You can be referring to two things, a visit to another institution (usually to give an invited talk) or you could mean a visiting student/researcher role:

Someone who visits a different institution for some prolonged period of time, usually to do research. You may even be able to register for classes.
It gives you the opportunity to work onsite with a different research group. You can think of it like an internship. Working onsite has a lot of benefits over working with a group remotely, such as direct access to lab equipment, data, participants, and your collaborators.
It can vary greatly, but I've seen it range from a summer to an entire year.

UC Berkeley has a page describing some benefits of visiting student researchers.


Can a university provide information about a student's activities?

In the US context, under the Federal Education Record Privacy Act (FERPA), students (whether they're international students or US residents/citizens) have a right to privacy.  This right begins when a student enrolls and continues even after a student graduates or otherwise leaves an institution.  In higher education, the student themselves has the right to privacy.  In K-12 education, the parents of a student have control over the privacy.

Under FERPA, information about a student consists of "Directory Information" as well as a broad variety of educational records that have stricter privacy controls.

The exact details of what constitutes directory information vary from campus to campus, but it can include name, address, phone number, email address, dates of attendance, degrees granted, etc.  Students have the right to restrict access to this information, but they must request that that this information is kept confidential.  In response to any request for directory information about a student who has requested confidentiality, an institution will simply not respond.  This can cause problems with potential employers confirming that you graduated with a particular degree and other situations where you might actually want to be acknowledged as a student.

Your other academic records are kept under much tighter control—under FERPA they won't be released without your explicit written permission.

So, depending on whether or not you have requested that your directory information be kept confidential, your institution might respond to a request by providing your directory information, or it might refuse to answer the request.  If the directory information is confidential, anyone who inquires about you should get an answer like "I can neither confirm nor deny that John Q. Doe is or was a student at Big State U."

There are certain exceptions to FERPA privacy rights, including situations where the student could be claimed as a dependent on the parent's income tax return, situations where university officials have a legitimate need to access the information, etc.


Advisors and publishing - new field for postdoc

Your problem is not uncommon, especially in post-doc programmes. The level at which an advisor would dedicate his time to a post-doc fellow would vary widely among universities and countries.

From the possible viewpoint of your advisor: as a qualified PhD, you are considered to have sufficient skills to do progressive research (even on a relatively new field) and frame a paper by yourself. Certain advisors merely proof check your work for their part. Some may do more than that and some even less.

This is not always negative. Some may recall this a luxury. It gives one freedom to explore. Hence the way you look at this is subjective.

Note that not all advisors come into the above category. There are dedicated advisors who provide substantial support for their postdoctoral fellows. It would be generally better to network students from prospective advisors to get a better idea of the support they provide before you enter another post-doc programme. Although it may not always ascertain that your situation may change.

If you believe you do require assistance for your new topic, the advisor is not your only hope; you could try to find a mentor who could provide you the domain support you need. If you could find another advisor to switch to who would suit your preferences (backed up by the networking as described), then you may make the move. The final choice is ultimately up to you.


Asked again to review a paper, when the authors don't wish to modify it

Personally, I would inform the editors of both journals. For the new editor, I would attach your earlier review, and recommend rejection.

Then it's up to the new editor to decide what to do in this situation. This falls in the category of ethical problems, and I think most journals recommend that reviewers contact the editor immediately in such a situation. Perhaps the journal has a policy for this, or the editor may discuss the matter with other editors or the chief editor.

Let me add why I find it unethical. Peer review relies upon the volunteer labour of anonymous reviewers. Reviewers may invest significant time, and do not really get anything in return. If authors of a manuscript completely ignore reviews, and instead submit an unchanged manuscript somewhere else, I would, as a reviewer, be quite annoyed. At the very least they could reply to the reviews, state point-by-point that they disagree, refuse to change anything and then submit it somewhere else; but completely ignoring is wasting peoples time.


I need to gauge my chances of landing a postdoc - should I send an e-mail to the contact on the job advertisement?

You seem to answer the question yourself that there would be no problem of interpretation. It is just an inquiry. However, you are not likely to learn very much absent a formal application giving the new institution to compare your credentials with those of others. But I see no particular reason not to ask.

However, there are other avenues you might want to consider, depending on how flexible institution "A" is. You haven't been offered anything there, nor certainly accepted it, so you are free to apply to the other place. If you then hear encouraging words you can try to explore at least a delay with "A", informing them that you are undecided about another offer or opportunity. There is risk in that, of course, but if you don't apply for the second position you don't have any chance at all.


Why Elsevier Journals don't change status of a paper?

See also: What does the typical workflow of a journal look like?

Of course Elsevier journals change their status when there's an update. "With Editor" is one of the earliest statuses, and not progressing is a bad sign.
You "come to know" about the paper's status by looking at its status. It's "With Editor" right now.
You didn't say which editor you emailed, although not getting a reply is another bad sign, of course. Did you email the journal office, the editor-in-chief, the handling editor, etc? Whichever you emailed, try emailing a different editor.
Considering it's been months and the editor apparently hasn't invited reviewers, waiting is not a good idea. Email the other editors, or withdraw your paper and submit elsewhere.


Your best bet is probably to ask your colleagues if they would have you let a look at their (successful) grant proposals. That way you can also ask questions.


How to mention a course that you haven't taken yet in an application

I understand your situation as I have been there many times. The answer really depends on the job I would say. Since you say that the job "strongly favors" but not "requires" CUDA, it can't hurt to mention that you plan to take it.

"But where do I do this?"

So depending on what is required from you as an applicant, there are a couple of places to mention your future course. If there is a cover letter then this is the ideal place to slip in the fact that you are an avid learner and plan to take and complete the course before the internship begins etc. etc. However, if it is a more informal application process that focuses mainly on a resume, then under your course work section (if you don't have one then I recommend putting one that lists all the relevant courses you have taken for the job) and next to it just list the semester you plan to take it, for example:

Intro to computing concepts, Data structures,
Operating Systems (In Progress), CUDA Programming (Fall 2015)

Feel free to put grades next to each one if they are impressive.


How to prepare a presentation if there is a visually impaired person in the audience?

From conversations with my wife, who is blind, you don't want to overthink this too much. Most of the things you can do to help the visually impaired will help everyone in the audience.

For starters, I'd suggest sending out the slide deck beforehand if at all possible, since this helps everyone be prepared. You should also make sure any figures have some sort of caption or title on them with a brief description of what's being shown. This will help anyone using a screen-reader to follow along.

The major thing that will help is making sure that you're giving general descriptions of the charts and figures, as well as the takeaway from those figures. This is good practice in general, since it ensures that your audience understands what you're trying to show with a figure and is invaluable to someone with low vision because it allows them to better understand the information being presented.

The true goal is to ensure that someone with only an audio recording of your presentation, no slides at all, can follow along to a reasonable extent. A couple of things may be missed, but the overall meaning should be apparent.


More years ago than I care to remember, I changed departments and started working for a new manager (NM). At the same time, another person (AP) also joined the department. My new manager put a weekly meeting on our calendars for the three of us. We would go into the meeting, and NM would start asking us what seemed to me to be really simple questions - what are we working on, issues with deliverables, who are we talking to about whatnot. Really simple questions. Almost insultingly simple questions, or so it seemed to me. Hey, I'm experienced and know what I'm talking about!

I started getting irritated by this meeting wasting my time. I could have had a meeting with NM to say it was wasting my time and why am I invited. Or, as I did, I took note of what was asked and what the answers were expected to look like (yes, there is problem A, we are trying fix B, and I'm working with so-and-so on alternative path, will know next week how to resolve). Then, I went 100% prepared to perform the data dump that NM seemed to want, whether or not I felt it was appropriate.

Fast forward 2 weeks, where I had started off the meetings presenting the necessary information (and only the necessary information) to NM at the beginning of the meeting in ~ 5 minutes. No questions addressed to me. Then, AP would get questioned, and generally fumble through the answers and need direction on what to do next.

Next week, I was removed from the calendar invite. AP was not.

Several months later, NM and I had a nice conversation over lunch about the purpose of the meeting. Basically, it was to establish that (1) I knew what I was supposed to do, (2) who I was supposed to work with, (3) I could rapidly summarize progress/goals/deliverables/budget stuff, and (4) I indeed could think for my self and be proactive in getting the right things done. In essence, I had passed the test and shown that I was, indeed, and as expected, an independent contributor and good team player. And, NM remained a good manager and mentor for me, just much more hands off (unless needed!).

What does this mean for you? You started a few weeks ago. You and your work style are a complete unknown to your advisor. What do they really want? What questions do they ask? Can you anticipate what they are and how to answer them correctly? If you need help, do you ask for it? Can you describe what you are working on in 60 seconds or less?

Be proactive. Show that you do indeed know the right things and are applying them properly. Do not go there to passively answer questions. Ask for help when you need it. And, learn to deal with people whose social interaction style is that way - you will meet many more in the course of your career.


How to get postdoc funding without a mentor

Generally you would select a few professors whose work you admire and write to them to say you are excited by their work, explain how you would fit in and ask if they would be willing to discuss the possibility of applying for a postdoctoral fellowship with them as the mentor. When you do this it will definately be in your interests if you were to mention specific fellowships you are thinking of applying for. It has been known for well funded professors in the US to offer to fund an exceptional candidate for the first year while they apply for funding, but I wouldn't assume this.

If the professors were positive you would then generally have a discussion about projects that would fit both of your interests. I would guess you would then write the application with their help, and cross your fingers while you waited for a response.


Have technical reports been subsumed by preprints?

While preprint archives certainly remove one of the major reasons that I used to submit technical reports, sometimes I find there's just no other appropriate title for a work.

To me, the whole notion of a preprint assumes intention to eventually publish in a journal, using a journal-style format and style of argumentation. There are a number of things that I write, however, that are worth archiving in citable form that just are not that.

In my own work, for example, I often end up producing formal project reports for funding agencies.  These may incorporate material from papers or that will later be extracted for papers, but the report itself can be a valuable document, especially for talking about implementation details or negative results.

Likewise, highly technical documents such as specifications, architecture documents, standards, best practices recommendations, etc., can be extremely valuable, but are often not appropriate to publish as journal articles.  One often also writes journal articles about such things, but there is a big difference between an article explaining the core concepts and value in a standard versus the full grinding detail of its complete specification.

I'm sure there are other examples as well, but the bottom line is this: "technical report" remains a nice catch-all name for any archival technical artifact that's a written document but not a journal article.


Price difference between master's and phd programs

Masters students are often unfunded. That is, they have to pay (most of) the tuition fee. Against that, PhD students are typically funded. That is, they are paid to study. Here's an example. The student here is not only paid a monthly stipend of $2000/month, (s)he doesn't have to pay tuition fees.

In other words, yes, it's often cheaper to do a PhD than a Masters. Caveats apply: it's possible you may not be offered funding (in which case a PhD is also more expensive). Also, since a PhD takes longer than a Masters, if you graduate with a Masters and then get a well-paid job immediately, the extra income might be enough to compensate for the price difference.


How can US universities check whether graduate students work outside TA/RA?

How can they or how do they?

The chances are pretty slim that a university is able to follow-up on graduate students extracurricular lives.  Perhaps it happens if someone gives them reasons to but it is still very unlikely. The exception to this is within the university system -- I would expect that to be easier for them to do (as pointed out by Jon Custer in the comments).

How can they?  Well, anything is possible. Someone could make this their investigative mission.  They could hire someone like a private investigator.  They could play secret agent themselves and follow you.  These all are possible but unlikely.


Not asking for Letter of Recommendation from Masters thesis supervisor

It will look a bit weird, yes. And the other faculty members in your department probably do not know you as well as your thesis supervisor, so their letters of recommendation will not be very specific. But I've never seen this be reason for an immediate rejection, which means you can make up for it in the rest of your application.

Probably an unnecessary tip, but: don't express your dissatisfaction with your supervisor in your applications.


Go with three strong LORs like everyone else and call it good.  No one needs five and seven is ridiculous.


Is it appropriate to email an eminent researcher in your field?

Here are some of my strayed thoughts.

Think from return of investments, of yours and your idol's

If you ever perceived that your e-mail would be a "waste of their time," then why send it? I feel that most eminent researchers have a trait of "ignore everyone and head for their goal;" getting acknowledgement and acceptance is probably not their primary concern. A specific e-mail describing how their work has inspired your study/project is probably fine, but I wouldn't go so far to expect they would reply and give specific comments on your hypotheses.

From your point of view, instead of using the energy and bandwidth to send the e-mails, there are a lot more you can do:

There are many ways to show your appreciation

First, they would probably like to see their work being formally cited and, more importantly, applied to the field or crossed into other fields. Each idea geminated from their work is an appreciation by itself, and in the mean time you can also enhance your publication and research paradigm. The plus is: if you have done enough of it, the big shot may actually contact you and give comments.

Second, you can help preaching the researcher's ideas and agenda. You can write blogs, answer other people questions, use their works in your journal clubs or lectures, etc. to subtly introduce the researcher's teaching to the public. Better yet, refine the researcher's ideas, and incorporate into yours. Become a spiritual successor with your own unique approach. And let your career be inspired by the researcher.

You can learn from someone without establishing communication

For some more senior researchers, look for their auto-biography, biography, interviews, and documentaries that feature them. I will probably never be able to talk to Itzhak Perlman, but I learned a lot about him through books, websites, documentaries, and musics that he plays. (And actually, he has a Youtube channel as well, but I am suffering from too much fanboy shyness to write any comment.)

For younger researchers, try look for their blogs, Youtube channels, open courses, or even biographies of their mentors. All these may help you become more familiar with them.

Another way is to indirectly know them. Most of these researchers would have a lot of students or proteges, who may be closer to your rank and more likely to communicate with you. You may build a relationship with them, and learn a thing or two about their interaction with their mentor.

Try technology

For their new publications... nowadays most online journals allow leaving comments online. You may try to say a nice thing or two there. If they write a blog, that's even easier. Some researchers maintain a LinkedIn page or a Twitter account, try connect with them and follow them. Hope for the best.

Use other famous people as leverage

If you really want to communicate with them, also try using other organizations. For instance, you can write to some online radio station and suggest an interview topic and some guests, which of course will include your idolized researcher. You can also write to some prominent podcast hosts and give them a couple reason to invite so and so for an interview. Make good use of crowdsourcing, invite your peers and friends to support your petition.

Some heroes/heroines are better left a bit mysterious

This is sad but occasionally painfully true. Some famous people are better left not known at personal level. They could be immensely arrogant, they may not have a nanogram of social skill, they may be a jerk... Unless I have reconstructed a pretty concrete and reliable image about the researcher from different sources, I would probably want to keep them as what they are in my mind, and as an inspiration for my work.


Why using ORCID iDs instead of DOIs to identify researchers?

Because I would rather be an Orc than an Object.  [/joke]

More seriously: from the horse's mouth

  Our members will be aware that CrossRef has been exploring the possibility of creating an “author DOI” or “contributor ID”  system. In doing so, it has become clear that the issues and use-cases involved in identifying researchers span a broad collection of stakeholders including libraries, institutions, funders, publishers and, of course researchers themselves. In short, this is not primarily “a publisher problem.” As such, we believe that the ORCID approach to creating an inclusive and open organization representing all the stakeholders in the scholarly communications process represents the best chance of creating a successful contributor identification system

The main problem with using DOI to identify authors is that the DOI model dishes out DOI identifiers through registration agencies, which usually charge some fee for the assignment. The use of registration agencies is fundamental to the design and operation of the DOI scheme. The main advantage of the ORCID scheme, as indicated above by CrossRef, one of the DOI registration agencies, is its openness and inclusiveness. Obtaining an ORCID is relatively simple.

As an aside: ORCID is a subset of the ISNI and is used for identification of researchers. For more general contributors to media, the ISNI is preferred.


Why would a conference ask for a title page if the submitted paper has been submitted somewhere else?

I'm hardly an expert on this topic, but I have coordinated the online content for professional conferences (as opposed to academic conferences), and based on how this requirement is worded...

I believe it implies that they ask for the title page so that any existing instance of the work online can easily be identified as your work specifically, and not any indication of plagiarism. I also would think it protects against an attendee later writing something that plagiarizes a paper which was presented at the conference, without proper attribution.

I'm not sure if there's yet another layer, of how they would cite a paper they first heard about at a conference, in regard to the container within a container format of citations. But it could be yet another reason they would make such a request, just to cover bases.


When I refer back to a thesis to find a piece of information, I find the lists of tables and figures to be extremely useful. I often have a general idea of what I am looking for. Turning that general idea into a simple text search that does not yield hundreds of hits is difficult. By reading the short captions in the list of figures, I can generally find the figure I want.


What to do if I have seen an exam before I have taken it?

In a situation in which you would suffer no matter what you do, you can also work to protect yourself.

An anonymous note to the professor that the exam has been compromised and that there are photographs of it circulating comes close to resolving the issue. The person who took the photo likely deserves punishment, of course, so this solution doesn't resolve that. But at least academic integrity is preserved. The professor will need to provide a new exam, of course.

The professor may also announce to the class that there is a problem and ask that whoever sent the anonymous note inform him of their identity. You may have to deal with that.

Also, you may not be the only student struggling with this.

If you are friends with the person who took the photo, you could also confront him/her with a suggestion that they step forward. If they do this before an accusation is made, I would think any punishment would be less than otherwise.


Can one do mathematical physics research without much knowledge of physics

Historically, most of the mathematics was developed to solve physical problems, and a fair amount of physical intuition helps to understand the ideas behind the mathematical methods, interpret solutions and check that their mathematical form is consistent with subject-specific problem, and also to develop new methods and communicate them to the users. So in general some background in Physics improves your chances to do a successful research in Applied Mathematics, and in particular to carry out PhD program.

However, there are some areas of Maths where you do just fine without any Physics. For example, general analysis of PDEs can lead you into functional analysis, and I don't think that analysis of properties of Sobolev spaces relies hugely on physical intuition.


Who launches a private non-profit university?

I'm only familiar with the US, but my understanding is that most (if not all) private non-profit universities were started with a single large gift from a wealthy individual, family, small group of individual, or a charitable foundation (usually started by one of the above).  In many cases the institution is named after that person.

I'm not sure in which countries the number of private non-profit universities is "rapidly growing".  I only know of a few recently started institutions in the US.  One with which I'm somewhat familiar is Olin College.  According to their web site, the college was started with a $460 million gift from the F. W. Olin Foundation, which in turn was founded in 1938 by Franklin W. Olin and funded by his personal wealth.

Such gifts are considered "charity" in that their main purpose is to benefit the community, and the donor doesn't receive a financial benefit.  Of course, any given donor could certainly have personal motivations other than a genuine desire to do good (attention, guilt, fun, taxes, etc.), but there is really no way to guess.


Tenure and tenure denial rates by universities

No.  Most institutions would consider tenure denial to be a confidential personnel matter.  This information probably cannot even be obtained using freedom of information laws.

A small portion of institutions have their newly tenured faculty announced in Inside Higher Ed.

You can estimate faculty retention rates by viewing archive.org's records of the list of faculty on the university website.  In practice, tenure rates are not as important as retention rates.  There's no point in getting tenure at an institution you don't want to work at.


How to turn a book chapter into a publishable paper?

There is absolutely nothing wrong with using research you've already published, whether in a book chapter or any other format, as a basis for further research that could lead to a new publication. However, it sounds to me like the way you are approaching this is a classic example of putting the cart before the horse.

Your goal should be to do new research that contributes something to your area, not to artificially boost your publication list by rehashing old material, which as I said in the comments is the definition of self-plagiarism. Once you have found something new to say beyond what you already wrote about in your book chapter, it will become naturally apparent to you when it makes sense to publish your findings, so the question you are asking here will likely never need to be asked. The point is that publishing is merely the last step of the process of doing research, and in some sense the least important step. It is the means to the end of communicating your research results, not the end unto itself.

As for the practical question of how much material from the book chapter you can include in a new publication, there are different schools of thought on this, with some people viewing any inclusion of substantially similar text from earlier publications, especially without an explicit citation and mention of the similarities, quite negatively. I advise you to consult your advisor or a senior colleague who is familiar with the norms in your area about such things.


International Code of Ethics for order of co-authors in research papers

The meaning of author order varies across fields. In some fields, authors are listed alphabetically. In others, the order reflects some sort of perceived contribution. Some people prefer to be the last author.

The only unified code, and it is unwritten at that, regarding author order, is to talk to your authors and be considerate to their feelings. It is academic misconduct to leave someone out as an author. Similarly, it is wrong to list someone who should not be an author. This means that it is up to everyone to decide. If your research group is so disfunctional that this is hard, have those conversations at the start. In fact, I advise everyone to have those conversations at the start and during the process just to keep hard feelings from developing.


Why don't publication venues systematically make the LaTeX source of papers available?

I suspect that this is a solution in search of a problem. Most likely journals aren't making LaTeX versions of papers available because they don't see a demand for such a service from the side of the readers; this would take effort to implement and maintain; and some authors would object to the idea of making it easier for others to reuse (read: plagiarize) their papers. In other words, publishers simply have (or at least think they have) better things to do with their time and money.

It should be noted that arXiv does make LaTeX source code available, and in fact will only accept submissions in the original source code rather than as PDFs (for papers that were written in LaTeX), so in those areas of math and physics where uploading preprint versions of one's paper to arXiv is the norm, this "problem" (such that it is) is already solved.


What criteria would you assess to gauge whether to quit a Ph.D for a job in industry?

"you think" you'd be happy working might not be enough, depend on the situation I suggest you to take a leave of absence (usually universities in the UK allow this) for 6-12 months, and get a job so you know for sure what ticks for you, then decide whether to return to your program or keep the industry position. Don't feel guilty for taking options that are readily available.

I had similar experience and this, to go or to stay, might be the hardest question I had to answer myself for the longest time. In the end I decided to stick it out, but I also have a close friend who's having the time of their live ditching their PhD 2 years in. You just need to work out the best approach for your situation, and the best way to do it is from a little bit of distance.

Good luck!


Is it bad for one's future career prospects if the PhD thesis topic is broad?

Coming from a somewhat different field (mathematics), I have seen some theses that were essentially bundles of not-strongly-related papers, each good enough to get published, and considered (by the advisor and the department) good enough to earn a PhD. Ok.

But this is indeed different from "getting a job". From what I have seen, job applicants don't succeed so much with "broad appeal" alone, but also must have strong appeal to a particular research group/interest. Thus, a too-diffuse body of work, especially if described in a fashion that makes it appear diffuse _and_unfocused_, will not get up to the thresh-hold of having a good chance at job opportunities.

To my mind, the point is how one portrays such work. If (in contrast to the situation of the question) the papers really are completely disjoint and unrelated, it is not easy to describe them as fitting together into a coherent research program. If, indeed, as apparently is the case in the questioner's situation, there is a coherence to the body of work, it is very important to re-describe things to emphasized that. "Novel computational methods whose potential is illustrated by making progress in several important problems"? That sort of thing?

After all, presumably/often the author of several papers does have some underlying theme/principle/concept/whatever that is merely manifest in various way ... that may superficially appear very different.

So, in summary, the description of the body of work would best emphasize the common thread(s) underlying the several instances. Although often labels are simplistic, hiring committees do use them, so figuring out how to position oneself among those labels is probably smart. (In effect denying the relevance of admittedly simplistic labels and categorizations is most likely just self-sabotage.)

One's advisor's approval of the body of work as meriting the PhD is a different issue from getting the advisor's recommendations about an appealing coherent description of the whole of the work.


Publishing referee reports I have written - Yes or No and How?

Take care with this. Since you write them, the words are yours unless the journal has required that you yield all rights to them or otherwise restricts your actions.

However, you should consider whether it is ethical to break the blind or double blind nature of review. There are reasons for that, though some are a bit esoteric.

If you need to say negative things about someone's paper and they take it personally, then you could find yourself in the middle of an academic war and those other people with an interest in an author's work might join the fray.

You also need to be sure that whatever you need to quote in a review is properly cited as in any other work. This makes publishing a double-blind review impossible, of course.

Some things might need to be confidential for various reasons, including patentable work. Some things need to be reserved until the paper is published, I think.

However, maybe the biggest issue is as follows. Often enough, by the time a paper is edited and re-edited, it no longer bears a lot of similarity to the version that you reviewed. In some fields this is a bigger problem than others, of course, but don't discount it. This will, potentially, reflect badly on yourself if you say things about a paper that aren't true about the published version.


What solutions exist to store data in text files and future-proof against tampering?

In addition to good recommendations on the InfoSec SE site, some of which are not that difficult to implement (for example, digital signing), I would suggest another rather straightforward solution (unless your data is extremely large or extremely sensitive): simply use one of Git repositories, such as GitHub or GitLab, or research data repositories, such as Zenodo or figshare.

Git and Git-based services now support large files, plus you will have an added benefit of versioning for data files that you can match with your research workflows to enable reproducibility.

Check my related answer on some arguments for potential preference for Zenodo vs. figshare.


Is there a way out of losing interest in science during a PhD?

You show strong signs of burn-out. It is unclear whether you really lost interest in science or you simply did not make the proper transition from being motivated by the triggers of your youth (winning competitions) to the triggers of scientific endeavour on its own.
Also note, competitions are fun, because they are hard, but solvable in limited time. Full Metal Science, however, is tough. You have no idea whether things work, whether there is a solution and, if there is, how long it takes. It's a completely different game. It's a 100-m sprint vs. a marathon.
There are a couple of ways out. If you can afford to, you should take time off for a few months, even half a year and do other things. Stuff you enjoy, sleeping, traveling, gaming, whatever, without pressure. Forget science for that period. Then, but only then, after your return, come back and take account of what really makes you tick. What is it that you would like to be doing for the next 5 years? Not your lifetime, just 5 years. And move from there.
If you cannot afford to go away for a few months, there is something else you could try, namely starting a scientific hobby. Take a bit of time apart where you do something that is PhD-irrelevant. Solving problems? Hacking some software? Or something entirely different. Make yourself clear that this does not have to be published, it's just something to keep you aware about what you enjoyed about science. There is Feynman's anecdote about the wobbling plate, very pertinent to you. In any case, absolutely make sure to hard-limit your PhD hours per day. Make sure you keep a hobby, and a network of people etc. It sounds like a waste of time, but it isn't. Your other hours will count more if they are boxed in.
TL;DR:

Take time off.
If not possible, find a scientific hobby and hard-box your PhD hours.
Keep your other activities on plan, almost without exception (except for isolated important deadlines).

PS: I have no advice concerning your mentioning of hypersensitivity concerning feedback from others. That's not really a question we can answer here, and some people's advice would be almost automatically to recommend therapy. I am not saying this is not the right step, but some people find this overkill. If validation of others plays a bigger role for you than the topic itself, you probably need to consider activities which get you this validation more directly by interacting with people, such as blogging, science journalism (if science interests you at all anymore, that is).


Perhaps the only other course is to get the maths professor and maths head of Dept. to petition the university registrar as a "special" case...

But don't hold your hopes up, it is worth a try though.


Should a professor recommending me talk about my (bad) grades in his or her letter?

It really depends on how the professor knows you.

If the professor only knew you "after the change", the letter might say "I am aware of student's relatively low grades during the first few years, but by the time of my class, they were a top-performing student", that kind of thing.

If the professor has known you for years, it might be appropriate to comment on having observed this change, and expressing confidence that you can handle the role in question despite the low cumulative QPA.


Correction of figure in galley proofs in Elsevier journal

Is the error trivial (i.e. does not need to be peer reviewed, no reasonable person would object) or not? If it is trivial, then don't worry about it now and correct it during galley proofs. A sufficiently obvious error might even be spotted by the publisher when they do copyediting. If it is not trivial then let the editor know, since they might need to get the reviewer to check it again.


Recommenders that are professors but not co-authors

People who cite your papers

A particular audience that is suitable for this are people who cite your papers. It is quite likely that the committee wants to see what impact (if any) your research has on your field, so they would want opinions from people outside your team that have read your research and find it useful. One way to find such people is to look at citations to your papers - they (obviously) have read your research, consider it valuable, and you should be able to find their contact information from their papers.


Is it wise to contact the editor of a journals with my concerns regarding the length of the acceptance process?

I was under the impression that such a process would take at most 3-4 months.

No. 3-4 months would be, in my experience, extremely quickly for Computer Science transactions. That would mean that your submission would get accepted without modifications in the first revision, which almost never happens (and even then 3 months would be very fast). 1 to 2 years for the entire process is more common.

However, this has nothing to do with it being your first paper. It is the same for every submission. Those journals have pretty rigours peer review, which simply takes some time.

That being said, it will also be similar for other non-spam journals. I am not aware of any reputable CS journal that would suit your 3-4 months expectation.

  Would it be appropriate/advisable to contact the editors of the journals with my concerns regarding the length of the acceptance process?

The answer would very likely be "deal with it or submit somewhere else". Frankly, if a journal had a reasonable way to cut down on the time required for the review process without hampering review quality, they would arguably do it anyway. They are not going to "make an exception" or anything of this ilk.

  my advisor and another professor, who is close to our research, both suggest that I should refrain from trying to aim that high, i.e. first publish in a lower ranked journal. They state that the reason is not the insufficient quality of the paper, but rather the length of the acceptance process

I would assume they meant not "a lower ranked journal", but rather "a conference". Review durations for conferences are indeed much more predictable (and, generally, shorter, in the 2-month range on average).

Submitting to a weaker journal to get your notification a little bit faster does not seem like overly good advice to me. If they indeed were speaking about a lower-ranked journal, you should consider the possibility that they were sugar-coating their judgement that your paper is not good enough for a very strong journal.


Is it conventional to point out harmless typos in mathematical derivations in lecture notes?

I think it is a good idea. While the typos you find may be harmless in their respective contexts, they can be a hindrance to properly understanding the concepts, particularly for students who find the material challenging and are not immediately able to identify when something is just a typo. A harmless typo, such as an incorrect expression that just happens to match with the correct answer for a particular problem, can lead to errors if applied to other problems. Furthermore, "do check this at home you will get X" not giving X is not harmless — students would not be sure if they did not get X because they applied a method incorrectly or because it was just a typo, which would waste time and cause confusion, as you also mentioned.
Whether you should report the typos depends on the professor. If they explicitly encourage students to report them, then certainly you should. If there is no explicit guidance, then unless they react negatively to your corrections, it would be a good idea to inform them, and as you say, get a confirmation that your understanding is correct. If you are still in doubt, you can always ask what they would prefer.
In your specific case, the fact that they maintain an erratum suggests that they see it positively. Some professors create a collection of notes that they refine and keep using for future offerings of the course, so you are probably helping future students as well. In fact, some may encourage it to the extent of giving extra credit for finding errors.
I am not aware if it is "conventional" or "normal" behaviour in general, but I see no reason to not do this, as long as your corrections are accurate, useful, and you have the (even implicit) support of your professor.


How many times is OK to register for a PhD program?

The fundamental issue here is that your first advisor left academia altogether—by retiring before his students were done. This is an awful thing to do to the people one is supervising—leaving them completely in the lurch in such a manner is unacceptable behavior. The advisor should not have taken on new students if he was planning on retiring.

As a result of this, it is obvious that some allowances for this will need to be made. The way to signal this is through your CV: list both advisors, including the dates for which you worked with them. If your first advisor is well-known enough, then this will automatically clue in others about what happened.

Overall, though, so long as the time required isn't too unreasonable for your discipline, an extended stay in graduate school isn't problematic. However, if you have mitigating circumstances such as these, it makes such problems a lot easier to overlook.


First of all, academic writing is all about the mind putting words on paper, you are really looking for tools to help you with the technical side of putting together the material. Looking at your list of examples, I do not see much that is not already implemented in Word (probably being the most common writing tool in academia). A second that contains everything except a solid version control (revision tool) is (La)TeX (which is also free). But, if version control is required you can use GitHub, as I know many LaTeX authors do.

On a more personal side, the difficulty in writing science is not about getting the technical aspects right, it may be tedious and boring but is easily done. What matters is the text and how to be precise and concise and no software will help you there. Version control is sometimes a good tool but really, is it necessary to see everything one has written and deleted? Isn't the present text what really matters and what one has to consider for improvements? It is easy to get bogged down with the wrong details so getting tools to sort those out is never wrong but I do not necessarily see how a special purpose academic writing tool will help much more than with the technicalities than existing tools do.


Attending conferences as a first-year undergrad

"keeping up-to-date with recent advances aren't really applicable to me..."

Not so; that's a myth. Your poster got accepted, and that means you are now part of the "recent advances" in the field.

So, go. Tell people what you are doing. No, people won't flock to your poster and ask for your autograph; however, chances are, someone there will find your work interesting. You might get to talk with people who have done similar work. You might get a few pointers. You might get some affirmation that you're working on an interesting problem.

I went to a conference once where I was just starting out in the field. One of the world's most renowned experts attended my talk. Imagine my surprise when, a year later, my advisor returned from the same conference, he told me that this same expert approached him, and asked, "Where is that student of yours? I really liked his idea..."

You never know what kind of benefit you might get over the course of a few days when everyone there shares expertise in some common interest. Sometimes it's someone who can help you out, or nudge you in the right direction, or motivate you, or challenge you (hopefully in a constructive way), or merely encourage you by nodding their head as you speak, seemingly interested in what you are doing.  Maybe you'll end up with a business card and a contact number of someone who can help you down the road as your research progresses.

Likewise, you stand to learn a lot from them, too. Who knows? Maybe someone will light a spark that will ignite a passion later.

By the way, most people like talking about their own research. So, if you attend a session that interests you, but a lot of it goes over your head, try to sit with that speaker at the lunch table. I'd bet that, more often than not, he wouldn't mind explaining some of the fundamentals to a bright and curious student.

Maybe I'm being overly optimistic, but I'd bet you'll come back a bit more rejuvenated, somewhat more enlightened, and a lot more encouraged.


What to do with what I've learned when writing my research proposal?

Having learnt something new does not mean that you can publish a research article. You need some new research to publish. So my answer to the question in the title is:

Use your new knowledge to do research.

If you still hold on to the idea of publishing something, you need to think hard about 1. a venue to publish and 2. what is it that makes your text publishable. If you can write a really good overview for some audience and can find a venue that may fit, you may try (but in fact, it is pretty hard and next to impossible to write a good overview when you just entered a field, this is something for more senior people).


How are the personal assistants for professors usually funded?

Funding for non-research positions comes from either direct or indirect sources.

Direct sources means writing a proposal that includes funding for personnel such as a lab technician or an administrator for a research center. In this case, the funding is obtained directly through grants.

Most of the time, however, the funding is indirect: the salary is paid by the department, rather than an individual research group. This funding is paid for through the "overhead" charges that are included in research grants. (In some cases, such as public universities in Germany, this funding is also indirect, coming from a grant by the state or federal government given to each professorship.)


Do I need recommendation letters from supervisors if I have a master's?

If I see you have been involved in lots of supervised research projects on your CV/statement, but that none of your letter writers are any of your supervisors, I will find that a bit weird, but it wouldn't kill your application.  Remember (I feel this has come up in a lot of questions lately), in mathematics research experience is not that important for getting into PhD programs (at least in the US).  What is, is having learned and showing a capacity to learn advanced mathematics (as well as work ethic + motivation).

Edit (in response to comments):

You seem to want to get a letter from your boss, and that's fine, and it may be helpful, but the point is that typically letters from the workplace don't provide too much insight into academic abilities, unless that letter writer is closely connected to academia (e.g., they have a PhD in your field of study).  This is why non-academic letters are usually not sufficient to get one accepted into a good graduate program, and you should get letters from academics as well.  (I would try to get at least 1 letter from a pure math prof from your bachelor's and 1 from a prof from your master's.)
Certainly having done well in advanced pure math classes, and having successfully gone through a master's in a related area makes you a reasonable case for grad school in pure math.  (How much the master's helps depends a lot on the details of program.)  Whether what you've done at work will be helpful in evaluating your academic abilities depends on what you were doing (see also the previous bullet point), but at least your boss can address things like work ethic and general intelligence.

Since I don't know the details of your situation, or what your application looks like, I can only say from what I've heard so far, I car guess there are several programs that would take you, but I'm not sure which ones.  I would recommend applying to a variety of programs at different levels of competitiveness and see where you get in.  It's also a good idea to try asking a couple of your profs advice on applying.


Advantage of pure maths courses in transcript for physics grad school

I think the real answer is that it depends on what it is that you're planning to do. The more closely your courses align with your proposed field of study, the easier it is for the committee to evaluate. So, taking pure mathematics courses makes more sense if you're going into a theory-based field than if you're doing something more experimental in focus.

However, you should also keep in mind that a strong grade in an upper-level mathematics course will at best be "neutral," and it might be possible to explain away a bad grade; a bad grade in any physics course will not go over so well. So you should factor your interest level and ability to handle the courses in your selection process. You should also consider if the course in physics is considered a "standard" course for undergraduates pursuing graduate admissions. If so, then it makes more sense to take that class than an elective mathematics course. (Otherwise, the question will of course be "Why didn't you take course X?")


Conflict of Interest statement for journal submission

A conflict of interest statement is revealing that you have some relationship with the journal, or, for example, its editors. It can also be a statement in which you reveal a relationship to some company or product that you discuss, analyze, or recommend in the paper.

Some papers are written as propaganda on behalf of individuals or products, for example. They want a statement that you aren't doing that, of if you have such a "conflict", exactly what is its nature.

A serious enough conflict can lead to rejection. But if your Mom is the lead editor of the journal, it is still a conflict, though it can be resolved by assigning the paper to someone else.

Anyway, there are a variety of things, but they mostly come down to the question of whether a careful reader would question your conclusions based on external factors other than what is actually written in the paper.

A cover letter  is just for introducing yourself and your paper to the managing editor with a bit of information that will help to assign the paper to an appropriate editor. Quite different.


Asking an external professor for a feedback on my BSc. thesis

Look for other magazines that don't require such a letter.  (Do they all?)
Find a professor that you can talk to. Or a postdoc.  Or a visiting scholar.  Some won't give you time of day, but some will be OK for a conversation.  Then maybe talk about what you've done that was interesting.  (Make some notecards and then be able to show/talk about the topics on the board.)  Keep it a little lighter than "read my manuscript".  That's a little leaden to be expected to read amateur work.  But a meeting where you are able to say interesting things like

"lots of people want to have geometric interpretations of analysis and say that is novel, but they most likely think in areas or volumes.  I like to think in decision trees and nodes.  It's not really novel, as Russian authors from the 50s like Guestanovitch have written this way.  But it's kind of rarely seen nowadays."

[Made up example...I don't know analysis...but you get the drift.


Which is more important in academic promotion: getting funding, or its secondary effects?

I think this is largely moot. Alice will only achieve that large amount of funding by being productive. If Bob is sufficiently productive, and in a place where external funding is important, then he will likely attract such funding since he would be foolish not to seek it. In that sense, productivity trumps funding.

But, again, the world of academia is very diverse. Some places external funding is an extremely important factor (maybe THE factor) in getting tenure. Other places not so much. But in research universities you need to be productive and to help others (students) be productive.

And it may be much more important what a lab overall is able to produce, not just the PI.


Advantages and Disadvantages of learning mathematics and physics subjects through lecture videos

For postgraduate research, neither watching video lectures nor just reading a book are going to help you enough.

You're going to have to actively engage with the subject matter, by solving problems, and keeping up with current research literature in journals.

Following on from the OP's comment: I do understand that your question is "which is better - books or videos". And the answer to your question is neither. It's a false opposition.

Neither are necessary, and neither are sufficient. You have to learn the core content of maths and physics by solving problems. And to do postgraduate research, you have to keep up with the current research literature in journals (including preprint archives where appropriate).


Should I apply to tenure-track positions if I'm fairly certain I won't be staying?

Apply.

If you accept a position, you are committed for the following year. Leaving after two years will disappoint people, but it happens fairly often, and the potential consequences of you not applying to these jobs are perhaps more serious than the potential consequences to the departments if you leave after two years.

Besides, I don't know what your circumstances are, but you are presumably not completely sure you won't stay.


Should correlation tables be half or full matrices?

For what it's worth, the convention in APA format is for the diagonals to be labelled with a dash and for the upper triangle to be left blank. See e.g. Table 1 in this paper.

Personally, I think that including redundant information in the upper triangle is wasteful and only serves to overwhelm the reader. A table formatted like a lower triangle is, at first glance, obviously a correlation matrix, while a fully-filled-in table could be anything. However, I'm not aware of any studies on the effectiveness of either method.


Does it matter where my academic website is hosted, for issues of intellectual property?

I can hardly see how writing your own comments on someone else's published work can come close to any sort of copyright infringement. Obviously, you would not re-publish someone else's papers in your blog? Small quotes are allowed in the UK under fair dealing exception (aka fair use). IANAL, but I would be surprised if it's any different in the US.

Obviously, if you republish someone else's papers in full, this is anything but a blog.


Since you did not specify the citation style, I chose APA at citethisforme.com, selected journal article and entered the DOI. This is the result:

In-text: ("A matter of scale", 2016)

Bibliography: A matter of scale. (2016). Nature Nanotechnology, 11(9), 733-733. http://dx.doi.org/10.1038/nnano.2016.180

Even so it is an Editorial and has no author, it is still sort of a journal article since it is published in a journal with volume and issue and has a DOI. Therefore, I'd suggest this solution.


Final graduation thesis - Team members won't cooperate anymore

Other team members may have been put off by your ambition to make the project publishable, rather than merely sufficient for graduation. They only signed up for a graduation thesis project, not an academic paper.

To meet their needs and try to get them back on board, I suggest splitting your planning into two phases, with two different objectives:

Graduation Thesis This should be a team project, but should only include work that is necessary for graduation. Do everything you can to limit the scope and difficulty, so that all members of the team can understand the project and contribute with a reasonable effort. You will then be in a strong position when asking the rest of the team to contribute.
Publication This is your personal project, not shared by the rest of the team. You should expect to do all the additional work for it after completion of the graduation thesis sub-project. It may involve rewriting material to give a more sophisticated treatment, as well as more research than is necessary for graduation.


Can a researcher hire 100% themself with funds from H2020 project (or other call)?

It's quite normal for people to pay 100% of their salary (or the salaries of researchers, post docs, etc) out of H2020 project grants. I'm not following what you see as the problem. It just means that person spends 100% of their time on that research.


Having students grade each other on group projects?

This can go well if you do it right. Undergraduates don't like to "tell on" their friends, so it needs to be a bit subtle. If you just ask for grades or points, they will uniformly give high points. Alternatively, if they think someone was slacking they will be pretty savage. But there is a way.

In a group of about five, ask each student (a) who were the most important 3 contributors to your project - including yourself, and (b) what was the nature of their contribution that makes you say that. You also need to ask each student to detail their own most important contribution.

You will learn a lot from this. If someone is never mentioned, you know they didn't contribute much but no one has to actually say that.

I've had situations in which a student that I thought was a bit of a slacker was praised by several of his teammates for keeping the group working on the problem.

Note that this method also permits students to contribute in different ways, not just technical contributions.

Giving a self-assessment is also important here as you get a sense whether they have a realistic view.

If the groups are only pairs, then just ask each member what was the most important contribution of the partner and what was your own most important contribution. Let them write a few sentences of explanation.

Of course, you will need to translate the comments to marks as you aren't asking the students to do that. They are likely to do it poorly in any case. In all but extreme cases you can just give everyone the same grade for the project as the contributions might be different, but each might be valued in its own way.


How to search who exactly to cold-email for a research internship?

You're right that it's hard for an undergraduate to know where to start, and you've done the right thing by asking professors at your own university first.
The next thing to try would be to ask those professors again, but instead of asking to work with them, ask for their suggestions of a couple of people at other universities who you could get in touch with. You can do this iteratively: each time you email someone to ask for an opportunity, say that you understand if they're too busy to take on a student and ask if they have a suggestion for someone else you can contact.
Those more senior to me may weigh in on this, but it's generally frowned upon to offer your work for free. If the professor isn't able to compensate you financially, would you be able to get course credit for your work? I'm not too familiar with the US system, but perhaps it is possible. I would avoid working for free if you can -- it sets a precedent and allows professors to favour those who have their own financial support (and thus puts less well off students at a disadvantage when looking for research opportunities).
Keep studying the literature if you can, and persevere with emailing professors. To maximise your chances of a response, keep the email polite and to the point. Good luck!


How to publish a paper that does not seem to be within the scope of any journal?

Interdisciplinary papers have this problem a lot. A - now - very influential paper in my field, I was told by the first author, was in limbo for 4 years before it was published, despite the senior author being world-famous.

Persistence is the key. Try to find someone influential who is knowledgeable and you can convince to help you expanding/adapting/explaining the work better and you could then co-submit with. Or else, you could consider aiming for a general-purpose journal such as PLoS ONE, and whose reviewers are advised to select by novelty and correctness, rather than (subjectively judged) relevance.

Learning to write for the specific audience of a journal can also help.


Duration of postdoctoral positions in pure math

This varies considerably from country to country.  In the US, the "gold standard" is typically a 3 year position (just a quick look at MathJobs reveals ones at Baylor, Dartmouth, Northeastern, and that was just on the first page of listings). Note that some will say that they are shorter with a possibility of extension to 3 years; the extension is generally just a formality. There are even occasionally 4 year positions.  There are also a mix of shorter positions: one semester or one year appointments at institutes like MSRI or IAS are usually intended to complement specific programs, and generally taken as a supplement to a longer term position.  Sometimes there are shorter grant funded positions, though in most cases I know in the US, the department will be able to step in to extend the appointment to 3 years.  "Postdoc" is also a kind of porous category; sometimes departments will hire shorter term positions when they just need someone to teach a few classes which fit somewhere on the continuum of postdoc to adjunct positions.

In the rest of the world, positions this long are much less common, due to some mix of cultural and economic factors, but certainly not unknown.  Generally positions outside the US are funded by grants, and it is hard to get enough funding to support a postdoc for 3 years (in most countries).


Distance Learning vs Free Online Education

Basically, is your question is "Is it worth it to enroll in distance learning when you could do the same attending free online lectures?" I believe you can have some good input from  Looking for sources of online graduate-level education and Does one get academic credit towards a degree for open online courses?.

The bottom line is: online lectures usually don't provide academic credits. So you can't show an official degree to an employer, so it depends on the kind of job you want to do: if it's enough to show what you can do (say, for instance, you want to be a web-designer, then your portfolio is likely to be more important than your degree), then why not. But otherwise, you might have to stick with the distance learning.


Submitting parts of my thesis to a journal, overlapping text fragments: self-plagiarism?

It is only (self-)plagiarism when you do not indicate that some text is being reused.

So there is a simple remedy: Add to your thesis some text that indicates which parts have been submitted where. This could be formulated for example as:

  This chapter has been submitted to journal as authors, title


How badly will bad grades impact future college and career life?

DISCLAIMER: This is based on my personal opinion.

I am studying in the UK, I failed a module during the second year of my undergraduate. I couldn't re-sit the module and took it on the chin.

I eventually worked extra hard and got a First class degree.

I went onto graduate school, MSc and PhD.

The grades are important, the Professors I spoke to told me, and it seemed to be the first thing they asked about, BUT, the average always appeared much more important for admissions etc.

You're not a robot, you can have a couple of bad grades.

Just keep working hard to get that GPA up!

The honest answer is yes it will have an impact, some firms or schools only want the perfect students, but for the majority, the overall average will have a bigger impact!


How do I stop assuming that someone is male?

Is your academic field male-dominated? I imagine that this is what might encourage you to make these assumptions, if you do not make them in other areas of your life.

For me the main thing was to try to systematically use gender-neutral pronouns, in writing and in speech. Training yourself to do this forces you to confront your bias, and eventually this should become a habit. You will also notice such assumptions made by other people, especially in papers.

This being said, if you are aware of the problem and of these assumptions, you are probably already halfway there. :)


Evaluating Grad Schools on grounds other than research

I applied to six graduate schools in my field, and was accepted at all of them. The criteria I used to whittle down the choices were:

Did I like the people in the department I was visiting?  (This surprisingly did eliminate one school.)
Did I want to go to live in the city where the school was for five or so years? (One more down, four left.)
Could I find enough people I was interested in working for, so that if I didn't get my top choice, I'd still be happy with the projects I'd be taking?
Can I financially afford to live in the city? (One more down, two left.)

At that point, however, the remaining criteria were all competing with one another: one school offered me a lot more money, the other had a lot better location. Both offered plenty of research, and both had excellent reputations in their field. Ultimately, for me, the location, combined with the slightly higher general profile of the school I attended, swayed the balance for me.

Remember that you're looking for individual groups or faculty members as well as entire departments. Students and faculty will both be considerations for you.


There is a fair option available. The professor could have insisted that both M and G could be first author. I have seen in research follows like this:

M*, G*, P or G*, M*, P

* Both the authors contributed equally to this work.

Your present authorship order: P, G, M is really unfair for both of you (G and M).


Etiquette - send a copy of my new book to the department I earned my PhD within or to my advisor?

To the department. The point of publishing work is to share the knowledge with others. This will be more greatly achieved in your previous department where other professors and up-and-coming students can have access to your work. This would be better than your work simply sitting on your old supervisor's book shelf. Your supervisor likely knows your work and therefore does not need a constant reminder sitting on his or her shelf. Also, I never knew an academic supervisor who cherished having a previous student's work sitting on their shelf solely for sentimental reasons, which I think might be your motive.


What to put in "affiliation" field when submitting paper without affiliation?

As noted by @mankoff in a comment on Does one need to be affiliated with a university to publish papers?, you can use "Independent Scholar":

  Here is a recent paper published by someone affiliated as "Independent Scholar": dx.doi.org/10.1175/BAMS-D-12-00171.1


In what format I should share a semi complete business & technical innovative idea in enterprise

To share new enterprise ideas, you should follow the procedure defined by your enterprise. I suspect a white paper would be suitable, since a yellow paper may reveal too many technical details that your enterprise might want to patent.


Should repeated course grades be included in GPA calculations for reporting to institutions in the U.S.?

Should I include both failing and repeated grades when calculating my
  GPA or just my last grade in that course?

If all your failings and repeated courses are reported in your transcripts, then you should report them too.

You should report all your official documents as they are and the applicant should never edit them or report them partially (by his own favor).

PS:

When you have your transcripts, your cGPA and also GPAs of each semester (including your passed, repeating and failed courses) is reported in the transcripts.

You can check whether the marks of your failed and repeating courses are calculated in your GPA or not. You should translate/report/recalculate your GPA exactly the same as they appear in your original transcripts.

Also, as you can see in one comment's liked question, the GPA calculation method differs from one country to another; so you don't need to re-calculate anything yourself (even, I think that by translating your GPA to another GPA-system by mistake may disturb your admissions opportunities); just officially translate your transcripts and send it to the admission office of the university you are aiming to study in. The admission office will recalculate your GPA based on their methods or they may then ask you for more supporting documents. Read the following quotation from the accepted answer to the question: How to convert from one grading scheme to another

  Most countries have their own system which doesn't really make sense
  as you try to "translate" them to some other system.

even, in this answer it is mentioned:

  Don't convert between different grading schemes unless it is
  explicitly mentioned what minimum grades you need for your own
  country. Just apply and hope for the best.


Is it reasonable to suggest a PhD thesis topic in an interdisciplinary area in which none of the faculty members specialize?

Well, no answer yet? I'll give it a try, even though I'm in CS and I'm residing in Europe. But maybe it helps a bit:

To adress your questions 1-3:

In CS it would - in math it depends on the will of the supervisor.
Depends on your PhD program and supervisor. It might depend who is sponsoring the PhD program as well.
I don't know enough about the US system to answer this one - but you asked for an other option and there is one:
Just quit the program you are in and look for an other one in a CS department! Sounds a bit disruptive, but if this is your research interest, you should follow it!


Shall I explain to grad school admissions that 'the first year didn't count' (UK)?

For the benefit of non UK members, the first year marks of a degree at a UK university is not used for calculating a student's final grade. The only requirement to continue on the degree is achieve at least 40%. It is therefore not uncommon for students to achieve marks in their first year which do not reflect their full abilities, and while it does not affect their grades it can affect how future employer or post graduate admissions view their application!

If this is the case you should address this in your personal statement. Tell them how you gained a new perspective and work ethic after your first year at university and demonstrate this with your improved results in your subsequent years along with appropriate participation in university clubs and societies.

If however your first year marks are consistent with your subsequent years, there is no need to mention it. Your application is about you as a potential student, not about explaining the intricacies of UK grade calculations.

Edit: The reasoning behind only requiring a mark of 40% for the first year is to allow students some adjustment to a more independent study style and also to give young adults entering university the freedom to have new life experiences outside of academia. The prevalent philosophy at UK institutions is that academic achievement is not the only goal of attending university (though it is obviously still important!)

Since the progression of students enrolled on a degree is decided on a department by department basis its impossible to find a single decree stating this how all UK universities operate it is by far how the majority work. Provided below are links to progression guidance from 2 UK universities, stating that only pass marks (40%) are required and that this mark will not be used to calculate degree classifications.
University of York Progression, University of Durham Progression


Is it wise to use the paper reference numbers defined in CV in statement of purpose?

Don't make anyone do extra work. They may not want to (or easily be able to) open a different file to find the reference. Give up part (1/4th?) of a page for references. Don't cram text in the main body, but references could be written with a (slightly) smaller/tighter font size/spacing if necessary.


How do academics in humanities such as philosophy apply mathematics or physics in their discipline?

First, a historical note: The idea that philosophy and mathematics are separate fields is a recent invention. A few hundred years ago, they were spoken of as one and the same. If you go back even further to the 16th century, physics becomes part of that same field, and even further back the term “philosophy” referred to any systemic investigation whose result was knowledge. For example, Newton’s great work was titled Principles of Natural Philosophy (in Latin) and while Aristotle more famously wrote on ethics and metaphysics, he also wrote on zoology, logic, physics, and biological taxonomy amongst other topics. Herodotus (primarily a historian by modern standards) and Hippocrates (a primarily a physician) were both considered philosophers. Herodotus wrote important religious theory in his history books and Hippocrates wrote important ethical ideas in his medical works (ask any western doctor about the “Hippocratic Oath”). These didn’t seem like digressions and interludes to contemporary readers. These were all works addressing topics of philosophy.

  What is the difference between the Philosophy of Computer Science and Computer Science?

Roughly, science studies X and the philosophy of science studies people who study X, ideas about X, and the connection between X and other philosophical questions. Topics in the philosophy of X (for every science) include questions that define the scope and nature of the field, as well as its epistemic standards such as research methods and standards of evidence.

Three examples of questions along these lines are:

In physics, there is generally a preference for a theory that possesses “mathematical elegance” over one that appears to be more ad hoc, even when the two theories have identical observed evidence. Is having this preference legitimate? If so, can it be justified based on the practice of physics alone or does it require appeal to other principles (maybe ontological principles, or epistemic ones)?
In computer science, one studies computers and computation. Given an object, how do you tell if it’s a computer? What does it mean to solve something “via a computation” or “via an algorithm” as opposed to via other means?
In physics, one studies the physical properties of objects. Someone might be tempted to say that mathematics analogously studies the mathematical properties of objects. However, we are used to thinking of physical properties as being those embodied by physical objects that exists in physical space (that is, mass is a property of this ball that exists in the world). Is there an analogous sense in which mathematical properties are embodied by mathematical objects that exist in mathematical space?

Over the course of the investigation of these topics, topic-specific questions tend to crop up. Contemporary philosophy of mathematics is extremely concerned with ontological and epistemological questions, while contemporary philosophy of medicine is primarily concerned with ethical issues and the philosophy of biology involves questions about the precise nature of life and the implications of extraterrestrial life.

It’s quite possible that someone could be an expert in subjects like this and not be able to do cutting edge mathematics and physics, though answering these questions certainly requires a substantial knowledge of the fields of science you are analyzing.

  Are there well-publicized research performed by religious scholars or philosophers that actually inform or advances or guides the development of mainstream theory in say astrophysics, biology, medicine, mathematics, etc.?

The answer historically is yes, even setting aside the historical note I opened with. Thales, Aristotle, Alhazen, Ptolemy the Second, and Jean Buridan are all famous people who would be considered philosophers by today’s standards who made substantial contributions to physics, astronomy, biology, medicine, mathematics, and other fields of science. If you’re looking for more recent contributions it’s more difficult.

There seems to be a historical bias in categorizing people as scientists when they did both science and philosophy (by modern standards). Although he’s far more famous for his work on calculus, Leibniz was also a very influential philosopher, and probably more influential as a philosopher in his time than as a mathematician. You’ve probably heard of his theory that we live in the “best of all possible worlds,” because an all powerful and all good god wouldn’t let us live in anything else. These ideas were so influential in his day that Voltaire became famous in part for attacking Leibniz’s philosophy, such as in his book Candide. Einstein, Minkowski, Turing, and Nash all did philosophy, but that aspect of their work is less well-known to the general public.

There are some people who are widely classified as philosophers who made substantial scientific advances in recent times. The work of the logician Gottlob Frege (1848 - 1925) was ignored in mathematics for a while, but the mathematicians Bertrand Russell and Giuseppe Peano would revolutionize mathematics by introducing axiomatic systems of logic and arithmetic grounded in Frege’s work. Linguistics is an example of a science that recently grew out of a field of philosophy, and so many recent philosophers have had substantial impacts on linguistics, such as Ludwig Wittgenstein (1889 - 1951) and Saul Kripke (1940 - Present). The philosopher of mind and philosopher of language David Chalmers (1966 - Present) is hugely influential in the development of fields of computer science such as artificial intelligence and human-computer interaction. Chalmers is one of those people whose ideas are used to benchmark and understand developments in AI, as he has written extensively on the concept of intelligence and coined the term “the hard problem of consciousness.”

David Hume (1711 - 1776) wrote a book called an Enquiry Concerning Human Understanding which is undoubtedly one of the 10 most influential philosophical works ever written in the West. Although it’s impact is most prominent in philosophy (Kant famously claimed that it woke him from his “dogmatic slumber”), it also was highly relevant to scientists and the sciences. Einstein had the following to say about it in a letter to Moritz Schlick, 14 December 1915

  You have also correctly seen that this trend of thought [positivism] was of great influence on my efforts, and specifically E. Mach and still much more Hume, whose treatise on understanding I studied with fervor and admiration shortly before the discovery of the theory of relativity. It is very well possible that without these philosophical studies I would not have arrived at the solution.

This wasn’t one of your main points, but I also wanted to address this:

  ultimately I am not certain about how subjects such as mathematics and physics can be made relevant to philosophy (or other areas).

They don’t need to be “made relevant to philosophy.” Anything that increases ones understanding of the world is something that is relevant to philosophy. However, one could wonder to what extent the technical details of scientific theories or scientific methods affect philosophy. Like any question about the interdisciplinary use of techniques developed in one field but applied to others, the answer to highly depends on the field of philosophy and the skill of the philosopher, but virtually every scientific advance gets used by some philosophers for something. There are ontologists whose arguments about the philosophy of time that revolve around technical details of Einstein’s theories of relativity, epistemologists who use category theory, philosophers of mind who use results from cutting edge neuroscience research, and ethicists and metaethicists who read and make extensive use of results from social sciences such as economics, behavioral psychology, and decision theory.


What is the mean in an standard exam? (For grading on a curve)

“Grading on a curve” means that you select what percentage of grades you want to correspond to a given final grade. It’s entirely up to you how you choose the resulting mean grade using that system. If you want to make the mean a 60 or an 80 or anything else, that’s your call. Ultimately, though, the point of the curve is to avoid having “grades less than 50 are failing.”


Is it really legal to submit a work to a venue although we already uploaded it as a reprint somewhere like Arxiv or researchgate?

The answer is simple: those same journals have an explicit exception for preprint servers.
Consider, for example, the Nature family of journals, whose current preprint policy says, in part:

Posting of preprints is not considered prior publication and will not jeopardize consideration at Nature Research journals. Manuscripts posted on preprint servers will not be taken into account when determining the advance provided by a study under consideration at a Nature Research journal.

If you are wondering about a particular journal, the Sherpa/Romeo database is a good information source and often easier than searching the journal's own pages for the applicable policy.


PhD Germany with British conversion MSc IT

To obtain a doctorate in Germany, you must have a qualifying degree from an accredited institution. Nowadays this is always a Master's degree with a thesis (Master's degrees without a thesis are effectively worthless if you intend to pursue a PhD). It should be in the field you are intending to obtain your doctorate in. If your degree is from an applied institution such as Napier, expect to have considerable difficulty finding a PhD program that will take you. (Though it is not impossible and things are changing.)

Don't expect the German system to be much like the British, as they are culturally and technically different. In Germany, you do not apply to a PhD program; you establish a relationship with a professor who is willing to supervise you, and the admission as a doctoral student follows from that. That is very difficult to do if you are coming in cold from outside the country. There are some EU-sponsored programs which explicitly solicit applications from other EU countries, but they are the exception.

How is your German? Anybody suggesting that you can get by in Germany without a decent command of German is not being totally honest with you. Even though PhD candidates here are often foreigners and the international language of many disciplines is English, you will be working in institutions in which the administrative language is German, and not being able to speak it will put you at some disadvantage. If nothing else, the competition will be much harder if you can only speak English as your second language, particularly if you are expected to teach.

Your best chance might be to apply to another academic M.Sc. program at a research university in Germany and get your foot in the door that way; this will expose you to professors and give you a chance to establish a relationship that could lead to a PhD.

The Friedrich-Alexander Universität Erlangen-Nürnberg long had a good reputation for computer science. There is also the Karlsruhe Institute für Technologie or the Leibniz-Universität Hannover. Freiburg is also an option. Note however, that these are the better institutions and the competition is strong. You may not be in a position to be too selective. Cast your net wide and look at all institutions with a computer science department.
PhD candidates are generally hired on as "WiMi" - Wissenschaftlicher Mitarbeiter - on time-limited contract. Pay varies but 1500 €/month is typical. How far that takes you depends on where you are living. In Munich, it will barely cover your rent if you have a family. In some east German cities (Dresden, Leipzig, Halle, Magdeburg, Jena) you might yet support your family and live decently. The situation in Berlin is changing rapidly and while it is currently just affordable, it won't stay that way.


How should I go about reading mathematics papers and textbooks as a PhD student

I'm a second year student too.

I think that one have to study what really needs to know, for instance, if I need the Feit-Thompson Theorem (for some reason) I cite and use, if you need to use the tools and ideas that were used in that long proof, then you read the paper. Now, how to read it, in first instance, keep the central ideas and go deeper if you really need it for your work. There is a lot of mathematics, and nobody can learn everything, even if you only study algebraic geometry (it is a broad field). My tutor says that one will have a lot of years to study and go deep in topics that are of our interest, and in the moment, work hard for getting the PhD (it is not easy, we know it), and publish


What is the benefit of 'voluntary page charges'?

The benefits of "voluntary" page charges are much the same as for "mandatory" page charges - you are paying them in order to support publication of the paper. The only difference is that, technically, you don't have to, and you can avoid it if you wish.

Why do we have such a weird situation?

There is a long and complicated history here; what follows is mostly a precis of this paper, which is an interesting read.

This particular journal seems to be using an unusual holdover from an old-fashioned way of handling page charges.

Page charges date back to the 1930s. (You may want to remember this the next time you see someone saying that paying publishers is a shocking modern development.) The majority of journal subscribers at this time were individual members of scholarly societies, rather than libraries, and so there was a fairly low limit to how much you could reasonably charge for a subscription.

However, particularly in physics, the amount of stuff people wanted to publish was growing dramatically - Physical Review doubled in size during the 1920s, and even then still had a growing backlog. Printing and mailing larger issues more often obviously costs more, but subscribers would balk at rapid subscription increases, and the societies were already (mostly) losing money publishing the journals to begin with. The solution by the American Physical Society (followed by many others) was to shift part of the cost onto the authors, allowing the cost charged to subscribers to stay the same even if they now got more pages in their journals, or if the amount of papers dramatically fluctuated in a given year.

But not everyone had the money to pay the charges. For the first couple of years, a generous benefactor paid for everyone who couldn't; after that, unpaid charges mounted up. Some institutions and funders were asked for donations to help cover the gaps, but, critically, authors were not penalised for failure to pay, nor were they chased for the money. The sense that these were "optional" charges became quite well entrenched, and while most authors paid, many avoided doing so without complaints. The US government gave tacit support to the emerging model in the fifties, when it was decided that federal agencies could pay page charges as long as they were the same assessed on non-federal authors, and they were voluntary. (You have to love the logic of "we'll pay if voluntary, but not if mandatory")

By the 1970s, page charges were well established in the scholarly landscape, and almost 40% of US-published articles were in page-charge journals - higher than 80% in some fields. (It was much lower outside the US.)

In the 1970s, the US Postal Service got involved. They took the position that a page charge was essentially a fee to distribute advertising about your research, which would mean that the journals got hit by much higher postage charges than if they were simply distributing public-good information. The IRS made a similar argument about payments being commercial and threatened to increase taxation. The negotiated solution was to very clearly emphasise that page charges were a voluntary contribution, rather than a mandatory one, neatly evading some of the legal issues.

Page charges mostly died out after this. American society journals were always the major users of page charges, but during the 1980s, most of them were absorbed by commercial publishers (who almost without exception stopped levying page charges). Many of the remainder, presumably, found that they could shift away from page charges by taking advantage of the very dramatic increases in subscription charges during the 1980s and 1990s (the famous "serials crisis").

But you'll still find a few today - eg PNAS, or the AGU titles. Most of these now structure page charges as mandatory - I suppose the complex financial issues from the 1970s have now been solved in other ways, or else the fact that you can ask for a fee waiver means they still technically qualify as "voluntary". Not quite sure how this circle got squared... but, regardless, that's where we originally got the "voluntary" text.


PhD funding agency, and conflict of research and development

Just try to explain that you cannot spend all your time on software development. Consider having your advisor present during the meeting to support this.

Show them the software, and ask them what they think about it, how they would hypothetically further develop it, what tips they can give you. Try to change the discussion to a constructive conversation where they help you and you can exploit their expertise. People generally appreciate when you value their knowledge, and are often happy to help.


Would participating in student politics as a PhD student without an advisor create a bad impression?

It very much depends on the quality of your PhD work. If that looks good, it can be a boost to your CV. However, if your work is middling, this may appear like escapism (or perhaps a political career is what you should pursue instead of a PhD).

This is always, as @user3209815 said, your decision. What is unlikely to work well is to take up this job and getting even further behind on your PhD work.


What is the difference between research and a thesis at the B.S./M.S. level?

A thesis is always research, but not all research is theses.

In a five-year Masters program, one would definitely do a thesis, but these programs often have very stiff course requirements, which leave little time for research except the thesis.  Given this, it is often the case that the only research that a student does is the thesis, and that only to the level of sufficiency to obtain the degree.  Many 5-year Masters Theses are thus no better than 4-year Bachelor's theses, but will indeed be held to a higher standard (e.g., as though one had gone through a separate 2-years Masters program).

Last-minute and "merely sufficient" research work of this sort will also be much less effective at building trust and relationships with a faculty member than a longer time working on research as an undergraduate, even at a "lower" level.  This significantly impacts one's ability to get a good letter of recommendation, which is another key for PhD admission.

I suspect this is why they recommend as they do, and think it's a good thing that they do so.


Can grad school admission recommendation letters be generic for all applications?

Recommendation letters generally do not need to be tailored for each school. Admissions committee members are faculty too, and in an age where people regularly apply to 10+ programs they understand the undue burden this would place on already busy faculty.

Occasionally a more tailored letter may have some advantages, for example if the recommender has close connections at one of the programs, but it is definitely not expected or required.


Model for the number of citations an article receives over time

I imagine you'd have an initial publication lag where citations might be lower for example in year 1 than in year 2 and that then aggregate citation counts over time would have to be monotonically decelerating. You'd also have substantial variability in terms of individual articles. For example, I've heard of articles which accelerate in their citation count over time as they become the standard citation for a particular topic.

Independent of overall number of citations received, journals and fields  differ dramatically in the rate at which citations accumulate. A good starting point is to look at "citation half life" (i.e., the median time it takes a journal or field to acquire half of its total citations). If you can access ISI you can examine how different fields and journals differ in citation half life.

For example, I just had a quick look at a few fields from ISI 2012 which yielded the following data:

Field                       Citation Half-Life (in years)
PSYCHIATRY                  7.6
ASTRONOMY & ASTROPHYSICS    6.9
MATHEMATICS                 >10.0
PSYCHOLOGY                  >10.0

So clearly psychiatry and astronomy tend to cite more recent articles, whereas mathematics and psychology often cite older articles.

The implication is that impact factors (which are based on the last 2 or possibly 5 years post publication) should be higher in psychiatry/astronomy than in mathematics/psychology. It also means that early career researchers in psychiatry/astronomy should accumulate a better h-index more quickly than researchers in mathematics/psychology, all else being equal.


How to build bridges between mathematicians, computer scientists and biologists?

Disclosure: I'm a mathematical biologist that came into it from the biology side.

I don't think it is necessary to retrain the biologists so they understand maths and retrain the mathematicians so they understand biologists, although these things should occur naturally to some degree with interdisciplinary work. Rather, I think it is important to understand the motivations of each 'type' and to tailor the language to the audience.

To grossly generalise, biologists are more interested in quantitative methods as a tool to answer interesting biological questions and mathematicians are more interested in the method/analysis used to answer that question.

So when mathematicians talk to biologists, they need to place less emphasis on the technical details of a model/analysis and focus on the general features. For example, if you are building a model to answer an evolutionary or ecological question, a biologist is more interested in the biological assumptions the model is making and whether or not the model is a reasonable abstraction of the biological system. In turn, the mathematician may need to explain why certain details of the system can't or shouldn't be included in the model (e.g. because they would complicate the analysis for little gain in intuitive understanding).

When biologists talk to mathematicians they need to frame their questions in a way that is conducive to a quantitative framework. If a mathematician is trying to build a model, they don't need or want to know every minute detail of a system. It's overkill and will just lead to confusion. What are the most relevant points? For example, if a biologist is interested in how the density of cows affects the density of grass in a paddock, then it isn't helpful for the biologist to give the mathematician a lesson on all the intricacies of grass growing and grass eating. It would be better if the biologist comes with a defined question, such as 'how does increasing the number of cows in a paddock affect grass regeneration?' and points out that the main elements in the system are 1. how grass grows (as some function of grass density) and 2. how grass is eaten (as some function of cow density).

If you want a book about mathematical biology that is written for biologists then I'd recommend "A Biologist's Guide to Mathematical Modeling in Ecology and Evolution" by Sarah P. Otto & Troy Day