Can my co-advisor be from another institution?

Yes, it's common in the institutions that I know. Where I graduated, at least one member of the committee even had to be an 'external'.
That doesn't mean the same applies to your institution. Read your local examination rules and check with your first supervisor if external (co)supervision is possible in your institution and what the implications are.


Would the professor leave the classroom if only 1 student uses their cellphone during class?

I've occasionally done "shocking" things to send an important message. It might be that all he intends is to make it a dramatic statement that you (the class) should take it more seriously.

I doubt that he intends to not return, and also doubt that he would get any administrative support for that.

I've always been willing to fail the entire class. Also willing to give full marks to the entire class. But that depends on individual, not group, behavior. Again, failing person A because of the actions of B would be unethical and would draw no administrative support.

If it is only one student then, perhaps, a more nuanced and less dramatic response would probably be called for.

In one of my "dramatic explosions" not every student was guilty. But even the ones who were more conscientious got an important message about proper behavior. In this case it was more about their own lack of preparation. There is a scene in Stand And Deliver in which the teacher, Jaime Escalante, denies entry to the classroom to a student who doesn't have his homework paper ready to turn in: "If you don't have a ticket, you don't get to watch the show."

But hopefully, the need for such drama is infrequent.


How to include experiments vs state-of-the-art papers with no code

In this situation we always just say "we attempted to compare our result against XYX et al, but could not access a working implementation."

If a reviewer were to complain, we might say (to the reviewer, not in the paper) "in what way does #3 move the field forward if it cannot be used by anyone".


What to do about fee from publisher for withdrawing unpublished accepted manuscript?

There is wrong on every side of this situation.

First, a journal demanding money for withdrawing a paper is suspicious in the extreme. I have never in my life heard of such a practice from a legitimate journal, which means that you were probably duped into submitting to a predatory (junk) publisher.  If this is the case, you should definitely withdraw the paper and refuse to pay the money, but they may not let you: a dishonest publisher may simply publish your paper without your consent and send you a bill.  If this happens, you can try to fight it, but you may end up needing to withdraw from the other journal instead and simply write off the paper and/or the $500 as a learning experience.

And what will you have learned?

Never dual submit a paper: it is scientifically dishonest, wastes everybody's time, and seriously annoys any legitimate journal.
Never submit a paper to a journal that you haven't thoroughly investigated to determine that it is not a shady fly-by-night predatory publisher.


Should a bachelor’s or master’s thesis include acknowledgements?

Acknowledgments are almost always an optional part of a document that you can choose to include but don't have to. This is true for PhD theses as well as MSc, Diploma theses, or any other kind of document.

The guiding line is: If there are people or institutions who you feel you want to thank or acknowledge their support, then do so. If you think that everyone in your life and your university has let you down, then don't.


You can use note taking to both save the information you later want to recall, and, more importantly, reinforce the learning that helps you recall it.

There is evidence that hand written notes are best for memory enhancement as they engage the brain in a different way than typing (or certainly more than cut-paste).

But you can go an extra step. You can, at a somewhat later date, summarize your notes, which, again, reinforces the learning.

And there is no reason that you can't also capture your original notes and/or summaries in some computer media for keyword searching and such.

This personal database of past readings and thoughts about those readings is better for recall than, say, Google, which searches a larger space than you are interested in and so comes up with un-useful hits.

But the key to it, is to use reinforcement tricks (hand written notes, etc.) so that deep learning is achieved and recall is more likely.

Personally, I prefer taking original notes on index cards. You can always carry a pen and a few cards for making quick notations and for noting questions you might have so that they can be explored later. The cards can then serve as the basis of summaries. See this answer to an unrelated question for more on the concept of the Hipster PDA.

Of course this technique works best if you start it before you need it. But it isn't ever too late. There is a Chinese proverb: The best time to plant a tree is forty years ago. The second best time is right now.


Is is possible to anonymously encourage one's US university to make content accessible (e.g., as per the ADA)?

The appropriate place to raise this would be through the Disabled Student Services at your university. Even though you're taking the course as a MOOC, the DSS office still has authority over the course (unless it's being run through a subsidiary or joint-venture similar to Ed-X) as well as the responsibility to make it accessible. C.F. Harvard and Ed-X accessibility settlement.

If DSS does not respond, then the next place to go would be the ADA Compliance Officer on campus. If the university is receiving federal funds, they should have someone designated as such (and this person might share multiple roles, such as the Title IX Compliance Officer, etc.).

If that fails, then the university ombudsperson.

If all university channels fail, then you contact your State office of civil rights or  the Federal Office for Civil Rights (OCR). It's unknown whether the Federal OCR will be proactive and responsive during the current regime, but technically they are where the buck stops right before you go with a full blown ADA complaint.

Also, you might also pursue hiring private legal counsel, especially if you absolutely want to remain anonymous during the initial complaint phase. Ask your local disability center for independent living for referrals to local attorneys who take on ADA/504 complaints against universities (note this is very different from run of the mill ADA cases against private businesses) or consult with a national firm such as Disability Rights Advocates, CREEC Law, or DREDF, etc.


Copyright in academic software in the UK

Many academics in CS publish their software and sometimes even their data, blissfully ignoring whether they are allowed to do so in their institution or not. It's unlikely to cause any trouble because institutions usually don't care too much: nobody will ever check, unless there's a potential commercial opportunity at play.

However my understanding is that IP rights for any outcome produced in the course of academic work [edited] might be shared between the institution and the author, depending on the institution/country (but IANAL of course). This doesn't mean that the institution forbids academics to publish their software/data, actually it's even very unlikely that the institution would oppose publishing open-source software, but the proper way to do this would be to ask the IP/innovation office for permission (afaik most institutions have one nowadays).

In my research centre there is an official process that we are supposed to follow whenever we want to make something publicly available. It's a simple software disclosure form where the author indicates what the software does and what kind of license they want to apply to it. The form is supposed to be reviewed by an IP officer who in my experience always validates the request.  I've done it a few times myself: this additional administrative step is a bit annoying but it's not such a big effort.


There are two questions, namely what you can do legally and what the community would consider acceptable.

Legally, distributing such a summary is probably a copyright violation if you borrow too much from the original; in the U.S., it would be considered a derivative work (the legal definition includes "abridgment" and "condensation" as forms of derivative work).  In that case, it would be illegal to distribute it without permission from the copyright holder.  On the other hand, you are not likely to get in trouble unless you offend the author or publisher.  The easiest way to offend the publisher would be if they view your summary as competition that might decrease sales of the book, but they might take a strict approach to copyright enforcement in any case (it depends on the publisher, and I would guess that a nonprofit publisher might be more understanding than a big commercial publisher).  In practice, the worst case scenario is probably being forced to take down any copies you had posted online.  You could be sued, but that seems unlikely to me.

The research community is likely to take a less strict approach than the law.  If you distribute the summary privately (e.g., just to friends or students), then nobody is likely to find out or care.  If you post it online, then it's more likely to attract attention, but it won't necessarily be negative attention.  That depends on how you've written it.

You should keep several things in mind to avoid causing offense:

You should be absolutely clear about what you have done: what's a direct quote, what's a mildly reworded version of the author's words, what's a summary in your own words.  You need to be careful about distinguishing your own interpretaton from the author's, and you can run into trouble in two directions, either by seeming to take credit for observations that are explained in the book, or by seeming to attribute your own ideas or organization to the author.  This is a difficult balancing act, which is easy to mess up.  Even if you are very careful, the author may still feel that you are distorting the emphasis on different topics, for example.
You should be very careful about correctness.  I would be unhappy if someone circulated a summary of a book of mine that had mistakes in it.

I would not recommend asking the author for permission, since that would put the author in an awkward position (of having to either endorse or object to your summary).  If the author discovers your summary and complains, then I feel professional courtesy requires you to make changes or take it down.

Personally, I would probably not post it online, but opinions could differ.


Is it unusual for a prospective university to offer a bonus to your stipend after visiting?

It's not too unusual. Lower-ranked schools know they need to work a little harder to attract top talent. For example, I did an REU at a lower-ranked school, and they admitted that the only reason they bothered offering an REU program was hoping that some of us would become grad students -- they normally couldn't attract grad students of our caliber. Offering a 15% stipend increase to particularly promising students seems altogether appropriate.
University 2. I might seriously consider university 1 if you didn't like university 2 for some reason -- what you do is far more important than where you go, and getting into a top school does not guarantee you an academic future (not even close!!). But in your case, both seem like good options, so if you get into university 2, I would go there.


Where to find computer science conferences which accept engineering work?

The three primary ways of finding a community and venues that suits you are:

talk with people familiar with communities that might be of interest to you (will be heavily based on luck and talking with a lot of different people about their work)
find publications that make the sort of contributions that you want to make (requires broad reading of the literature in your field, and possibly beyond it)
find venues that sound like they are on-topic for you and read papers from it to see what variety of papers seem popular there recently

In short, there is a three-way link here: People <-> Publication <-> Venue

Find one and you can work your way to the others. Find a publication that fits what you want to do, and you can find the venue it appears in, as well as the people involved with it. Given people, you can find what other papers they publish and where they publish them. Given a venue, you can find what sort of papers are published there, and who is responsible for those papers.

All of these are in a constant state of change, so what contributions are valued, what work people do, and what are top/good/ok/bad places to publish changes at least yearly. Ideally you would have local contacts (advisor, other professors, fellow researchers) who can help you, as the search space is so large, but sometimes you are (or want to be) in the minority and so what works for most people near you won't work for you.

Specific to engineering, you should be aware (and look for) the fact that not all engineering contributions are the same, either. Some focus on novelty, technical difficulty, real-world application, industrial applicability, actual deployment, etc. You'll discover that as you read through papers.

I should also clarify that math is not a short-hand for academic or scientific work. While math is often a part of papers, there are many types of paper where you could remove the math completely and the contribution would be the same. Sometimes math is part of the key contribution, sometimes it is sprinkled on for effect (like a garnish), sometimes it is just for clarity, and sometimes it is just because it is standard to include some definitions/equations but they aren't otherwise important. Learning to distinguish them is just part of the process of reading through them - though I suspect you are getting hung up on the fine details before you get to the general big picture, which will actually make it harder to figure out what is going on.

I would suggest you try to read the papers in a less detailed way on the first pass or two, and basically replace the math with this: input -> (magic happens...) -> output. First understand the general gist of what purpose the math is to serve, and then you can go back and look at the math more closely when it seems relevant - but most papers won't be relevant enough to the task at hand to bother with that level of detail. It can also help to join a reading group so you can get the experience of seeing how other people talk about the papers and work through them. This is especially important with unfamiliar math, as there are many natural language ways of talking about the math that makes it make sense, when you would never get that from only reading the paper itself.

Eventually you will be able to find papers and say, "hey, this is the kind of paper I want to write and the work I want to do, only instead of this detail here I would instead like to do this other thing..." - and there you go. Since you have less time to do this than a full PhD, I suggest you be a bit less picky and instead focus on the lower-hanging fruit of being closer to the work your group does, or at least focus on papers you feel are more intelligible to you and settle for an OK fit.

Finally, don't be afraid to ask for help from those around you, that is part of the process and point of being in a program. Well, you can be afraid, that's fine - just ask for help anyway. You will not understand every last bit of what you do, much less what other people do, and that's part of the work - don't worry about it. Much of the goal of the field you are in is to try to make advancements even though the level of complexity has long gone beyond what any one person can understand fully, even with many more years of experience than you have. Do what you can, muddle through, and accept that you will only understand a small percentage of what there is to know.


How much should I charge a colleague for a translation project?

I imagine the answer here is slightly subjective, but my personal thoughts are that you should charge whatever you feel your time is worth. The industry price is probably a good starting point -- don't undervalue your time for sure. And remember the time and energy that went into developing your language skills too, not just the time it will take you to translate the article.

That being said, the industry price is just that -- a starting point. If you want to reduce the price for a colleague, you can certainly do so. You may have political reasons for doing so (you want their support on something within the university), or they may have services to offer you in return (as in a barter economy). I'd caution you against reducing your price too much -- you don't want to be inundated with requests like this in the future.


Which licence choose for a new academic computing language?

Oh, no, yet another format!

Now seriously, you can legally register a format, but I don't see a big benefit from doing it.  For what I see, licensing is essentially a copyright of the actual text. In most practical purposes, having a public, freely available document explaining it, should suffice.

To support my feeling, I have been digging in some academic examples I am familiar with and they don't specify any.

If you want to be sure, you could see what other people have done, for example, OpenDocument format.


Can an editor review manuscript without sending to reviewers?

Yes, an editor can review a manuscript themselves, but you cannot infer an editor is reviewing themselves when a manuscript has been with "a journal [for] one  month...and the status is 'with editor' up to now."


Is a joint science PhD/JD a bad idea if I end up pursuing academic science?

Interesting question.  There are so many factors to consider, including time, cost, workload, etc.

It does seem though that having credentials in both disciplines can give you both a unique perspective and a means through which you can influence public policy. Forward-thinking academic departments may see that as a plus.  Of course, others could see it as a lack of commitment to pure science, but I'm speculating.

You should consider that the merging of science and law is not uncharted territory. A great example is Vanderbilt's law and neuroscience initiative, funded by the MacArthur Foundation. See
Vandy Law & Neuroscience for details.

However, Vandy does not have a 'law and neuroscience' department, and I doubt that the law school or school of psychology (housing neuroscience) would specifically look for a candidate with both a PhD and JD.  But, it would certainly fit. This may be true of other institutions as well.


In my opinion professors are normal people and can have friends as everyone else, as long as it does not affect your grades and how you are treated in the classroom. I used to give classes where I taught my friend who I started studies at the same university with (he took a few gap years...). In the classroom and when grading exams and homeworks I treated him exactly as other students.

There is also a possibility that your institution's code of conduct has regulations pertaining to this situation. Nevertheless, they should be more of concern for your professor than you.


Applying to a PhD program whose offer I rejected last year

It is likely that you will need to contact the particular program director to receive an answer specific to your situation, as a number of elements are specific to the program, the department and the institution or university. However, allow me to respond from the point of view of the director of a graduate school in a Russell Group university in the UK.

Given that you accepted an offer from University A about a year ago, it is likely that you would have turned down the offer from University B or allowed the offer to lapse. Either way, as a year as passed, it is highly unlikely that the offer from university B is still valid. Thus, you will need to reapply.

The administrators of graduate programs, whether operated centrally as mine is or devolved to individual departments, will retain records from previous applicants. The type of information stored and the duration of storage will depend on the individual unit. Regardless, it is highly likely that some record of your information -- perhaps even your full application -- will have been retained, given that only a year has passed.

Thus, I wouldn't hide the fact that you had previously applied, been accepted and declined a place in University B. It's quite the opposite, in fact. Your application should now contain some explanation about the following:

Why you are reapplying
What was the reason for your decision to decline the offer
What have you been up to in the period of time between applications

These explanation should be made on top of the information you'd be providing about your proposal, your qualifications, etc. It might form some part of your personal statement.

Once your application has been received, it will be assessed in the usual manner. A flag will be raised that you'd applied before and (at least in my graduate school) your previous record would be appended to the new application. This forms the evidence on which a decision is made.

You need to be aware that submitting an application in this round that is identical to the one you submitted previously is not a wise move. First, it's been a year or so since you wrote the proposal and the science might have moved forward in important ways. Second, you have had more experience and may have had time to produce research relevant to your proposal. Third, the program or department's staff mix might have changed, so that potential supervisors are now unavailable. Fourth, the program or department's research priorities might have changed so that the areas of research are now different. When crafting your new application, I suggest taking these issues into account.

Contacting program directors is always advisable, at least to receive information specific to your situation. Don't expect them to know your case if you cold call, but if you prepare them sufficiently, they should be able to provide you with valuable advice that you can use to your advantage, even if that advice is "don't bother applying".

Finally, reapplications from applicants who've previously been accepted into one of our programs and who've subsequently declined is unusual, but not unknown. This year, we accepted about 400 or so new PhD students. About 2.5% were from students who'd deferred their entry (that is, they accepted the original offer, but asked permission to delay their start dates by a few months). We had one reapplication, which was eventually rejected.

Good luck.


Would it be acceptable to report a professor for poor teaching / attitude in a Masters graduate course?

You should discuss this situation with your department graduate chair or a similar authority.  It is important to give your program feedback so that they can improve.  However, keep your feedback constructive.  The word "report" is excessively negative.

I think you should adopt some perspective.  Often, graduate level courses are not treated as seriously as undergraduate courses because graduate students are expected to spend their time on independent research, not course work.  Also, while you may be paying a lot of tuition, it is unlikely that an adjunct professor is receiving very much pay.  Many adjuncts are working many jobs to pay their living expenses.  They often receive no training from employers.  Poor teaching by adjuncts can reflect problems with the structure of the institution rather than with the individual adjunct.


What are the criteria for degree revocation?

Please feel free to edit this answer to improve it.
Short answer: will my degree be revoked?
Almost certainly not. Degree revocation is extremely rare, and almost always involves some major, willful misconduct such as plagiarizing long sections or falsifying data. Almost everyone who has raised concerns on this site over the years had nothing to worry about. The different answers below discuss different criteria that could lead to degree revocation, but these are generally edge cases. The typical person who earned their degree in good faith has nothing to worry about.
But this site cannot give you a definitive answer. Different schools have different staff and different policies, so it is impossible to predict how a particular institution will respond to a particular situation. Nor can we decide whether you committed misconduct (and even if we did, our decision would not count for anything). We recommend checking your school's policy on degree revocation (often available online). If you are concerned about degree revocation, you could discuss the issue with a legal advisor or the school in question, though you may be better off "letting sleeping dogs lie."
Finally, note that degree revocation may be discussed or threatened rather more frequently than it actually occurs. Individuals and/or organisations may respond to some incident or action by 'calling on the university to revoke the degree', and this may gain traction on social (or indeed traditional) media. However, this does not mean it is actually likely to happen.


Mentioning LGBTQ Identity in Personal Statement for PhD Applications

Edit (in response to revised question):

In light of the revised question, this sounds like exactly the sort of thing they are asking for, so yes feel free to talk about L, G, B, T, Q and X.  However, my guess is that whatever you write here won't make too much of a difference (as long as you don't make yourself sound crazy or anything), for the same reasons I indicated in my original answer.

Original Answer Below (where it sounded like this was about a personal statement):

Unless they are asking specifically for you to address diversity issues, I don't think it matters much what you say about LGBTQ issues in your personal statement, as it has nothing to do with physics.  Note: depending on the department and admissions committee, the statement of purpose may be important or not important (e.g., Why do admissions committees consider the Statement of Purpose to be important? and How important is the statement of purpose in a PhD application for admission to a top school in the US?).

What I look for in a statement of purpose (in math, which I imagine is similar to physics) is basically what I look for in the rest of the application: your preparation for grad school, your talent and work ethic, your interests/fit with our program.  Though it also helps to get a sense of your personality (so it's not good, e.g., if you sound like a crackpot).

I don't think the issues mentioned in your question reflect too much on these things.  On the other hand, I don't think it will hurt your application if you want to briefly mention at least (1) and possibly (2) if you can weave them in naturally, but these things shouldn't be the focus of your personal statement, as they say nothing about why you want to go to grad school.  (Certainly your CV is a suitable place for (1), so it can make it onto your application there.)  Academia is relatively LGBTQ friendly in my experience.  However, we don't want to know your whole life story on your application, just the part of your story related to (in your case) Physics.


What are the different components of degree titles called?

To take one of your examples:

Master of Arts in Psychology: Behavioral Health
|_A__|_B_____|_C___________|_D________________|

"Master" is the degree. Etymologically, "degree" comes from "degré": the step of a stair (or  rung of a ladder). "Degree" can be synonymous with "level" or "extent" - it is a measure. You could say "the level of a degree", but that would be a tautology. It's not incorrect, but "level" is redundant there - "degree" already says everything that you'd be trying to get from "level". Degree is a very flexible word, and can be used to refer to just part A, parts A+B, parts A+B+C, and parts A+B+C+D.

Then either:
"Psychology" is the subject and "Behavioral Health" is the speciality, or "Psychology: Behavioral Health" is the subject. You might also hear "field" used instead of "subject".

"of Arts" doesn't really have a well-recognised name. You could call it type, kind, field, sort, school or faculty, but in the end, if you want to ask what sort of Master's someone has, you'll probably end up saying something like: "What kind of Master's? Master of Science, Arts, MBA, something else?"


Further improving PhD thesis vs publishing as a post-doc

You can always revise and extend your old work. Make your dissertation work as good as you can in the available time and then move on. If the problems you work on are sufficiently interesting there is always room to continue.

Whether you continue the work with your advisor or not may be a question that depends on the expectations of your field.

Most doctoral students hopefully finish with a notebook full of problems that were interesting but couldn't be completed during the graduate program. The ideas don't die just because you graduate.


How to deal with a micromanaging supervisor?

It is a difficult situation but you can try the following:

Tell your supervisor the following:

  I would prefer that he gives his opinion by saying I prefer this idea better and pointing out a wrong assumption by saying I don't think this works. Evaluating me (monthly for example) instead of just saying directly you are wrong (because most of the time the mistake does not affect the work). -

It is not guaranteed to work —  if he's certain he's always right, he's probably certain that he's right in how he does the supervision. But it may hive him the food for thought and eventually lead him to adapt to your needs.

Take a more leading role in collaboration. He explicitly expects you to do it. Yes, you will probably be criticised for your mistakes, but if you manage to process this feedback constructively, you will get  a lot of useful knowledge and experience.

  I don't feel that I am allowed to do thing by myself because he is pointing out everything so I just wait for his orders.

Don't wait for his orders. He explicitly wants you to try and fail and receive his feedback on it and try again. This is his supervision method. It's annoying but it's not the worst. Maybe, ask him also to note and appreciate good things about your proposals when he sees them.

Micromanaging requires a lot of time, effort and thought. It's not an easy or pleasant strategy. Being control freak is not fun. PI's are pushed into it often because they:

are responsible for large and complex projects
do not have time to do all the work personally and have to rely on postdocs
do not receive the expected outcome from their postdocs — for various reasons postdocs may waste project time and funds and achieve nothing.

There is a delicate balance to strike between developing a postdoc as an independent researcher (i.e. allow them to take lead, try and fail), and achieving project goals (i.e. get excellent results and produce top-level publications). These two goals contradict each other, and any PI is under a pressure to deliver both. This may lead to the conflict you describe as:

  he behaves as a micromanager and wants me to take lead. The two things don't match in my opinion.

Unfortunately, this is a direct consequence of modern funding system and culture of success in academia.

I disagree with another answer suggesting to "blame the professor". My advice is to try to help your professor.


What is an "evidence based" teaching statement?

I think the verbage "evidence-based" is often a little misleading to a STEM researcher. When we hear "evidence", we think of proofs or scientific experiments with significant sample sizes and controlling of confounders. Clearly, such hard data is not usually available in your teaching statement. However, it's also not really what people are asking for when the want to see "evidence" - normally, plausible anecdotal data is entirely sufficient.
More generally, what people often mean when they ask for evidence is that the current text is simply not sufficiently convincing, often because it "tells" rather than "demonstrates". It's not so different to how we tell PhD applicants to write their Letters of Motivation - everybody can write that they love teaching (by itself this is a meaningless, empty statement), it's better to explain what you do that shows that you love teaching.
I can give an example from my own teaching statement for promotion to Associate Professor a while back. The initial version had a paragraph that read something like this:

I redesigned course XYZ and improved student success as well as student evaluations.

I received the fair criticism that I should be providing more evidence, because the current statement isn't particularly convincing. So my final version instead read something like this:

I redesigned course XYZ [explain changes]. After implementing these changes in 2017, the percentage of failing students dropped from an average of 20% to 13%, despite a technically more challenging exam design. Additionally, the course evaluation improved from an average of 3.2 to 4.4. This leads me to believe that my changes were effective, both in terms of student learning and student motivation.

This is clearly not hard proof that my course is now indeed better - maybe my exam wasn't actually harder, or maybe I just got a smarter class this year. But it's a whole lot more convincing than simply writing "I did well".


Can posting to arXiv ruin your reputation?

I think your comment has very important information:

  This paper is just that. It presents helpful information but doesn't develop any ideas or utilize the scientific method.

So, it is not crappy, they are not unbacked claims; it is just nothing new. As long as you are aware of it, and it is clear you are not trying to make it look different, it cannot hurt you.

You can think of this paper as a small review or class notes.

The only thing that may hurt your reputation is if it had very serious mistakes, and you don't address them. To be safe, just ask some of your colleagues to review it, even if it is not a thorough one. They should be able to tell you if it is correct, informative, and clear. And by all means, if it is informative, go ahead and publish it.

Also, ArXiv is not only for preprints of papers. For example, I have seen philosophical dissertations on QM very non technical (a second year Physics undergrad should be able to follow), or another about the story of protein folding research in a certain institution.

Edit:

Regarding your comment:

  but are arxiv posts considered publications for what you're talking about? i could put my grocery list there if I wanted to, right?

ArXiv is not peer reviewed, so the quality threshold is not so high. You can publish not so technical pieces, or sneak a bad article that looks just fine, they don't count as official publications. But, on the other hand, they are better than nothing. Specially if you are at the beginning of your PhD, when you are not expected to have publications yet, your ArXive papers are an example of your capabilities.

No one will use the sheer number of submitted papers, but if you have some fine pieces (for example, a good, brief review of your field, previous research and terminology), can show you have a promising career for, for example, applying for summer schools or extra funding.

Depending on your field, this kind of papers can be extremely useful. For example, in Bioinformatics, most people come from a CS background (programming experts and good Mathematics, but knowing nothing about Biology and Chemistry), Biology (lacking in Algorithmics, Machine Learning, and Statistics), Physics (lots of Maths, but basic knowledge of mostly everything else)... For me, having a quick reference of the basic terminology of other disciplines would save me a lot of time, as I have to look up many simple concepts that would be obvious for, for example, a Chemist undergrad.


Should I share my course notes with my co-students?

You have just discovered some of the seemingly irrational ways in which students sabotage themselves and behave contrary to their own interests, and how they sometimes do this precisely in response to an attempt to help them by offering them useful resources.

Professors constantly struggle with this issue: do I offer my students lecture notes? A practice exam? Homework solutions? A detailed outline of the topics I covered in each lecture with precise references to the textbook? Etc. What one observes is that sometimes by the very act of offering such resources you paradoxically hurt the students by reducing their incentive to come to class or take other action that is important for their educational success.

What makes these decisions especially tricky is that almost always, offering these resources does in fact help many students while at he same time hurting others who have the inclination to respond in this counterintuitive and self-defeating way. So it is a real dilemma about whether you insist on helping the "deserving" students who are not tempted to slack off because you made their lives a bit easier, or take a more "social engineering" approach that tries to optimize the success of the class as a whole without getting drawn into moralistic judgments about which students' needs are more deserving of being addressed.

To summarize, I don't have a good answer to your question. All I can say is that you need to think what goal exactly you are trying to achieve by sharing your notes, and then consider (keeping in mind my analysis above) whether the sharing actually helps or hinders that goal.


Inability to secure any research position after PhD and postdoc. I am stuck with my low prospects research field. How do I proceed with my career?

Never look for the job only in computational modelling. Start making a list of your skills:

Programming
Math
Mechanical engg
surface treatments

Take all the keywords from your paper. Or list common things that you can relate to industry. Search for these.
And it is not always necessary to always be in research after Postdoc. Even PhD in biology have found their way into programming.
Good luck.


Regarding co-authorship for a research paper

They repeated my experiments with my optimized conditions

It sounds like they repeated the work you did and acknowledged you for running the preliminary experiment. While it sounds like you could have been included to a greater extent in the "new" research, they decided for whatever reason to not include you. By recollecting the data, they have essentially eliminated your contribution. In addition to the acknowledgement, providing a reference/citation to your "preliminary" data would not be out of place, but if those data are not publicly available (and in some fields in a peer-reviewed and/or archival form) providing a reference may be out of place.

There are really two things you can do. The first is talk to your former supervisor, not the corresponding author, about authorship on the current work and any other work you were involved in while working in the lab. It is quite possible the corresponding author does not really know who you are or what your role in the preliminary studies were. The second thing you could do is attempt to publish your data first. You would of course want to include everyone who deserves authorship (which likely includes your former supervisor) and this could get messy. Getting to the finish line first could be difficult. You may be able to get the work "published" on a non-peer-reviewed preprint service (e.g., arXiv) first, but the value of those types of preprints are very field dependent.


How do I address a colleague in an 3-way email with a student?

This answer is a bit meta, I guess. I would probably use a form of address that would seem comfortable to the student, since you are jointly teaching him/her. It would seem to make things like reply-all in an email more comfortable for the student. I'm sure your colleague will understand. If you are being a bit formal with the colleague you can echo that with the student. Ms. James and Prof. Smythe.

However, some places are first name only and always. Then it would be different.

One option, of course, is just to ask each person how they would like to be addressed and go with that. You will want to give your own preference as well when you ask.

Just note that whatever you do, you will be either emphasizing or de-emphasizing the authority structure. Either could be appropriate depending on other factors.


How should I thank this person who wrote a letter of rec for me (but to a different school than the one I'm attending?)

Directly, as if they were an actual human being.

"Thank you for providing letters of recommendation for my graduate school applications.  I will be joining the musicology PhD program at the University of Southern North Dakota at Hoople next fall.  Although I did not need your letter for my USNDH application, I still very much appreciate your support through the application process."


Assignment extensions for no apparent reasons (USA)

The short answer is that opinions on granting extensions vary between institutions and even departments. Some universities view extensions as a way to support student learning. They argue that they want students to be able to get the most out of each assignment and so when the student completes the work is less important than that they do eventually complete it and are able to focus their full attention on it.

Other universities hold the same perspective that you do, that learning to manage deadlines is an important piece of being a student, and that allowing for extensions whenever asked is doing a disservice to students.

The chair of your department or even the other faculty should be able to give you insight on expectations that you should follow and on what is customary. I strongly recommend that you talk to them, since they know your students.

Another option is to pre-emptively institute a limited extension system for all students. The mathematics and computer science courses at my undergraduate college used this tactic to great success. On the first day of the semester, the professor told the students that each of them had a certain number of "late days" (usually 4 for a class with weekly assignments), which would grant a student 24 hours of automatic extension. These could be used at any time on any assignment except for group work or exams. Students did not need to provide a reason for using a late day, although they did need to inform the professor/a TA that they were. There was usually a form online for students to fill out. Students could use them as they wanted- all at once or one at a time. Some professors gave small amounts of extra credit for having late days remaining at the end of the semester, and some allowed students to earn extra late days throughout the semester by doing extra credit work, handing in assignments significantly early, or going to relevant talks, etc.

The benefit of a system like late days is that most students will feel less stressed and more in control of their own time. It thus enables you, as the professor, to hold a quite strict "no other extensions unless absolute emergency" policy. It was well understood that if a student used up all of their late days early on and then got minorly sick or had a job interview or had something else come up, that was just too bad. They would turn in what they had. Further extensions were typically only granted if the student or a family member was in the hospital or if they had formal accommodations through the college itself.


What are the benefits and drawbacks of rotating professors to teach subjects not in their areas?

Most programs I've ever heard of don't randomly assign professors - but the typical system in the US I'm aware of has each professor required to teach X number of credits. The department has requirements for what class must be taught (like standard intro classes, courses required for the major, etc), as well as the opening for a variety of specialty courses (often called "electives") - but the core courses have to be taken up first.

While departments differ, it seems the most common system is one where professors pick the classes they will teach (sometimes by seniority or department rank getting their first pick, sometimes by some other method). The natural order of things is that it's easier to teach a class the second time than it is to teach it the first time (since you already have so much material prepared and you have had some practice now), so professors naturally end up teaching many of the same classes year after year. However, most departments have comings and goings nearly every semester - retirements, people leaving, sabbaticals, medical leave, changing course load amounts (buying out of teaching, becoming a department chair, not being the chair anymore, winning a big grant, having a big grant run out). Thus things are constantly in flux, so even if you really, really wanted the same courses taught by the same professors every semester - you can't have it, it isn't possible.

There is a downside to having things static, even when you somehow manage to have so much stability that it's possible. Some examples:

Many professors get comfortable with the material enough that they don't make large updates, and it can get stale and out of date over time (both materially and in method used).
Professors, being human beings, get bored of saying the same thing over and over and their excitement, passion, and patience can begin to wear thin even with classes they once enjoyed.
Some students aren't a good fit with some professors, and if a required class is always taught by a professor they don't get along with this may interfere with academic progress.
Professors can lose sight - or just not have a good idea to begin with - what the goal of teaching some material actually is. Most programs have courses that build on each other, like Introduction -> Research Methods -> Stats -> Advanced Research Methods. If you only teach stats and don't ever run an advanced class, are you sure you are teaching the stats students will need - and are you emphasizing applications that best prepare them for the advanced material? If you teach a Calculus I class, are you making sure students get all the groundwork they need for Calculus II? I've had students tell me "the Professor assumed we all had JavaScript in the previous class and designed the whole class around it, but half of us had never seen it before!" - with not very encouraging results.

However, there are downsides to moving people around a lot too:

The first time is always the hardest. No one knows what to expect, every question asked will be one you might not have answered before, the teacher's idea of pacing and time required to complete assignments will basically be wild guesses, etc.
Sometimes someone is asked to teach a class because no one else is available. I talked with a visiting academic who was a statistician, and he said in his first semester they came to him and said, "Hey, have you ever used C++ before?" He said, "Well, I guess a little bit in undergrad..." And so they said, "Great, don't have anyone else to teach this required class - will you teach a C++ class for us?" So he just had to figure it out as he went. It isn't ideal, but the alternative: no class offered that semester, which may mean students can't take required key classes or they will just miss out on learning important material entirely. Sometimes everyone just has the make the best of a non-ideal situation - come to think of it, that's what most of us have to do most of the time!

In the end, there is a first time for everyone. Experienced professors had to teach a class for the first time too. Sometimes this can even be a positive experience for everyone, if the professor and the student choose to handle it that way. One of the hardest things about teaching people is when you've forgotten what it was like to not know. You can all learn together, and it can be easier to have empathize with students confusion and anticipate their questions when you are confused and have questions too! The job of a teacher isn't always to be an expert bestowing their grand accumulated wisdom, but instead sometimes they are just a guide and skilled companion to help you through difficult territory.

...and sometimes neither of you want to be there, but it's a required course and the department is making them teach it so you suck it up and move on. :)


What reasonable steps can I take to report misbehavior by publishers to the wider research community?

If the matter concerns a mathematical journal, you can submit your case to the European Mathematical Society ethics committee

Note that even if this committee has been established by the EMS, they should consider non-European issues as well as issues from European publisher, journals and authors.

Of course, their power is somewhat limited but given their status, they could have some impact by simply issuing a public statement.


Attending graduate school at my undergraduate university

Pros

If you stay at the same school (this applies even more when you join grad school immediately out of your undergrads), it'll be a matter of remaining in your comfort zone - same department, a faculty who know you, even the same apartment/neighborhood! This can be a major factor, depending on the person concerned - the pros of staying at your Alma mater are all about convenience IMO.
If your UG department has an influential professor with whom you've worked before and are planning to continue as well, that can be very advantageous -  as having such a faculty get to know a student's work as an undergraduate can lead to a very strong recommendation (since he has accepted you in the grad program, it is reasonable to assume your work had impressed him during your undergrads).

Cons

An important advantage of going to another school is that you will be exposed to a completely different department, with faculty who may have diverse research ideas for you to work on. The department, in turn, will benefit as well as a new student from another school will cross-pollinate their department with fresh ideas. This is so important that some top universities have a strong bias against accepting their own undergraduate students into their graduate programs.


Fine to put as an appendix to my statement of purpose the paragraph explaining the gaps in my transcripts?

This would be fine. One fundamental point of the personal statement is to allow you to comment on anything unusual in your records (gaps in education, a semester when you got sick and had low grades, etc.)

In general, you can format the statement of purpose however you like. Using clear signposts (such as section headings) can make it much easier to follow.

Remember that the person reading your personal statement probably has a large stack of them to read, so making their job easier can only help you.


Why and how to reference chemical vendors in paper

Just do it in the experimental section, in text, without an endnote.

"The starting materials were X% stuff and Y% other stuff (cation  basis,  Aldrich  Chemical  Company, USA).  Vendor  supplied  ICP showed the following major impurities: Z ppm blalba, W ppm blablabla."  (I have seen master batch numbers listed as well.)

The main thing is to share enough info so that someone can repeat the work or can find a flaw if there was one.  For example if 5 9s purity is important, at least list that (probably make a comment to that effect as well).  If you had relatively low purity or possible impurities that may affect your results, just be honest and disclose it. (Feynman, Katzoff advice on sharing possible limitations of the research.)

However, I think for routine synthetic chemistry, probably well into the high 90s% of experiments are not really dependent on the starting materials.  That is, it is possible to get sufficient purity relatively cheaply and the experiment is more about what you decided to do and the methodology.  But there may be cases where this is not true or where your results are particularly noteworthy.  All that said, synthetic chemistry, in my experience has very low replication problems.  It's just not like priming research.

EDIT:  Just noticed you had a 1, 2 format.  I believe I address both questions.


Convert UK Bachelor Degree Grades to German Grade Scale

There is no universal system available for converting grades between national systems. For instance, in Germany, each university and even each faculty within a university may have its own system for "translating" grades from one system to another, and grades obtained between courses are not necessarily directly translatable. For instance, 70% of the points on an exam in one subject might constitute a 1,3 in one subject but (for instance) a 2,3 in another subject.

The only reliable rules are:

A 4,0 (4.0) is the minimum passing grade in any subject in a German university.
In classes where written exams are administered, the scale above 4,0 should be as uniform as possible. (In other words, the difference between the minimum points for a 1,0 or a 1,3 should be the same as between a 2,0 and a 2,3.)

But, as you can see, this still allows for a lot of latitude between different subjects.


There are an endless amount of resources for this question available on the internet here is just a handful of ideas

Developing a study-guide yourself is a default option for most lecturers. You include all of the concepts that will appear on the exam plus additional ones that you believe the students should know but that you will not assess. The additional information prevents the students from focusing only on test content.
Jigsaw involves dividing the work for the review by groups. Each group reviews their part. After each group reviews their part you remix the groups so that each group includes all of the pieces of the review. Everyone in each group shares their part to form the complete picture.
Some professors have students make potential sample questions. Developing and answering questions is a useful technique in content mastery. Students are able to articulate what they know through such an approach.

There are also an endless supply of games that can be modified to help with reviewing, for example

Jeopardy
Wheel of Fortune
Monopoly
Bingo

This provides some basic ideas.


How to work efficiently under loose supervision during graduate studies?

I think the more general form of the question is: (a) what do I need from my supervisor and (b) if my supervisor cannot/will not provide this, then what can I do?

Here's a few things I think supervisors are most important for early on in graduate studies:

Discipline and Motivation

So you need to put in long hours to succeed in graduate studies and oftentimes you need to work "blind": you need to work on things you don't know will succeed or not, or where you have no fixed goal in mind. Discipline can thus be a major issue for any relatively normal human being. Supervisors are supposed to track your progress on a regular basis and ensure you are putting in the required levels of effort, to encourage with a carrot and to use the stick if necessary.

If your supervisor is not tracking your progress and setting goals for you, then you need to take your own discipline into your own hands. The simplest method is to set your own goals with deadlines, focusing on achieving one thing at a time. Make TODO lists that follow a rough plan you have in mind. If a task is too broad, it will never get done: each task should be small enough and phrased in such a way that you know how it can be achieved (even if the task is just "problem solve X for one hour").

Assign yourself regular hours to work. If procrastination is a problem, just start. Starting is the hardest part so unplug yourself from whatever you were doing, minimise the potential for distraction as much as possible, take a deep breath and start. It's that simple.

Experience

It is not enough to work hard, but you need to work smart. Inexperienced students often tend to invest more effort into unimportant minor details that they feel they can control, rather than important details where the outcome or process is uncertain. The job of the supervisor should be to provide context on the relative importance of various tasks, to stop students from getting bogged down in minor details and to keep the bigger picture in mind.

Experience comes into play in other areas. For example, if you're starting out in publishing, or trying to publish to a venue you haven't before, experience is crucial so as to know what form the paper should take, what sort of narrative is accepted, what sort of "boxes" have to be ticked.

There is no replacement for experience. However, you can find experience elsewhere than your supervisor. Are there more senior students or PostDocs you can collaborate with? Maybe there's a group outside of your institute you can collaborate with remotely? Working with other people (i.e., not having a monogamous relationship with your supervisor) is an excellent way to quickly level up your own experience and gain new perspectives!

Technical Expertise

Your supervisor is also supposed to apply his/her technical expertise to your supervision, particularly in the early days. But if they do not provide you sufficient time and effort in this regard, or if their own technical expertise does not cover your interests, or as you progress into more detail on your PhD, you will need to find sources of expertise elsewhere.

Again, talk with other people. Try to seek out people with the skills that you require and try to develop a mutually beneficial working relationship with them (i.e., don't expect them to help you out of the goodness of their hearts). Perhaps you could even find a co-supervisor or a "mentor" who can be credited on a thesis?

The Web is also your friend. When I was a graduate student, I learned far more from playing around and trying things and from reading (on the Web) than from anything my supervisors (or lecturers) taught me. One of the most important lessons from graduate studies is "independent study" ... learning how to learn. When you do a PhD you are supposed to be the world's leading expert on your chosen topic. The only way this can happen is if you develop your own technical expertise in your area beyond that of your supervisor and your other colleagues.

Funding

Presumably if you already have a supervisor then you have a fixed source of funding. However, you may need additional funding if you go over length or funding for conference travel, etc. This can be very difficult for graduate students to get involved in.

However, there are often calls that are aimed at students and require minimal input from a supervisor. These include student travel grants for conferences, governmental scholarships, prizes for submitted work, etc. Furthermore, other senior researchers will often have funds they can provide for part-time contributions; talk to people if you are stuck.

Summary

I think some of the most important lessons that have to be learned during graduate studies are:

How to discipline and motivate yourself and organise your own work
Understand the nature of research itself, the broader research community and how your work will be viewed by them
How to find, initiate and follow through on fruitful collaborations with other researchers and research groups
How to find your own sources of funding

The main goal of graduate studies is to gradually reduce your dependence on your supervisor until, by the end of your PhD, you don't need them any more. A good supervisor should understand and support you in this, particularly early on, but if this isn't working out, then you need to learn how to rely on yourself more (or find another (co-)supervisor).


Fairness of assigning different reviewers for final decision on paper

When you submit a paper to a journal, you agree, in essence, to go by their rules and procedures for that paper until and unless it is rejected. It is too late, now, to object.

The fact that the editor wanted additional views of the paper is a good thing, for the journal and its readers. Their goal is to publish high quality papers.

And, if you are rejected, by whatever process, you have the opportunity to submit the paper elsewhere, of course.


What do I write as response for an academic misconduct investigation?

If I understand this correctly, you were under the impression that proper quotation of sources means to have them in your bibliography (and nothing else). You then quoted from those sources without quotation marks and footnotes to the reference quoted.
I’d explain that to them, apologize, and ask for a good source how, in the future, to quote according to their specific guidelines. That’s the truth; it doesn’t strike me as terrible in your first year, but you’ll have to hope your professors agree.


How do I convince my department that not all research needs to be profit-oriented?

I have gotten a job in a sort of university of Applied Sciences; this work place wants to start a small research group, but one issue that I started to notice is the orientation they want to give it. I mean, they want that all research to give a profit.

Well, that's a direction that many research centres around the world go. Fundamentally, IBM does not maintain IBM Research to contribute to human knowledge, but so that IBM Proper can get an innovation advantage (and patents - lots and lots of patents).

A University of Applied Sciences is usually not a research university in the traditional sense. They are not funded to do research, and, by and large, it is not their job. It seems perfectly reasonable that they expect their upcoming research group to fund itself or even be a cash cow. There is no obligation that a research centre needs to also do unprofitable things.

To make this perfectly clear: building up a for-profit research centre is a perfectly valid strategy. Clearly, it is not the kind of research you want to be doing (which is perfectly fine, even very understandable for me), but you cannot expect them to change their global strategy to fit your idea of research, especially if you just joined them.

  should all research be profit oriented?

No, of course not.


What to do to speed up the paper publication process?

You cannot speed up the process.  Everyone’s in a hurry to get their stuff published so your own situation is repeated with pretty much every submission.
More importantly, what are the odds the manuscript will be accepted as is, with no revisions?  Be ready to quickly make revisions, and be sure to address all concerns of the referees, and this will speed up the process.


How to tell advisor I'm declining a scholarship?

Just honestly tell him your reasons. They are very understandable.

Making a commitment to work for years an institution that you aren't sure you want to work for, at a location thousands of miles away from where you want to be, is a very big deal for your life.

Yes, it might be somewhat less convenient for your advisor, but so what?  This decision is about you and what is best for you, not about your advisor.  A reasonable person would not expect you to re-order years of your life, just so it is slightly easier to fund their lab.

I would just give your reasons and not worry about it.  It will probably be fine.  On the off chance that your advisor does get upset, just try to remember that it is not your fault.  And certainly don't change your plans in response.


Which software converts academic publications from PDF to Word without mangling complex formatting?

UPDATE: The question has gone through 10+ revisions since I wrote this answer. I haven't checked to see whether it is still relevant. I'll try to respond to comments.
I'll start by disclaiming: My initial solutions do not follow the prescribed pdf to doc conversion (whilst my last solution does, albeit, it's probably a bad solution), and I haven't tested them, which violates the OP's constraints. I disregard these constraints because I don't think they are particularly relevant.
It isn't clear whether on-screen, digital reading or printed, physical reading is preferred, nor how much adjustment in text size is desired, clarification may allow more focus.
The trivial, obvious solutions, which have surely been tried, are: Large screen plus zoom and printing to a larger paper size, e.g., A3 or A2 (the former being more commonly available), rather than A4. Annotations and highlighting can be applied to pdfs with numerous tools.
For various other enhancements, numerous tools exist on Linux, which can be scripted to suit needs. For instance, a page could be split into smaller parts and manipulated in various ways, e.g., split a portrait page into top- and bottom-parts, and blow up each part onto a horizontal page (optionally of larger size). All operations can be automated. This approach cannot fail particularly badly for academic papers. At worst, perhaps the split is applied in the wrong place, but, the two parts can be displayed simultaneously, aligned at the lower/upper edge, or by folding the top edge of a printed page.
Linux tools can also be used to convert to word processor format, for instance, pdf2ps and ps2txt can be combined to convert pdf to plaintext, which any word processor can open. (This is my worst solution. I doubt tables, footnotes, formulae, etc. will be handled particularly well.)
Converting to a word processor format seems like a misdirection. That's why my last solution probably won't work. Extracting another format from a pdf seemingly goes against the design goal of the pdf format, namely, to present documents in a [software independent] manner...encapsulat[ing, in each file,] a complete description of a fixed-layout flat document, including the text, fonts, vector graphics, raster images and other information needed to display it (source: Wikipedia).
My apologies if I'm way off mark here. I'm unsure of your precise requirements.


List of all the Universities/Colleges in USA

At  http://ope.ed.gov/accreditation you can download a list of all accredited US colleges, universities, and similar educational programs. I counted 9746 unique institutions.


Will writing MSC instead of MSc in an application count against me?

While it is possible for an applicant to be harmed by sufficiently bad grammar in a personal statement, I cannot imagine something on the scale that you describe -- writing MSC instead of MSc -- having any impact whatsoever on the evaluation of your application. Bad grammar can count against you because it indicates that you are not be a poor writer and/or you didn't take time and care with your application. Switching between MSc and MSC signals neither of these things, so you should be fine. There are so many ways to sell or sink an application that something on this scale is miniscule noise compared to the other signals that an application provides.

Note, by the way, that there is some variation allowed in this abbreviation, though I don't think MSC is among the accepted forms.


Should a "good" Ph.D. student still get some strong supervision?

Some advisors have a style of viewing supervision the same way ER doctors look at treatment. The key word is triage. Where there's a need to make things okay, he/she will be there. My advisor had the same viewpoint as he was very busy with other work and saw our meetings more as a checking-in as a friend than supervision.  I thought that when all the other students graduated, he'd give me the same amount of time as they got, but that was untrue. He continued with the same amount.

I asked him about this at the end, and he just said there weren't many crises (there was exactly one, in which he met me within 8 hours to make a game plan with me). Rest assured that your advisor probably is allowing you to create your own research programme and become independent earlier than usually scheduled. This will help your letter from him. From having more of a mentoring friend instead of being strongly supervised, I had an easy transition to postdoc, which is basically how your advisor is treating you now. In my fourth year, I felt almost abandoned. A year into my postdoc, I see that my advisor was the best advisor I could have asked for.

Seems like you're doing great as an independent researcher and your advisor will give you his input if needed but is curious what you'll come up with on your own. A loose leash is a good thing if you're self-motivated.


Why are computer science related degrees at some good European universities not ABET accredited?

I have not found much value in accreditation; it may serve to identify poor-quality schools, but most decently ranked departments sail through accreditation without any of their real deficiencies being exposed.  The process is thus little more than a bureaucratic checkbox for government or company sponsors of students.

If you want to gauge the quality of a department ... look at where its
graduates go.  What companies hire them, what universities accept them for graduate school/academic positions, what are their successful graduates doing 10-15 years after graduation?


Scanned Letter of Recommendation versus Saved as PDF

The instructions seem simple enough for your professor to follow. However, if still in doubt, you could contact the University concerned and see if you could come to a conclusion regarding this matter.


How do you write a letter of recommendation for someone who got an A in your class, but who you've never talked to outside of class?

Here's my understanding of the issue: A student, who you do not know very well outside of the classroom, asked you for a recommendation letter, and you said "yes."

So, assuming you thought highly of the student's performance in your course, you write the strongest letter you can under these circumstances.

This means you focus on the student's performance in your course, and compare the student's performance to the performance of others who have taken the course. If your course is particularly challenging in some way, you may also extrapolate on how the student's performance is indicative of some key strengths which are relevant to the student's target grad programs.

There is no need to overthink this, and if the student is not successful in getting into a good grad program, and they think it is because you weren't able to vouch for them the way that they would prefer, then, if they're a fast learner, they'll ask someone else next time.


How to prepare and what is discussed with professors at a PhD interview session? US application

Typically, the point of the interview is two-fold: to help the professor to judge whether you are smart and have potential (two separate things), and to help you judge whether you want to spend the next 4+ years working with this guy as your boss. To that extent, you're being judged on your potential, which means you need to show excitement about his research (in that you've read about it and are familiar with it, see below), and lots of enthusiasm. Knowing your stuff is also helpful so you don't look like an idiot.

In most cases, you'll discuss your undergrad work, you'll be asked about your familiarity with the professor's research (basic familiarity goes a long way here), and you'll be told about his current research work. Different professors have wildly different interview styles, so it can be anything from conversational to almost exam-like.

The best way to prepare would be exactly as you suggest; read two or three papers from that professor. I would recommend choosing one with a recent publication date (i.e., within the past 12 months) and the one he has with the most citations. Different search tools allow you to find that for different fields; for example, hubmed allows that for biology/medicine fields.


How to present a review paper at a conference?

In 12 minutes, the best you can do for your audience is highlight four to six broad observations or conclusions about the state of research. Here are some questions you might address with your observations:

Are the lines of research diverging and multiplying, or converging and consolidating?
Has it divided into "factions" or "schools" that define problems, methods, and solutions differently?  Or is all research operating under a single paradigm?
What's the influence and interaction with other fields and disciplines?
Where has research made progress addressing fundamental questions?  Where has research made no meaningful progress?
Where should researchers look for the most promising research directions and under-explored areas?

Don't try to make more than six observations in 12 minutes. By trying to say more, you are actually communicating less effectively.  Any one who wants the full story can read your paper.


How to avoid plagiarism when you come up with an argument for a class paper and later discover that another author has the same argument?

From your description, it doesn't sound like a question of plagiarism (you say you're referencing the relevant paper, and I assume you're either paraphrasing it or using quotation marks as appropriate), but a possible lack of novelty. Lack of novelty is more of an issue when you're trying to publish in a journal or present at a conference. Usually class assignments don't have to be novel; they just have to reflect your own work. If your professor is satisfied, I don't think you have a problem. I would do my best to extend the ideas from the other paper, i.e. add something to their analysis.


As a reviewer, should I act when the second reviewer did not seem to review the manuscript carefully?

I see that the 2nd reviewer wrote only one sentence in his review to
the first draft of the manuscript, although there were major issues at
the theoretical, methodological, and linguistic levels.

Are these issues not addressed in the revised submission (based on your comments)? Have the authors addressed all your comments carefully and satisfactorily?

Should I tell the editor that I consider such a review insufficient?

I would not do this. It is the job of the editor to see whether the reviewer has done justice to the article.

However, if you think there are still some issues with the revised manuscript, give it a fresh read and add more comments, e.g.
"I can see that the authors have addressed all of my previous comments. But, I still see that the article could be further improved if the following few points are addressed..."


Approaching a master's in humanities after STEM-focused undergrad

There is no reason not to try to do this and many reasons why you should. But the only valid advice will come from an admissions committee or a professor in the field who will look at your qualifications and goals.

Be sure to present yourself in the most positive light relative to the new field, of course.

There may even be advantages of your STEM background. Mathematics and CS, for example have applications in the humanities and the background can lead to many fruitful collaborations if you speak the language of both fields.

But until you apply somewhere you have no idea of the possible outcome.


Improving my profile for cs phd admissions (math undergrad)

As far as marks and grades go, that will depend very much on where you apply. Checking the admission requirements for the 'top 50' PhD programs is the best advice I could give there. I'm assuming you're US based given you're referencing GPA, midterms etc, and providing you want to remain in the country looking up admission requirements should be then straightforward (the same would apply in any country with regard to undergrad marks and PhD admission expectations).

As you're intending on moving to computer science, the most important thing to have would be programming experience. Some of the 'exposure so far' that you detail might imply you have done actual coding, but it is not clear. You should definitely explicitly highlight what experience you have there on any application you make (and it would help if you did the same here!) If you are a competent mathematician (or scientist, or engineer for that matter) making the move to computer science should be well within your capabilities but it will, again, depend very much on where you apply as to how much foreknowledge they will expect / require you to have. I myself moved from chemistry research to being a C++ computer game engine programmer and I know plenty of programmers who have started out with degrees / careers in maths, engineering etc before ending up in computer science masters programs. Switching straight into a PhD may have more stringent requirements, but that'd be another thing to check on with the particular places you want to apply to.

There are no professional or academic repercussions as such to carrying out doctoral research in the same place you studied for your undergrad degree. However, moving elsewhere will most likely expose you to new ways of thinking and working, which is generally a good thing where research is concerned!


Should a student keep asking questions to a faculty even if the faculty is unsure of the answer?

You're studying psychology. That doesn't make you telepathic.

There's a wide variety of possible reasons for what's going on:

you are mistaken, your lecturer is not uncomfortable. Crazy, I know, but you just might be wrong.
your lecturer has indigestion, or piles, or tight shoes
your questions indicate you're missing basic knowledge
the questions take the group away from the core material that the lecturer has to get through, and answering them will slow the teaching down
your lecturer doesn't know the answer, and can't bring themselves to say as much, and doesn't have the nous to turn it around and ask you or the rest of the class to find the answer. That's quite a failing in an academic, to be unable to say "I don't know".

Note that repeatedly asking "why A?" "So why B?" "So why C? ..." is something that toddlers do, it's often just time-wasting and attention-seeking and is likely to annoy a lot of people; even if those aren't your motives, be aware that it could come across as that. So instead of just asking questions, look for some answers yourself. You are doing a higher degree, after all, so you should be looking for answers yourself, as well as seeking help from staff and other students.


What to expect when pursuing a second doctorate in an unrelated field

In my experience, nonstandard paths like what you propose are initially viewed with surprise, and with varying degrees of suspicion. That includes admission committees, potential supervisors, fellow students, etc. However, that comes from uncertainty and unfamiliarity and can be shaped by the narrative you supply, and how you follow through.

Basically, people will probably have 3 archetypes in mind when you first contact them. The most positive one is that you are some sort of polymath genius. The most negative one is that you are a serial fail-to-deploy-in-life perpetual student, a model everyone in academia has encountered. And the 3rd is that you want to do research in some unexpected interesting intersection of your old and new field (which you've said is not the case). You therefore need to replace that narrative with a truer, credible, if possibly slightly airbrushed one, something like: you've always been interested in both X and Y, initially pursued interesting topics in X leading to a Ph.D. and start of a promising career, but are increasingly passionate about Y and want to refocus on that. I would be open that you don't expect to directly harness your expertise in X, but that you do expect that your background will help you be a very effective student in Y.

And then you need to back that up with your actions! Your Ph.D. is a credential indicating you have demonstrated the ability to advance the state of the art of knowledge in some field, and that you have learned sufficient academic "tradecraft" to be an independent researcher, at least from a competence point of view. (Footnote: The at-best only partial independence of a post-doc, and indeed the whole post-doc position, is more a reflection of funding realities than of a junior academic's presumed research abilities). So if someone with a Ph.D. and post-docs would approach me, I would expect them to be able to motor through the usual initial stages of a Ph.D. much more quickly than a "new" graduate student. I would expect that they will have done a fair amount of foundational reading in the field already -- that's something that hardly needs an advisor, though an advisor will be helpful in helping identify important strands that may be nonobvious from the outside. And I would expect them to arrive with some well-developed thoughts on potential research topic, though of course we might well adjust it together.

If you were to come with this type of pre-preparation, I'd consider you a lower-risk admit -- as a committee member or prospective advisor -- than someone whose basic skilset is unproven. Conversely, if you were to arrive, with the background you describe, with the typical keen-but-blank-slate mindset a fresh-out-of-undergrad student usually brings, then I would be more worried you belong to the serial-failure-to-deploy archetype instead.

Second, I would suggest you be very open about discussing your financial expectations. Do you need/expect funding (and is it usual in your target field)? Or can you fund yourself by continuing to work in your current field part-time? Or do you have enough saved up from a well-paid science/tech job (and academics in the humanities/social sciences tend to assume all science/tech jobs are well paid....) that you will be self-supporting? All of those are acceptable, just avoid unpleasant surprises from failing to bring up the topic.

Good luck!


Should undergraduate researchers expect payment?

Usually, undergraduate research assistant positions are compensated in two ways: 1) academic credit or 2) hourly wage.

From my own personal experiences, paid undergraduate research assistantships are hard to come by. In the United States, a lot of these positions are considered "work studies" where it's considered an on-campus, part-time employment. However, even then, a lot of these positions were restricted to lower-income students who were able to document financial need. Usually, the research labs would be using their research grants to fund these paid positions. As many people in academia may know, research funds are also hard to come by. A lot of labs may have limited funds that they prioritize for hiring more important positions like Graduate Research Assistants/Associates or Lab/Project Managers.

Undergraduate Research Assistant positions compensated via academic credit are much more common since they allow for students to take fewer classes (and also saves the lab's funds).

However, when neither options are given, then it's ultimately just a volunteer position where the undergraduate may take on the position for intrinsic value or to gain experience.

Ultimately, a lot of professors and researchers may agree that it makes sense to compensate undergrads for hourly wage if possible (especially if they're putting in significant amount of work every week!), but a lot of times, it's really just the fact that the labs do not have the adequate funds to do so.


Can a PhD student publish a paper outside PhD topic without supervisor approval only by its own?

There is no general reason why this should not be possible/allowed.

You will have to check the regulations of your department/university for PhD students: They may require you to seek approval of your advisor prior to submission of papers. Potentially a journal could have a similar rule in place, but I have never encountered this.

That said, I do not believe this to be advisable: If your relationship with your PhD advisor is so bad that do you not feel you can ask them about your intention to submit this paper, you should probably seek a new advisor. If you are so close to graduating that your prefer sitting it out, then rocking the boat is probably a bad idea.


Getting back to academics / independent research

There are two ways in which you can be involved in research, coming out of industry.

It is possible to enroll in a PhD program.  There are normally no age requirements, and it is not unheard of for people to start a PhD later in their career.  Depending on where you are, this may require a Master degree first.  I suspect many PIs are happy to enroll someone with substantial industry experience.

It is also possible to find employment at a company that cooperates with university research.  It's quite common for small and medium enterprises to cooperate with universities in projects (for some funding agencies such as the European Commission, this is in fact a requirement), so with the right skills, expertise, and contacts, that should be possible.  For example, within the EU, Horizon 2020 projects always must involve such enterprises.

Gaining full employment (not counting RA/TA/PhD studies) at a university without already having a PhD degree and recent publications is not feasible.


It is not possible to give a concrete answer without knowing which area in Chemistry you did for your PhD. I assume you are from India. There are other options for you to consider irrespective of your field of research.

Try to get an INSPIRE Faculty position, which is not really a faculty position in usual sense.
Apply abroad which will increase your chance of finding a similar field at least statistically.

I don't think appearing GATE once again is a good idea. Also why don't you try industry, there are plenty of jobs for chemists, once again its hard to say for sure without knowing your area of research.


Clear explanation of Conflict of Interest with examples in journal articles

I recall having seen some papers (say, on a method of electrode modification), where an author has been a shareholder in a company implementing this method on an industry scale, commercially. This is an example of a COI; a person is gaining money from another entity (in this case, his company) working in the same sphere.

Here's what I found on the web.

  A potential conflict of interest exists when an author has a direct or indirect relationship, through the research-sponsoring institution, with a company that may benefit from the results of the study. The following types of relationship are considered as potentially conflicting and must be disclosed:

  If over the past two years one of the authors:

  Received fees for consulting services, delivery of lectures and text writing or payment for any other type of service rendered to the manufacturer of the product.
  Received any kind of contribution from the manufacturer of the product (funds for the project, equipment, drugs, personnel) related to the project under analysis or any other involving the same product.
  Received funds from the manufacturer of the product to participate in congresses/conferences.
  Owned stocks in the company that manufactures the product.
  Is employed by a company that may direct or indirectly benefit from the results of the study.
  The manufacturer of the product has been involved in data collection, analysis, interpretation or writing.

My example falls under 'owned stocks' part.


Is being a volunteer useful for academic prospective

If you apply for grants where "Broader Impact" (or something like it) is a criteria, then a demonstrable history of volunteer and outreach activities related to your academic field of study can be helpful. Same goes for awards that consider "service" as a criteria.

(The reviewers of my NSF graduate research fellowship application commented favorably on my volunteer experience, which I mentioned towards "Broader Impact".)


Cover letter and feelings - use or avoid

Personally, I think your sentence fragments all suggest both a lack of evidence and a lack of confidence.  But more importantly, I think you're simply asking the wrong question.

Instead of focusing on the detailed language of your cover letter, focus on the content.  Who are you?  What have you done?  What makes you an asset to your target departments?  Instead of expressing your interests, demonstrate your accomplishments and your vision.  Instead of stating your beliefs or your confidence, show the reader clear evidence of your expertise and your impact.  Show, don't tell.

The advice that I give my own students and colleagues when they apply for graduate school or for jobs or for tenure is to aim for the next target.

Graduate applications should not say "Please admit me" but rather "I will become an independent researcher.  Let me get on with it."
Thesis proposals should not say "Please let me pass" but rather "I will have a strong PhD thesis. Let me get on with it."
Thesis defenses should not say "Please let me graduate" but rather  "I will get an academic job. Let me get on with it."
Job talks should not say "Please hire me" but rather "I will get tenure. Let me get on with it."
Tenure packages should not say "Please give me tenure" but rather "I will be a full professor. Let me get on with it."

And the way each application should "say" its message is not by stating your interest or belief or intention or confidence that you'll pass the next stage, but by presenting clear and compelling evidence that you'll pass the next stage.  And of course you never want to actually suggest the impatience implicit in the phrase "Let me get on with it"; rather, you want to convince your audience to let you get on with it.

Don't try to convince that reader that you believe that you'll be successful.  Make the reader believe that you'll be successful.  Show the reader that you will be successful.


Learning More CS, Physics, or Math on side as a Physics and Electrical Engineering major

If you want the most fundamental skill, Math is surely the most fundamental as the other sciences are built on top of it to some degree. However, whether the math you learn will impact your future research is debatable. I had a friend with your passion for self study who went off the deep end for about a semester on Group Theory. To my knowledge he hasn't used an ounce of it in his current work, but of course that doesn't mean it was a waste of time.
There is a point after which "getting a head start" has diminishing returns. It's like if you're running a race, but you don't know the course layout, your ability to predict where you should go rapidly diminishes once you leave the starting line. In this case, getting too much of a head start could work against you as you might have fully left the racetrack.
In that case I would simply spend your free time studying what seems most interesting to you in that moment, and let the future take care of itself. If, down the road, you start to think you really do need to brush up on your fundamental CS (or whatever), you can always take the time to study that at that time. The good news is that in most roles you will fill in the future as a scientist or engineer (and many other career paths, too), your job is not to know all the answers, your job is to know how to learn what the answer is.


How many "Cambridge"s in one line? (Citing a book from C.U.P.)

There's really no harm in adding clarifying information.  Obviously, we need a city name if we get "University of Georgia Press" because there are two very different University of Georgias in the world.  One located in Athens (Georgia, USA — not Greece!) and the other located in Tbilisi.

Likewise, if we see a publisher we're not familiar with, and the citation is only "Athens", it's nice to know at a quick glance whether we're talking about the American Georgian city, or the Greek one.  The topic of the paper make dictate which one is the "expected" one — if we're talking Atlanta politics, we can assume Georgia, unless otherwise specified, and if we're talking Plato, we can assume Greece.

Ultimately, though, it depends on the house style. If the house style includes the city, they'll do it for all publications, no matter how obvious one would think.  In your specific example, it's undoubtedly an overzealous copy-editor who is probably accustomed to having "Harvard University Press, Cambridge" and fixing it to "Cambridge, MA" to clarify.


Can who you pick as "faculty members of interest" make-or-break your PhD application?

The answer depends on the admissions process at the school.

Some departments will look through all applicants together, choose the top applicants from the entire pool, and then assign them to faculty advisors. Student and faculty preferences on the advisor has some impact, but these students are competing against all other students.
For other departments, individual faculty primarily look through students who want to work with them (as stated on their application), and admission decisions are made for individual research groups. For these departments, the preferred faculty advisor that you list can have a large impact on the extent to which different faculty review your application, and which other applicants you are primarily being compared with.

As an externally funded PhD student, you are not competing for the limited funding like other applicants. Of course, there may be other constraints such as lab space and available time for specific professors, but available funding is often one of the main active constraints. That gives you a greater chance of being able to work with a specific advisor.
You will likely be working with the same professor for 3-4 years, so requesting an advisor whose research interests and/or working style are a good fit for you could make for more enjoyable and productive PhD studies.


What are the benefits of doing a PhD on a case study?

Case studies offer researchers the opportunities to dig deep into the rich details of the case.  In social science, this can frequently mean being able to answer "how" and "why" questions, use qualitative data, and generate rather than test theories.  I am not a physical scientist or engineer, but I imagine that similar principles apply:  the details of specific settings can be more informative than a more generic approach.

Case studies and quantitative/comparative studies are (in an ideal world) complementary to each other.  One tries to build up a deep understanding from looking carefully at a single (or smaller number of) cases, while the other seeks to establish generality, test theories, and (depending on the field) establish causation.

That said, in my experience (again, social science), the communities of scholars who work on case studies are frequently relatively disconnected from the communities of scholars who do statistical/quantitative work.  When choosing your career path, be sure to think about which community you will be happiest in.


Does recording video of a scientific presentation violate the privacy of a PhD student?

EDIT: This post has been restructured into a clear answer, rather than the discussion format it was originally in. Thank you Stella Biderman.

Recording a video of a scientific presentation by itself need not be an invasion of privacy. The invasion comes if and when the video is shared, depending on the nature of sharing medium, the control over shared content and agency to withdraw/clarify one's statement.

A departmental talk may be recorded for internal review. A conference talk may be officially recorded (though I have never seen this personally). As long as these are not shared, and are stored for internal use (quality control, archive, proof of the event), privacy is not invaded. Even so, many individuals may find this distasteful, uncomfortable and even repulsive. This should be respected to the extent possible.
Personal choice is crucial. A conference is certainly a (restricted) public presentation, but presenters go there voluntarily. If someone wants to go on YouTube, that's fine. But nobody is allowed to make them go there. The concern of agency is also important- does the presenter have the right to retract or clarify their stand? Once on social media, it is near-impossible to issue 'errata' or pull something down once people start sharing it.

Yes, video is different from writing.

The medium is of crucial importance, because it determines how the content is disseminated. A journal paper is restricted to subscribers (let's leave illegal downloads out of all discussions).  An open access paper is open to all, but typically accessed by those with a prior interest. Both have restrictions on how it can be further shared and used. This is not the case with videos on social media. Those are seen by a mixed population with different levels of interest. They can be shared very easily and without accountability. They lend themselves to defamatory and potentially abusive comments and unwanted, non-constructive scrutiny.

The nature of delivery determines the audience. YouTube is not an academic medium. Neither is a regular newspaper. Both are good for certain purposes, both may be used for outreach and even educational purposes, but are sub-optimal for sharing research. The packaging of academic content to make it engaging to the general public is a serious and involved matter, which should be handled by dedicated workers with necessary expertise. A typical PhD student is not expected to have this expertise. (After all, how many academics after Feynman do you know who did this on a large scale?)


Using Microsoft Publisher to draw high quality flowcharts?

You can use any software and later improve the quality of your chart with a vector software like Inkscape (or actually, you can draw the flowchart directly there). I could recommend you using Draw.io (https://www.draw.io/). It performs quite well, you can save your flowcharts directly to the cloud, and you can export your flowcharts in SVG format.