What should I do if I submitted more recommendations than needed for an academic job application?

What's done is done.  Five is no big faux pas, just more than needed.  I would move on and, perhaps in the future, trim the number you submit.


How to find suitable PhD programs in Computational Social Science?

There are several/many programs in Communication (which may sometimes refer to itself as Mass Communication and some related terms) that would be good places to study social media, online behavior, etc. using computational methods. Just going off the top of my head, I'd look at the PhD programs at University of North Carolina, University of California at Santa Barbara, Ohio State, University of Wisconsin at Madison, Northeastern University. I also know that Northeastern has an interdisciplinary network science program.
Basically every Communication program that I know of is actively trying to enhance their capacities in this area and would probably be attracted to prospective students with such interests as well. You should also know that competition for faculty jobs in this field is also much less fierce than in most other fields that I know about (there are typically more open positions than new PhDs in a given year). Of course, COVID-19 will cause a hopefully temporary downturn in available jobs in all fields.


How widespread are electronic-only dissertations?

The first page of a Google search shows UVA and USC do this already.  You could try contacting colleagues at those schools and see how the experience has been.  (Sorry, I don't have a statistic.)

P.s. I am sympathetic to those who prefer the bound volumes.  I think you can in some ways scan a text and multiple texts more easily in the hard copy than electronic.  Also, there are excellent arguments that books on acid free paper are a superior storage media than computer files (longer lasting, safer, future readable).  Finally I think that the granting university is more likely to have future students working in the same general area.  Thus they benefit especially from a printout.


What supporting documents to send along grad school application?

Ask them. I very much doubt there is a uniform document package requirement. If you come from a different country, the documents they'd want to see might be quite a bit more detailed than if you come from the same country.


Your question is not really about Academia, it is more of "figuring out what to do with your professional life".

Academia can certainly help you in the following ways:

you might take several courses from different areas like Psychology, Animal Behaviour, and many others to find what you are leaning towards.
those things might inspire you to get a certain graduate degree. However, going into a graduate school is a big decision, and will require time/money investments, so have to be chosen wisely and not instantaneously.
it can try to accommodate interdisciplinarily (software engineering + something else) research if you decide on going to a grad school.

But you certainly have to take the following things into consideration:

not every hobby can/should be a profession. While it is awesome to do what you love and follow your passion, you have to really understand how different are the professional and amateur ways. That can be achieved by getting experience in those areas, both from the academic and professional directions.
advice/support from your family and friends will be important. Though they might not immediately support you in your immediate decisions (which depends on their personalities), you will need their opinions and wisdom.
you seem to have a very scattered vision of yourself, combining psychology, animal behavior, entrepreneurship, software engineering, etc. You might want to explore those things one-by-one but in a quality way.
getting rid of software engineering completely doesn't sound very good. You may want to incorporate your knowledge in this area to some other (like psychology) and take advantage of interdisciplinary research.
changing career path comes at a cost of suffering from the shortage of money. You will need to think of backup options to support yourself, especially if your family is not totally aware of your plans.


From the ResearchGate website:

Advantages:

  Make your research citable. DOIs provide information on where your work can be found online. They are guaranteed to never change, making them a great way to provide a reliable link to any of your research.
  Showcase all of your research. DOIs provide the ability to find all publications associated with a single author, including research that hasn’t been published.
  Put a date on your discovery. DOIs include the publishing date of your research, to make sure you get the credit you deserve.

Disadvantage:

  Once a ResearchGate DOI has been generated, the research cannot be edited. Instead, you should remove the research completely, re-upload it with the edits and then generate a new DOI.

Also see:
Should I include a DOI/website URL for a publication in dissertation bibliography?


Is it normal for a potential supervisor to not reply to a student even after they replied before?

Is your deadline for this opportunity within a month or two? If so, a gentle nudge would be appropriate after a week. You could reply to your own email to bring it back to the top of the professor's inbox, saying something at the top like:

  Dear Professor X, I am sure you are very busy, so thank you for your previous response about the PhD position. Please let me know if you would like to further discuss my research experience (details below) or the projects I hope to pursue with you.

If the deadline is extremely close (within the next two weeks?) it might be appropriate to further inquire, "Given that the application deadline is XXX, may I ask whether you are still considering me as a potential student for this PhD position?" (It would be courteous for the professor to tell you if you were out of consideration, but it also might not be necessary to ask for this clarification unless your next action hinges on the response, e.g. asking another faculty member at the institution to sponsor you.)

Edit: Advice on getting replies from busy professors suggests saying that you're "sending a follow-up in case your original message went to spam, or something similar". However, that is less plausible because you previously received a response. (Unless the attachments may have gotten it sent to a spam filter.) I'm not sure whether there is another courteous "little white lie" to deploy here rather than taking the tack of "I am sure you are very busy."


How should I fix the problem of two part surname taken as middle name by google scholar?

Google crawled your data from somewhere, I suspect that source gave Google the wrong data. E.g., perhaps a bibtex listing is wrong. So, to fix the problem, you could fix the source.
Taking Mahmoudi as the middle name in Alireza Mahmoudi Kamelabad is a standard reading. To avoid that reading, you could use Alireza Mahmoudi-Kamelabad in the future.


Reference management software to get the link of references

Digital Object Indentifier (DOI) names might be a possible solution. Sometimes article citations in major databases come with them - if so, you can use them to directly access the paper (in a web browser, at least).

For example, for Claude Shannon's seminal work A Mathematical Theory of Communication, the DOI name is 10.1109/9780470544242.ch1. This can be resolved either by using this website, which also describes DOI names in detail; or by using a direct link, such as http://dx.doi.org/10.1109/9780470544242.ch1.

You can find these DOI numbers either by checking reference databases (which often include them) or by checking a website such as crossref.org.

IIRC, Mendeley actually includes a field for the DOI name, if known. I've seen it automatically populated when I use the browser clipping tool (sometimes, not always).


You should report this immediately, but be sure you collect evidence.
Edit: The reason that you should collect evidence is that you are accusing your fellow students of gross academic misconduct that would result in serious consequences. Not only will it be impossible for anyone to pursue the matter without evidence, but making baseless accusations could result in negative consequences for you.
Screenshot correspondence (if it’s in Chinese get it translated or find a native speaker among the faculty who can translate). Emails, text messages etc should be saved as well. If your university is reputable, it will deal harshly with these cases.
The actual procedure varies by institution but the first person to contact is the professor. They’d likely want to know that this is happening and would be furious to hear this. It’s quite possible that the professor is unaware, or simply unable to obtain evidence that something is going on: if everything is happening on a non university server there’s little they can do to catch cheaters.
Would anything be done? That depends on the institution, but what you’re describing is pretty clear cut. Students can get expelled and in the case of international students, have their visa revoked as a result. If this happened in my class I would do everything I can to ensure those students are punished as much as possible. The likeliest outcome is failing the class and getting a remark on your transcript.
Help make academia better and report them.


Should I inform authorities of someone falsely claiming a non-existing PhD?

It is certainly appropriate for you to bring this to everyone's attention. However, it is also important that you do so in a way that will protect yourself from retaliation as you seem to suggest the person has some power.

The dilemma, of course, is that an anonymous accusation is easy to dismiss. But if you can just direct people to source of your information so that they can independently verify your claim it will stand a better chance of being heard.

It is also possible, that the "authorities" are already aware of this and are, in fact, invested in the career of the person. This happens in some places, so, depending on the norms of your location, it may be especially important to protect yourself, and in the worst case prepare for the situation that it won't be addressed.


Benefits of including short and/or long-term visits abroad on my CV?

I don't see any drawbacks adding your grants and visits in CV, but it will surely increase the weightage of your CV in this competitive world. I have been a Travel Grant Reviewer since last 5 years to select suitable candidates to attend the meetings/conferences. My experiences give the following merits to add them in CV.

Grants/Awards/Prizes proves your ability to be considered in top researchers.
Visits abroad proves your ability to work in different environments/places and with different peoples.
Listing your conferences and presentation details proves your ability/interest to present your work in the international forum.

So all the points have their own meaning to define your potential. If you don't mention them, then how do you think that you will be evaluated properly?


Is it ethical for the postdoc to be listed as a co-author and the corresponding author on all group publications?

I come from a field that is rather (let's call it) pragmatic about co-authorship, and I have never heard of a postdoc automatically being a co-author of papers. Sure, sometimes the input of the postdoc is not extremely large, but having a postdoc as a default co-author of each paper irrespective of contribution seems very uncommon to me.

  The reasoning behind this practice is that the postdoc needs publications for his academic career.

Who cares? The same is true for you. If he cannot write papers himself or actually advise students that write good papers (not the same as just being on a paper without contribution), he should not be able to progress his career.

  As a consequence, emails are prepared for the postdoc by the PhD students, and sent out under the name of the postdoc.

That's ridiculous. Don't do that (either for a postdoc or a professor). If they are not able to answer questions about a paper, they need to at least be honest enough to defer to the person that can. Pretending like the postdoc is the real brain behind a paper is certainly not ethical.

  Is this a standard practice in your field of research?

Nope. Never heard of that, and Applied CS is certainly not a field that is well-known for its die-hard adherence to ethical guidelines re: co-authorship.


What would you do if the author of a published CS article does not respond to code requests?

Simply nothing, but trying to implement it yourself!
According to my experience, there would be four potential reasons because of which authors may refuse to share their code:
1- Their code needs to process some particular data that they are not allowed to share. Thus, the code by itself, without that specific data, does not reproduce the results of the paper. So, sharing the code does not fulfil any reproducibility purpose.
2- They feel that they may still release more "major" contributions of that code. Then, they would postpone the public release of the code until they feel that the code is milked enough, and they have run out of further remarkable ideas.
3- They may believe that if one is really interested in their work and the cultivation of ideas to expand its results, she herself codifies the paper since personal codification often leads to way deeper levels of understanding of what's behind a piece of code, rather than just running some already-cooked snippets.
4- They don't have further access to the code. Not everyone may keep a clone of her contributions on her personal hard drive depending on the policies of the academic or industrial body under which that code was written.


As a candidate, the best answer is probably: do nothing.

You don't know for sure that there is an impropriety.  It's not clear that anything unethical or against institutional policy is taking place.  At my institution, for example, those on a hiring committee are required to disclose any personal relationships with candidates, and make a declaration that this won't affect their decision.

There isn't an automatic policy of removing someone from a committee because of such conflict of interest.  This is often a good idea, but it's not always possible.  Some committee members may be essential for organizational reasons.  For example, the head of a research group that is hiring a new member would rightly insist on being integral to the hiring decision. They can't be removed because of an issue like this--nor can people with a personal relationship to committee members be stopped from applying for a job.

In the real world, this sort of thing happens, and it can't always be avoided.  It may be that everyone already knows of the relationship and has decided this is not a problem.

It's not clear that this would affect your chance of getting the job.  Sometimes a personal connection unfairly prejudices hiring decisions.  Sometimes people strive to avoid letting this prejudice their decision.  And for something like "previous romantic relationship", it's not even clear whether the prejudice would be positive or negative.

You don't really know whether or how this affects your chance of getting hired.

Reporting is more likely to hurt than help your candidacy.  To report it, would be to assume bad faith on the part of at least one person who is making a decision about hiring you.  Reporting it would likely give you a bad reputation in at least that person's eyes, and maybe others as well.

If everyone already knows about the issue, your reporting comes across as questioning the work of the whole committee--not a good thing!

You could report it and hope to remain anonymous, but there's no guarantee of that.

Really, there is nothing unusual about the situation.  Even though protections are put in place, hiring is almost never a level playing field.  Very often, internal candidates have a leg up on everyone else.  Advertised positions that are actually earmarked for a predetermined candidate are common.

This is unfortunate, but it's also reality.  And because hiring decisions are always largely subjective, there is only so much that can be done about it.  I don't think the information you discovered makes this situation unusual in any way, really.  Try not to worry about it, do your best, and move on if you don't get the job.


Is it good practice to teach using real life experiences of the student?

Yes - to answer your question. If it helps them understand the materials then you should do it.


I would presume that you have to inquire with the lab/director/hiring manager/program manager to fix the actual start date by mutual agreement. You can't normally just choose unilaterally, and they may have a fixed date in mind. In general, the hiring entity decides on the employee's start date.


References must be cited vs. need not be cited

This sentence is present on page 5 in the IEEE guide at:

https://www.ieee.org/content/dam/ieee-org/ieee/web/org/conferences/style_references_manual.pdf

The guide gives an explanation to it as follows:

References in Text: References need not be cited in the text. When they are, they appear on the line, in square brackets, inside the punctuation. Grammatically, they may be treated as if they were footnote numbers, e.g., as shown by Brown [4], [5]; as mentioned earlier [2], [4]–[7 ], [9]; Smith [4] and Brown and Jones [5]; Wood et al.[7]

This clearly means that numbers rather than the author name (s) are preferred to be used in the text. When author names are used, the guide gives some examples on how to cite them.


Check with your advisor, and if they do not know, check with your department director of graduate studies (it may have a different name, but it is a faculty member who is "in charge" of the PhD program).

In general, there shouldn't be any problem, but your institution may have special policies and what not. As always, it is better to be open about any changes. More communication is better that less.

Be positive when you write to your advisor and motivate the changes.. E.g., "I would like to add these results because they improve the dissertation in such and such a way ..."


In a paper, how would you name a part that describes the big picture before the technical details

In my research area (software engineering), a widely used name for this section would be Overview.


How to review bogus science without hurting feelings?

So, I see that you're conflicted by the desire to give your honest opinion and your desire to be nice. While some say you should let go of the desire to be nice, I think in this case it might be more productive to first look at how you can be nice. But first, let me briefly talk about 'cranks':

What are cranks?

The following quote from Nature is prominently placed on the Wikipedia article on cranks:

  A crank is defined as a man who cannot be turned.

Less cryptically, an important property of crank is the unwillingness to change their line of thought or accept being wrong (they likely admit to make 'unimportant' mistakes and will immediately explain what they 'actually' meant). This will become a very useful definition. Suppose for the moment that exactly one of the following is true about the motivation of your correspondent:

"I have a brilliant idea about the universe and by showing this to an expert, I'll get the recognition I deserve."
"I don't know much about Physics, but I think this is a good theory and want to know what the experts think."

Note that person 1 is a crank, for when you tell (1) that this idea is 'bogus', the reaction will be likely hostile, as (1) will refuse to be 'turned'. Any conversation with (1) is a waste time. If your know for certain that you're dealing with person 1, ignoring, aborting and running away in the most polite way possible is recommended. However, as you desire to be kind to your correpondent, I doubt you are certain that you're dealing with person 1. (Also, assuming 1-ness might be dangerous. Applying Hanlon's razor seems like a good idea.)

How to be nice to person 2

Now, is person 2 a crank? (2) could be a crank, but not necessarily. Perhaps (2) is simply a layman who always had an interest in physics, but never had (or took) the chance to pursue this interest with proper study and thinks this is how physics can be done.

For person 2, I think the best way to be nice is to not give your opinion on the  work, other than that it simply is hard for you to judge (2)'s actual ideas as they are very non-standardly presented. (This can be a lie. But I think it is a very useful lie.) It is important that you add the advice that if (2) has an interest in physics, (2) should learn more about physics so that (2) can properly present the theory. It is good to add some explicit method for (2) to do this, such as some introductory books, courses or videos.

In the best case, (2) will start learning things and eventually will realize that his theory is 'bogus' by themselves! In the worst case, (2) will show the inability to 'turned'. But thereby, (2) reveals to be (1) all along and you can therefore safely abort communications with your correspondent.

Conclusion

I think it is good you ask this question, because I believe there is a true dilemma here. You must choose at most one of:

Share your (brutally) honest opinion with your correspondent.
Help your correspondent by gently directing them to the path of learning.

Any combination of the two will likely act as a discouragement for your correspondent from attempting to learn, for your correspondents idea that they might be able to do some physics is likely crushed by the weight of an experts opinion.


As a referee, is it okay to ask for references to be removed?

Yes, the spurious references should be removed, as stated by @Solar Mike. There is a diplomatic way to accomplish this without making any assumptions or accusing anyone of anything. Write something along the lines of

  The current bibliography contains a number of references which are not explicitly cited in the main text. They are: (insert complete list of numbers). The main text should either be extended to include a discussion of these references or the references should be deleted.

You compile the list by ticking of all explicitly cited references as you read through the main text. Any entries left are spurious.

A tool like LaTeX typically has a command which is used to print the entire bibliography. Spurious references are often generated by forgetting to disable this command when the final draft is compiled. If you can identify the tool, then you can insert a helpful statement to that effect, i.e.

  As you are using LaTeX, please check if manuscript contains a \nocite{*} command.

EDIT: I just realized that my original text does not cover the case where the manuscript contains references which are cited in the main text, but appear to be irrelevant. A diplomatic approach can proceed along the lines of:

  The author(s) should extend the discussion of the following references: (insert complete list of dubious references). Currently, it is not clear to the reader how these references relate to the subject under discussion.

This allows the authors to either explain why the references are relevant or remove them if they are irrelevant.


Discussing authorship/sole authorship with supervisor

Note: things may vary by field. Single-author publications has never been an important metric in any field I've ever worked in, but can't say for sure about math.

I think your advisor should be a co-author. Here are some things to consider:

Reputation. Even if you did good work, the paper will get more circulation with an established researcher's name on it. So, you probably want him to have authorship, though you should of course be first author.

His contributions. As you say the project "would never have been born without his guidance." It sounds like he did not contribute only offhand comments, but actually proposed a line of research and helped you to follow it.

Funding. I'm assuming he funded you to do this research. In itself, this doesn't mean he deserves authorship -- but I suspect that a lot has been going on "behind the scenes" to help you with this work. Grant proposals are a lot of work, and he probably put a bit of thought into your general research area before he even hired you. (This may not apply in your particular case, since the advisor didn't fund you.)

The bar for co-authorship is not so high. I have seen questions on this site where people have been given co-authorship for reviewing the grammar! I think this is ridiculous, but adding your advisor seems altogether appropriate. In particular, you will be first author, so it costs you very little -- and it likely means quite a bit to him. In fact, the old supervisor would have a decent case for being added as yet another author.

Edit: OP has clarified that single-author papers are an important metric in this field. If this is true, the advisor in question surely knows this as well. So, if you want to ask for sole-authorship, you could say something like this:

  I wanted to ask about the authorship for this paper. As you know, single-author papers will be important for my career. So, I wondered if you thought it would be appropriate for me to be the sole author on this paper.

Note, I still think adding your advisor as a co-author would be more appropriate. Perhaps a "compromise" would be to ask the question in a more neutral way, something like:

  I wanted to ask about the authorship for this paper. You obviously made a lot of contributions and maybe it makes sense for you to be a co-author. On the other hand, this paper might be a good chance for me to get a single-author paper, which as you know, I will need for my career. What do you think?


Why is Paper Publishing and getting a patent completely unrelated?

not all, but many papers (that are accepted and published) are based on ideas that can be patented as well

This is a misconception.  Even in engineering, only a small minority of papers contain ideas worth patenting.  The further you get from engineering, the smaller this fraction gets.

  So, why is that there is no system in which a person can apply for a publishing a paper and also getting the idea patented at the same time?

You can indeed do both things in parallel, but not via the same process.  Publishing a paper is an academic process, whereas filing a patent application is a legal process, and the two things just don't overlap very much.

It's kind of like asking why you can't write your dissertation and apply for jobs via the same process.  You can certainly work on both at the same time, and there is a relationship between them, but fundamentally they aren't the same thing.

  Is it possible that I publish a paper, do not get it patented and during that time someone else patents my work in his name?

No, it's not possible.  Well, technically someone could try, but they would be wasting their time, since your paper would serve as "prior art" that would invalidate the patent.

  Or someone else picks up my theory, develops it further and gets a patent?

That could happen, whether or not you file for a patent.  They would own the intellectual property rights to the extension of your work, but not to your work itself.


Formatting and desired content depend mostly on the publication venue. Most journals have a citation style, and will often provide a style file for the bibliography manager that you use. So it depends on what venue you have in mind.

If you don't have a venue in mind, then you can use any standard format that's used in your area of study.


Indentation of the first paragraph in a section

Copied from this answer on writers.SE:

  [...] in Robert Bringhurst's Elements of Typographic Style, he states that
  "opening paragraphs" should be "flush left" because "[t]he function of
  a paragraph indent is to mark a pause, setting the paragraph apart
  from what precedes it. If a paragraph is preceded by a title or
  subhead, the indent is superfluous and can therefore be omitted".


How to remove my name from the editorial board of a journal on Beall’s list?

The best way to deal with this is to get legal help. Keep a copy of all your communications (email, etc.) with the journal, bring it to a lawyer and state your issue. Legal help can be expensive, but if you're seriously concerned about being listed and consider a high priority to get off the website, then I advise you to seek quality legal help as soon as possible.

In the mean time, you can also make a note on your personal website/blog/social media/profiles/wherever people access you and your work that you are not an editor of that journal.


In my experience, service lecture is used to refer to a lecture (course) about your field given to students of another field, usually an introductory course to give those students the basics that they need for their studies.

For example, at my university, there is a course Physics for Chemists, Biologists, and Geologists which is organised by the department of physics and given by a physics professor and which teaches essential concepts of physics to students of the named fields. In contrast to “physics for physicists” lectures, the department of physics does not benefit from the effort put into this lecture as it’s not teaching its own students. Thus giving this lecture is a mere service to the departments of chemistry, biology and geology.

Of course, to be sure about the intended meaning, you would have to ask the issuers of the form.


How can I Get a Job Reviewing Math or Comp Sci Articles and Books in Advance of Publication?

The kind of thing you're looking to do can be fun, but does not pay. That's because your progress will be painfully slow. For example, say I have a 300-page mathematics monograph. How much do you think is fair to charge for your content editing? Don't forget the total revenue of that book is likely to be less than $10,000 in total. Further, how many more copies of the book is one likely to sell if they engage you? In the best-case scenario, you'll catch every error, and the reviews will be glowing ... but translating that into books-that-are-sold-that-would-not-otherwise-be-sold, I'd estimate that to be ~5-10 books. From there, we could say that the publisher might be willing to pay you $100. For a 300-page monograph, it's just really hard to see it as worth it.

You could make more money by handling the entirety of the publication process. You'd need to do copyediting (i.e. English editing, not just content editing), send proofs to authors, liaise with the typesetters & printers, and so on. Publishers have people whose job scope is to do this ("editors"). Unfortunately, you still won't be able to do the kind of content editing you want to do. I used to work in academic publishing, and when I did this, I handled 8-9 projects at the same time. There's just no way you can treat each manuscript in the detail you want to.

Having said that, one part of the job scope of editors is to acquire more projects. If you do a good job with editing, you can impress authors who might in turn either write more books or refer their friends & colleagues to you. This will be good for your career. If the project you're handling is aimed at the general public, or at undergraduate level, you have more of a chance to offer content critiques, but you won't have time to understand deep mathematics.

If you still want to do this, then you can find such jobs the same way you find other such jobs: by reading job advertisements and writing to employers (in this case academic publishers). You can also put up your own advertisements to do this kind of checking, in which case you'd use message boards that mathematicians or computer scientists look at.


Is it problematic to use a Wikipedia article I wrote in my PhD thesis?

No, but make sure you cite it and mention it, to avoid being accused of copying and pasting from Wikipedia.

In any case, it is great that you have contributed to Wikipedia and I wish more people considered using pieces of their introductory chapters for Wikipedia. Just make sure that people know that you copied to, not from, Wikipedia. (I mean, the order is irrelevant, i.e. whether you first wrote text for Wikipedia or your thesis, but the authorship is.)


What would a good written policy for scaling exam grades look like?

In general scaling is a mistake as it introduces uncertainty into the student's calculations. But some adjustments are proper and you can publish statements about them.

First, you can agree that no one will "miss" the next grade by a small percentage. This is better done overall, than on a per exam/paper basis. But if it takes 90% (overall) to get an "A", then, at the end of the day give the A to someone with 89. This merely recognizes that your grading scheme isn't perfect and may disadvantage people in small ways occasionally.

Second, agree that your grading rubric is clear that you are allowed to adjust upward when you think it justified. Mine would say something like, "If you get 80% you will get at least a B". This is just a reinforcement of the first point.

Third, permit people to do work over if they have fallen short. Regrade it for "most of" the lost points. My policy was 90%. If you lost 30 points on an assignment you could get 27 points (max) back if you re did the assignment properly. My policy was generous, permitting several attempts. The repetition was good for the students and worked to assure learning.

Fourth, at the end of a course, look at how the students did overall and compare it mentally with what you think they really learned in the course. If you think the learning was actually better than the distribution shows, bump it a bit. This will push a few students up to the next partial grade, say from B to B+.

Finally, avoid marking using only a few high-risk exams, but spread the marks over a large number of tasks. All or nothing final exams eventually leads to trouble, even in less extreme cases than the one you mentioned. This leads to a practice of continuous study and learning rather than "cramming" for the big one. Cramming results in more memorization (short term learning) and less deep learning.

My students all knew everything about the above policies. I seldom got complaints about grading. I could be as demanding a professor as I felt necessary (students viewed me as very demanding). At the end of the course surprises were always happy ones and students felt good about themselves and encouraged to continue.

Finally, let me note that strict scaling, making the course distribution into something like a normal curve is, IMO, always a mistake. It turns the course into a zero-sum game for students who can only win if someone else loses. In theory it should be possible for everyone to do well, even full marks, based only on their own work. Such scaling is also unjustified as it assume that a given sample (your students) perfectly match a population (all students). Statistically that is a serious error to make unless your scale is huge.


How to get through with an unsupporting supervisor?

Show your supervisor why you are right and the other guy is wrong. Gather solid proof, wait until you are less emotional, ask to meet your supervisor and tell her in a neutral, professional tone. Maybe she just wasn't able to see your point at that moment.


Do LOR writers need to be someone who's taught you a class?

Whether they taught you a class or not is irrelevant. What you need is people who can confidently and honestly predict your future success. This implies that having worked with someone in a research environment is probably more valuable than having them as an instructor.
In fact, given that many places now have very large classes and student interacting mostly with TAs, instructors may not be nearly as valuable as they once were.
So, no, it won't hamper you provided that your letter writers can make that prediction honestly and enthusiastically.


Should the explanatory text come before or after the animations in tech articles?

Before the animation, introduce the graphic.

Below the animation, include a caption.  Your first example has a nice caption but I would format it so it looks more clearly like a caption.

Provide a way to turn off the animation.  It is hard for some people (like me) to focus on the text that follows while the movement is continuing to take place.

Thank you so much for asking.  Animation on the web can drive a person nuts.  On the other hand, it can be helpful in gaining understanding.


How long does it take for the first round review of physical review letters?

It can be long; 4 weeks is not uncommon, but much past 6 usually triggers some editorial action.  Fortunately APS has a good manuscript system so it’s easy to see of the editor is trying to move things along: watch for reminders sent to referee(s) in the audit trail.


Start it with a compelling question that add some context to your talk. A recent talk at a conference I attended started like this:

  What is the largest sumfree subset of the numbers 1 to n?

This is a well-known problem first posed by Erdos, and if someone can say that their research leads to a nice way to solve it, a lot of people will be interested (or at least more interested than if the speaker starts by saying "I'm going to talk about containers for hypergraphs").

Otherwise, start by presenting a situation (or amusing anecdote) where your results would be applicable:

  Suppose 11 of your spouse's charming relatives are visiting for two weeks. How do you seat everyone around the round table you had to drag out of the garage so that everyone has everyone else on each side of them at least once during the two weeks? What if you want to avoid their annoying cousin but would love to sit next to their mother-in-law more times?

Both of these were very interesting beginnings, and as the speakers continued through their talk, they kept connecting back to the original problem, explaining how their result provided easier or more convenient solutions to the basic problem. There is really no need to start with "thank you for attending". Wait with that until after, and save the title and collaborators until you've explained why everyone should care what you and some other people they don't know wrote a paper about. You have already been introduced by the organiser, so you can just dive right into the motivation.


Is it possible for a student to TA their entire way through graduate school?

The ability of a department to fund TAs depends on the courses being taught, the number of students in a class, and the overall budget. Often, a department will use this number in combination with the amount of funding faculty are pulling in as well as other sources to decide how many students to admit and how much TA funding support to provide.

Independently, a department might make a determination of how long any one student might be guaranteed a TA position (this is often detailed on the admissions letter), with the expectation that students will look to be supported by research funding, or are expected to support themselves. Again, this depends from department to department and from university to university.

I don't think there's any area-wide standard. In computer science, I see all kinds of models, ranging from full support through the entire program to no funding at all (although this latter model is rare).

So to answer your question: maybe, it depends.


What are typical examples of 'Reference Misuse' when defined as 'using references to support predetermined arguments rather than illuminate debate'?

The definition provided seems a little opaque to me, but I can think of a couple of situations to which it might apply.

Reference misdirection: I write a paper in which I include some assertion, perhaps only tangential to my main argument.  Maybe it's something that I remember hearing from someone at some point, but I can't quite remember who.  The referee or a co-author calls me out on it and says that I need to provide a reference.  I type a couple of keywords into Google Scholar and find a plausible-sounding reference.  It looks related to my assertion, but it doesn't actually prove it.  I cite it anyway knowing that the reviewer will probably not follow up on it.

Overstating the impact of a reference:  I write a paper that depends crucially on some Theory X.  There is a paper that provided some evidence in support of Theory X, but I cite the paper as claiming that it found "strong evidence in favor of Theory X".  Or perhaps the paper did indeed find strong evidence in favor of Theory X, but I state that it "proved" the validity of Theory X.  Moreover, perhaps the paper provided a number of qualifications to their claims (which maybe invalidate its application entirely to my case!), but I ignore these qualifications entirely.

Presenting a one-sided history: I write a paper in favor of Theory X (or maybe my paper depends on the validity of Theory X).  In my introduction, I provide an extensive survey of the field and cite dozens of papers that have found evidence in favor of Theory X.  However, there are just as many papers which have found strong evidence against Theory X, but I do not cite any of these.  Although there is clearly a lively scholarly debate surrounding Theory X, I present Theory X as though it is a settled fact.  While this won't fool anyone who does serious research on Theory X, it will be a source of confusion for those who work in other fields and are not aware of the controversy.

This last one is particularly common and isn't as egregious as the others since the reference is not fraudulent, just superfluous.

Scratching someone's back:  I've written a paper in a related field to a colleague.  I know that they would appreciate a citation to one or more of their papers.  Or perhaps I would like to cite them to help bring my work to their attention.  Their work is not directly related to mine, but I figure out a way to add a few sentences to the introduction that vaguely connect my paper to their work so that I can work a citation to them into the paper.

Since researchers are all human (and hence biased and involved in academic politics), it's impossible to be entirely immune from all of these.  If you do a lot of research on Theory X and believe it to be true in your heart of hearts, you will be more aware of the limitations of studies purporting to disprove Theory X and will be more easily able to justify omitting references to them in your work.  But the goal of research is to discover the truth and present it as clearly as possible, and part of that process is being as aware of one's own biases as one can.


What is the best course of action when approached by predatory publishers?

Flagging as spam and deleting them is the right thing to do.  Also, if they seem to be using the name of a legitimate researcher, warn that person.
Anything else is a waste of your time.

There is no organization that licenses scientific publication, nor is it clear such a thing is possible.  Even if there was, it would likely make no difference: if we cannot even limit the activity of 419 scams, which are clearly illegal, how can we do any better against predatory publishers, who are often essentially the same thing in a more legitimate mask?


How to reference "letters of gratitude" on the CV?

I am working on two separate areas (academia and industry); in the second one, it is sometimes useful to acknowledge these thank you letters when applying for jobs.

I'd recommend having two versions of your CV/resume, for use in applying to different sorts of jobs.  The industrial version could take whatever approach is standard for such applications.  For the academic version, it would be safer not to list these letters of gratitude under "Honors and Awards", since that's usually reserved for more clear-cut cases (such as prizes, awards, competitive fellowships, etc.), so including them there could look odd or like you are padding your CV.  If you'd like to mention them on the academic version of your CV as well, one possibility would be to write "received letter of gratitude from university" in parentheses after your description of the training course.


Is it ethical to cite a reviewer's papers even if they are rather irrelevant?

Don't speculate about who the reviewer(s) of your manuscript are. Nothing good can come out of having the knowledge. In fact thinking you know who the reviewers are can cause you quite a bit of grief.

Forget about who authored the review and focus on the facts. You think the paper suggested is tangentially related and not really relevant. Therefore you think you shouldn't cite it. As in similar situations, the next most natural thing to do would be to not cite it, giving your reasons. It would take a pretty unscrupulous reviewer to reject your manuscript because it doesn't cite his paper, and even if the reviewer attempts this, he would also have to convince the editor that he's actually rejecting your manuscript for valid reasons. Remember the editor can see who the reviewer is, and will notice if the reviewer is pushing his paper even if the relevance is tangential. Further, remember that the editor can accept a paper even if the reviewer recommends rejection.

Finally, about whether to report this, there's no point. You won't learn anything about it anyway because the editors can neither confirm nor deny the identity of the reviewer.


Graduate school admission without college degree

I see no particular reason why a graduate committee may not admit someone without an undergraduate degree. But you'd have to have outstanding -- and well documented -- talents for a committee to take a chance on such a candidate.


Why is citing to old publications seemingly the norm even in fields where much research becomes obsolete as technology progresses?

Coming from the same field as you, I know what you mean. I also wondered the same thing at first. Note that in other fields, citing papers that are 100 years old is the norm so saying a paper is old because it is a decade old might not resonate for them :).

There is much to take from an old paper. Even if the problem was solved with "obsolete" technology for an obsolete problem, the method employed, the problem tackled, the method used to test the results, ..., all this might still be relevant to your problem.
You might also use related works to show that a research direction was taken as to explain why you don't have to do it yourself. But at least you will show that you know it has been searched and your reader will also know.
The last reason you might want to cite those paper is to put your own work in contrast to those present there. You say the works are obsolete and old ? Perfect, explain how your research tackles a problem they have not resolved. This is something especially important in robotics where everything is new and shiny and cool and changes so fast. Make yourself unique by citing close related work but showing how you differ from them. And those similar work might be those older highly specialized work:

  This method solve very specific problem 1. However, it cannot solve novel situation while the method we present in our work can.

There is more to a paper than meets the eye.


Is it rude to change universities/supervisors after already indicating research interest with a current supervisor?

If Y is what you really want to do then go for it. There is no point in going down a career path just to please someone else.

Talk in person to your current supervisor once you have a written offer from the university that does Y. Explain to him that it is your dream to do Y and you hope to keep in contact with him even though you are leaving the university.

A good supervisor will understand - if not then he was not a good supervisor anyway. It's a win-win for you.


Is this tenured professor plagiarizing his lectures?

While there are a number of issues with this teaching style, there is no plagiarism because there is no expectation of originality in teaching. He could teach better, probably, but it's not like you can report him for plagiarizing his lecture notes.


Would a B grade PhD-level course in part time help or hurt graduate application?

Hiding the grade is unethical and if discovered will haunt you. But lots of doctoral courses in the US, at least, result in B grades. It isn't a huge problem if you learn something in them. Their purpose is to prepare you for comps, not to show a high GPA.

I'd call in more or less neutral for your application. But the application, overall, needs to show both preparation and likelihood of success. I don't think a B in a difficult course is a negative for either. But the application overall has to demonstrate excellence. It needn't be perfect in every detail.

For students already in the program, a B grade is considered acceptable.

But, if you restrict your search to "top 5" graduate schools you are already likely to miss the mark due completely to the small number of slots and the large number of highly qualified applicants.


How can I use my mathematical background when applying to physics PhD program?

I actually think the problem isn't that your math classes are off-topic. I know lots of Physics PhDs who double majored or minored in math.
The problem is that you're focusing an awful lot on your coursework in your SOP. Your classes really shouldn't be the focus: anyone reviewing your application gets that information from skimming your transcript. Most professors in physics departments are familiar with the classes you took by their titles and already know how they would relate to physics research, so making it a centerpiece of your SOP is a waste of space. You can give the double major at most one paragraph to tie it into your goals.
You should talk about your research more. It doesn't necessarily have to be impressive, but your ability to function as a researcher is more important to your promise as a PhD student than how many upper div math classes you took.
A double major will not totally make up for a lack of research experience in a grad school application. Succeeding in classes is a different skill set than succeeding in research.


There might be exceptions of which I'm not aware of, but usually, no, you don't reply, unless there are specific queries from the editor.


What type of books to read to improve Academic English?

The best book is one you will actually read. Your English won't improve by looking guiltily at that tome gathering dust on your nightstand because it's a slog to get through. So yes, novels (in your favorite genre) are excellent for that purpose.

Academic English isn't that different from regular English. Once you have a firm command of English, picking up the academic style is just a matter of reading a few papers in your area.


Advisor dies suddenly, advice needed for research students

We had a similar situation at my university when a professor running a large group with millions of research dollars passed away. There are a few issues that have to be dealt with, and usually the department chair and/or the dean play a major role in this

research funding: often this can be transferred (in consultation with program managers) to faculty in related areas who (depending on the degree of involvement in the research) either merely manage the money for the students involved, or might play a more active role in spending it.
students: students need committees and replacement advisors. Again, the department chair, in consultation with the students and related faculty, might be able to assign faculty as caretakers for the students.
teaching/committees: while there are likely significant teaching/committee disruptions, these don't affect the former students of the researcher, so I'll ignore this component.

My view is that students that are close to graduating need someone who can sign off on their thesis work (hopefully without too much modification). They hopefully already have a few other people who can write letters for them for jobs, and can mention the advisor's demise in their letters to explain the absence.

Students earlier in the Ph.D program (say just post-qualifying) are in the biggest bind: they've spent enough time in their research area to have committed to a topic, but now they have no one to guide them. They are the ones who probably need the most help from senior students, other faculty and the department.

Students early in the program have the option of switching advisors, or even schools if there's no one else in the department who can advise them/fund them/works in their areas of interest. Again, the department is usually sympathetic and might be able to provide such students with short term funding via TAships if that's an issue.

None of this of course addresses the feelings of grief and loss


Is it bad to ask the editor about the status of a submission on seeing that referees' reports were submitted a week ago?

Once reviewers reports have been returned, the editor has to assess the reviews in light of the paper and provide the author with indications on how to proceed. Exactly how this come through will differ between fields and editors. The main point, however, is that a certain amount of work is usually needed to process the reviews before passing the manuscript with comments back to the author. Since editors also handle, sometimes, quite large volumes of papers in parallel, your manuscript will be placed in a queue and the editor will likely take each manuscript in order. In addition, many, if not most, editors do their editing in parallel to ordinary faculty jobs which may at times further limit their available time. It is thus reasonable that this process may take several weeks. In "my" journal we as editors have three weeks for this process before being reminded by the electronic submission system that the manuscript is "due". We often make this deadline, but not always depending n workload.

So, one week is definitely too short a time to expect a response. Three weeks seems to be reasonable in my field but I would maybe allow even additional time to pass. It is probably good to talk to your peers who may have experience with the particular journal and also your field to get feedback on what is considered reasonable.

Added to clarify a comment: it is never "bad" to contact anyone, but it is only fair to allow a a "reasonable" (in the sense of the field and specific journal) amount of time to pass since the early contact will not likely yield anything productive. What, on the other hand, is bad is rather the attitude with which some contacts are made. Insights into appropriate time frames will help to keep communications as fruitful as possible.


I found a nontrivial mistake in my currently-under-review paper. Should I send a correction to the editor?

If the mistake is important, you should send a correction now, rather than waiting for the referee report.  (If it's not important in the context of the overall paper, then the right course of action is more debatable, but in your case it sounds like an important enough mistake to require notifying the referee.)

If you wait, you are wasting the referee's time figuring out something you already know.
I think it looks better to catch your own mistake than to have it pointed out by the referee.
If the referee doesn't notice the mistake and suggests accepting the paper, I imagine the editor will rescind the acceptance after you point out the mistake, or at least suggest further refereeing (since not noticing a completely wrong proof calls into question the reliability of the referee report).  On the other hand, if you point it out, the referee may still recommend accepting the revised manuscript.

  For context, this is one of three main results of the paper, but its proof only takes up about two manuscript pages (out of 18 total).

This sounds like an ideal case for pointing out the mistake: it has real importance, but I'd bet the chances of acceptance remain reasonable.


In a research paper, is it acceptable to include expletives in the results of a text analysis?

Yes, it is ethical.  When you play Scrabble with other enthusiasts, bad words are perfectly acceptable and no one bats an eyelash.


How does LibGen/SciHub affect researchers' research and publishing process?

Let us call J. DOI  (for  "John DOI" or "Jane DOI", gender aware, see Jane Doe and John Doe) the anonymous researcher whose opinions follow. S(he) could be just  everyone, either from a rich or poor country, either with paywall capabilities or not. Being able to do this from home, researchers in universities with paywall access use it as well as others.
At the beginning, J. DOI used the LibGen/SciHub source scarcely. J. was not sure whether it was dangerous or not, or legal or not. J. DOI probably had a little more casual "hacking skills" than her/his colleagues. Earlier, J. DOI knew how to fetch documents that did not appear directly on the  first pages of  classical search engines. He/she knew about gopher, wais, ftp, and wget, to name a few.
When you find a novel gold mine, sometimes you don't say it loud, especially if you don't know how safe the atmosphere is, but you may share some gold you have dug. So J. DOI did not tell friends of the tricks, but he/she was very  keen on "helping colleagues" find a buried paper, because they  knew that J. DOI could. At first, J. DOI gained local fame as a web-search wizard.
This boosted J. DOI's confidence. And gluttony began. This affected J. DOI's health. Positively, because J. DOI could travel with less favorite scientific paper books, less printed papers. And this probably saved J. DOI's back, spine and joints. J. DOI could now use a much smaller and lighter bag, with travel essentials  only. But J. DOI would spend night hours grabbing electronic scientific works, often unrelated to his studies, only because "they were accessible", not knowing how long this will last. J. DOI remembers when  library.nu closed in 2012. J. DOI became physically healthier, but more tired.
Past the sheer amazement of the treasure, J. DOI became aware and overwhelmed. Aware of the legal and ethical  issues first and foremost. Some Johns and  Janes probably decided to refrain their greed, and to stick to official ways. The  other J. soon began to actually build a reference management policy with assorted software, because directories full of pdf, epub, djvu unnamed files are of no use. J. DOI created collections, used ontologies and keywords. J. DOI became organized.
But gathering papers and books is not science. J. DOI began to trace so-called "new  ideas" back in time, quoting the appropriate papers. J. was not stopped too early by paywalls, and was allowed generalizations. J. felt doing a more accurate and honest scientific job, standing on shoulders of more ancient or obscure but deserving giants. Science news does not invent everyday, especially in a time of publish or perish, paper avalanche and retraction.
J. DOI was now a little less interested in the most novel papers, and browsed journal table of contents less often. J. DOI was a FOMO (Fear of Missing Out) for the recent papers, and  became a FOMO of older stuff. Luckily, the number of published papers decreases when going back in time. J. DOI was more focused, and more curious as well.
Finally, J. DOI became more self-assured, meeting fellow researchers of the same kin. J. DOI could draw more connections between seemingly afar fields and ideas.
Now, J. DOI still dreams about (electric sheeps and) cumulative science and a global open access, for the rich and the  poor. J. DOI  knows that the present situation is not morally, ethically or even financially satisfactory, but (s)he hopes that it will slowly modify practices, toward better open science.

This topic is being reactivated in the context of paywalls, open access, archives. See for instance Why are most scientific articles locked behind a paywall?


Getting accepted to present at a conference, but choosing not to go - including this in SoP

It's not unheard of for someone to be unable to attend a conference after having their work accepted. This can happen for any number of reasons that may be seen as having varying levels of validity in someone else's eyes, ranging from "death in the family" to "I have better things to do". I don't see a compelling reason to open yourself up to such value judgments about your reasons for choosing to not go to the conference. Having your work accepted at a conference is an accolade in itself, so it's worth mentioning, but you could simply say that you were "unable to attend" and leave it at that. Your particular reasons for not attending aren't relevant to the point you're making (that your work is good enough to get accepted), and may or may not be viewed unfavorably depending on the individual, so there's not much of a reason to go into the details.


Breaking the (perhaps perceived) academic (poverty) cycle

One possibility IMHO is to try to use the Internet to your advantage. In my field (bioinformatics/statistics), there are a few online communities (discussion forums, Twitter) with relatively low barrier of entry. But once in an online community, how do you make useful contact with others - especially those that can "lift you up" (who may easily turn out not to be from the top western universities, but skilled and friendly people from all walks of academia)?
My answer is: be useful. Can you spend some time answering/helping beginners on the forums? Can you proofread and (very politely) suggest improvements to educational materials someone posted? Can you write a tutorial for some tool/technique you've learned? Are there calls for open online collaborations you can join? Can you code and fix bugs/improve documentation in popular open source packages in your field? ... Note that there might be hidden norms on how "good members" of the community should behave and especially if you look foreign it may unfortunately be easy to end up being judged negatively for a good-faith effort - so some social knowledge/skill may be needed.
If the community is healthy (which unfortunately not all communities are), this lets you develop some "currency" in the community and you become more likely to get help yourself when you need it. Once you are not a "nobody", you are more likely to succeed when you ask some members of the community explicitly for mentorship or for consulting and becoming a co-author on your upcoming paper or for joining a multi-lab effort to collect a larger sample of subjects for a study. And if it fails (and it can fail), your effort made the world a better place and that's also not nothing.
My experience with this approach is that being the first person to enter a subfield (Bayesian statistics) at a somewhat lower-prestige Central European institution with basically zero contacts, it was not that hard to get (over a few years) into productive contact with some of the top researchers in the subfield while only attending a single in-person event - you are definitely facing a tougher "prestige gradient" than me and being white and having a western-sounding name surely made my life easier, so my advice may not apply to you or may not apply completely. I still hope it is a useful suggestion and I believe it is actionable even with relatively low resources.
Also my field is less dependent on expensive equipment/reagents/... so keeping up with the top research is easier. And all of this requires quite a lot of time, which you might not have.
You are facing a tough challenge but I hope you succeed!
P.S.: One thing I don't want to suggest is to "compete for attention" of prestigious colleagues. This is IMHO both unhealthy and unlikely to work well. Instead, I think there are many ways in which a good-faith effort to help the scientific community in your subfield can help your career/connections as a side effect. This is a game many can play and all can win without somebody losing.


How to ask "Do you have any projects for me?" to a professor (who is not your own advisor)

As JeffE would say: "Ask it directly, just as if the professor were human."

  "Do you have any projects on which I could work under your supervision/with your collaboration?"

Sounds just fine.


What is the point of a non-confidential reference letter?

From the perspective of UK higher education, the 'point' of a non-confidential reference letter is that there is no such thing as a confidential one; any data held on that student (such as references) can be disclosed by the institution holding it.

How does the old saying go? Dance like no-one's watching, writing an email like it's being read aloud in a deposition.

References are a tricky grey area, and I do preach caution in case a student ends up seeing what you have written - which can be embarrassing, or even libelous if you can't prove statements that purport to be truth.

I do not think that this undermines the referencing process, however; if you can make true statements about a candidate, including your opinions about them, then, in my opinion, you are within your right to do so.  After all, your student has asked you to do this.


Is it possible to upload expository papers to arXiv?

The official line appears to be that:

  arXiv accepts only submissions in the form of an article that would be refereeable by a conventional publication venue. This excludes [...] reports that do not contain original or substantive research [...]

That said, I see expository and survey papers appear there all the time, and nobody seems to mind.  I think if your expository paper is of a quality that you would consider submitting to an appropriate journal (there are many that publish expository papers) or lecture notes series, then it's fine for arXiv.  If it's just your course notes on the fundamental theorem of calculus, don't do it.

I don't see why they should be moved to "General Mathematics"; they should be categorized with the topic that the paper is about.


Self-plagiarism and supplementary information

Methods sections (supplementary or otherwise) are one of the few places where self-plagiarism may not apply.  This is because the typical format for a methods section is not narrative (for which creativity is expected) but a highly compressed sort of recipe (e.g. "DHT5a cells in LB, grown in 96-well plates, 150 mL per well, at 37C for 18 hours while shaking at 300 rpm.").  In this form, method sections are essentially a computer program to be executed by a human, and as such the question of self-plagiarism is irrelevant, just like it is if you attach a computer program to your supplementary information.

If you have a "long-form" method section, however, where you give a narrative explanation of an approach, its reasoning and justification, how it relates to the experiments, etc., then the narrative aspects are expected to show originality and self-plagiarism does apply.  This is because you have explanatory text that should be contextually adapted to the rest of the paper, an using it in a new paper changes the context and should thus change the text.

For an example illustrating this distinction, here is the supplementary section from on of my own recent papers.  Section 9, "Additional Methods" is a "recipe section" for which I would not be concerned with the question of self-plagiarism.  All of the other sections are "narrative sections" where one does need to be concerned about self-plagiarism.


How do you decide between two PhD offers?

I am answering this on the basis that I was making this same decision myself a year ago.

Firstly, the LRI will be joining the Francis Crick Institute next year as it opens, which may end up being esteemed in it's own right if all goes according to their plans. It depends what you want to do after the PhD, if you want to stay in academia and cancer research, then it is the supervisor's esteem that is more likely to help you in the long run, as well as the impact of your papers. The label on the institute makes less difference as you go on (within reason of course).

Have a look at the recent publications of the group, maybe see how many have PhD students on good author positions in good journals; that's what will get you a post-doc ultimately.

The two being 4 year funded, the London one may be better financially overall. Integrated PhD programs (where you have 3 small projects in the first year, getting an MRes, then pick the final PhD project for 3 years, I presume this is the case for Oxford) in my experience tend to be more trouble than they're wort, unless you're not sure on picking a definite research project yet or don't have a Masters.

The issues can come from firstly, not getting the project you were hoping for after the first year, after the MRes, but now you're tied down to Oxford (may not happen, but does all too ofter) and also you now have 3 years to do your PhD, not 4. Why waste time on multiple smaller sub-projects at the start if you have a clear idea on what you want to do for your final project? Of course, the corollary here, if you don't have a clear idea exactly what you want your PhD to be on, then integrated programs can be a godsend.

My best advice on the rational decision front is don't. Relationship with group and particularly the supervisor is the main factor in a PhD, with a bad supervisor able to kill your career dead in the water, intentionally or not.

If you have a passion for the research, and get on well with the group and supervisor then I would definitely go for that PhD. Lack of these both for 4 years will likely mean you either drop out, or have a horrible 4 years and then hate your research.

I went for the lower paid, lower ranked Uni offer, and have no regrets. In fact, the higher paid one was industry funded, and they've since gone under, so I dodged a bullet there.


Same literature survey in first and final reports, Is it ok?

In some institutions, one of the goals of the provisional report is to get the student to write something that will eventually be included in their dissertation/thesis. In this way the student feels that he or she has already made a start on the (dreaded) writing up process and therefore feels confident that - in further small, incremental steps - the rest of the document can be created.

In such cases, it would be unreasonable to consider the re-use of the literature review appearing in the provisional report in the final work as being plagiarism.

Matters may be a little different if the initial report was published in some manner, and released outside of the institution. As per one of the comments to your question so far, get your advisor's input.


Graduate coursework not taken for a degree- still relevant for graduate admissions?

The coursework is helpful, especially if you do well in them. It will show that you have understand and have experience with these concepts. The work is not as important as your research, but will be of some benefit. That being said, whether you can transfer them as academic credit towards your graduate degree will really depend upon the school.

As to your CV, simply add a section under education mentioning that you took courses at your new institute. You can list the courses under that and submit a transcript for them when you apply to graduate school.


Is shifting from one field to another helpful for a good career?

Shifting among several fields is definitely exposing you to different fields, and as the comments indicated,  being an expert in more than one field is helpful for a successful career in academia. Answers to other questions on this site make it clear that shifting (or even completely changing fields) in the duration of an academic career is normal and advantageous.

For example, see Bitwise's advice here, where he says

  Changing fields is very common in academia, especially at the PhD/postdoc transition. In many cases it is actually considered an advantage, since you can import your skills, expertise and a certain thought-process into a field in which many people do not have those skills. For example, many physicists, computer scientists and mathematicians have migrated to biology and have made significant contributions. In fact, there are even postdoctoral fellowships that specifically fund this type of field-change.

The question was specific to changing fields at the PhD/postdoc transition stage, but his advice holds at any stage of an academic career.


How should I interpret "English is poor" review when I used a language check service before submission?

There are several possibilities here, although generally they all have the same solution.

The English is poor or incorrect and the company did not check it well

It is possible that the company that checked your article did a bad job. This happens. Maybe the service did not have a native English speaker check your article. Maybe they had a bad day. Maybe they don't provide good service, and you just got lucky on previous times. It's hard to say.

The English is grammatical, but not idiomatic

It is possible that the company that checked your article fixed all the grammatical mistakes, but that there are still some phrasings which are not idiomatic or particularly natural. This is essentially a function of how detailed the corrections were. For example, here is the first paragraph of your post:

  Recently I had submitted a Manuscript to an International Journal. Though it is accepted as a Minor revision, but I am worried about the reviewer's comment. First reviewer has commented that the Paper is well written, still needs some English improvements. Second reviewer has also commented that English improvements is required.

There are some small grammatical errors, and I can correct them as follows (in bold):

  Recently I had submitted a manuscript to an international journal. Though it is was accepted as a minor revision, but I am worried about the reviewer's comment. The first reviewer has commented that the paper is well written, but still needs some English improvements. The second reviewer has also commented that English improvements is are required.

While this paragraph is now grammatically correct, it still does not feel like it was written by a native speaker, and the way some words are used is a little odd. (E.g. using though and but in the second sentence; you really only need one of them.) So, a more thorough checking would suggest edits like the following:

  Recently I had submitted a manuscript to an international journal. Though it is was accepted as a Minor revision pending minor revisions, but I am worried about the reviewers's comments. The first reviewer has commented that the paper is well written, but still needs some English improvements. The second reviewer has also commented that English improvements is are required.

The checking service could have done the first step (making it grammatically correct) without following through on the second step (making it idiomatic). The second step is much harder, of course, as it requires knowledge of what style is appropriate for your field (and for the journal you are writing for), and, to some extent, it requires technical knowledge of whatever you're writing about.

The English is fine, the reviewer is just being picky

Academic articles are complex and often involve detailed theoretical or technical discussion. At times, they can be hard to follow. Sometimes this complexity is interpreted as poor language skills, and reviewers complain. I know more than one native English speaker who has received reviews asking them to check their article with a native speaker. In essence, this criticism relates to how the content is presented rather than linguistic concerns like grammaticality or phrasing.

The solution

It is not easily possible for you to determine right now which of the above scenarios has happened. However, a big help would be for you to show the manuscript to a trusted colleague who is a native speaker of English, and ask them how it reads. If the English is really atrocious, then you know you have a problem with the checking service; if there are some unusual phrases but it's otherwise fine, then you know the problem is that it's occasionally un-idiomatic; and if there are no obvious problems, then it's probably just an issue of reviewer interpretation.

The other step you should take is to re-read your manuscript and attempt to make complex exposition more clear. (This is a step I advise everyone to do at basically every stage of the writing process...) This will help your article in the case that the English was fine but the reviewer was just confused.

Finally, breathe and relax. Your article was accepted, congratulations! Clearly the reviewers and the editor thought that the scientific content was sufficient to merit publication.


Why is research assistantship decoupled from masters/phd program?

This is very difficult to answer authoritatively because each program is different but here are some reasons:

As @Brian Borchers noted, sometimes the admissions and RA funding committees are separate. At some universities, admissions is handled by the department while the RA funding has to be petitioned from the graduate school.
At some places, the lack of funding in the 2+ year is a weeding mechanism. Weaker students aren't offered funding, so they are disappeared (or they pay full fare which is even better than disappearing).
University or department finances may be such that they are not permitted to make a 2 year commitment. They hope that funding will continue but they are being cautious.
They may hope that rather than a university RA position, you will be switched to an external grant funded RA position. They can make a stronger case for funding "unfunded" students this way.
Something else.

The best thing for you to do is to talk to the director of graduate studies AS WELL AS to current graduate students in the program. People on the internet can't tell you which scenario it might be.


Are there situations where taking an honorarium for trying a textbook on a class is acceptable behavior?

I think if you'd not seriously consider the text without the honorarium, that clinches a "don't do it". That is, external monetary motivations should not be allowed to color your professional judgement. And, given that the appearance of impropriety is itself a potential problem, even if the text is plausible, better to be able to later claim objectivity by not taking an honorarium/bribe...


Assessing students in exams with negative points?

Grade that goes below zero doesn't make sense.

What makes you say that?  In some real-world scenarios, thinking you know the answer and being wrong is worse than realizing you don't know.  For example, I'd rather have my doctor or lawyer recognize when something goes beyond their expertise, so I can consult a specialist rather than following mistaken advice.  I imagine the same is true for most professionals, such as engineers.

If not answering at all yields a grade of zero, then it's reasonable to award negative points for a truly bad answer.  (Of course an insightful but flawed answer may still deserve a positive score, just not as high as the correct answer.)

In practice the most common case I've seen negative scores used is multiple choice exams, for the reason given by GeneMachine, but one can make a philosophical case for applying them much more broadly.


Risking declining a postdoc offer for a potentially better one

Accept the "good postdoc" position, get paid whilst you finish your PhD (during evenings/at weekends) and benefit from the position. Apply for the "reaching for the stars" postdoc. Should you be successful, quit the "good postdoc," optionally after negotiating a delayed start date to allow more time in that position.

The OP has declined their other, so this answer is for other readers.


How can a person switch from Arts to STEM?

I admire the enthusiasm, that's for sure. The practicality of the situation, well that's different, but have a go! If the goal is to work in IT, which it sounds like it is, I'd skip the MSc altogether and focus on, for example, software development, system administration, IaaS via AWS or Azure, network administration, whatever. The shortest path, as you ask for, requires laser focus at this point. Best of luck to all involved!
Added
There are numerous avenues in IT. Two roles that might not be obvious, but perhaps worth consideration for someone with a nontechnical background, are business analyst and scrum master. These tend to require broader skills, maybe with more emphasis on interpersonal skills, than others.


APA: Citing an annual report over multiple years

I don't work in APA much, but in the several papers I have had published the journal has had particular requirements for special cases like that. Step one would be to reach out to the editor of your chosen publication.
In the mean time I would probably cite them separately.

  Smith, J. (2002) Annual Report
   Smith, J. (2003) Annual Report
   Smith, J. (2004) Annual Report
   etc.

with the in text citation (Smith, 2002, 2003, 2004 ... ). I find it preferable to include too much detail and be asked to scale back than vice versa.


How do CS graduate school admissions weigh an unrelated master?

If your final goal is to have a CS Ph.D., getting a masters in sociology first will in no way help you reach that goal.  Doing option II may be viewed as a "waste of time" by CS admissions committees, though it probably won't preclude you from getting into a masters program afterwards.  I'm guessing the net effect will be slightly negative from the point of view of a CS admissions committee.

However, it doesn't mean you shouldn't do option II, especially if you think you'll enjoy it.  You might even find your career plans changing after getting a masters in sociology.


Should I pay the teammate of the research if they don't contribute many things?

Use the money for whatever purpose it was assigned: If assigned to pay project team members equally plus your bonus for the leader position, do that. If assigned for submission fee, pay that. If assigned with no remit, do as you see fit. Personally, I think everyone deserves to be paid for their work, after costs (i.e., the submission fee).


Master's studies in France and Greece (one year per country) plausibility

If your plan is to live in each country one year, you would be better off by doing a master course of 2 years in Greece (or France) and being one year exchange student with Erasmus program in France (or Greece).
As far as I know, you can be Erasmus student without scholarship (which means you will fund yourself through the abroad stay).
Bureaucracy can be complicated (transcript of exams must be translated, syllabus not matching, etcetc) but being under the umbrella of the Erasmus Programm will help you a lot.


Potential PhD supervisor expressed interest, but had a short response. What do I reply?

I think he is busy and just responded in the quickest way possible to your query. If you are interested in it, respond that you are and would like to take it up. More importantly, respond that you want to take it up under his supervision and will be following up with your formal application.

If you come up with any deep thoughts on the problem or partial solutions, you can (now or later) communicate that you have progress and maybe share some of that. Since you don't really know much about him, I wouldn't lay everything out early on, however. Wait until you can assess one another first.

If you read other questions on this site note that some of them are about unethical behavior by supervisors. I have no reason to even suspect this is the case here (and since it is rare, I doubt it). Others questions are about misunderstandings. If you are familiar with the game Poker, don't show all your cards early.


How to deal with advisor writing a thesis chapter for you?

A few possible reasons:

The advisor is not very experienced with advising students and is not clear on what they are supposed to do.
The advisor intends to publish the thesis with the student and is therefore interested in ensuring that the specific chapter is properly written.
The advisor is not confident in the student’s ability to correctly formulate certain ideas.

What can the student do? Ask the advisor politely to lead the writing of the thesis, write a first draft that they can later review. If the advisor insists, I suggest letting it go. It’s one chapter and is not a very big deal if it is indeed an undergraduate thesis. Helping students write is not unethical unless the student is really not leading the project. However in that case I fail to see why the advisor would take the thesis writing as their own project...


Teaching duties in Italy for researchers, associate professors, and full professors

I'll answer about where I teach, but I think it is similar in the rest of Italy. Typical amounts of teaching are:

RTD-A 50-70 hours of frontal teaching / year
RTD-B 70-100 hours
Full and associate professor 120-130 hours.

In addition, exams take quite a lot of time. You have to offer the students up to 5-7 opportunities to take each exam each year (yes, you read that right), plus 2 make-up exams for certain protected categories such as parents and workers.  Many undergraduate courses have a written and an oral exam, at least in the STEM area.
You have some leeway in scheduling your exams so that you can fit in conferences and/or visits, but typically lectures and exams will keep you busy for more or less the whole year, apart from August and a 2-weeks Christmas break. (Or you can arrange to have courses only in one semester, especially at the earlier career stages when you have less teaching.)
There are regular faculty meetings (at least 1/month). In addition, there are some committees for stuff like outreach, teaching evaluation, attracting new students; you can expect to have little administrative tasks at the beginning of your career but it will step up as you progress.
Paperwork is mostly tied to national and European grants.
EDIT to add more detail: As a professor, you won't have to sign a contract detailing your obligations: all the regulations come directly from the Italian codes of laws (yes, this is weird). In practice, there are very few hard requirements written in stone; one of them is the amount of teaching activities: as a professor, you can be required to cover at least 120 frontal teaching hours/academic year, and you have to devote to all teaching activities at least 350 hours/academic year overall. In practice, people usually talk to each other, compromise, and share the burden of department administrative activities. I don't know what would happen if someone decides to do the bare minimum and refuse all additional assignments, because in practice this doesn't happen.


Should I mention a mistake made by a third person?

It was your task to ensure the book gets returned. You need to take responsibility and apologize. You can mention that you had made arrangements, which failed unfortunately.

It's unlikely that the professor cares about the details. What he cares about is that he didn't get the book (that's why you apologize) and that he can rely on and trust you (that's why you promise it doesn't happen again and make sure it doesn't). This is a learning experience, i.e., you know now that your relative is not reliable and as a consequence your professor trusts you slightly less (but that's not permanent damage). Obviously, make sure he gets the book as soon as possible.


What is an optimal reading order for a set of related papers?

I often struggle with the same question.  One approach which I find often gives good results is to start by skimming through all the papers (typically in chronological order) and use this first reading to decide on a more appropriate reading order, typically starting with the ones which seem more introductory or survey-like and ending with the more detailed ones.


List of accepted papers: Why do notifications take 10 more days?

Most likely, the program committee needs some additional time to edit reviews and provide a summary of the PC's discussion of the paper.  Reviews may require editing to remove bugs (for example, if a reviewer misinterpreted a result, but the misunderstanding was cleared up in discussion), or to professionalize the language (a reviewer might have described an author as a jerk or worse), or to remove references to other submissions under review need to be purged.


Would a Professor be responsive to a meeting request from a PhD student like this?

@Penguin_Knight's comment is the best advice in this situation: ask Professor C to introduce you (via email with you in CC) to Professor X and mention that you will be in town and would like to chat.  Professor X may not have time to read all the messages she gets from students and other people she doesn't know, so there is always a chance your message -- not matter how well-crafted -- may be overlooked.  But a message from a coauthor will immediately stand out and is sure to be read carefully.

This is a very natural thing for Professor C to do (assuming she has a positive opinion of you and your work); you should make the request politely but you don't need to feel that it is a huge favor.

If you leave a good impression, this introduction and the subsequent visit will usually drastically improve your chances of admission.


Does a thesis have to have a "Discussion" chapter?

Do you discuss the results and their implications?  Do you present the insights and conclusions?  Do you make your argument and present your evidence in a logical, persuasive way?

I find that chapter/section headings are much less important than the overall document strength. If your thesis fits the following, the I'd defend it.  Worst case you may be asked to restructure; best case you make your point and it is accepted as is.

Key Points:
Thesis should
- be organized and logical
- clearly articulate the main points and supporting evidence
- discuss any conclusions and insights

I'm sure there are others.  Section/chapter headings are author's choice - use what you need to accomplish your purpose.


What can we do to increase student engagement?

My school has a mandatory attendance policy (which I know several members here disagree with) but because of that policy I have had to face with engagement in a different way that you. Still, I hope this answer will help.

Without engagement I find myself in large classes (sometimes >100) and classroom management gets to be a real challenge (for me and the other students). So, after trying a few different things I've found that challenging the students almost like a game show seems to be useful.

For example, in one module, I will give them scenarios (one at a time) to analyze (with multiple choice answers where each requires them to come up with their own reasons why that is the right answer). The scenario is short enough to fit on one slide and while the students are encouraged to read before class, they can still participate even if they did not do the work. This is particularly helpful to me since the ones who do not do the homework tend to be the hardest to control and, therefore, are the most disruptive to the learning environment. They tend to find it a challenge to see who can 'guess' right.

On top of this, I try to inject a little humor while walking around the room asking for analyses which tends to add a little entertainment aspect to the whole event.

For another module, I assess through an extremely difficult test which is quite common to fail unless extensive research is done. In this case, I alternate lecturer sessions (where I do most of the talking) and discussion sessions (where students do most of the talking). Engagement is not quite as strong with this module but I'm still honing it.

On a somewhat related note, you might check into this article on discovery based learning. I found it quite interesting.


Should I contact the reviewers I suggested during the submission if the manuscript is still under review after one year?

No.

You don't (and shouldn't) know who your reviewers are.  The editor could have ignored your suggestions entirely, or even used them as a list of conflicted people not to ask to review your paper.

Feel free to bug the editor again, but leave it to the editor to bug the referee(s).


Quitting a job after spending ahead on a grant

Most grants are not given in a lump sum, but in a sequence of increments---typically 12-months increments, but sometimes shorter or longer.

It is true that when you get a chunk of money for a increment, there is typically quite a bit of flexibility in how you spend it within a phase (though some funder require notification if you go significantly "off plan").  You cannot spend more than you've been allocated, however, and asking for an increment in advance is typically either impossible or else requires negotiation and approvals from the funder.

In your hypothetical situation, then, if the funder (university or external) gave all of the money up front, and the spend plan was within contractual bounds, they really have no place to object if you happened to spend it faster than anticipated (assuming no other regulations were violated).

However... the money was never actually yours. It belongs to your institution in some way (probably via your department via appropriate contracting and accounting personnel), and you probably never even had the right to sign for the money.  You were just given authority over allocating its expenditure.  As such, when you leave, the remaining money (and any tangible assets, like equipment) stay in place.  The money will likely go away, since the terms of the grant specified key personnel (you) who are no longer available, but if the parting is friendly enough it may be possible for somebody else to take responsibility and the project to continue with you as a subcontract or consultant.

Reputational consequences based on the particulars of how you quit, of course, are another matter entirely.


Evaluating red flags in potential advisors' scientific production and impact, past students, research interests and personality

Well, first of all, this is a master's thesis. I would argue that it doesn't really matter that much, because you will at most be working with this person for a year or so and then leaving to go somewhere else.

Given what you've written here, I wonder why this is even a question for you. You know Prof H and have taken courses with him and done well. You know that he gives good mentorship and feedback. You know that his former students end up very successful. You know he's productive and well-known, which could be helpful for getting into a PhD program. The only question here is does he have enough subfield knowledge in your area to advise your thesis?

Also, if he has 30 years of research and is a household name, how is his work not impactful in terms of citations? You don't become a household name as a scientist unless you've written some papers with impact.

Prof K might not be a bad choice either. The fact that he has had no doctoral students is irrelevant because you're writing a master's thesis. But why go for an unknown if you already know Prof H and know that he's a great advisor?


A working paper or a discussion paper or something else?

JEL classifications are just that: classifications. Anyone can put such a classification on his paper, and it doesn't have anything to do with publishing in the JEL - it's more like a keyword.

To your question: I don't think there really is such a big difference between a working paper (which is work in progress, typically distributed to be discussed) and a discussion paper (which is work in progress, typically distributed to be discussed). All of these are essentially manuscripts under preparation for submission to a refereed journal (in CS, a conference). So I would file all of these under "non-reviewed papers".


ieee membership discount on overlength manuscripts

I believe there is confusion about what the charges mean. Generally, IEEE has two types of page charges:

Voluntary Page Charges
Overlength Page Charges

In 2020, for IEEE Transactions on Information Forensics and Security, the voluntary page charge rate is $110, while the overlength page charge is $220 — which correspond to the numbers in your question.
However, the meaning of these charges is very different.
Voluntary charges – are actually voluntary. They are not obligatory, usually paid by the institution, and help IEEE to offset some of the expenses incurred in publication.
Overlength charges – are different. They have to be paid for all submissions exceeding X number of pages (X=6 and X=10 for short and regular papers in IEEE Transactions on Information Forensics and Security, respectively). This small note from 2004 might explain things a bit more elaborate; I simply was not able to find the relevant page on the IEEE site directly.
I have never heard of a discount on overlength charges. Often, these charges are paid by the advisor from a grant. I once paid the charges myself as a student when I was in transition between affiliations.
With all that information, it is highly unlikely that you can get the charge lower than $220 pay page over the limit. However, in some circumstances (the reasons have to be very serious), I believe IEEE can waive the charge altogether.

Disclaimer: I serve as a Vice-Chair of Membership and Benefits Committee for IEEE Antennas and Propagation Society; however, this answer is not within my direct area of expertise — thus, posted solely as my opinion as an individual familiar with IEEE practices.