What to do when you have obtained very similar results with two different groups and you want to publish them both

I'm surprised you did not mention the option that I would probably do: combine all data into one paper. Based on your description it sounds as if both data support a similar hypothesis/line of enquiry. If that is the case, publish one much stronger paper using two independent sets of data. All authors would need to be included. You could check with both teams to see if they agree. Speaking of which, have you asked them what they want to do?


Advice for dinner with prospective Ph. D. advisor and grad students?

To add to the Massimo's comment on not taking notes, yeah I think that would seem weird. If the conversation is about science, and a particularly interesting point comes up or you want to take note of someone's name to look up a paper, make a note on your phone.

Offering to pay might be polite, though if the prof's paying through his department or a grant I wouldn't insist. I think it's safe to say that if the grad students don't pull out their wallets, neither should you.

Just act normally. Be yourself - it is not a formal occasion. The prof will have invited his students along for two reasons:

Because dinner with just the two of you could be exceedingly awkward
So that everyone can get an impression of how you'll fit
in with the group.

Just make the usual small talk with his grad students to (hopefully) find some common ground, talk a bit about their projects, and make sure to have a good yarn about non-work-related things too. Your scientific prowess will not be assessed at the dinner table!


You're not really a student at your new institution until you have actually arrived and registered there.  At this point, it would appropriate to say something like:

  I will be a graduate student at Institute X with anticipated start date D

You can certainly update your CV to convey that information immediately.

As for other sites, typically they allow you to list a number of positions with starting and ending dates.  If their system lets you list a start date in the future (I haven't tried that on the particular sites you mention), then that would be a clear enough communication of your current and anticipated status.  Otherwise, you can write the same sort of "anticipated start date" line in your free-text personal description.


Choosing between Bachelors's in a higher uni vs masters in less reputable uni?

Paying for a masters degree in physics is a poor idea, even a poorer idea is a second BS in physics.
Get an engineering degree if you're going to spend your own money.


You’d have to check with the conference organizers. However, usually when such dinners are organized, the conference has already contracted a reduced price per attendee in exchange for a volume order with a fairly limited menu selected in advance. You usually don’t get to order à la carte off the restaurant’s menu.


Is writing an expository paper helpful for math PhD admission?

An expository paper is useful in the abstract, but how much it will actually help you depends on the circumstances.

The basic problem is that if you hand a random mathematician an expository paper on microlocal sheaf theory, they won't know what to make of it.  Is it even correct?  Is it plagiarized?  Is it completely routine (closely following standard sources), or does it show creativity in the organization or explanations?  Unless the reader has real expertise, they won't be able to judge it without a lot of time and effort, and there's a real chance that nobody on the admissions committee will have that expertise.  If everything goes well, they'll forward your paper to an expert who will give them an informed judgment.  But if that expert turns out to be busy or disorganized, your paper may fall through the cracks and end up not counting for much with the admissions committee.

You can get around this by making sure at least one of your letters of recommendation discusses the paper.  If the recommender can vouch for the quality and originality of the paper, then that will mean a lot.  Of course this means you have to convince someone to take a serious look at it, but your chances of doing this are at least as high as the admissions committee's.

If you are writing the paper under the supervision of a faculty member who is happy to read it and write a letter of recommendation, then that's great.  I'm not sure I'd recommend just writing one on your own, however.  It could work out well, but there's a risk of not getting much admissions benefit from it, so this would make sense only if you feel writing the paper would be a rewarding activity even aside from graduate admissions.

If you've already given talks that will be discussed in your letters, then that could be good enough.  An expository paper comes across as more serious and convincing than just some talks, but not necessarily enough so to justify the extra work.


How much background detail should go in the introduction section in a paper?

How much detail to provide in the introduction depends on the circumstances.  The minimum requirement is to give enough context and references that a diligent reader could fill in any missing background, at the cost of some extra work.  However, that's a pretty undemanding requirement; a few papers fail to do this, but they generally fail by not even trying.  It's often valuable to do more to make life easier for the reader.  How much more depends on who you expect will read the paper, and on what you believe they want or need from the introduction.  (Some papers are read only by impatient experts, while others attract a broad audience.)  What's considered appropriate may vary between fields or even subfields, but here are a few general principles:

Targeting an audience for your papers can be a self-fulfilling prophecy.  If you aim at a very specialized audience, it becomes much less likely that anyone else will read your papers.  Attracting a broader audience is on the whole a good thing, both for scientific progress and for your own career, so it's best not to limit your audience unnecessarily.  If modest changes will make your writing much more accessible, then they are probably a good idea.
It's easy to overestimate how much readers really know.  In an ideal world, every researcher would remember all the details of everything they ever studied, but life doesn't work that way.  Of course you can't re-teach things from scratch (and shouldn't even try), but sometimes a brief reminder can be really helpful.  This is particularly true when the details matter: if the reader really needs to know exactly how a certain algorithm works to understand your paper, then restating the algorithm can be worthwhile even if you suspect most readers will already be somewhat familiar with it.  Those who already know the details can easily skim just enough to convince themselves that their version is the same as yours, while those who don't can read more carefully.
The introduction plays a crucial role in describing the context and explaining why you did these things and what the consequences are.  It may not be the part of the paper that most excites you, but it will almost certainly be the most-read section (not counting the abstract).  The purpose of your paper is to communicate your discoveries, and making the introduction more accessible is sometimes the best way to achieve this.


How to contact professors for PhD vacancies?

To supplement the other answers, here are some do's and don'ts for email contact.

  The worst thing you can do is make it seem like you're trying to cast
  a wide net and don't have a clear focus. That's a guaranteed delete.

Therefore,

Narrow your search to the people whose work you're really interested in
Read their papers (especially recent ones - I've had people email me about stuff I did 5 year ago - I've moved on :))
Think about their work. Find something intelligent to say (even a question).
Email the professor and focus on those questions.

That's most likely to get my (their) attention.


Problems with gift authorships on papers and how to solve it

You should not agree to submission of a manuscript that includes an inaccurate author list.
Your coauthors should not submit a manuscript without your permission.
If they do that knowingly, you should tell the editor the manuscript was submitted without your permission.  This will lead to rejection or retraction of the manuscript.
You should be transparent with everyone involved about the author list.  People who might think they should be gift authors should not be surprised when the paper is published without their name.

In your case, it sounds like your colleagues cannot retaliate against you for doing the right thing.  Usually gift authorship occurs in a situation where retaliation is a possibility.


My internship is going to sponsor my bachelor's thesis (which will require more hours in the office). Should I ask for more money?

I don't think you have a lot of leverage here other than by disadvantaging yourself.

First, scholarship money is not always abundant and people like to spread it around to help more people, rather than to concentrate it.

And, you are getting something for your work, beyond the money. You are getting a degree. It isn't that they get your work for free. You made an agreement, I think, if I have a accurate reading here. Live up to it.

I think your statement that the company is holding you hostage is misplaced. In fact, they are helping enabling your future. Even just providing a project that you can develop into a thesis should be worth something to you.

I suspect that starting over with a different situation would be worse for you in every way: time, money, and more.


What do search committees really read in a CV during initial screening for a faculty position?

I'm serving on a hiring committee this year that received roughly 180 applications for a tenure track position in mathematics.  All of the members of the committee reviewed all of the applications.  Most could be very easily eliminated from consideration (PhD not completed yet, PhD in a field other than mathematics, wrong area, etc.)  Although I got through some of these easy applications in a minute, the better applications took considerably more time to review, and I ended up spending about 15 hours reviewing applications for the first round or an average of about 5 minutes per application.

When the committee met, we wrote down our top 20 lists, and it was relatively easy to select phone interview candidates, since only 18 candidates were on the top 20 lists of at least two of the committee members.  We offered phone interviews to 18 candidates and had 14 candidates who agreed to phone interview.

I don't blame applicants for submitting to lots of places, but the reality in mathematics today is that nearly all institutions will be able to find enough applicants to phone interview that meet all of their requirements, are in the preferred area of specialization, and have some post PhD experience (post-doc, VAP, or both.)    If you don't have these qualities, then you're not likely to get through the first round of screening.


What is the IEEE citation style for content obtained from wikipedia?

For correct citation of Wikipedia, see Wikipedia's guide to citing Wikipedia.  Since you are using IEEE styles, you should probably be using BibTeX to manage your citation, in which case you can directly use the BibTeX formatting template provided.


Publishing paper as a PhD student without advisor's name

I think there are actually two questions here. Firstly, the question you explicitly asked:

  Can I publish my own work(not my dissertation work) as a PhD student without including my advisor's name ?

Yes, of course you can. Assuming it will be of high quality, it will be accepted. That being said, it is somewhat unlikely that you will be able to generate first-class research completely on your own, without a professor or at least a more senior student or postdoc to help you get started. A problem might be that if you decide to submit to a conference, your advisor may refuse to pay for your conference trip. However, from your previous posts I understand that you work in a field where publications happen mainly through journals, so presumably that is not a big issue.

However, I think you also have a second question that you did not explicitly ask:

Will publishing alone, behind the back of my advisor, help me get a faculty position? (this is assuming that you are indeed able to get some good publications accepted without help)

Not at all. You will need a glowing reference letter from your advisor to have a shot at any reasonable tenure track. Communicating explicitly or implicitly that you decided that your advisor was an "idiot" and hence took matters into your own hands will not in any way reflect positively on you in a hiring process. Hiring committees, by and large, tend to be risk-averse, and your story has a big flashing warning light all over it. What you will need to do to get out of this is transfer, to a different professor or to a different programme.


Can I Publish a Book Based on my Ph.D. Thesis and Other Practical Findings I Found After My Ph.D?

There's several issues here.  One is the copyright of existing work, for instance your thesis, work you did for a company that now belongs to them, papers published in journals where you assigned the copyright.  That covers the specific words, figures, code and data you used in those places.  You may or may not have rights to those, depending on the terms of the agreements you made.

Another is confidentiality, for example obligations to your employer, trade secrets, upcoming patent applications, state secrets, etc.  You don't want to reveal things you aren't allowed to reveal, by either contractual obligations or law.
Law may also cover libel, hate-speech and other restrictions on freedom of speech.

Beside that, what's in your head belongs to you.  So if you sit down with an empty piece of paper and just write, all that belongs to you.  And if you want to publish that, nobody can stop you.


What to do when university has not yet reimbursed travel costs for a job interview?

In general, don't attribute inaction to malice or fraud when it almost certainly is just due to laziness, disorganization, or incompetence. University bureaucracies, especially in some countries, can be unbelievably slow. Sadly, three weeks is often not a particularly long period to go unreimbursed. Be patient and persistent and this will almost certainly work out eventually.


You should certainly list it, whether it is treated as a big deal or not. It won't have a negative impact. But if it is a formal course with evaluation and a grade, then it probably also shows up on your transcript. In that case, listing it again, probably has less value.
But, in an application for grad study, you could list it as part of your motivation for current study in some appropriate place. Certainly a willingness to learn "beyond the curriculum" is a good thing.


How to cite a deck of powerpoint slides with two titles?

This should be applicable for your problem in APA sytle.

  [Authors (if known)]. [Title of the matter]. Retrieved from [URL]. Slides [start]-[end].

Just keep in mind that the main purpose of citation is to facilitate the reader to be able to refer the materials you've referred. As long as you show clearly where to look and what to look for, your citation is considered valid. Citation formats are there for uniformity within the bibliography within the concerned journal.


How to ask a professor to join a project in a way that leaves him a "graceful out"?

I do not want to end up trapping either of us in an advising relationship that would be bad for both of us in the event he was just trying to be nice when he agreed to be co-advisor on my master's thesis.

Give him some credit and don't assume he would agree to a bad advising relationship just to be "nice."

Ask him directly. If he wants to say "no," there are any number of ways in which he can say it.


Do you need to read a whole article before citing it?

No, you don't have to read the whole paper.
If you think you do, ask yourself this:

  do you also have to read all papers cited in the paper?

For example, I recently needed to know a certain function of n. Some computer experimentation suggested that it might be 3*2^n, let's say. Then I found a paper published in a reputable journal that claimed to prove exactly that. As the reasons why it was 3*2^n were probably rather unrelated to what I was trying to do, I cited them but did not check their proof.

On balance, I think that making every author read every paper they ever cite would slow down the progress of science.

Caveat: this may be field-dependent. For instance, if the paper can be thought of as consisting of just one long definition, then yes, one should read the whole thing.


How to prevent an idea / innovation from being stolen or plagiarised

If you have an invention, patent it. It's an expensive and long process though. But it may be dangerous to publish the paper first. Your patent could possibly be denied if the paper is deemed "prior art". This varies by jurisdiction, of course. Keep it as a trade secret until you file the patent.

You can't actually "prevent" plagiarism. You can only try to reveal it.

If you publish the paper without obtaining patent on the "invention", then people are free to use the idea. They just can't legally violate your copyright nor morally plagiarize the paper. But, ideas are free to use.

If the idea is valid and novel, you might be able to partner with some company to exploit it. Don't reveal it, however, without non-disclosure agreements in place first.

Much of this requires a lawyer, of course.


Replacing a shorter manuscript with a longer manuscript on arXiv

If the new manuscript version supersedes the old one, and includes all of its content, I would suggest replacing it. After all, if, say, PRL would have asked for Supplemental Material which would have added up to another 10 pages, you would also have updated the arxiv version.
An added advantage is that people don't get confused by the fact that there are two different versions of the same result on the arxiv, and they don't know which one to cite.  (You would also loose citations this way, except on google scholar, where you might gain some; this could of course be resolved by adding the Journal-Ref field for both of them.)
Finally, if you decide to post two different versions, it would be a good idea to add a corresponding comment field to both publications, informing the reader about their relation.


I've developed a close relationship with my past graduate teaching assistant, and I'm very interested in her: is it appropriate to pursue this?

Since you are not working under her supervision right now, then assuming you are both adults, you are in the clear ethically, legally, and university policy-wise.
The only real caveats are that if you end up involved in a romantic relationship with her, she will not be able to write you a letter of recommendation, and will not be able to assume a supervisory role over you in the future. However, academia has plenty of dating and married couples working in the same department and sometimes on the same project. There are well-established norms for dealing with such situations, and no one thinks this is anything to get worked up about.
Good luck!
Edit: as I somewhat feared would happen, people are volunteering unsolicited advice about whether it’s a smart idea to enter a relationship with someone you may end up sharing a workplace with in some hypothetical future, based on further hypotheticals about what would happen if you end up splitting up or whatnot. Since I respect you as a fully autonomous adult capable of making your own decisions, I have restricted my answer to things you actually asked about and that are in the scope of the sort of advice this site is designed to offer. I would advise others to do the same. There’s nothing inappropriate about a romantic relationship in your situation. It may be a good idea or a bad one, wise or unwise based on numerous factors as with any question about whether two people are a good match for each other. But that’s not what you asked about, and has no connection to academia.


I got a C in a core class. Should I retake it?

An easy answer, from the viewpoint of grad admissions, at least: iffy grades are a blot... but/and, also, a serious question is about the extent to which "bad grades" reflect you understanding ... of things that need to be understood, not just gatekeeper stuff.

Also, you'll be competing against people who have reasonably-good grades... for whatever that's worth... but/and grad admissions committees will not see much up-side to admitting people who "show" worse than others.

Also, btw, it's not so hard to get good grades in undergrad stuff, even if one isn't ultra-conformist. True, it's also not hard to get iffy grades even when one has a pretty good understanding. But/and (!) in these days when everyone on the planet hopes to make a living as a computer-scientist (for example), not being prey to the standard tropes/weaknesses may be the selling point.

That is, maybe retaking courses to generate better grades that will mask old, not-so-good grades, is worth your time... unless, on a different course, you can do "genius-stuff" ... which makes schooling irrelevant, ... maybe.


You have no need to do anything. By contacting the author, you pointed out what you believe to be a flaw. It could be you are incorrect, it could be that they deal with this in a future version, it could be that they simply don't care. To me, this situation is akin to the following xkcd comic:

People perform research, good and bad, every day. Once it's published you can feel free to write an article refuting their conclusions, but until then it's just informal academic discussion, and there's nothing you can really do about someone else being wrong.

Disclaimer: Some disciplines may treat preprints as actual publications, and if so, the preceding does not apply. I do not know of any fields for which this is the case, but then again, there's a lot of things I do not know.


When is it acceptable to report classmates who cheat on an exam?

The answer to the title question is:

Always

(barring some sort of really bizarre circumstances that I am not able to think of right now).
The specifics of the situations does not make me change my answer in this case.


Applying to PhD Programmes with novel undergraduate degrees

Note that I'm answering this from the perspective of an applicant rather than someone on a PhD admissions committee.

  "(...) how would having one of those degrees affect an application as opposed to having a standard degree in physics?"

I don't think that the name of the degree itself would affect your application. However, I think it would be a good idea to make sure that you carefully explain the content of your degree (for instance, in your research statement/ statement of interest/ personal statement, or get one of your referees to do this in their letter), so that the admissions committee understands what courses you have taken and how these relate to a more "standard" degree scheme.

From the degree titles that you mention, I'm guessing that these will involve a large amount of normal undergraduate physics and maths, the names of which will also be on your transcript for the admissions people to see.

  "I'm also worried that such novel degrees would spark cynicism and
  distrust that could be disadvantageous to a potential application for a PhD."

The most important component of a successful PhD application is your demonstrated aptitude or ability to perform research. If you can do this, and do it well, then I think the name of your degree will matter less.

I speak from personal experience on this; my undergraduate degree is in Astrophysics, with a lot of specialised astro modules, but for my PhD I'm moving into theoretical cosmology, an area which is more commonly populated by applied mathematicians and theoretical physicists. I just had to make sure I "sold" my degree to the admissions committees by explaining that my degree was sufficiently theoretical. Getting some research experience by writing a dissertation during my fourth (Master's) year undoubtedly helped this.

If you're still worried about people distrusting the value of your degree, I would recommend trying to find out if the degree scheme is accredited in any way; for example, here in the UK, all reputable physics degrees are standardised and accredited by the Institute of Physics. I don't know what country you are in, but something similar may exist there.

Finally, as I mentioned in a comment, it might be best not to specialise too early (although you sound as though you have a pretty good idea of what you want to do). The option in this case would be to enroll on a straight physics degree scheme and specialise later on by taking any optional modules that are available (modules which would probably be mandatory if you were on the Quantum Engineering scheme, for example). The best person to advise you about the possibility of doing this would be the admissions tutor at the university offering these courses. They will be able to tell you what combinations of modules lead to which degree.


Lack of research opportunities in Israel

Are there any reasons for Israel seemingly not being (a) involved much in international research collaborations and (b) interested in foreign students/researchers?

Your assumption (a) is completely incorrect — it’s hard for me to think of a statement that’s further than the truth.
Assumption (b) is correct in the context of foreign students, and this has a simple explanation. It’s mostly a language issue: PhD programs in Israel are offered in Hebrew, and it’s extremely rare for foreign students looking for a place to do their PhD to be willing to invest several years to learn the language at the level they’d need to know it to be successful in doing a PhD. The ones who would entertain that possibility are small enough in numbers, and highly motivated enough, that there’s no need for graduate programs to do special outreach targeted at them. Any postings for PhD programs or positions will be in Hebrew, and if you are not a Hebrew speaker you will not be able to find and read them.
There are a few exceptions to this. The Weizmann Institute of Science has English as its official language and does attract a reasonable number of foreign students. Tel Aviv University has an English speaking medical school program and, I vaguely recall, a business master’s program. There might be other isolated programs for which the language barrier wouldn’t be an issue.


Well-acquainted professor does not respond when I share my work?

If you want a reference then you should send an email specifically asking for a reference.  Send it now, there is no point in waiting.

This doesn't really have anything to do with his response or non-response to your previous email, but if you like you could include a postscript: "By the way, I was wondering if you had a chance to look at the paper draft I sent recently?  If you have any comments I would be glad to hear them."

Two emails in a summer is certainly not a "burden", so forget about that.

Visiting the professor's office would also be fine, except that since it is summer he is not so likely to be there.


Journal sent review request to my supervisor but the email was addressed to me

Your supervisor does not want to accept this review request. Your course of action depends on whether you want to review the manuscript:

if you do want to review the manuscript, contact the editor letting them know about the mistake, asking whether you were the intended recipient, and expressing your willingness to accept the review. If the editor confirms that you were the intended reviewer, or that your review would be welcome, proceed with the review.

if you do not want to review the manuscript, just reject the request. It might be worth contacting the editor anyway and letting them know about the mistake, in order to make sure that future review requests arrive at the intended recipient.


Does it make sense to make exam grading very transparent?

Transparency is great, when you can do it.  Many of my large undergraduate classes would show a score histogram for every major quiz or exam, and some would explicitly give the grading rubric.  This was generally very much appreciated by the students for exactly the reasons you give: better understanding of how they stand and why they got the scores they got, letting them judge fairness and know when to reasonably object (which sometimes happened).

From the TA side, my experience was that transparency actually decreased my work, because it meant that I didn't need to deal with many spurious complaints, and that many of the complaints could be resolved directly through reference to the rubric.


My feeling is that unless there are funding issues, there would be some resistance to firing a postdoc unless there were real problems: the startup cost/time for a new postdoc can be high.

Having posted ads like these myself before, I can say that one non-funding-based reason to mention a 1-2 year postdoc is to allow for a hedge in case the hired person turns out to be really bad. In that case, you have the option of doing a first-year review and dismissing the person (i.e the default bit is set to NO and some activation energy is required to make it a YES)

In the reverse case of a two-year postdoc, the default bit is now YES and significant activation energy is required to make it a NO. If not done right, this could even lead to charges of unfair dismissal and so on.

So since there's a glut of postdocs and a short supply of positions, the "buyers" have some power to shape the position to suit their needs.


Letting another author know I'm using one of their results

Citing another is in no way "leaching". It is the natural course of scholarship. It took a long time for my dissertation to be extended, but I was very happy when it occurred. I was, in a small way, an inspiration for another. That is what we do in academia.

Send the email. Moreover, wait and hope for a similar email to come to you in the future. Too seldom do we get to actually thank the people on whose work we build.

And if the person is still working in that field, asking for collaboration is completely proper. In my own example, I'd left the field and had nothing to contribute going forward, but it was still a nice feeling that someone, somewhere, still cared.


Paid leave for a graduate teaching assistant

In the program I directed for many years, there was no provision for TAs to take paid leave.  They could take unpaid leave.


Are reviewers required to check for originality?

As I see it, the reviewers and editors don't have an obligation to redo the literature search.  However, the reviewer should be someone who is sufficiently familiar with the topic that they would be reasonably likely to know about relevant prior work, and should be able to identify serious omissions in the literature search. A reviewer who doesn't have that level of expertise should not be assigned, and if assigned should probably decline to review the paper.

Of course, if the reviewer does know about prior work that duplicates the paper under review, then they should require the authors to cite it, and evaluate the paper based on its novel contributions only, if any (or as an independent simultaneous discovery, if the timing makes that a possibility).

Final responsibility for the content of the paper always rests with the authors alone.  However, if the paper is accepted and later found to be a rediscovery, a common course of action is to print an "acknowledgement of priority", a short note citing the previous paper and acknowledging that it was first.  Typically it wouldn't be retracted.  (Of course this only applies if the editors believe the paper is really an honest independent rediscovery; if it is plagiarism then it should be retracted.)


What can I do when my e-mails to professors go unanswered?

Variants on this question come up a lot: "I sent an email to a professor about X and they didn't reply, now what?"

My untested pet theory is that it's related to imposter syndrome somehow.  People in graduate school, or entering graduate school, or otherwise just trying to enter academia, never feel like they belong.  You're clearly not good enough to be there, so you had better try not to make waves lest someone notice and rectify the situation.  So when a professor fails at something basic, like replying to an email, the automatic assumption is that it's probably a reflection on how little you belong, even in their inbox.

Don't get me wrong, I and every PhD student I've talked to have felt the same way, and I imagine that doesn't change at the post doc level either.

But the general answer given is "what you asked is reasonable and they should have replied.  Don't assume the worst, they're probably just busy.  Yes, you should absolutely follow up again after allowing enough time to go by from the first attempt."

From what you've said, this advice exactly fits your situation too.  Following up with a phone call might be even better - you're not accusing them of anything, or upset they didn't reply.  You're just helping them out with fitting you into their busy schedule.

The bottom line for me is that if they are actually sending you an implicit "no" by not replying, it is they who should feel sheepish when you follow up, not you.  We all face rejections at various points in our academic careers, and there's no excuse for avoiding giving timely, professional rejections to others when necessary.


The Formality and Informality Relationship in Academia

I do think that interpersonal skills are important in academia. A few ideas:

1) Tell your supervisor you would like to improve at this. Ask for suggestions on improving your verbal communication and email communication. Consider asking if there is a particular person who is effective at this that you could learn from.

2) Ask your friends to read over your email and have “practice conversation” with you while you are working on improving this. In important situations I always have friends read my emails before sending (common among my group of Asst Professors who are trying to climb the ladder).

3) Keep examples of effective correspondence. I have a coauthor who is loved by everyone and who is a master at asking for things in a polite yet firm way. I often refer to his emails to get ideas for my own.

4) For the arrogance problem, be careful how you state your facts. I have a student who will often state his opinion as a fact. Or will state something I taught him the day before as a fact he is explaining to me without acknowledging that I was the one who taught it to him! I know this is a cultural difference, so I try to be patient with this, but it is difficult because really dislike it. Consider using phrases like “As you know,...” “As you explained to me...” “I recently read in X journal that...” “To the best of my knowledge,...”

5) It also seems that your supervisors don't respond well to your disagreements. First, you are right to "pick your battles" as you have stated. In some cases you might decide not to disagree. My old boss used to say, "This will become self-revealing," by which he meant that the incorrect party will eventually realize the problem without a direct disagreement (it will become clear in the data, from other sources better positioned to disagree, etc.). Second, you need to learn to disagree diplomatically and tactfully. One approach is to distance yourself from the disagreement. Instead of saying, "I think this approach is wrong." you might say, "I understand that many people use this approach. I have also read some papers recently that argue that another approach is an improvement on that method in certain cases." You might also try to lead them in the direction you want to go by making it their idea. This usually comes down to asking questions. "Are there any extensions of that method in the recent literature? Are there any cases where that method is less preferred? What feedback about that method have you received from reviewers?" Basically, you want to disagree without being disagreeable and always allow the other party to save face.


Is it possible to remotely engage in a side project with a postdoc in order to gain experience?

You end your post with multiple questions. It is usually better to try to write one focussed post per question on these sites. However, I will focus on two questions that I feel are key here:

Would it be possible to do this project remotely?
How should you contact the postdoc?

Would it be possible to do this project remotely?

You can always ask to do a side project, research is about collaboration. Remote collaboration should be fine, given that that is how a lot of companies and universities are functioning now due to the pandemic. Zoom/Teams/Slack or something similar should work fine, use whatever the postdoc is using. Do go to your advisor first and see if they agree that this fits in your PhD or if you should do this on your own time.

How should you contact the postdoc?

An unprompted message might go unnoticed. Ask your professor if they by any chance know the postdoc you want to collaborate with. If they do, ask if they can introduce you and already vouch for your work. If they don't, look for another possible connection to do this. This will give you the highest probability of success. If you end up not being able to find somebody to help you, send them a message directly. Keep your message brief, direct and describe your background and how you'd like to help (depending on the topic you could help with for example data cleaning, analysis or visualization, literature reviews, etc.) and ask them if they have something for you, now or in the future.


How to address an Editor if I have new proof techniques of old results?

What makes this question challenging to answer is that it’s addressing the wrong level of generality: you’re asking about a very specific situation (publishing a simpler proof of a known result) but your questions suggest you’re missing basic facts about publishing of math research in general (how to “address an editor”, how to select a journal to send your paper to, and how to know if your research is even publishable) that have little to do with the specific situation you’re describing.

In terms of answering these questions, only one strikes me as answerable with the information you’ve provided: in math you don’t “address an editor” in any special way, you simply send in your paper using the process described on the journal’s website. If this involves an email to the editor, this need not contain anything more than a factual statement that you are submitting your paper to the journal. There is no need to “address” the contents of your paper or attempt to support the paper’s case for publication in the email - that’s the job of the paper itself.

For the other questions, I think you’ll have to find a knowledgeable person to actually look at your paper and give you advice about whether the results are publishable and what journal they will be a good fit for, how to choose a good title, etc. Those are all important questions but they would depend on much more detailed information than the mere fact that you’ve found new proofs of known results - papers meeting such a description can range anywhere from near-worthless to something that belongs in a top journal. Anyway, good luck!


Is choosing a journal editor in submitting a paper an important step?

Editors could be specialized.

For instance, I work in forecasting, and in an editorial board of a general forecasting journal, some editors may be specialized in sales forecasting, others in macroeconomic forecasting, others in judgmental modifications to forecasts, others in demographics or crime forecasting and so forth. I certainly make an effort to steer my papers towards an editor that is most familiar with my specific topic.

If the editor you picked is not a specialist in your particular topic, he will likely route your submission to an expert colleague on the editorial board, so just picking one should not be too important apart from causing a minuscule amount of additional work. Unless, that is, your abstract does not sound promising to the not-absolute-expert, or the editor you picked is busy, in which case the re-routing could cause a small delay.


PNAS citation style for chapters in a book series

Among other things, on its webpage PNAS supplies a LaTeX template for authors.  This template includes both examples of references and also a BibTeX style file that you can use for preparing references in PNAS style.


Funding after getting an Integrated Masters Degree

After much searching on various goverment websites, it turned out Find a Masters had the answer.

You are not eligible for a UK postgraduate student loan if you already hold an integrated Master's degree.


Where to send my research work for evaluation?

It seems that what you are looking for is a peer review. This is the first step after you submitted your work to a scientific journal that covers your field of work. Its purpose is to ensure the quality of your work and the contribution it makes to ongoing research. This said, in order to publish something in a scientific journal, you should have brought "something new" to the table. Nonetheless submitting your article will certainly lead to some feedback.

The second option I see and that you should consider first is finding a person on a close by university, who might help you out by reading part of your article and giving you some feedback.


How can a decent student find a doctoral advisor from another faculty?

Just in order to formally mark this question as resolved:

Thanks a lot to the people that showed concern in the comments! The things have worked out pretty good for me. The thing that I've personally learned from this struggle is that one should explore all the possible options, knock on every possible door and keep trying - if you are really interested in your subject, there will always be somebody who will be ready to share your interest.


Asking senior scientists for a subreview

You can always ask and they can say "no". It's surely not rude and weird; people are asked to review stuff all the time. The probability is not too low that one or more of them will say "no", but you may be lucky.

In my experience, more senior people are more likely to say "no", but of course if they say "yes" they will be the more competent reviewers. And some say "yes".

Don't be worried about asking somebody something that they don't want to do. If you ask and they say "no", it won't reflect in any way negatively on you.


It is unclear to me 'why' you want to give the job more time. Do you expect your workload to decrease? Do you expect your chair to become more reasonable? For academia to change their approach to work/life balance? If the answer to all (or even most) of the questions like this are 'no', then there is no point in waiting. And from my personal experience, the longer you wait in transitioning from academia to industry, the more challenging it is going to be -- and less satisfying.


How to overcome feelings of incompetence/failure in a PhD programme?

You have to accept that you are rusty and need to brush up on things. It is what it is, but there are others, myself included, who started a PhD after a few unproductive years.

The number one thing to do is not to take more classes than you're required to. If you are in the US system, there will be tons of homeworks and class work, so you need to make sure you will not fall too far behind. Your first objective is to pass the qualifier exam if your university has one.

But, you will also need to get an adviser, who will want you to do research. You need to pick wisely. Your adviser must be able to support you, especially if you are not allowed to teach. It is better to find someone who is a good planner and doesn't expect a student who takes classes and probably teaches to also do 60+ hours of research work. Not that it wouldn't be beneficial.

If teaching is included in the time balancing act, you have to be careful that your students do not abuse your time. Be strict with office hours, and be hard to find especially when preparing for your own exams.

The part with getting up to speed is harder, but be open and let people help you. If you have questions, do not be shy to ask your younger peers, or the course instructors. Also, participate in group study, especially if you feel it helps you and check homework results and discuss them with colleagues. You will learn a lot, but it will also help you understand more accurately where you stand in terms of knowledge compared to your colleagues. Even if you are more of an introvert and work a lot better alone, you still need the interaction with your peers.

Another thing is to plan alone time far from work. You have to have a more relaxed day, at least, when you don't have any work planned or you will end up burnt out and depressed. Also, if you have a family already, you have to understand that the PhD will take you from them more than a normal job would. Make sure you have a discussion with them where you set the expectations, and also try to leave the work at work as much as you can.


Does publishing books help with PhD admissions?

Certainly it would be a plus---even a good technical blog or a nice portfolio of posts on SE can be helpful.  It speaks to your level of sophistication and interest in the subject.  One can tell a lot about scientific maturity by reading someone's expository works---it betrays the way one thinks about things and can also give an indication of scientific awareness.

At least some of your letter writers should be familiar with the book and be impressed with it.  If you're lucky, some faculty at places you're applying may also be familiar with it as well.

For me, publishing with a well-known publisher would make a little stronger first impression (the publisher can lend the book a little credibility), but really what the letters say about it, or how the book reads if I decide to look at it myself (which is much easier for open access books) is much more important.  (Note: open access books or online notes can actually get wider circulation in academia than traditionally published books.)

This is not to say that writing a technical book is a good way to get into a PhD program.  It takes a lot of effort that could be put to other use if your only goal is to get a PhD.  But if you already have one written, it would be silly not to mention it.


If you can afford to do all that graduate study without a TA-ship or RA-ship, more power to you!  Perhaps you could get the two masters concurrently... or at least get some of the coursework for the aeronautical/aerospace engineering masters out of the way.  Maybe there will be some nice overlap that will speed things up a bit for you.

You could also take those a/a courses in the early stages of a PhD program in either field.


Recommendation letter from a supervisor after falling out

To begin with, most supervisors are reasonable, decent people.  So, the option of communication, depending on the nature of the falling out, is quite reasonable.  It is perfectly possible to finish a PhD with a substantially acrimonious relationship.  It might be best to study communication skills a bit first.

If that isn't practical, typically, the former supervisor has a lot of power.*  However, very few things are absolutes.  The purpose of a supervisor's letter is to gain insight from someone who has previously worked with you.  In the USA, in my experience, a certain amount of creativity is acceptable as long as you can fulfill that purpose.

For example, my PhD supervisor switched continents and became quite busy with startups without leaving a forwarding address...  So, I provided a letter of recommendation from another supervisor along with a note describing the circumstances for some fellowship applications.  No problems. Albeit, I worked in research in industry for several years.

*One thing many graduate students overlook is properly researching potential advisors.  The cost of a PhD, typically, significantly exceeds the price of a home.  And, typically, is much riskier.  Yet, somehow, students jump into PhD programs far more easily than they'd buy houses.  On the positive side, in departments I have been in, there have been a few supervisors with known personality issues and, within the department, accommodations were made for students leaving those groups.


Applying for a postdoc. Should I mention that I completed my PhD with no supervision?

Should I mention that I completed my Ph.D. with no supervision?

Definitely not.  "I had no supervision during my PhD." could be interpreted as "Nobody taught me anything during my Ph.D. so I am unqualified." or "I am incapable of giving credit to other people who deserve it." or "I am so obnoxious my supervisor will not interact with me." or "I refuse to work with others."  It is likely none of these are true, but the misinterpretation is a possibility.

What should happen is that your supervisor writes a letter of recommendation saying that you have shown a high degree of independence and that you now have more expertise in Y than they do.


What is the name of the interviewing/research technique where one sample generates questions for the next?

It sounds like grounded theory:

A study based on grounded theory is likely to begin with a question, or even just with the collection of qualitative data. As researchers review the data collected, ideas or concepts become apparent to the researchers. These ideas/concepts are said to "emerge" from the data.

Data are collected so as to let concepts emerge, and these emerging concepts are then used in the further collection of data. The concepts that emerge thus 'update' or 'feed back' into the next step in the empirical approach.


Letter of Recommendation from an unofficial college email ID

“Will it harm my application?” — Maybe, maybe not… it depends on the mindset of the persons who will review the application. The likelihood that it impacts negatively your application is probably not very high (there are more people than you think, even in non-rural non-Indian areas, who use commercial email accounts rather than institutional ones).

However, you are right there is some slight risk: there have been recent cases of people using faking email accounts for other researchers, e.g. in order to increase their chances in peer review. Because these cases have been publicized recently, people may be more wary of non-institutional addresses.

But more to the point: what can you do? — Not much. If the format  of the letter is free, ask your letter writers to use official letterhead from their institution… Otherwise, try and see if your letter writers are listed on their institution's public pages, at least, with their email address: that way, the person receiving the application will be able (if he wants to) to check their identity.


Listing awarded grants not affiliated with a university research position on a CV

Your CV is a list of all of your scientific credentials, not just all of the credentials that you happen to have gathered while in a university research position.  Whether you obtain your grant at a university, a non-profit, or a for-profit company, in all cases it shows evidence of your ability to engage with funders and obtain external support for research, education, outreach, technology transition, or other such activities that are important in academia.  Certainly, for my own part as a scientist working at a for-profit company, I quite comfortably and proudly list the funding that I have obtained for my work on my CV.


Should I include a "prestigious" invited-only conference/workshop on my CV?

I'm afraid of appearing over-proud of a minor deal.

In general, you should not worry about this.  A CV is a document where you are supposed to "sell yourself".  Everyone expects you to highlight those things that show your ability, experience, and recognition by prominent people in the field.

This makes many people uncomfortable, since talking up our own achievements is not the norm for most of us.  However, it is the right thing to do for a CV.  List anything that provides evidence that you are a strong candidate.

Is it possible to have a CV that appears "over-proud"?  Yes, if you did something like clearly exaggerate your experience, or use boastful language.  But merely factually listing something you achieved or participated in is not going to create that impression.

As for this specific workshop, definitely put it on your CV.  The fact that prominent researchers thought you were worth including in this event speaks well of you.  I wouldn't call that a "minor deal", especially for a PhD student.


I cannot tell you what authors would care in general, but I can tell you that most authors I know would not care at all. No one gets a dime from a paper anyway.

I advise you however to not mention such a detail: it's actually irrelevant in that context, because you would be writing to discuss the content of the paper, not the ways to get access. When you write to someone, especially someone you don't know, avoid irrelevant details: people are busy.


How much study gap is acceptable in New Zealand?

It sounds like you have still being doing research and publishing since your masters. If you have still been keeping your skills fresh, that means you haven't really had a gap, regardless of whether or not you were registered as a student. Just explain this when applying and your gap will not be a concern. Your recommendation letters and publications can attest to that fact.
Age should not be a concern from the university's perspective. Although, a prospective supervisor may wonder about your perspective -- why do you want to do a PhD now? why not earlier? If you can give a good answer about your aspirations, then that will allay any concerns.


The Directory of Open Access Journals (DOAJ) is an attempt to create such a list for all fields, including the social sciences:

  DOAJ is an online directory that indexes and provides access to quality open access, peer-reviewed journals.

They have a search function that lets you drill down to specific fields.


Citing multiple Github repositories with a single citation

There are really only two solutions to this problem, and which is appropriate depends on the customs of your field:

Name the repositories (and possibly give their URLs), but do not formally cite them. In some fields this will be unacceptable, others it's up to the author, and in yet while others it is considered unacceptable to cite a non-peer-reviewed source like a repository (I have had journals force me to de-formalize software citations before!).
Shrink something else to make space for the repository citations. You may think this is not possible, but I promise you that you can get the few lines you need without significantly affecting content through minor tweaks in wording, layout, and such (including in reference contents!)


Possibility of doing PhD in astronomy with only masters in CS

In Sweden there is no hard requirement. (In Spain, for that matter, there isn't either, but I don't recommend going for a PhD there). You just need to convince a professor that you are a good asset for the team. The way it works here (and in some other countries in Europe) is that the PI gets funding and hires whomever he wants, based on whatever criteria. Other countries make the decision at a department level, usually putting stress on the marks. Anyway, the difference is convincing one party or a few.

It is true that all the people I know in the closest related department, are physicist, but they do a lot of programming and data analysis. Your strong points are:

You can improve code quality. (I have seen code that gives me nightmares.)
You can implement new algorithms.
You can learn the physics along the way.

CS backgrounds are, by the way, quite common in Bioinformatics and, to a lesser degree, Biophysics.

References:

I am in Sweden working in Biophysics, and my girlfriend is doing a PhD in Astrophysics.


May I upload the preprint version of my article to ResearchGate before publication?

First you should note that ResearchGate is unlikely to be considered self archiving by the publisher. While they may allow it, you should confirm. You should also ask about embargo periods. Assuming the publisher has told you the publication date is compulsory when self archiving, it is not unreasonable to ask what you should do at this stage.

In the absence of guidance, you could use something like forth coming or in press in place of the date.


Can I tell the PI who has offered me a postdoc job that I have not decided yet waiting for other results

I think you are right about not accepting multiple offers. But that isn't the same as not considering multiple offers.

Unless you have a special relationship with the PI you don't actually owe him or her an explanation of why you are waiting. It would, however, do you good if you could give a date, not too far in the future, by which you will let him/her know.

Of course, it is possible that the offer could be withdrawn, rules permitting, but if you wait to accept you can't control that.

I wouldn't probably say I was awaiting other offers, or give a false reason instead. It is enough to say that you aren't yet quite ready to make a decision on such a big step. Yes, that sort of thing is a bit of hedging, but probably called for, since you are actually hedging.

But don't put them off too long.


What could be the reasons to be rejected as a Doctoral Candidate in Germany?

Without knowing more about your specific case, here are some potential reasons (in no particular order) why you might not be getting the job(s) you are applying to:

your profile/prior experience is not as relevant as you think it is for the position
they already have somebody in mind
they might think, having been in the industry for some years, you will look into doing research as a "9-to-5 job" (for better or worse, in most countries academia is different than industry). I am guessing this is what you refer to, with mentioning kids? I have plenty of colleagues with small children, that alone is not a problem.
they are concerned you do not fit the rest of the team
they found somebody better than you
they might be concerned about your reasons for switching to academia

Without more information it's impossible to say which one, if any, or which ones apply to your case. Your best bet to ask for feedback when you are given a rejection. It's important, and I cannot stress this enough, to be polite when you do so. The idea is to get meaningful feedback so you can improve your chances for your future applications, and definitely not to get a justification for their decision. They have absolutely no reason to justify their decision to each individual applicant.

What kind of feedback you get back will ultimately vary, sometimes you get a meaningful message with relevant feedback, other times you will get the boilerplate "we regret to inform you..." and not much more than that. Most often you will get something that is general enough, but with some nuggets of feedback.

For example, I recently got a rejection from a consultancy company I sent a general application to. I was introduced to them for the first time last year, when they were attending a career fair part of a conference I helped organize. I asked for some feedback, and in between the typical corporate HR BS, there was the indications that they had pivoted away from the areas where my skills would be valuable to them. So my take home message from that is that this company is not relevant for me anymore, even if it may have been last year. And yes, even if the job description fits my CV really well, they are not looking for someone like me.

I am giving this example only to serve as an example, I am sure your situation will be very different. But the point is, try to read into whatever feedback you might get.

Lastly, if I were you, I would try and see if there are any possibilities to get some career coach or something like that. It would be good to get some recruiters point of view on your CV.

EDIT: I noticed that I didn't address some of your questions

  Are there some special differences applying for jobs in the industry compared to academia?

Well, yeah... I would guess that academia would put more weight on your prior education, what courses you have done, whether or not you have published anything etc.

Industry, I reckon, cares more about your prior work experience, i.e. what you have done before.

The core difference is that academic positions are aiming at you developing your skills, learning new things, acquire a critical understanding of complex subjects. Industry positions primary require you to do something, have a contribution in the value chain in whatever the company is selling to its customers. You improving your skills, learning new things etc is a secondary concern. You being critical of your own, others' or even your superiors', work would not fly as well in industry as it does in academia, I would guess.

  all applications were the same as I would apply for a job in the industry, which was always really easy and successful - max timespan from sending the application over the interview to job offer was about 1-2 weeks

How many jobs have you applied to? Think of it as a sports stat, if your 3-point percentage is 1/1, sure it's 100% but you are hardly league's best 3pt shooter. :)

In general, I think academic positions are not filled as quickly as industrial counterparts. There are many things that need to be cleared by the dept/faculty/university admissions etc. Also the positions need to be open for a minimum of X working days, depending on the institution.

TLDR: Stay patient, ask for feedback, keep trying


Is it recommended for a professor to not entertain advanced questions for a basic course?

1) How should a professor react to the most advanced questions from her students of a basic course, if (s)he knows the answer?

I would distinguish between reasonable and obnoxious questions.

If the question is reasonable, then I would give a concise answer and encourage "offline" follow up. The question in your example seems reasonable -- it's essentially "how wide is the gap between what we're learning and what's actually used?"
If the question is obnoxious (e.g., student is just trying to show off), then I would consider giving a very concise answer (one sentence), or else explaining that you don't think the question is a good use of the available time (and, optionally, encouraging follow up in office hours).

  2) How a professor has to react in the classroom for the advanced questions that (s)he doesn't know the answer?

I'm not sure one has any choice but to say "That's a good question, but I have no idea" or "I have no idea, and I doubt it matters for the purpose of this exam."


How to find out if an author is practicing pseudoscience or is fraudulent?

Context: I'm a PhD student in Computational Social Science, so I'm very knowledgable about Complexity Science and related fields and how they are applied to design, architecture, organization science, and economics.  Also, my adviser is a leader in the field of Design Science, particularly how Cognitive Science and AI can be applied to understand design and designers.  Finally, I have a lot of domain knowledge regarding Pattern Languages and generative models of conception and design.

  Is there any way to find if I can trust these authors?

I've encountered many authors, researchers, and consultants who I have identified as "charlatans" when it comes to applying Complexity Science or other models or theories to social systems.  For the most part, they apply Complexity Science only in a metaphorical sense (e.g. "edge of chaos" concept), but have no basis or foundation in empirical or theoretical research.

But to determine whether any particular author is a charlatan or not, there is no substitute for you understanding the underlying theory or method. There is no reliable method for you to determine whether author A has a valid foundation in theory X unless you do your homework and develop a working understanding of theory X.  If, on the other hand, you stay with your position that "I'm not a mathematician", then you have no basis for deciding either way.  Looking at what other people say or citations will not help you, in an academic sense.

If you don't want to do the work to understand the mathematics, computational science, and formal methods that these author use, then just go another direction.  If you must include them in your papers, then just say that you have no opinion on their validity or significance because their methods/theories are beyond your grasp.

Finally, just because you don't understand the mathematical and computational methods these authors use their theories doesn't mean there is any "junk science" going on.  As Steven Covey (7 Habits) advised: "Seek first to understand."

Edit: Whether or not these authors have tenured positions at important Universities is not very good evidence regarding whether their "science" is "junk" or not.


If no funding is available at the time of admission, what are the chances of getting funding later, and when would I find out?

Yes it is possible, but more likely during the PhD level (it happened to three friends of mine). So basically they got the acceptance letter, they might even gave an initial fee (e.g., for first 3 months); and then, the supervisor worked out how to apply for a funding from the university or put them in a funded project.


How do I cite or refer to the sources I am using?

Different institutions/publishers prefer different citation styles, there is a whole range to choose from. Popular ones include IEEE, MLA, Chicago, Elsevier, etc. You ought to refer your thesis writing guidelines as mentioned by your institution or ask your advisor for further clarifications on this one.

  In which places is it appropriate?

If you understand why citing is important, you would know that you ought to cite every source you refer. Especially considering that your academic thesis is work you claim as your own, you ought to differentiate between what comes from you and what comes from others.

  If I include a theorem from some source, internalize the proof strategy and then formulate a proof without peeking at the source, should I mention the source of the theorem?

Yes, you should. The theorem proof may be yours but the theorem itself isn't. As @JeffE suggested, cite the original source of the theorem, if you could find it. Otherwise, search for another secondary, yet credible and accessible, source of information that would point to your theorem.


I think that this will be good practical experience for you, regardless of whether you're proceeding to further study.

A few things to note:

Discuss your plan and involve your supervisor in your preparation of the manuscript. The reason for the first is that statistically significant results and a potential research gap aren't sufficient in and of themselves in guaranteeing acceptance. The reason for the second is because there's more to submission of a paper than simply writing it. Your supervisor will be able to provide you with guidance.
Read and dissect some papers from the journal to which you plan to submit. This will orient you about the style of writing, formatting, referencing, etc. Certainly, read the instructions to authors, but also be guided by good samples from the same journal.
Prepare emotionally for the review process and the decision. First time authors are often surprised by the delays, unhelpfulness or viciousness inherent in the peer review system.

Good luck to you.


In other words, can I go to a postdoc looking to talk and ask questions related to our field?

It depends on what you mean by "can", as well as the culture in your field and department.

If you are asking whether it's an ethical and reasonable thing to do, then the answer is certainly yes.  You can talk with and ask questions to anyone you'd like, provided you appropriately acknowledge any assistance you receive.

If you are asking whether the postdoc has an obligation to provide substantial assistance or tutoring, then the answer is quite possibly no.  It's hard to give a definitive answer, since precisely what the word "postdoc" means varies between fields and departments, but you shouldn't assume supervising graduate students is a serious part of the job unless you have some confirmation that this is true in your scenario.

If your questions are genuinely interesting and thought-provoking to the postdoc, then they will probably be happy to chat with you.  You may also get a good response if you ask about topics that are truly difficult to learn about elsewhere, so that the postdoc will be sympathetic.  On the other hand, if you try to lighten your workload by asking the postdoc relatively routine questions so you don't have to bother looking things up, then they will probably lose patience with you.


How do I cite CVPR workshop conference "short" paper?

Clearly.
The main purpose of a bibliography entry is to properly identify the work, with enough information that (at least in principle) your readers can find the work and read it for themselves.  If the github.io repository doesn't suggest a citation format, make up something reasonable that serves that purpose.  The precise formatting doesn't matter (or if it does, the editor will fix it for you).  For example:

[10] J. Smith and R. Tyler.  BADWOLF: A temporally agnostic relational
database information system.  Presented at the 13th Gallifreyan
Workshop on Untempered Schismatics, Arcadia, December 2020.
https://torchwood.github.io/badworf.pdf


What is a "Graphical Table of Contents" Abstract?

Some publishers (ACS I'm lookin at you) have what they call GToC, which is like a ToC with small images. You might have seen such in some magazines, here's an example.

Accompanying the image is usually a short text that is sort of like a teaser for the article, in a way the coolest tidbit about what you have written. I believe that's what they are asking for here.


Can a professor grade students based on what she "remembers" with no proper record?

Check if your school has a grade appeal process.

Many schools in the US have one. It will bring in some other administrators (e.g., chair of the department or dean) to review your argument and assess the professor's rationale for giving you the grade.

You might have a good chance with this since she has no written justification for your grade or other student's grades and relies only on her memory. Additionally, if you can remember what you spoke about during the class on specific days (and the students who spoke immediately before/after you), you might want to go ahead and write that down so that you can bring it up with your appeal.


Can a person of average intelligence get a PhD in physics or math if he or she works hard enough?

I recently reread Malcolm Gladwell's book Outliers, which has a discussion of this very point, i.e., IQ versus academic success.  The gist of it is that, like it or not, the IQ test robustly measures something so that a score below X will, with high probability, prevent academic success at level Y.  E.g. a child with an IQ below 50 will have trouble taking classes with other students.  I just checked the passage, and he claims, quoting from Arthur Jensen's book Bias in Mental Testing, that with high probability someone with an IQ of below 115 cannot graduate from a university with grades that will get them into graduate school.

One key phrase in the above is with high probability.  Thus no one is claiming that such success is impossible, but it becomes significantly more unlikely.  Another important point -- in fact, the whole point of this part of the book -- is that while having an IQ above the threshold seems to be important, the importance quickly disappears past the threshold.  In particular, though we may disagree whether the IQ threshold for getting a PhD in mathematics is 100 or 115 or whatever, beyond a certain level there is no significant correlation between IQ and academic success.  You might expect someone with an IQ of 175 to have a huge mathematical advantage over someone with an IQ of 125.  But this really seems not to be the case.

Let me say finally that this answer should not in any practical sense be discouraging to anyone.  If you or anyone else is wondering whether you have the intellectual capacity to get a PhD in mathematics -- you don't find out the answer by taking an IQ test, you find out the answer by studying mathematics and doing the best you can.  Someone who has a measured IQ of, say, 95 but gets a degree from a reputable university with excellent grades in challenging courses and competitive test scores: of course such a student should seriously consider getting a PhD in mathematics if they are interested, and should not be dissuaded at all by their "low IQ".


How to cite something when you cannot remember where you've read it?

Since you're already here, an obvious step would be to post a question on a relevant Stack Exchange site. (Other websites are available.) Such questions are routinely asked and answered on MathOverflow, for example.

Similarly, asking colleagues can also work. They don't necessarily need to be people you know personally either. There's often someone in a field with a reputation for a "near-encyclopedic knowledge of the literature" you could send an email to.

However, if nothing works, honesty is the best approach. Just present it as a known result of unknown origin, or something to that effect. Here's an example where that kind of formulation is used for a problem, not a result, but the same idea applies.


I suggest studying the techniques used in one-room schools.

The idea is not to even try to teach one lesson to the whole class. Instead, you get small groups doing work appropriate to their level, while moving around and giving instruction to groups as needed. Generally, the younger students will need the most attention.

For example, you could set a group of the most advanced students to first translate a passage individually, and then discuss, in French, the differences between their translations. If they disagree about a translation and cannot resolve it themselves, they will need your help for a few minutes. Gradually make the passages more difficult, so they go on learning. Periodically, explain an advanced point of French grammar or usage, and then set passages to translate in each direction using it. You can tell them to use the new structure when translating to French.

You can also use more advanced students to help teach. Trying to explain e.g. a tricky point of grammar can be a good way of clarifying it in one's own mind.

Meanwhile, you can be working with the beginners, who will need more direct instruction.


When should one publish code publicly on GitHub: during or after journal review?

Particular to your situation, I think the exact answer is highly dependent on some missing information:

How do you plan to license the code once released?
Do you have some sort of agreement with the journal that the code is part of the manuscript that they will own the copyright to?

In General: When should one release the code relative to publication? Before! (Allow me to explain)
My knee-jerk response was "why isn't the code already on GitHub (or another hosting site)"?
By publicly posting the code, publicly affiliating yourselves to it, and having a time-stamped "paper" trail of commits. I would expect this provides a good hedge against being "scooped", similar to, but more robust than, the old signed-and-dated lab books for maintaining development records in the case of IP/patent disputes.
I work, directly or indirectly (and often in a very minor way) on computational chemistry code, but we write the code and store it in a GitHub repo where it's public facing and has open source licenses. The code either gets cited in papers that use it (not necessarily well - see this question) and/or there's an article written up detailing the software that provide details specific to it (and maybe even later publications of new major versions with added features, e.g. RMG and RMG 3 with actively-developed source here)


Elsevier's 'MethodsX' journal as an additional article to my original research article (plagiarism)

The MethodsX journal says, as part of its guide to authors:

  Your submission can also be an extension of a previously published original research paper, whereas your MethodsX paper will include all of the technical details that might not have been included in your research paper.

It also has an extremely abbreviated format,

  an abstract to outline the customization
  a graphical abstract visual to illustrate what you've done
  the method(s) in sufficient detail to help people replicate it, including any relevant figures, tables etc
  at least one reference to the original description of the method you're using

Thus, for a properly prepared MethodsX article, I think that any question of plagiarism will be moot. Abstract and context material will need to be heavily paraphrased for its new context, and any repeated material on the method will be explicitly cited as an adaptation (with permission) of the original paper.


Co-authors decided to remove most of my contributions from a Nature paper without my consent

First, take the time to carefully consider your options.

From your description the problem looks like a disagreement between co-authors: the behaviour of the corresponding author is careless and disrespectful, but it doesn't look like a major breach of ethics. Turning this into a legal battle might cause a lot of trouble, especially in a large multidisciplinary project. This could damage your reputation.

This is why I would suggest a more subtle approach first:

Ask your co-authors why the article has been shortened and why your parts have been removed.
Try to negotiate with them: explain why you think some parts you wrote are really important and should be added back
If this does not work or if too much of your work has to be removed, ask to use your contribution to write another paper for a different journal/conference. This time you would be the main author and present your work as you see fit. Your co-authors can hardly refuse this to you after cutting your part.


Journal does not tell me why they rejected my paper, even on request

"Following a review of the manuscript by the editorial board, we have regretfully decided not to consider this work for publication. We thank you for your interest in our journal and..."

This sounds like an editorial ("desk") reject more than anything else. Hence, there typically is no formal, written review that the editor could forward to you. It is just that the handling editor and/or the Editor-in-Chief have decided that the paper is either of low enough quality, or so clearly out of scope, that running it through the full-blown peer-review process would be a waste of reviewer time. While this is of course a harsh judgement for your submission, the editors are entirely allowed to do this - there is no formal "obligation" that any submission will have to be peer-reviewed before it can be rejected.

  What can I do in this case? Note that the only thing I want is to know reasons for the rejection.

Realistically, not much. Of course it would be nice if the editors at least gave you some informal pointers why your submission was desk-rejected, e.g., "I am sorry but your submission is out of scope for this journal", but maybe if your request was combative enough, the editor decided that she/he rather did not want to get into an argument with you about this. Anyway, I doubt that there is an obligation on the editor's side to always fully justify each rejection. At the end of the day, acceptance of papers is always a discretionary decision by the Editor-in-Chief, and not something you can formally object to.


Is it bad to apply to one PhD program with the intent of leaving for another (more prestigious) one?

This would be wrong.

The reason the PhD is subsidized, while the master's is not, is because you are making a longer-term commitment to the university, and they expect to benefit as an institution from your PhD work.  You would be accepting this under false pretenses.  In my opinion, this is just wrong, apart from whether it harms you or not.  You should not enter into agreements where you never intend to hold up your side of the deal.

It would also not work as well for your plan.

I think it will be hard to produce evidence, based on 6 months or a year of a PhD program, of your improved academic performance.  But you could actually complete a master's degree in a year's time, and that would be something that would really help admission into a PhD program.

Leaving shortly into your PhD program is definitely frowned upon.

Universities actively try to stop this from happening.  For example, they usually do not allow people in PhD programs to convert their work into a master's degree after a year or two of study, precisely because people would try to take advantage of this loophole to get a free master's.

This will look bad to the institution you are leaving.  I'm less certain about how the institution you are going to would view it, but it seems a potential negative there, as well.


Is it ok for an applied mathematician to research a topic that she has personal experience with?

I do not have experience with specifically applied maths, but in general, there is no problem at all with conducting research in a direction that you have some personal connection with. One could argue that many applied research projects are driven by concrete needs, and I fail to see why those would have to be needs of other people rather than a researcher's own.

That being said, you will need to remain cautious of your own bias in your endeavours. As a researcher, it will be expected of you to work on the topic from a neutral, scientific, "big picture" perspective, which is easy to lose if you are at the same time also part of this "picture".

Let me provide one example from my own research. I conduct research on software engineering. Many of our best PhD students have worked as software developers prior to starting their PhD, so in a way they are also part of the same demographics that they research. What can now happen with inexperienced students is that (s)he will, for instance, interview developers with regard to a specific problem, process, or practice, and, during the analysis phase, discard statements that go against their own prior experience as "obviously wrong" or "bad". In that way, a student may overemphasize results that resonate with her/his own prior experience, and discard results that don't, essentially guaranteeing that the results are in line with what the student expected going into the study based on her/his own experience.

You will need to make sure that you do not run into the same trap - don't assume that everybody experiences your health issues the same way, that you are some sort of gold standard of this specific condition, or that your specific variation is more important or relevant than others. However, these are definitely issues that a good advisor can help you with.


How I can politely ask him for his contribution?

Just sent him/her an email with a brief summary of the ideas you are interested in and ask him/her if he/she is interested on the project, it has worked for me. Otherwise, try to attend one of his/her talks and approach him/her and the end of the talk, if possible.

How about the contribution, to be more exact, the order of names?

Perhaps it is too early to discuss about this ("Before one brings home the bacon one must kill the pig"). Who knows whether he/she is going to generalise or improve the ideas you propose or he/she would barely be involved in the project (you will come across all sorts of characters while doing research). A safe option is to use the alphabetical order. It helps to avoid many ego-fights. Start with a document without the name of the authors. If you end-up with something worthy of publication, put the cards on the table and ask directly "what order would you be more comfortable with?" or "would you be happy with the order 'ME and John Doe'? ".


Consequences of applying for two (or more) programs in one university

When I applied to graduate school, I sometimes sent applications to two departments within the same university because I could see myself being a fit for either department. In fact, at least one school had explicit instructions for applicants to two or more departments, so it is likely not as uncommon as one might think.

My experience was that it didn't really matter that I applied to two different departments within the same school. The biggest issue was making sure that things like my GRE scores and letters were sent to both departments instead of just one, since somehow there were mix ups along the way. In terms of the review of my application, I don't think there were any drawbacks because there was no overlap between the two review committees (i.e., no one who reviewed applications for department #1 also reviewed applications for department #2). As such, expressing different ideas in different SOPs, etc. did not have any impact on my admissions to my knowledge.

I would, however, caution you against applying to two degree programs within the same department (e.g., the Master's degree and the doctoral degree). Since it's within the same department, chances are high that the same people will be reviewing both applications, or at the very least, it is likely that someone will notice that you applied to two different degree programs. This might come across as a sign that you do not fully know what you want to do, which can hurt your application to both programs. Many departments (although certainly not all) have a policy where if you apply to the PhD program and are rejected, you can automatically be considered for the Master's degree program. If you know you ultimately want to apply for a PhD, I would apply for the PhD and see if you can be considered for the Master's program if your application is unsuccessful.


Professor not replying to my email. Why?

Expecting an overnight reply to any email is unrealistic. He may have some issues of his own to deal with, given the worldwide pandemic. He will probably reply "in good time", but by his standards.

Whether you are allowed to take a make up or not we can't say here. It is up to him and to the institution. I hope it is allowed and expect it would be given the family emergency. But the other things you mention have little bearing on the issue.

But waiting a week after the missed exam wasn't wise, and expecting an instant reply after you didn't offer an explanation for a week is a bit "over the top".

I suggest that you wait to see what the reply is. There probably isn't really a need for instant action at this point.


What does it mean when it says on a grad school application to choose recommender "familiar with the candidate's scholarly abilities"?

It doesn't necessarily mean your research advisor. It could be a faculty member you've taken classes with, someone you've worked on a project with, etc.

What the admissions committee is looking for is evidence that you will succeed in graduate school - and that means evidence that you can think independently, tackle difficult problems, and so on. Choose faculty members who can speak to your abilities as a student and a (future) researcher.

When I asked for LoRs, I asked (1) a faculty member I had taken several classes with and with whom I was working as an undergraduate research, (2) another faculty member I had taken several classes with and had a good working relationship with, and (3) a faculty member who I was currently taking a class with (and who admittedly was an alumnus of my top school) :-)


How to respond after co-authors revise rejected paper without informing first author?

A lot depends on the particulars of the situation, but the principles of academic honesty are pretty straightforward here, and an answer for the particular situation can be derived from those principles.

The basic principle is that every involved author in a work has a stake in that work and the consent of all authors must be obtained before a work is submitted.  Most journals actually explicitly ask about this, and the better run ones will send email to every author to inform them so that they have a chance to object.

Somebody who was once author, however, can become uninvolved in one of several ways:

The author may object to the nature of the paper and explicitly withdraw from authorship.
The author may stop fulfilling their responsibilities for authors, in which case they should be kept as an author but might have their position in the author list change based on how the manuscript continues to evolve.
The author may have had a minor role (e.g., in a many-author biology or physics publication), and choose to give blanket consent to whatever the primary authors believe is acceptable, rather than be involved in detail.

So the first thing to determine is, did the first author effectively drop out of their responsibilities?  As the lead author, a first author needs to discuss the fate of the rejected paper with the other authors in a timely fashion.  If the first author instead vanishes (e.g., changing positions and not staying in communication about the work), then it is entirely reasonable for the others to pick up the paper again.  The first author might or might not stay first then, depending on how the paper evolves, how much new experimental work is done, etc.  If there is a decision not to proceed, however, then anyone who changes their mind and wants to revise and resubmit needs to re-involve all of the authors again.

If it is the case that the others acted inappropriately, then the action to take depends on how important the paper is to the first author relative to the relationship with the other authors.  The range of options includes (from least to most bridge-burning):

Ask to be involved in further revision and authorship discussions (assuming the paper isn't already published)
Stop collaborating with the other authors (if the first author is aiming to be a career scientist, there will be many other papers with better collaborators)
Request a correction or retraction from the publisher

Scientists are people like everybody else, and have everything from stellar working relationships to innocent miscommunications to nasty misbehaviors.  Start from the assumption that there is an innocent misunderstanding, but if there is real misconduct involved, the best thing to do is to balance protection of yourself and warning of others as best fits your situation.


Applying to a masters program based on university rankings?

Is it stupid to go to a university which is ranked around 160 by Times Higher Education for a Master's degree?  You should consider additional information.  First, I recommend deciding what you want to do after getting your master's degree.  Then consider if the degree program you are applying for will help you achieve that goal.  If you are not sure, check the program or school website for statistics, or contact the program's alumni for advice.

Since this is the academia stack exchange, let's assume for the moment you want to continue in academia.  In this case, the university's reputation (which is correlated with its ranking) is very important, but the specific program's reputation is even more important.  (edit: People who know little about you will judge you based on the institution/program where you got your degree, because it is easy for them.)  Working with a well-known faculty member can also have great importance.

Certainly rankings will not inform you if you will like living or working at an institution.  Finally, normally each time you change institutions the prestige of your new position will decrease.


What is a good way to tackle difficult technical questions during graduate interview

Relax it is the most important thing; if you are stressed it will show. Also people ask tough questions not only to see if you get the answer right, but also see how you get to the answer, and to see how you respond to the answer you gave being challenged and questioned.

Also If you don't know something or are unsure but think you could have a stab at it say so. Some people may not appreciate this but other really do. I have left a couple of interviews (I got the role) where people commented on my honesty. The person asking the question generally knows the answer, so don't BS them.

Talk of people knowing the answer, I worked with one guy who used to want to know the answer to esoteric or difficult technical stuff, so asked the same question to at least 2 candidate, and had a set of 5/6 questions. They would design chunks of the system in the interview, and then he'd pick the best guy. He had no idea what the answer should be, but figured if two people gave the same answer it was probably in the ballpark.

As I said at the start relax, one way to get a second to think is take a sip of water before answering. It allows you to get your thoughts in order after the shock of the questions. Also ask for clarification, even if you understand the whole question, again 5 seconds can be enough to pull you head back to the task, and dredge up those critical facts.


Quality of English in a college recommendation letter

The people reading a recommendation letter are interested in the following two things:

What is the assessment that the recommender makes of your skills and potential?
How much should they trust the recommender's assessment?

The style and errors of the recommender primarily speak to the second point.  It is hard to see how an occasional "normal" mistake will make a significant difference in how your or the letter-writer are perceived.  Likewise, if the writer is not a native English speaker, but makes mild typical grammatical errors that do not impede the sense of the document, it is just part of the normal "friction" of cross-cultural scientific communication and should not be a problem.

If, however, the mistakes are frequent and significant, then it may undermine the credibility of the recommendation.  Frequent or severe mistakes can make a reader think either that the recommender doesn't really care about this letter or that they are sloppy and perhaps don't have very good judgement to begin with.  Fairly or not, this can also apply to foreign-language issues, since a professor who knows their English is not good can get proof-reading help from any number of sources.


Do we mention the work that we did ourselves while giving a research proposal?

Including preliminary results that indicates the strength of the proposed research is never wrong. If your work has just started and your results are just inconclusive then you may consider not including them, simply because they do not contribute much to indicate the potential success of the proposed project. Mentioning that you have started work could still be useful to mention since it indicates you have thought through the process very carefully but then you should probably also consider adding something that makes it clear you cannot complete the research without additional resources. Otherwise, someone might get the idea you do not need any support and that you will complete the work anyway.


Graduate school applicant visiting a department he has applied to - advantageous?

It may not give you an advantage at being admitted, but it could help in other ways.  I visited my first-choice program (also in physics) around Thanksgiving of my senior year, and scheduled meetings with two PIs I wanted to work with.  The first stood me up, but the second took several hours to meet with me and show me the lab, and at the end of the visit he told me "If you get in and want to start early, let me know and I could probably give you an RA for the summer".  This ended up being a big help -- the visit made clear who would be better to work with, and also helped me get started with research shortly after graduating.


Here is another perspective: a professor offered you substantial help with your application and you end up complaining that they wasted your time. Trying to figure out whether you’d be a good fit, they discussed research with you  at length and help you draft a research proposal (which you hopefully use to improve your acceptance chances in other applications). After several days (or weeks) of discussion they decided that you’re ultimately not a good fit.
There can be a million reasons: another student was a better fit, funding was denied, research needs changed and so on. Rejection sucks, and I do sympathize, but it sounds like the professor went waaaaay out of their way to help a stranger; their reward? Getting trashed online for it.
Your lesson from this should be to not place all your chips on one advisor so to speak. When I interview candidates I implicitly assume they’ve applied to at least 10 other places and discussed their work with others. I had prospective students and research fellows rescind my offers after I had invested a ton of time and effort into getting them admitted. It sucks, but that’s life.
Edit: seeing the discussion in the comments regarding foul play, I don’t think that’s likely. While there might be a chance of that, think about it - why would anyone not want to hire someone who has great ideas? I don’t see the causal relation here. Coming into research with a non-cooperative mindset won’t help you in the future.


Successful survival strategies for academic departments threatened with closure

Once you are threatened with closure, it is probably too late to fix your problems.
Increase enrollment of new students with marketing.
Increase retention of students with better teaching and extracurricular experiences.
Seek donations.
Find a new source of revenue.
Unionize.  A union contract can force cross-subsidies from money-making departments to money-losing departments instead of closure.  However, this will not work if there are no money-making departments.

These decisions are all about money, and there's no easy way to get money.
A more detailed answer: https://ep3guide.org/toolkit