed to get through it.  Many who go for PhDs drop out somewhere along the way.  You would have gotten thrown out at any other university... but you got your degree from a top 50 school?  No.  No, that does not compute.  You got your degree from a top 50 school.
From the facts on the ground, you do have good qualifications.  Further, your core is a lot stronger than you think.  You state the it taking too long was "mostly your fault".  Probably you're describing running out of psychological resources of various sorts and therefore not being able to utterly power through at every point.  Yeah... that's the kind of marathon a PhD is.  The fact that you had to pick up a bunch of this stuff from self-study actually reflects well on you.  It's additional difficulty that you had to plow through on your way up, and your willingness and ability to do so are also good traits.
Mostly?  You sound seriously burned out.  You spent all that you could of your psychological resources in order to make it across the finish line, and then you went looking and dug deeper and found more, and spent those too.  You finally got your degree (go you!) and now the bill is coming due.  This is normal.  It sucks, but it's normal.  Coronavirus is almost certainly making it suck worse, because Coronavirus makes basically everything suck worse for everybody.  What you need is rest.  Rest, take care of yourself, re-establish a degree of a social life, reconnect with the things that you enjoy, and generally take care of yourself.  Nourish your soul, and allow yourself to heal.  You have a solid position until April.  There's time in there to recover, and you should take it.  Once you've had some time to recover, I suspect that you'll find the situation is not nearly so terrible... and there are places in industry where "I have a PhD" is a serious qualification all by itself.
Actually, I suspect that that's the final part of your problem.  You've been aiming at the top of your target range at every level up until now.  You got into a PhD program at a top 50 school, after all.  That's how you do that thing.  Now you've hit a point where you look at the top of the target range for "graduated a top 50 school with a PhD" and you don't think you can hack it.  You know?  You're probably right about that... but that's also normal.  Every time you hit that top bracket, the people around you get smarter and the challenges greater.  There's no shame in being the middle of the best of the best rather than the best of the best of the best.  Once you recover emotionally, start looking at positions a notch or two down from where you were looking before.  I suspect that you'll be able to find places where you can do things you enjoy and contribute meaningfully without burning yourself out in the same way, and places that will be delighted to get you... especially with your demonstrated willingness and ability to self-study when necessary.
One little anecdote: I have an aunt who ran one of the shared biochem labs at her university for many years.  It was a position that only required a Masters, but she had a PhD.  Still, they were happy to have her there, and happy with the moderate amount of low-pressure experimentation and publishing that she did with spare time and resources.  She, in turn, rather enjoyed being able to talk with the grad students without being terribly intimidating, but also pull out her doctorate when one of them was insufficiently respectful.  There's lots of positions out there that you're plenty qualified for, or even overqualified for.  If you're willing to put them in your view, I suspect that things will not look so dire.


How to publish an [La]TeXified version of an old typewritten book in mathematics?

This material is almost certainly under copyright, so the appropriate thing to do is to get in touch with the publisher and propose this project.  They may, in fact, be receptive and willing to work with you to make this an official new edition.  If they are not interested, then they may at least be willing to give you an official permission for your "remake."

If, on the other hand, the publisher is non-responsive or for some other reason cannot be contacted, then it would be reasonable to assume it's OK to go ahead with the remake and post it informally, e.g., on your personal website.  Because of the copyright issue, no third party is likely to want to publish it, and if the copyright holder eventually decides to take notice and that they don't like what you have done, you may have to take it down (there is, of course, a chance that they may sue instead, but that is relatively unlikely for such a document).  In the meantime, though, it would be a reasonable public service to provide for an apparently abandoned property.


I do not think it is necessary to cite or give exact bibliographical information during a written exam. Even in publications, textbook knowledge does not have to be equipped with references.
In more detail:

I almost write everything as it is and without paraphrasing or even citing, is that plagiarism?
I get some ideas from outside the book and I do cite them in that case, however I do not paraphrase as I am learning by heart the thoughts in order to answer a specific question in the exam, is that plagiarism?

What troubles me here is not that you do not cite correctly, but that you just reproduce the exact wording from the textbook. To the examiner, this does only show that you are able to find the relevant section of the textbook to the question, but not that you understood the subject sufficiently to explain it in your own words. With this approach, you are completely lost in essay questions, and later in your thesis.

And lastly, since I am memorizing by heart, I sometimes misspell the name of an author or even change a bit of details in his or her idea, is that a bad thing?

Misspelling the name is certainly not a problem. Changing the ideas depends on what exactly changes, but I think this is a problem that arises from learning by heart instead of learning the theory, facts, and connections therein.


Terms agreed upon for PhD offer are being unilaterally rescinded—what to do?

It may have been mistakes and over-optimism, not deliberate misleading, on the part of your advisor and the dean. If so, they should be feeling embarrassed at making promises they could not keep.

The contractor plan does not help with your goal of "Doing research and earning a PhD.". At most, it is a temporary stopgap, but accepting it may weaken your negotiating position when trying to get what you really need. You need to move to a university, possibly your old one, as a PhD student, not a contractor.

I suggest asking your advisor and the dean for help finding a PhD student position, including writing letters of recommendation and calling associates. That is the best way of compensating you for their unfulfilled promises. Give them something to do that is within their power, unlike keeping their original promises, but that will help you to your real objective, unlike the contractor offer.

Here is a way to get that discussion going:

  Thanks for the offer of a contractor position. Unfortunately, that
  does not let me achieve my objective of research leading to a PhD. It
  does not seem that I will be able to do that here. Could you help me
  with finding a PhD position elsewhere? Do you know other researchers
  in [your area]? Could you make some phone calls to find out who
  can take me?

Before doing this, you also need to compare your situation if you continue as a PhD student with your current advisor to not having a PhD student position.

You might also review your advisor's and the dean's known contacts, such as their co-authors, advisors, former students, and people who had the same advisor at about the same time. If you can, identify professors on that list who you would like as advisor. That way you can specifically ask them to contact Professors X, Y, and Z about you.

If they do start helping you with your position search, remember to thank them, even if you feel they owe it to you. Always give positive reinforcement to behavior that benefits you. That will encourage them to go further down that line.


Updating CV with Grant Funding Awarded but not used/PI internally but not externally on grants and contracts

Just list them as honestly as you can manage.
For the first, that you were named as project director for a grant awarded to XXX (either the individual or the institution or both).
For the second that you developed and submitted a grant that was awarded, but that you left before the work was executed. If the grant was awarded to you, specifically, say that. Or say what the grant lists as your role, had you stayed.
It doesn't take a lot of words to get it right.


Is it acceptable to extend deadlines for coursework delayed due to student activism?

Much would depend on the concrete situation. But, by default, I would think that activism is part of student's life that the student needs to learn to manage themselves; if they do not have the resources or ability to manage their  activism effectively so as not to have them interfere with their studies, then, largely, I would consider this to be their responsibility. One would probably not see any concessions given for extracurricular sports/music activity, and the question is why political activism should be exempt.

Some may argue that political activism is important as a part of society and therefore of a higher rank than, say, sports or music, but how this is evaluated would probably depend on whose side of the activism one sees oneself.

That being said, times which are more tolerant of studies as an opportunity for character development would probably give more leeway to activism, while times (such as ours) where studies would be considered more a means to an end (development of employment skills) would probably be less tolerant. I would see the former as an ideal of times past, but the latter as the reality today.


Is it possible to get in to Genetic Engineering after completing a bachelors in computer science?

It is common for graduates to jump between communications, electronics, computer science domains. But it is usually not so for something like genetic engineering even though it is considered an interdisciplinary field. Institutions might expect graduation from either of biotechnology, molecular biology, microbiology or biochemistry.

This would however be different for fields such as genomics and bioinformatics where institutions do accept CS graduates provided they have a background in areas like data analytics, machine learning, data mining, data science and the like.

As this would depend on the eligibility and preference criteria of the institution concerned, it would be better for your to consult with the prospective institution that would offer the program desired.


How damaging is it to have been a co-author of a retracted paper?

The effect of retractions on scientific careers has been studied, and the conclusion is essentially that retractions don't hurt scientists who are behaving carefully and ethically.

For your case, it sounds like you were clearly exonerated, and that your only fault was being a junior researcher who wasn't proactive about ensuring honesty on the part of your collaborators.  Since you've since gone on to be more fully educated as a researcher and to establish a good publication record, I would not expect that this past retraction is likely to have any significant effect on your current prospects.


Is there any time limit for writing comments on research article?

Yes, you can publish comments both informally (e.g. on a blog) and formally (by writing a paper that references the 2009 article) irrespective of when the original work was published. Much older articles get referenced and followed up upon.

The only issues to be aware of are:

The authors are somewhat less likely to notice and react to the comments.
Research on the topic may have gone on and your comments may be "old news", or already superseded of their own.


Negotiating Part-Time Lecturer in Germany

Given that the position as you describe in the comments "offers the possibility to enroll in [their] PhD program or to complete a habilitation", this should be interpreted as a typical qualification position in the German academic system. The concept of these positions is that you are an employee of the university, with some tasks in teaching, administration, and/or research, but you get time to work on your next qualification in an academic career. There is a dedicated federal law (informal name "Wissenschaftszeitvertragsgesetz", officially "Gesetz über befristete Arbeitsverträge in der Wissenschaft") that governs these positions.

In some fields (yes, usually the less well funded ones), it is quite common that only the "tasks" part is funded, but you have to do the "qualification" part unpaid, especially when working towards a PhD. Nowadays there is indeed a recommendation to fund all such positions for least at 65%, but given budget constraints etc. you can not always count on that. Nevertheless, with this type of position, the university needs to make sure that you have sufficient time to work on your qualification, so in principle the setup should be such that you need not more than the ~ 20 h / week to do the administrative / teaching part. Depending on the culture of the research team you're joining, you may still be expected to spend most or all of the "qualification time" there, so things may get a bit hard to keep apart.

The HR department will not negotiate with you about the part-time ratio nor about the salary group (such as E13 or E14) for this position. That is decided by the person that is filling the position, taking their budgetary constraints into account.

What the HR department will indeed do is determine the salary level (step 1, 2, 3, ...) that you are rated at. However, step 2 typically already requires at least some years of experience in a very similar position, and step 3 or 4 is indeed next to impossible, as you already figured out.

My recommendation would be to only take this type of position if you are more interested in the qualification part than in the teaching / administrative part. In the specific case you describe here it worries me a bit that the qualification part seems to be hardly described in the posting, which may indicate that the university "abuses" a qualification position to get some core teaching / administrative tasks done cheaply. At the interview, definitely ask about the research part, i.e., what topics you could work on, or come with some ideas of your own, and if they don't seem interested in that it's a big warning sign.

If this is for doing a PhD and you're in principle qualified to do that in Germany, then it should not be too difficult to find a position where the funded part is a small teaching support role or even working on a funded research project that can be connected to your PhD topic. Any of these would be much more preferable for doing a PhD than the type of position you describe here.


Given 0s on Assignments with suspected and dismissed cheating?

It seems that you are being treated unfairly, but it is a situation that can only be judged and handled locally. Your university probably has appeal processes and you can always go to the department head.

In programming as in mathematics there is often only one clear way to do something and if different students  do "the expected" thing, then their programs come out similar - occasionally very similar.

"Suspicion" of cheating should never be the final determinant.

But no one here can help you. Seek a solution locally.


Would receiving an award from a recognised conference in the field boost my future academic career?

There are two issues here. The first is about whether getting nominated for the award is a good reason to go to the conference. The second is about the project coordinator here, and how to convince them that you should go (it sounds like you want to).

As to whether getting nominated is a good reason to go, it depends on how selective the award is. Were only a handful (5-10) students nominated? I would say that is then quite prestigious and you should include it on your CV, and it would be a good reason to attend. Also, will they be presenting the award (or announcing the nominees) at the conference? If so, it would be good for you to be there, in case you are awarded it.

I think you should specifically reach out to whoever is organizing this award and ask them if, since you are nominated, you should attend. That may also be a subtle way for them to tell you "please do make sure to attend", if they are planning to give you the award. You can also ask your supervisor to reach out on your behalf, if that would be more comfortable for you.

As to the project coordinator, she does seem difficult to work with, but we should not be too harsh, perhaps she is receiving a lot of pressure to be tight with the budget, it is not clear. Anyway, there are two things you can do here:

If you get confirmation from the organizer of the award that you are expected to attend, you can use this to pressure the coordinator to let you go.
Get the support of your advisor or another higher-up in your university, as appropriate. It sounds like your advisor is on your side, but afraid of the coordinator, and you are already getting your advisor to persuade the coordinator, which is good. If that is not enough, you basically need to find someone who has more influence than the project coordinator (someone who is their boss, or the equivalent) to get on your side. If you do that successfully, then they can talk to the coordinator and get them to agree to fund your travel.

It sounds very reasonable, given that you are nominated for an award, will present at a workshop, AND have already received funding (waived fees) for all except travel, so I hope you can attend. Good luck!


Student asks TA if his result (figure) is correct

Welcome to the most standard "trick" students use to get answers out of professors/TAs :).

My answer is as a professor, but I think the basic principle works for TAs as well. What I usually do is turn the question back to them. Something like:

  S: Is this answer correct ?

  Me: Well, what do you think ?

now things can go in different ways:

case 1: S says "well I'm not sure". In which case you can say, "well how might you go about verifying that your answer is correct" ? this might then lead to a discussion of how to check answers without you having to commit to commenting on their particular answer.

case 2: S says "Well I think it's correct". Then you can say "Ok then :). I understand that you think it's correct" and leave it at that.

They might persist and say "can you tell me if you think it's correct". At which point you can say "No, but how would you go about checking its correctness" taking you back to case 1 and the "methodology" of checking.

The underlying pedagogical point is this: you don't want students checking answer correctness with you ahead of time because

a) learning to check your own answers is an important part of learning. It allows you to diagnose problems and identify the correct path to an answer.

b) it's unfair to those who don't ask, and it's a waste of your time

c) using this socratic approach allows you to assess how they are approaching the problem, and allows you to guide them in their approach, rather than spoonfeeding a prescribed answer. Everyone approaches problems differently.

p.s Students often also ask for hints. The material I teach is usually mathematical, so they're asking for hints for a proof. There you have some more leeway, but the trick is to draw them out into explaining their thought process, and then trying to gently nudge them without revealing the answer. It takes some practice and a lot of Socratic dialogue.


How good of a conference can I realistically submit my first paper to? How can I figure out which conferences I'm good enough to submit to?

You learn to evaluate these kind of things by experience.  You read the papers published in the conferences, form your own opinion of their quality, see how they impact the field over time, see how they are viewed by others, and revise your opinions.  Eventually you get a general sense of how "good" a paper should be in order to be published in this conference, and you compare it with your evaluation of your own paper's quality.

You bootstrap the process by drawing on your advisor's experience.

So: Ask your advisor.


Name spelling problem in recommendation letter

Do not worry about this. Just use the letter and ignore the spelling mistake (which most people will consider very minor).

As long as it is clear that this letter was meant for you (which is the case here), you are fine. People will care about the content of the letter, not about really minor spelling mistakes in your name, address, etc.


Why does the number of publications for computer science and economics PhD students differ by so much?

I don't believe what you say is univesally true of all CS areas; it is certainly not true of mine. But more to your point, based on my conversations with colleagues in economics, one factor (possibly of several) is definitely the submission-to-publication delay: A conference turnaround is about three months, but a journal can be much longer, especially if major revisions are involved.

Here's some insight on the subject (published a while ago).


How should a reviewer provide comments to a journal's special issue in a field he is not familiar with?

I have been receiving a lot of invitations lately to review proposals for special editions -- mostly open access.  These proposals have been way outside of my area of study (and sometimes discipline).  My guess is they scrape the web for potential reviewers and use a shotgun approach -- but that is just a guess.

I ALWAYS decline serving as a reviewer if I am not sufficiently expert on the substantive or methodological issues.  I also try to highlight in my review where my expertise may fall short so the editor knows where to fill the gaps.

I suggest you decline any invitation if you are not qualified to review the topic.


How to promote research commercialization?

In the US, at least, there are lots of different mechanisms intended to try to facilitate commercialization.  The major players are:

Universities, who want to make money by licensing patents
Entrepreneurs and venture capital groups, who see new technology as  one of the best sources of profitable market disruption.
Large established companies, who want to acquire new technology in order to prevent their markets from being disrupted and to disrupt their competitors.
Local, state, and national governments, who see tech transfer as a both a major economic benefit and an important justification for investing public money in research.

A few of the many significant mechanisms:

Every research university has some form of Technology Transfer Office, whose job is to get researchers and business people introduced and help them figure out opportunities for commercialization.  Many universities also have "sabbatical for a startup" programs for their faculty, official or otherwise.
Regional associations, like the Massachusetts Association of Technology Transfer Offices or the Northwest Future Energy Conferences do the same thing on a larger scale.
SBIR/STTR programs are a whole family of programs where significant amounts of government grant money is allocated specifically to commercialization of new technology by startups and other small businesses.  Some small businesses effectively set themselves up as independent research institutes with this money.
Within subfields, there are often specific joint industry/academia programs specifically designed to facilitate technology transfer.  For example the Semiconductor Research Corporation is designed to serve as an industry/academia bridge in, well, semiconductor research.  Another example is SynBERC, a long-term NSF project in synthetic biology which includes a highly successful program for industry involvement at all scales.

The interface between academia and industry, in the US at least, is much more intense and complicated than many realize.  You just have to go looking for connections into it.


Can ibid. be used under the Harvard referencing style?

From the examples at the University of the West of England:

  Generally ibid. and op.cit. tend to be used more in the body text for the Harvard system, and more in the reference list for the numeric system, as you can see.

They also note:

  There is no single authority that defines the 'Harvard' referencing style. Please seek guidance on the preferred scheme of referencing from your home institution or the journal in which your study will appear.

So I'm going to say yes, there is no reason as to why you couldn't use ibid with the Harvard citation style.


Would it be beneficial for one to mention schools that already accepted him/her when applying for MSc programs?

I doubt that it would do you any good in most cases and it might do you harm. There may be some upside, but consider the down. People might decide that you aren't very interested in them if you mention another school. People might decide you are gaming them. But even the best case is that people might decide that you already have options so they would want to give similar options to others. A "better" school might wonder why you applied to a "worse" one. A "worse" school might conclude you won't accept an offer from them.

It just seems too risky to me.

Focus your application on what you have done, on your interests, and on those things that make you a candidate for success in the program you are applying to. If you are a strong candidate it will be assumed that others will evaluate you similarly. You aren't desperate, so don't sound as if you are.

On the other hand, I don't think you need to actively hide your other acceptances. If asked, explain why you would prefer the new institution.


Importance between the American Mathematical Monthly and Research Journals

You're probably right that more people would see something published in the Monthly than in a "research" journal. But if you are aiming primarily to optimize the positive impact this paper would have on a CV for grad school (in the U.S.) I think it would be much better to say that it has been published in a good-quality research-oriented journal, since that will attest much more strongly to the quality of the research (as opposed to attesting to general interest).

EDIT: in contrast to some other answers' implications... The Math Monthly is not at all a research journal. It is an expository and (mostly elementary) problem/puzzle-oriented journal. Publication there is viewed (in my experience, and in my own opinion) as a good thing, but no indication at all about "research potential" or such stuff. That's not the fundamental criterion for publication there!

So, if you are wanting to give evidence that you have already made (and thus in the future can make) research contributions... publication in the Monthly gets you close-to-nothing. Sure, "it's nice", but it's not at all about making significant new contributions to live subjects. It's an entirely different thing. It's not just "a somewhat different journal"... it's in an entirely different category.


How to correctly mention 'Ranked 1st in undergraduate class based on GPA' on CV?

I don't know if this is applicable in your case, but another way to emphasise that you were at the top of your class is to ask the people writing your recommendations/references to include this piece of information.

Not only does it sound much better coming from someone else (and supposedly that someone is a reliable source), but also recommendations/references are typically the place to brag about such things.

That doesn't mean you shouldn't include it in your C.V. as well, though. Unfortunately, I don't think there is any way to write it so that it doesn't sound (at least a bit) pretentious.


How to anonymize submissions and ensure each student gets exactly one chance to submit?

In an online file sharing system (e.g. dropbox, google drive, onedrive...) create as many folders as you have students. Create a share link for each folder with write access.
Send the share links and the list of student emails to a trusted third party, and ask them to randomly assign a share link to each student.
Tell the student to upload (anonymously) their submission to the shared folder they were assigned to.
Upload your own feedback in the same folder.

It's a bit of a hassle but it works. There is a trusted third party involved, but you cannot get around that (just like for your exams proper, there is a trusted third party involved, namely, the online system).

Federico Poloni asks why a third party is strictly necessary. As this is a rather trivial question, I do not expect to be able to find a citation in the literature, but here is a mathematical proof. For simplicity, assume that there are two students, A and B. The instructor must give some information to A and B such that

the instructor can verify that no student submits the same work twice;
a student cannot impersonate another student to get around this restriction;
the instructor must be able to provide feedback regarding some submission and ensuring it arrives to the correct student.

Because of 2, the instructor must give some different piece of information to A and B to "sign" (in a cryptographical way, for example), their submission. A different key must provide a different signature because of 3, but the same key must always yield the same signature because of 1. Without a third party, the instructor must know what key is given to each student. It is then trivial to reuse that information to know what key yielded what signature, which can be use to breach anonymity.


Should I choose a postdoc with greater potential for collaboration over a higher ranked institution?

I would suggest going where you think you'll be happiest and do the most productive and visible research, taking into account whatever factors of these places are relevant to you.    Ultimately your chances at a faculty position will depend on the strength of your results and on your letters.

The advantages of going to a more prestigious place is that, in general, such places have a higher concentration of good mentors and collaborators.  Such factors make it easier for most people to get good results and high visibility.  But in your specific field, for your specific needs, a lower ranked department might be the better fit.

If you were saying you were considering department #100 over #5 (via some standard ranking), I might suggest you consider such a choice very carefully.  However, a "30s" department might easily be a better choice than a "top 15".


Writing about complex ideas without getting stuck

I am not sure what you have tried, so bear with me if some of these techniques are obvious to you:

Write from an outline: Complex matters need to be broken down. Writing from an outline helps with focusing on one thing at a time. It also helps with making sense of the big picture without having to go down each and every rabbit hole simultaneously. Remember that your outline isn't set in stone; on this consider the points below.
Explain your ideas verbally: You seem to be struggling with putting words on paper, perhaps because putting words on paper means fixing them. Explaining something out loud takes this pressure away, as everything can be qualified and corrected the next second -- you develop a sense of flow and can focus on the idea rather than the phrasing. Either talk to colleagues, or just to a mirror, a pet, or your left thumb. Programmers call this rubber duck debugging. You may find it useful (or maybe too restraining) to record your voice. I like to move around as I explain stuff to myself, and I had some good insights while running (alone and with a friend).
Either write in draft mode or in edit mode, never both at the same time: Draft mode is all about collecting ideas. Get the word count up as quickly as possible. In draft mode, you want to collect the raw material out of which you build your masterpiece later on. Silence the critic that lives in your left brain, and don't allow yourself to polish your draft yet. If you're really stuck, you may even try some free-writing exercises, like disabling the backspace key or writing with the screen switched off. Going off on a tangent is not only allowed but encouraged a this point! When later on you switch to edit mode, the first thing is to identify the key ideas that are now buried like raw diamonds in your draft. Highlight them, relate them to your outline (or write a new ex-post outline from them), and then structure the rest of the text around them, as you revise. Now, decide which parts are tangential and which are central to your argument. Cut the former and develop the latter.
Iterate! You will probably never completely avoid tangential thoughts proliferating in your draft, but you also can't tell which is which before you have written them down in draft mode and critically evaluated them in edit mode. As you progress through iterations of drafting/editing, the tangents become less. Before you ask: Yes, this takes time. Thinking does. None of the papers you admire has been written in a day, in one go.
Never delete big chunks of your draft once and for all. Instead, save the draft under a new file-name or use a version control system and make regular commits. This allows you to go back to earlier versions if you lost one of those raw diamonds somewhere along the way. It also permits you to be bold with revisions and deletions, making your text more concise and clear.
Reconsider the boundaries of your project: As you revise your draft, you may realize that what you originally considered a monolithic project is actually stuff for two or more projects. This is a good time to go back to your outline and split your draft in two: Decide what you want to focus on now, what you might look into next, and how these parts are related. The latter is part of your concluding section ("further research is needed..."). (If you will, this is point 4. on a meta-level.)


Does this count as a quantitative research?: word association

You answered your own question. You plan to "quantify the strength of word association." In this instance, yes, your work would be considered quantitative research.

[Wikipedia] defines quantitative research as "the systematic empirical investigation of observable phenomena via statistical, mathematical or computational techniques" 1. The example you cite does exactly that.

Yes, everything is quantifiable some way. The greater question is whether or not that quantification has meaning. Yes, you can quantify emotions (countries are compared on happiness scales all the time). How that concept was measured and what is done about it is much more important.

As evidenced by the comment left "the example you give is peculiar," there is a level of debate that scholars could have about the validity and credibility of your methodology. Whether or not your methods were quantitative is not at question (they were).

I then add one more question to your question: Does it matter? I would much rather argue the value of your research with you than whether it would be considered qualitative or quantitative in nature.


Following up on an email to a potential adviser for feedback on research proposal?

When to email somebody a follow-up email depends on how time-sensitive the topic is and other factors you may be aware of.  For people in close contact (e.g. a student taking a professor's class, or colleagues), a day or two is typically an acceptable wait time. For somebody that you initiate email contact with, a week is more typical. Other considerations are how much thinking the response might require: if you asked lots of questions, they may need more time to think about it before formulating a reply. Do you have reason to believe the person may be busier than usual (e.g. exam season or a conference)? If so, it would be polite to give them more time to catch up with their email.

In this case, a week or two is probably a sufficient amount of time. Less than a week would be too soon, as you haven't met them before emailing them. More than two weeks is getting close to winter break, at which point most academics check their email less frequently, and you need enough time to contact other professors if she suggests any. It's also possible other people are asking her similar questions. It's a busy time of year, so one follow-up couldn't hurt. (If she doesn't respond after a second email, I wouldn't send a third email.)

Here are a few resources you could check out about how to write your follow-up email:

How to write a polite reminder email?
How to remind a professor about sending papers to read?

You'll find other resources linked from these questions and by searching online, too. Most formal reminder emails follow a similar format. Remember to be brief.

It's certainly worth contacting other professors! I do not see any reason why not to.


How exactly do graduate students collaborate on a research project?

It's really like any other collaboration. Presumably the (student) researchers are working together because they have a common interest in a problem and possibly have some complementary expertise that's useful for solving the problem. So they'll interact and as the situation merits it will divide up tasks (or work on some aspects together). There really isn't a single rule for this.


Should numeration of a list of axioms be continued?

I would recommend thinking about this presentation problem in the following way: if you were inclined to be verbose, it would be perfectly correct to say:

Definition Monotone system of sides is a system of sides conforming to the axioms:

...
...
...
...

As such, it is not so much that you wish to continue a list of axioms, as it is that you wish to take advantage of the similarity of the two lists of axioms to present this information in a way that is more streamlined and easier to understand.
As such, I would recommend making the elision explicit, as in:

Definition A monotone system of sides conforms to the same axioms 1-3 for a system of sides, plus an additional axiom:

...

Definition A distributive system of sides conforms to the same axioms 1-4 for a monotone system of sides, plus an additional axiom:

...

Notice also that I have extended the italics to the whole statement "X system of sides," rather than just the adjective, since you are not defining e.g., "monotone" but rather "monotone system of sides."


Starting a PhD without wanting an academic career afterwards: should I tell my advisor?

This is pure opinion, of course, but I don't see anything wrong with getting a doctorate purely for the love of the field and a desire to know more. There are plenty of people in doctoral programs to fill the needs of academia in the future and some will be disappointed in their inability to find a suitable position. You don't need to apologize for anything.
But you may be a bit naive about the future and your ability to make a living. If you really aren't concerned about that, then there shouldn't be any problem, but understand that you may not find any position in which your new knowledge can be leveraged. But, there are other opportunities outside academia and industry if you have the financial resources to manage it.
Whether you talk about this with your advisor or not is a personal decision, and should be based on your understanding of how they might react. No one here can predict that better than yourself.
But you really aren't deceiving anyone. As you say, your future is yours to manage.

Back in the day, previous century, actually, we didn't worry about what came "after" since the economy was good and there was a lot of interest, both in academia and elsewhere in our skills (math, in my case). We were just able to assume that jobs would be there. But all of that ended when we successfully landed on the moon. So it was a shock to graduate into a terrible economy for folks with doctorates. But now the situation is very different. There is an abundance, not a lack, of skilled people, so the future is much less "certain" now than it seemed to be in the 1970's. Make sure you have plans, and back-up plans as well.


Can a University put a Creative Commons document containing a NonCommercial element (NC) behind a wall?

Creative Commons "NonCommercial" prohibits uses that are "primarily intended for or directed toward commercial advantage or monetary compensation."  Under U.S. law, where exactly the boundary lies can only ultimately be determined by development of precedent in case law, since the U.S. has a common-law legal system.

It is pretty clear, though, that this type of use would be non-infringing, for the following reasons:

Virtually no person pays to become a university student for the primary reason of access to online documents.  Likewise, it is an exceedingly minor perk for employees and could not be considered to give the university a significant commercial advantage (rare historical documents might be a different matter).
The actual barrier is a University ID, which can typically also be acquired in many ways that do not involve compensation passing in either direction (e.g. research affiliates).


Reference request for research on images or colors used in quizzes and exams

With a quick Google search, I found the following, but I am interested if there is anything more than these, especially with mathematics or studies with images:

"Effect of Paper Color on Students' Physics Exam Performances" by David R. Schmidt, Todd G. Ruskell, and Patrick B. Kohl

https://www.academia.edu/5702205/Effect_of_Paper_Color_on_Students_Physics_Exam_Performances

"The Non-Impact of Paper Color on Exam Performance" by Michael J. Meyer and Jennifer Bagwell:
http://aaajournals.org/doi/abs/10.2308/iace-50142

"Effect of Paper Color and Question Orderon Exam Performance" by Ilanit R. Tal, Katherine G. Akers, and Gordon K. Hodge

https://www.researchgate.net/publication/233180281_Effect_of_Paper_Color_and_Question_Order_on_Exam_Performance


Summary high School Mathematics in the USA

Every state has their own standards of what is covered in high school math classes. Many states (but not all) modeled their standards on the Common Core standards found in this link. http://www.corestandards.org/Math/

The topics covered are sorted into the categories of 1. Numbers 2. Algebra 3. Functions 4. Geometry and 5. Statistics and Probability. Each category gives more specific standards students are expected to master.

If you would like to see how topics covered by standards are presented good resources are EngageNY (https://www.engageny.org) which provides sample lessons/worksheets for the entire Curriculum. One note is most most teachers I knew who used EngageNY would modify/scaffold the material extensively for their students. Also to see sample exams JMAP has archives of New York's standardized tests by year/subject http://www.jmap.org/JMAP_REGENTS_EXAMS.htm and also with questions sorted by standard http://www.jmap.org/JMAP_REGENTS_BOOKS.htm

An important note is that Common Core standards go up through Algebra II but it is possible that some or even most of your students also took Pre-calculus and maybe even Calculus in High School as well. If you want to see what might be covered in a high school Calculus class one option is you can look at the course overviews for Advanced Placement calculus https://apcentral.collegeboard.org/pdf/ap-calculus-ab-course-overview.pdf?course=ap-calculus-ab and http://media.collegeboard.com/digitalServices/pdf/ap/ap-course-overviews/ap-calculus-bc-course-overview.pdf


How to recognize/ judge whether the PI/ recruiter has selected me as post doctoral fellow?

There is a very easy way to recognize when you have been selected: you will get a signed letter offering you the job.

If you haven't got one, then you haven't been selected (yet).

Everything else is irrelevant. I can understand that it's tempting to try to guess from subtle cues, but it's really a waste of time.


This is one of the harder questions you'll have to ponder, and one of the most useful. First off, realize that your choices are not (completely) irrevocable. Many researchers shift areas every 5-7 years or so - the changes are not dramatic, but over time you can make useful contributions in a number of different areas.

Having said that, what you are looking for is a broad topic that will presumably take you through the 5-6 years of a Ph.D. To look at your questions one by one:

  Where can I see if "getting my PhD to write software to guide probes
  to Jupiter" is even a viable option?

Do you know of people working on this ? maybe at NASA ? Where did they do their Ph.D ? what kinds of topics do they publish in ? What I mean is that one way to figure out if "Ph.D in X" is viable is to see if there are people doing X, and then figure out what their trajectory was by looking at their publications, CV etc

  Must I choose a area that is currently being researched at the
  university I attend, or am I free to come up with my own?

It depends. You're in an MS program, and you haven't mentioned whether you're planning to apply elsewhere for a Ph.D. An MS is a good time to explore your options with people at the university, burnish your research credentials, and build some background in areas of interest. Obviously it helps if your area of interest is covered, but even if it's not, figure out related background that you need, and maybe look for someone doing research in a related area. Also see which places/people you'd like to do a Ph.D at based on the area, and that will give you a sense of what kind of extra reading/prep to do.

  Can/should I be reading recently released papers on Computer Science
  topics for some inspiration, and if so where do I go to find those?

But of course ! but you should try to focus your search a bit. There's a large body of work in each of the topics you listed, and google is your friend. Once you find even a few papers, you can figure out where they were published, and then look at other papers in those venues, and repeat.


Why didn't more people graduate with a college degree when it was "affordable"?

There are many factors!

In the past there was much less demand for highly educated people, as there were many more jobs that were mostly manual labour. Technology is largely to blame for this, as computers and machines take over what we had to do with our heads and hands.
People were more likely to work in one job for their whole life, so there was less incentive to get a more general education.
Apprenticeships were more common, so you'd learn on the job rather than study at university.
It was easier in the past to "work your way up the company" – you'd start as a front-line grunt, and have a good chance of becoming a manager later on.
Children with poorly educated parents are much less likely to go to university. Starting off 100 years ago when almost everyone was poorly educated, it's actually taken remarkably few generations to get where we are now.


Assistant professor position in USA (9 months). Is it badly seen to spend the summer to work at distance in my home country?

A lot of this will depend on your department's culture regarding 9-month appointments. There are at least two different aspects of this I can think of:

How are 9-month appointments actually viewed? In some places I've been, 9-month positions, especially if the pay is spread over 12 months, are functionally just "75% Hard Money" positions, and there's a pretty clear expectation that you're working in the summer, etc. rather than "an unfunded summer is a summer off". If the summer ends up having a lot of committee meetings, etc. that could be a problem.
How are long absences viewed? There are some departments, especially those with lots of field work, being gone all summer would be quite typical. There are others where it would be extremely conspicuous, and probably be the source of some concerns about collegiality come evaluation time.


Is it a good idea to apply for PhD during my second Master degree?

As long as you can justify why you pursued a second master degree at first and why you want to quit (if I well understood), then you will not look bad.

I know many people who worked in the industry after their master and then turned back to academia. They could explain why they want to do a PhD and were convincing.

If you are motivated and have good reasons to do a PhD instead of finishing the second master degree, then go for it. However, remember that any employer will ask about critical decisions in your professional life. Examples include: 1) why did you leave your last job? What motivates you to pursue a PhD? What motivated you to pursue a second master? etc.


Would it be OK to in-text cite a paper without mentioning the name and year explicitly in APA?

I think this is covered in the APA style blog. The example they give boils down to instead of using

  This idea was recently explored by Palladino and Wade (2010). Palladino and Wade’s (2010) results indicate that “a flexible mind is a healthy mind” (p. 147).

you can write:

  This idea was recently explored by Palladino and Wade (2010). They noted that "a flexible mind is a healthy mind" (Palladino & Wade, 2010, p. 147).

So yes, you need to give the full names and year of the reference in the body of the text.


How do I work on research independently?

There is a chicken-and-egg problem here: you don't have the attention of the experts because you haven't demonstrated achievements in their field, which you can't do effectively without their vetting. To get those experts' attention you need to demonstrate that you have something new, without wasting their time.

Publishing something in the field is the best way to command their attention; the experts will be professionally required to digest your work. Usually only people with substantial academic credentials achieve this.

The alternative is seeking their attention in some way. This means being thankful and brief. Many academics are kind people who will answer a quick question.  Don't rely on a hunch; be sure you are on the right track before asking for their attention. Be ready for no response or a no, and take your time; you may find after writing that the question you asked was not quite the right one. Connections can also be made indirectly; though you have no friends working in related fields, you may have a friend-of-a-friend who is doing so.


Does EBSCO's "Peer Review" search filter filter out junk journals?

Yes.
However, keep in mind the various (read: broad) definitions of what peer reviewed means. EBSCO uses following definitions:

Blind Peer Reviewed - (or Double Blind Peer Reviewed) - Articles appearing in a journal are sent outside of the journal's publishing or sponsoring organization for review by external reviewer(s), whereby the either author's identity or the reviewers' identity is unknown.
Editorial Board Peer Review - articles appearing in a journal are reviewed by an internal board of editors, not solely by one editor. The author's identity may be known or unknown.
Expert Peer Review - articles appearing in a journal are reviewed by experts (either internal or external to the journal) whose credentials are known and who are experts within the subject matter of the article under review. The author's identity may be known or unknown.

According to EBSCO, you can also restrict your search to peer reviewed articles by suffixing your query with AND RV Y.


Where can I look for post-doctoral positions in Europe?

More information is always helpful.  Most students who do postdocs find them in the following ways.

1) A recommendation to a company or university from the faculty of their current institution.

2) A recently graduated Ph.D. student who may know of a great fit for you at their new postdoc.

3) A place you've interned in the past that is open to bringing you on as a postdoc.

4) University mailing list for graduate students in your field.

5) Your academic network you build from all those years attending conferences and presenting your work.


What to write in the email for sending PhD application to a research group's head?

Your CV has your background. Hopefully you have written an SOP (Statement of purpose) giving your goals for grad study and beyond. In the email you can probably best help yourself writing about why you want to work with him, but make it honest and not too "over the top". But a bit more than just your last suggestion. How does this group fit your SOP?

If he gets a lot of applications he will quickly sort them into two piles. You want to be in the pile for "further consideration".


I submitted my own code on someone elses account

Given that the student Honor Council has already found you guilty of cheating, maintaining that what you did was simply out of curiosity does not seem like a good strategy.  I don't find that explanation so convincing myself: your "curiosity" got you an unfair advantage in the grading of the assignment.  Your position that this advantage was not relevant to the final outcome is really not the point: many if not most students who cheat on assignments and exams could have reached the same outcome honestly if only they had been more patient (and honest!).  If you were really "just curious", you could have asked about it, and you certainly could have submitted only the allowed total number of submissions in a single day.

The real question is whether you deserve the punishment you've thus far been given, of a 0 on the entire assignment.  Generally, when students don't follow all the rules of an assignment, they can reasonably expect to be penalized for it in some way, but the penalty need not be the entire value of the assignment.  I think your position should be that you agree that you did not follow the rules and that you did this out of a combination of curiosity and stupidity.  You can make a reasonable case that you did not violate any fundamental principles of the assignment: all the work you turned in was your own, and you got it 100% correct well before the final deadline.  So all in all you did more good work than bad.  You did exhibit poor judgment and agree that some penalty is reasonable.

I would suggest that you ask to be given the score that you got on the last attempt before you submitted on your friend's computer.  This score is undeniably legit, and giving you that score for the assignment seems like a nice compromise between giving no penalty for breaking the rules and ruining your entire course grade.

On the other hand, all this is to answer your question "Is this really a serious offense?"  (TL,DR: probably not too serious, but you did do something wrong.)  What I suggested above is really more a suggestion for what I think a just outcome of the faculty deliberation would be.  Depending upon how your system works, you may or may not have the opportunity to suggest a punishment.  As others have said, your real strategy here is to remain calm, explain all the facts as clearly as possible, accept that what you did is wrong and convey the impression that you are nevertheless a good student overall.  What they decide is really up to them.


I do not know what they will do in your case. However, in general, the procedure is such that when the application process for PhD happens, most students doing Bachelors or Masters degress in other countries are in their final year and do not have grades to send. However, if you do fail, then the offer of admission no longer stands, in general.

For a PhD program, the minimum required standard is a bachelor's degree and if you fail that degree then why would they allow you entry? Having said that, now consider this. In certain countries, there are make-up exams for failed courses in a particular semester. If these make-up exams are taken before your offer of admission stands, i.e. Fall 2013 then you are good to enter. If not, then its bad luck for you. An offer of admission to a doctoral program only stands (in general) for that mentioned semester. You could potential defer the offer of admission another semester or year in order to take the make-up exams and then join the program. However, your chosen program may not allow this or may not have funds for you if you choose to join at a latter stage.

Basically, it all boils down to this. Contact the department immediately to ask for advice and tell them what options you have to finish your BS degree at home and whats the fastest route thats possible. Then see, what they have to say and take it from there. I speak from anecdotal evidence of a close friend who was forced to leave the offer of admission because he failed a couple of courses in his final year.

Do not try to fake your way through. I-20 or visa means nothing really for this problem and you will not be checked in general for proof of degree during your visa application process. But, be rest assured that you will be asked for proof of bachelor's degree once you join the program.


Safely negotiate a salary for a PhD offer - Germany

One of the mods here is a professor in a german university, I think he is able to add a better answer or at least confirm or discard mine.

Some considerations:

As far as I know, many german PhD students, at least in CS, are actually employed full-time, which I assume means 100% TVL-E. In that sense, both 50% and 65% seem somewhat on the low side to me. At the very least, negotiating for 65% does not seem so unreasonable that it should offend anybody.
However, don't be too disappointed if your negotiations go nowhere. I have heard from multiple people that academic salaries are oftentimes entirely unnegotiable in Germany (though not always)
German PhD student salaries are internationally quite on the high side (also if you take costs of living into account), so even if you cannot negotiate, 50% might still be ok compared internationally. That being said, the question is always if the salary is enough for your standard of living / circumstances. If you have a partner and two kids, maybe 50% simply does not allow you to live. If you are alone and live in a dorm, maybe 50% is plenty.
In germany, some amount of teaching is usually part of the job. That the one professor told you this before is a good thing. However, there is teaching and there is teaching. I have certainly seen groups where teaching load could add up to about 75% of a PhD student's work time. This is obviously terrible (independent of money issues). The hard part is figuring out whether this is the case in your specific group. The best way is to ask one of the current PhD students.
Don't be too afraid that you may annoy your future professor. In my experience, the entire "academics frown upon money issues" is a bit of a show. The same professors who says such things at the same time have no quarrels at all negotiating their own contracts or department budgets. If your future professors gets annoyed by you mentioning that you have a number of better offers, you should likely go somewhere else anyway.

Now, for the actual negotiation, I would follow moriary's remark from the comment - simply mention (friendly and non-threatingly) that you are torn on accepting the offer, as you have counter-offers at 65%. As said, nobody should get annoyed by that. We are all adults, right?


What's the difference between regular (aka full), position and short papers?

Here is what I have observed at the peer-reviewed conferences that I attend:

A regular full paper is your basic standard peer-reviewed paper.
A position paper is for ideas that don't have and results, per se, but are worth communicating to the community, or for announcing a result that has been published with another community.
A short paper is for work that is worth publishing, but doesn't rise to the level of quality or significance of a full paper.

Short papers are generally significantly less respected than full papers, but may be worth it anyway: a short paper in a high-profile conference is often better than a full paper in a less significant conference.  Position papers are funny and in a different category: they aren't attempting to be the same as a full paper, and are typically judged more by a standard of "interesting to discuss."


Depending on the rules of a given journal, an editor could take on the review task themselves or not. Some will permit it and so some editors will also review. Most will want some independent advice, I think.

I also think that editors are most likely to take on the obvious and simple cases, however. So a long delay is most likely (not necessarily) something else.

There are a lot of reasons for any delay. This could be all sorts of things. The preferred reviewer might be overloaded at the moment. The editor might have been having a hard time finding appropriate reviewers. There might have been fast reviews and it bounced back quickly but the editor hasn't made a decision. The editor may not have found a "suitable" slot for the paper and is holding off sending acceptance. There may be a negative review and the editor is seeking clarification. Lots of possibilities.

And "quite long time" feels different to you than it does to the editor. It can be frustrating. Either ask for a status update or be patient. But "weeks" is not very long. For some journals "months" isn't excessive.


I think you're creating a false dichotomy by saying

  the internship is certain to eat into vital amount of time he could
  otherwise spend thinking about research problems

Internships are places where sometimes REALLY interesting problems come up. Especially in engineering, while it's not critical, it's very important to keep a finger on what's happening in industry - the industry/academia divide is a matter of time-horizon rather than fundamental nature of the problem.

Of course you need to have enough experience to recognize interesting problems, which goes back to @aeismail's answer. I will also say that doing it late in your career isn't that bad either, because then you get a three-month interview for a job. That's how I got my first one :)


Should I tell my recommendation writers about my self-studying since graduating? Should I also mention my illness and depression?

First, I agree completely with Arno's answer here. The logic from that answer applies to these questions as well. Specifically...

Should I email the professors which will be sending letter of recommendation [and tell them] what I have been doing since I completed my masters in June 2020? (It would only list topics I have studied till now)?

Those reviewing your application may be interested to know what you have been up to during the past year. The answer appears to be "studying." So, it may be worth listing this briefly in your application somewhere. Just one bullet on your CV, or one sentence in one of your essays.
To your question: I see no harm in also providing this information to your letter writers. For the most part, their letters will focus on what they know about you directly, not what you say you did after graduating. But, it's definitely a good idea to stay in touch with your letter writers, and mentioning your recent activities is a natural thing to say in this context.

[Should I] include episodes of depression along with stomach infection?

No. It's usually better to declare victory rather than make excuses. In your case, there is no need for excuses; it is quite straightforward to say "since graduating, I've been studying topics X, Y, and Z." This sounds much better than "I've been trying to study, but between depression and illness I haven't made much progress." Why volunteer these extra details?

[Should I include] the reason behind the depression [issues with my father]?

Definitely not. This is very much oversharing. It is understandable that you want to discuss your difficult circumstances and are seeking forgiveness, validation, and/or reassurance. But you should have this discussion with your family, friends, or therapist, not with your professional references.


Potential postdoc advisor threatening to fire other postdocs

Can a PI fire a postdoc?
Surely they can, and sometimes they really have to do so in order to save research money and do the best for the group.
Can PI signal to the postdoc that their performance is under review?
Yes. This is an honest thing to do. It gives postdoc a chance to improve their performance and fix things, before guns will fire.
Is it a good idea to tell this as a joke?
Absolutely not. The job contract is a serious personal matter. The discussion should be private and professional, not public and semi-serious.
What can we tell about PI's personality?
He cares about the performance of the group and he tries to manage it. He doesn't know/feel what is a professional way of doing it. Perhaps, he struggles to maintain a distance and tends to become a bit too friendly with people in his group. As a result, it is hard for him to communicate difficult decisions and unpleasant messages and he tries to disguise them as a joke.


Etiquette for notifying personal contact on faculty search committee about applying for a position

Is it appropriate for me to tell him that I am putting my packet together and that I will let him know when I submit the application?

You most definitely want to respond ASAP and let him know that you are in the process of applying. It is not necessary to follow up further and tell him when you have applied, but nor would a quick email saying something like "Just to let you know, I submitted my application on the HR system today" be out of place.

  Following (1), is it appropriate for me to ask him to be on the lookout for my application when/after I submit it?

I would not use this terminology. Your communication with him is implying that he should keep a look out for your application. No reason to be blunt.

  Is it appropriate for me to ask follow-up questions about the person they are looking for, for example whether there are specific courses they're trying to develop within their department, whether there are research areas they're specifically looking for, etc. so then I can "tailor" my cover letter/teaching statement/research statement to what they need?

One can always ask a search chair this, but as they are the search chair and do not personally know you, you should expect a non-informative answer. This is a much better question for your personal contact/friend. In your case since the search chair used to work at your current department, someone in your department (possibly your advisor) who knows the chair personally, could also reach out to the chair.

  Should I be taking advantage of the fact that the search committee chair is still friendly with several people on my dissertation committee by having them contact him?

YES! YES! YES! I really cannot say YES enough. As awful as it sounds, this is how you get a job. You want to do this in a coordinated manner. You do not necessarily want every member of your department calling up the chair. You need to sit down with your advisor and discuss this search (but also all the searches you are applying for) and figure out your application strategy.

  The expected start date is sometime in late fall of this year, but the posting shows a closing date sometime in the summer next year. Can I ask my contact when he expects to start reviewing the applications?

This falls into one of job postings that is confusing for applicants. Presumably, they want someone to start ASAP, but do not want to lose the position if they do not get a good applicant. They also could have screwed up the deadlines. This is something you could ask the chair. If the posting suggests a person to contact about questions, you could also ask them.


Contacting a professor in the university you are applying

Only contact professors if you are genuinely interested in working with them and can demonstrate that you might be a good fit. Profs get a lot of generic cold emails so it isn't worth it if you aren't excited about them specifically.

But if you see someone's work that really does interest you, then definitely reach out! In a short email, use a few sentences to demonstrate that you are interested, know what they actually do (take a look at a few of their papers), and why you are a good fit (relate your experiences to their work).


Is the expression "Deputy Head of Research" correct?

"Deputy Head of Research" is someone who deputises for the "Head of Research".

By contrast, "Deputy Head for Research" (or, sometimes, "Deputy Head (Research)") is someone who deputises for some generic "Head" in the specific area of research.

"Research Deputy Head" is unidiomatic and sounds like a command "go and research the deputy head" rather than a title. The "research" coming first somehow stresses it as a verb rather than a noun.

Even more common than any of those constructions, at least in my part of the world, is the simpler "Head of Research".

In practice, there will be a definitive answer to this question which you can only find out by asking within your university.