Difference between 'PhD by Published Work' VS 'h.c. PhD' VS 'Dr hab'?

While it may be common for universities in the UK to offer such a degree, I'm not sure it's at all common to obtain a PhD in this way (i.e. 'by published works').  I think it is mainly aimed at people who have been involved in research for some time (especially as university staff members) without a PhD, but who have published material equivalent to a PhD thesis.  (As you will have read, for the Warwick program one must be either a member of staff at Warwick or have graduated with a Bachelor's degree or equivalent at least seven years ago.)
Generally someone applying for such a program would have already published the works they are planning to submit, and therefore as you say the program will consist primarily of preparing for the oral examination (often called 'viva' in the UK).  Although you probably have to prepare some kind of extra document as well (in the Oxford Brookes program this is a 'critical appraisal' of the works being presented).

This is, as Pieter has already explained, very different from either a habilitation (which is at a higher level than PhD) or an honorary PhD (which in general can honour any kind of accomplishment and doesn't require the holder to have done research at PhD level or indeed to have a university education at all).


Professor withholding course grade until submission of conference paper

I am a professor at a state school in the US, and American professors are currently the targets of a lot of undeserved grief (e.g. it is currently fashionable to believe that we are "lazy" and work much less than a full "business week"; that is not only a mistake but likely a dishonest, politically motivated mistake).  So keep that preamble in mind when I say:

  This is one of the most unambiguously unacceptable behaviors from a course instructor that I have heard.

Let me try to count the ways (but there are so many that I may get tired before I finish):

1) One of the most basic understandings between the student, the instructor and the university is the duration of the course.  By a certain extremely public, agreed upon, well-publicized deadline, all of the coursework must be complete, and by a slightly later date that your instructor has been carefully informed of, the course grades are due.  Planning to defer submission of the course grade after this date is just not the way the American academic system works.

2) Giving a grade of "incomplete" is not withholding a grade: it is assigning a certain kind of unsatisfactory grade.  [Once in college a rather elderly professor literally did not submit any of the grades for the course I was taking.  It was a little strange -- in these days we actually received transcripts in the mail over the break so the inquiry was less immediate than it would now be -- but he apologized and submitted the grades very soon after the start of the next quarter.  That's withholding a grade.]  In order to assign an incomplete, the student must not have completed the official coursework.

3) The instructor is not suitably respectful of the obvious problem which can occur if you assign students' grades too late: you may prevent them from graduating.  Many American universities have policies to expedite final coursework and grading for (would-be) graduating students.  Moreover, in the universities I've been involved with, beyond the written rules there is an unwritten culture that as an instructor you should think twice about any course practice that interferes with a student's timely graduation.  (Sometimes it turns out the student fails your course and therefore does not graduate on time.  That's "okay", but most of instructors would indeed think more carefully about assigning a failing grade under these circumstances and feel honorbound to convey the failing grade to the student sooner rather than later.  What if their parents show up in town only to learn that the student did not actually graduate?)  This practice is not hard to understand: one of very few commonalities among American academics is that we were all students at one time, so we should have some sympathies for the student perspective.

4) This course requirement is unusual and potentially problematic, and it is not listed on the course syllabus.  I think that the whole point of the course syllabus is so that instructors cannot totally change their course requirements / grading schemes in the middle of the course, and that seems to be what is happening here.

5) Teaching a university course is not like playing a game of Truth-or-Dare: it does not give you authority to compel the student outside of the classroom and the dorm room / study carrel.  Submitting a paper to a conference is a real-world action with real-world ramifications (the OP is rightly aware and concerned about this).  It is creating work -- possibly rather pointless and frivolous work -- for other busy academics and/or professionals.  It is setting a student up for harsh critique even up to the point of ridicule.  It is also bullying a student into publishing something they didn't actually want to publish.

Okay, I got tired.  What should a student do in this situation?

  Talk to the faculty member in question.

This is an in-person conversation.  You should think carefully both about want you want to say and how to behave in such a conversation.  Your goal is to convey the specific problems and hardships this course policy will impose on you.  (You don't want to frame it as an ethical or hypothetical discussion.)  Be calm but very specific.  Bring in a copy of the course syllabus and refer to it at some point during the discussion.  Bring in a copy of an academic document that says you need to have your grades by a certain date in order to graduate.  Say specifically: "I'm concerned that this course policy will jeopardize my graduation.  Can we address this?"  If your instructor says "Don't worry about it right now" then explain why you are worried about it right now.  Talk about your family's travel plans, talk about the financial implications of having to enroll for another semester....

(The point of the above strategy is this: I imagine that your instructor likes this course idea from his perspective.  Clearly he has not taken the time to think about it from your perspective.  If you make him see the negative consequences, he is much more likely to repent.)

You should not be brushed off in your meeting: this is a serious matter.  If in the course of the meeting you don't see things working out to your satisfaction, you should let him know that you intend to talk to (e.g.) the department chair about it.

By the way, apparently this took place almost a year ago.  What happened??


If it's published in a journal you will usually get a hint right at the page of the paper that there is an erratum.


How can a PhD holder safely negotiate the salary level for a TVL E13 position?

First, talk to your future supervisor. If they do not support it, chances are slim. Or, if they say it is impossible, equally so.
If they support it: Find out what the rules are - well, probably your supervisor knows.
Generally, there are two options, depending on the place: Either, the administration decides on their own.  Still, they might not proactively put you  in a higher level, but wait for you to ask for it and supply documents proving that you have previous experience.  In that case, the support of your supervisor will certainly help the process. And it is not unlikely that the administration would ask them if they judge the qualification equivalent.
Second, it could be that your supervisor has to write a justification why you should get a higher level, and then the administration decides.  Certainly, in that case the support of your supervisor is essential.
Finally, it could be that the administration has very rigid rules on this, and the supervisor has no influence on that. In particular, they could have the rigid rule that they don't recognize anything which was not in German public service (that would be the most conservative option, since they don't have to vouch for anything).
Good luck!
(In any case, I would say that level 2 is realistic, since, it only requires >1 year of experience. Level 3 is more ambitious, since it requires >3 years of experience.  In any case, also check the salaries for the different levels - the steps are not uniform.)


Primarily by succeeding in the informal respect economy that operates in these fields.

He or she needs to impress the people they collaborate with (especially those who work with them daily or weekly) by some set of

Playing an active part in a large number of useful side projects and analyses.
Spotting danger to the physical apparatus coming before things actually break.
Building, fixing and maintaining parts of the physical apparatus.
Contributing significant parts of the production software.
Dealing with difficult parts of the analysis (covariance analysis, systematic uncertainties, finding way to measure irreducible backgrounds, etc).
Doing a good job of promoting the project, giving talks and interacting with the press.

but most of all

Taking a leadership role in planning and organizing the experimental effort (from conception though feasibility analysis, design, construction, commissioning, calibration, operation through analysis and publication).

Starting at the level of a junior professor dealing with funding becomes a very important part of the mix, as does providing students and post-docs who are themselves good contributors.

The flip side is the way you evaluate candidates is heavily driven by who you know (it is easier to get a foot in the door if you have worked with someone at the hiring institution), by letters of recommendation and by word of mouth inquires (so gossip plays a part here).


What's the editor's benefit in setting deadlines for manuscript revision?

Editing a journal is a non-trivial exercise, something which tends to drag on forever and requires lots of pushing of reviewers and authors to complete their tasks on time. It is time-consuming. Without deadlines, reviewers and authors will submit their work arbitrarily late, making it very difficult to get each issue out on time.

Authors may well be motivated to get over the final line, but when there are other things to do and the possibility of delaying one piece of work yet another day, then it is easy to delay that work.


What to do about a citation that may be wrong

A polite way to deal with this is to say "We need the following known result (c.f. [A] and [B])  and include the proof for the convenience of the reader."  If someone writes you to clarify before this is finalized, you can revise.
If you are worried about giving credit that is inappropriate, take a moment and reflect on how citation counts are often misleading.  Your primary concern is the reader (including referees) and the above allows them to be as informed as they need to be.
If someone (say a referee) asks you to cite [B] for the proof, ask for a page or theorem reference.


Remote writing of master's thesis vs. taking a course

I am sort of confused. At least here in the states, at my university, a masters student is not expected to do novel research. When you state:

Actually this is what most students do, because generally it's thought that an advanced course is time better spent unless you have a clear path towards solving a problem in an area you're comfortable in

It sounds more like you're in a PhD program. In this case maybe speaking to your advisor and being appropriately direct ("I am not sure what my goals are and I do not understand the problem domain") may give you the insight you need. Your advisor is there to first and foremost guide you through the relatively rocky terrain that is academia.
Next up:

On the other hand, my institution allows one to replace a master's thesis with an additional advanced class.

To be blunt here this sounds like you are copping out on a very good research opportunity. These options are great for students who wish to achieve a masters and head into industry, perhaps as an analyst of some kind, but you don't want to do that. In the comments you stated clearly:

@Vladhagen Being a research mathematician

Having a desire to be a researcher means you should take this opportunity to struggle. I have yet to face a problem where I had all the answers and many times exploring a subfield I am interested in results in me having to do significant research just to understand where I am going. Knowing this I have some suggestions:

Speak to your advisor. You meet for 2 hours once a week. That is a lot of time. I was fortunate to get an hour with my advisor once a week. Manage your time correctly. Since you are stuck now would be a great time to compile a list of things you are stuck on, ideas you've had, things you've tried, and direct questions on how to proceed. Speak to your advisor like a time-crunched colleague or a boss. Don't waste their time but instead come to each meeting prepared with things you want to discuss and things you want to get done. This is great in industry too. Never be the person to show up to the boss with problems and no solutions. If you present a problem have a solution. This will earn you respect in more ways than you'll realize.

You will never have complete knowledge on a problem domain. The more theoretical your field the worst this gets. So start from first principles. As you're reading literature on your problem domain highlight things you don't understand and make an effort to understand those things. Then return to the paper, proceed until you hit another point you don't understand, and repeat. Knowledge, like research, is built in a step-wise fashion. Knowledge cannot be willed upon you. You have to climb that hill on your own.

Good luck. If you wish to be in research you should complete your thesis and not take the class. The experience will be worth it's weight in gold. You will ALWAYS be able to take another class. If your research is impressive you may be able to even ask a field-adjacent colleague to write a recommendation letter for you. The politics of academia are often obscure and you can source recommendation letters from people you've worked with or people who are aware of what you're capable of. Many times it's not necessary to take a class. Please, if you plan on being a researcher do not fall into the "milestone" trap. Enjoy the journey and learn from what it gives you. The rest will follow.


Looks right to me. That's how they ask to be cited, and it seems reasonable. Indeed, this discussion also agrees that citing the user manual is the right choice.


Will following a famous professor as a research internship be bad?

This is indeed a tough choice.

In principle, if you manage to establish a strong positive connection with the "famous professor" and will collaborate or simply keep in touch with him, this could be beneficial for the rest of your academic carrier: he may not only write a strong recommendation letter for grad school, but also introduce you to his professional network (traditionally conservative academic circles will accept you more easily), help to find a postdoc and a tenure-track position, and, finally he could write a letter for tenure promotion for you. On top of this, if you will continue to collaborate with him, your co-authored papers will be more easily accepted by good journals, etc.

On the other hand, "as they said mostly I will follow his phd students." This is a very strong indicator that he will not have time for you (this is typical for famous professors with large groups) and you will be supervised by his PhD students. In this case, interaction with the professor will be minimal, and, if he agrees to write a letter, he will ask students who supervised you to assist. There is a chance that you would remain a sort of unknown to him.

The "less-famous" professor, however, is likely to have more time for your. And you could learn (and benefit in other ways) much more from him than from PhD students of the famous professor. Remember also that a very strong and enthusiastic letter from a less-famous professor is better than a modest letter from the top one.

So, as I said, it is a tough choice.

I would recommend:

Try to find out what happened with other undergrads who where interns in both  groups (famous and less-famous). Where are they? If possible, contact them and ask about their experience.
Focus on how comfortable it is for you to communicate with both professors on a personal level. You could also ask them how often you should expect to interact with them.
Don't reflect too much on "The thing I am concerning is as he is a leading person in top universities, he must be surrounded by lots of smart persons." You got the internship. They would not offer it to a stupid person, since they are "surrounded by lots of smart persons". You are smart.


Is the quality of work done in PhD a measure of my abilities to pursue academia?

I think you are overly harsh with yourself, actually. There are several things going on here. First is that you are now more mature intellectually than you were when you began the work so are more likely to discount it than others might be. You know it best and if you were starting now, with what you now know, you would start higher up the ladder. That is just growth.

Just as important to answer your wider question is that for successful academics their first work, the dissertation, is seldom their best work. The more you work, the better you get. Just like an athlete.

I'm impressed, actually, that you taught your advisor something about your methodology and, it sounds like, developed that yourself.

But, the work doesn't get easier as you go along. It is just as hard, but you gain additional insight into the nature of things, especially that which it is important to study. I'll predict that if you don't give up you will do pretty well. A bit of letdown burnout is pretty common at your current stage. Power through it.


Making an unrequested change at revision stage to a journal paper

Make the improvement
The review process is there to improve the paper. If there are things that you can do to improve the paper without the reviewers help that's great! Making the changes is helpful to everyone.
From the reviewer's point of view - there will always be comments from other reviewers which I didn't think of. I wouldn't expect all improvements to come from my comments.
From the editor's point of view - they way to publish high quality papers. The review process is one (very important) aspect of this.
From your point of view - you want your papers to be as good as possible.


An invitation to join the editorial board of a newly launched journal

There are two types of "new" journals:

A genuinely new journal
A predatory/semi-predatory spam journal

Deciding whether to join an editorial board is largely about trying to figure out which category your invitation falls into. The first step is the email itself - is it written in clear, professional language that suggests actual editors? Stop by the journal/publisher's website - does it look legitimate? Check into the publisher's other journals if they have them - do they look like actual journals, or junk journals?

The next step is looking at the existing editorial board/editors-in-chief. Are these people you recognize in your field, and would make sense as the people to be on board? Are many of the "big names" in your field conspicuously missing?

The final step, if it passes these checks, is to actually email the editor-in-chief to talk about the journal. This serves two purposes:

It's possible for a scam journal to list someone as an editor without them knowing - contacting them directly should confirm they are indeed the editor.
It lets you talk about the journal's goals, the expected workload, etc. to make an informed choice about whether or not you have time.


Would having two words in my surname in my passport be a problem for US colleges/GRE/TOEFL?

I am Latino, and as a result have an even worse version of this issue. My full name is of the form
A B C D E, with A and B being given names, and C D  and E being surnames. An extra complication is that D is not a name by itself, it's just a preposition.
I have given the TOEFL and GRE tests before and that has not been an issue. Minor errors may occur depending on who handles the documentation, but they have never been an actual issue. For example, my names have been agglutinated as CDE, AB (surname, first name). In a visa, I had it once written as B C D E, A. In academic papers, it has been cited as E, A B C D; D E, A B C; C D E, AB; B C D E, A. The preposition itself sometimes vanishes leading to C E, A B.
No clerk has ever questioned my authorship, or my documentation in my travels.


In what order to list potential future advisors?

@Bill Barth, @Jon Custer and @jakebeal said "Order of Preference" (subjective, of course), and requested their comments be written as an answer so that it could be upvoted. I'm happy to oblige!


How to negotiate when professor asks for your help with a grant

You negotiated for 30 minutes to agree upon a 20 hour contract (four hours per day, for one week). That's an overhead of 2.5%. I doubt you can do much better...


What is wrong with conference publications compared with journal and transaction papers?

There is absolutely nothing wrong with conference publications. This sounds like your professor has something specific in mind and wants his students to achieve that target. In general, publications in journals are more detailed (and deep) so would make the students work harder I suppose since there is more information to process. Having said that, some journal papers are smaller than conference papers in length too (but that's not very common at least in computer engineering)

There is also a perception amongst a good number of academics that many conference publications are just small/quick pieces of work submitted hastily and later followed up with a journal publication. Again, this may depend on the conference itself. For example, the flagship conferences in your area would feature very good papers compared to a localised regional conference. So this may be a concern of your professor that his students may end up selecting a paper that is not of a good quality. In the end, only your professor can answer that.


How many professors should I contact before applying to Graduate School?

I didn’t contact any faculty, and I got into the programs where I was an obvious fit. I didn’t get into any others. Honestly, it did not even occur to me to contact professors. I am not sure this is particularly common in the social sciences and humanities in the US. In my program, only the international students pre-contacted professors.

To check, I would recommend reading “The Professor is In” to lean more about the graduate admissions and hiring process for the humanities.


Spelling mistakes in published conference paper at IEEE Xplore

It may be impossible to get a change made, but a possible approach would be to contact the program chair of the conference (or the conference chair if necessary) and ask for advice. They will know what is possible and what is not.

But it is also likely that the errors are merely a nuisance and not fatal to the work. It hasn't been a long time, yet, but over a longer period things get harder to change and more likely to be ignored.

Print versions are quite unlikely to be changed for anything but books that go through multiple printings with some editor intervention between printings.


How much does it matter the mentioned intended major at grad school in GRE registration?

I wouldn't worry about it because that portion is used for statistical purposes like compiling average test scores by major, like in the example here: http://www.ets.org/s...uide_table4.pdf

The information that schools look at that regard majors are if you take a subject test, like in computer science or physics. And of course all of your undergrad data.

Additionally, marking undecided is possible if you really dont want to choose one.


This data is available for the United States as part of the NCES Baccalaureate and Beyond Longitudinal Study (B&B). You can create a free account, then run some basic data analysis on their data using their PowerStats tool. (You could definitely use it to compute what "percentile would you be in if you had x GPA in y major" - I just tried it for myself. I was apparently a 95.1st percentile student as an undergrad :))

Here's a table I just made there of 10th, 25th, 50th, 75th, and 90th percentile GPA by major:


How many articles should a PhD candidate in applied linguistics /humanities optimally publish during their PhD?

To add to GrotesqueSI's answer, while it might be meaningless to associate an exact number to "hard-working" students, as a lot of other factors matter, I am guessing you are asking this question as a way of setting a goal for yourself (or assessing your work-in-progress).

A simple solution might be to pick a sample of 10-20 alumni that you consider to be successful or "hard-working," or at least in a place career-wise that you hope to end up one day. Take a look at their publication record from graduate school: what is the average number of papers? Is there a large spread, or do they all exceed some minimum number? For those who succeeded with few publications, were they particularly influential publications?

This can help you to find the answer that is personally most useful to you.


Asking the Editor-in-Chief about the reason of the review delay

In general, yes. The time for the review process varies between journals and between fields. you should, first of all try to assess what is normal for your field and particularly of the journal to which you submitted your work.

For me as Editor-in-Chief of a journal in the Sciences, it seems long but not unheard of. I have had rare cases where I have had to chase reviewers for a paper and where I have had to wait about three weeks to dismiss anyone or to just get a negative response. All these requests add up. Add to that reviewers that do not return the review despite, even repeatedly, promising to do so. So, it could be a case of bad luck, but before you send off a polite request, check so that such time frames are not normal for the journal. In any case, do not assume that the problem is only with the editor. It could be but as mentioned can results from many steps in the review chain.

Regarding a template, just write a short and polite mail or letter asking what time frame you can expect. You can, for example, say that you wish to know so that you can free up time for your possible revisions or something to smooth the request. But a short question is never wrong as long as the time frame is obviously longer than common for the journal


How much independency does a postdoctoral researcher have?

I would like to ask your opinion on whether it is normal for postdoctoral researchers to have collaborations with other people as well?

Our opinions don’t matter. The professor in charge of your grant is considered your supervisor, and whether it’s okay for you to spend significant time on outside collaborations depends on, and only on, the professor’s opinion. It’s likely okay, and yes it is somewhat normal at least in some disciplines (e.g. math), but you should simply ask them.


How important is the meeting with the dean in a faculty interview?

In US institutions I'm familiar with, the meeting with the dean serves the following purposes:

It is a way for the dean to exert oversight over the hiring process. While the dean is usually not able to tell if the candidate is really as amazing as the department will claim he/she is when they later ask to hire him/her, the dean can at least provide a basic sanity check, filter out obviously unqualified candidates, or detect various red flags indicating that there may be something seriously wrong with the department's candidate selection mechanism.
It is a way for the dean to signal to the department that he/she takes hiring seriously and is involved in the process. This may lead the department faculty to also take it more seriously and approach hiring with more respect and integrity.
It is a way for the department and dean to signal to the candidate that they take him/her seriously, to the extent that the dean is making his/her precious time available for the purpose of having the meeting. If the candidate is a hot commodity being sought after by several schools, this can be important.
It is an opportunity for the candidate to impress the dean with his/her brilliance. Usually the dean will not be so involved with decision making that this will make much of a difference, but nonetheless, there are subtle ways that the dean being particularly impressed with a candidate (or conversely, particularly unimpressed) can be communicated down the hiring chain, and in cases of extreme brilliance/lack thereof this could end up making a difference.
It is an opportunity for the dean to impress the candidate with his/her own brilliance. The interview is a two-sided event in which both parties are evaluating each other, so this is part of the package of the university trying to sell itself to an attractive candidate. Again, usually candidates won't care so much about the personality of the dean where they are interviewing, but in extreme cases a super-amazing dean can make the school seem materially more attractive, and a super-horrible dean can make the candidate run for their life.

Usually none of these effects are very significant, and not meeting the dean almost certainly won't make any difference one way or another on the outcome of the interview. The final use for the meeting that I can think of is the only one that actually matters somewhat (though still not very much), which is:

In the event that the candidate met with the dean and was later hired, they arrive at a campus where they already met the dean. This contributes to their sense of familiarity with the place (and presumably confidence that it is well run) and gives them a feeling that if there is any trouble at the department they know who to go to. A small thing perhaps, but still worth something in my opinion...

Bottom line: in your situation, don't worry about it. If you end up being hired you will meet the dean sooner or later.


Is it ok to withdraw from a PhD when receiving another job offer?

In the US, you can withdraw at any time, even after starting. If you  have signed a contract for some services, then you may have to deal with that, but most universities will let it go since those services can almost always be handled by other people.
People leave doctoral education for lots of reasons.
But I suggest you think long term about your career and whether a job is preferable to a doctorate.


lecturing one subject with other lecturer's material

In Academia there is always a lot of egos involved. Do not take it personal and let your ego get in the way. As you admit, you are not the main lecturer. He is. He prepared the slides, exercises, exams, practices, final project and so on. Excellent. Less work / stress for you. It is not your time to shine. In any job (academia or not) you must learn how to play "second fiddle" if needed. And this is one of these times.

On the other hand, teaching is much more than the slides, exercises, final project or exams. It is the teacher's personality, how he is in sync with the classroom needs, how to make the students participate in the course and how to make the lesson an unforgettable experience. You can and must try to do all these, regardless of the slides you use. So you can still make all the students want to watch your lecture (instead of his) if that is what it takes to boost your ego. Although it clearly is not a competition. It is just a job. So, do it as best as you can with the tools you are given. It is really that simple.

Update.

From the comments I see, there is too much focus on "No-one should tell how to teach...". But this is not really the point. If professor B was supposed to teach both lectures and due to a newly assigned duty he cannot, would not that be impolite / inconsiderate for the new professor (Layla) not to give her (at least) the materials and slides he uses? If someone steps in for me, I would most certainly do all the necessary work for my coleague to have the most seamless transition by alleviating some of the stress /work for preparing lectures / slides, exercises. And if I was the subsitute I would appreciate this offer. Why must egos be involved in such a process and why should anyone not accept the offer given? If this situation continues for the next semester - year, Layla should have a saying on how the lecture should be done. But for this year I do not see the point in making too much fuss over it.


Accepted conference paper but changing job before the conference

The only thing that can be said for sure is that the conference is unlikely to cancel the submission. I don't know of any conferences that would do such a thing.

But whether anyone wants to pay for attendance is another question altogether. It can be explored with the company and with the university. In many cases either would be happy to help you attend as it increases their own visibility. In other cases they would not. In some situations the institution (company or university) won't pay anyway depending on the paper and the cost.

The safest thing for you is to assume that if you want to attend then you will have to pay yourself and to hope that, upon asking, either the company or the university will pay instead. It isn't then end of the world if a co-author presents in your stead. You still have the publication on your record.

Withdrawing your name from authorship seems to me to be the worst option as you have done the work but won't get credit.

It is also possible that you can submit something in addition to the conference and have the university pay on the basis of that, instead.


Submitting an improved/extended version of a journal article under review

The main issue here is whether the so-called extensions or improvements are substantial enough to classify the revised version as a separate paper. In general, I think not. In addition, that you've "improved" a paper means that the older version is "deficient" in some way (or else, why "improve" it?). If so, then you are doing the original journal a disservice by having them review a deficient paper.

I am part of the editorial team of a number of journals. In none of them would we appreciate you submitting essentially the same paper to another journal. In fact, if we found out, then we would contact the new journal and discuss the case in tandem. In addition, if we received a submission, we expect you to assert that the manuscript was not being reviewed elsewhere. It i likely that you would not be able to make this assertion to us, knowing that an earlier version of the paper was being reviewed elsewhere.

Perhaps you're thinking, "why not submit the revised paper to the same journal because it has improved on the original manuscript?" Even this is pretty frustrating from an editor's point of view. It is likely that, as editor, I'm waiting for reviews of your original paper to arrive. If you were to submit a revision to me during this process, it would be rather disruptive and I would ask why you submitted a half-baked manuscript to us in the first place.

What can I advise you? I suggest that you contact the Journal and ask for the deputy editor who's handling your manuscript. I would discuss your situation citing these two significant issues: (1) 10 months is a long time to wait and (2) during that time, we've made improvements to the manuscript. Then I would ask them what to do.

Deputy editors are human, too. If they understand your situation, then they can advise you accordingly.

Good luck!


Should I leave this PhD and start another one? Would I be in trouble?

The comment of astronat is good. Most people would support you.
But there is more. If you are happier, then you will probably do better work. Being in something that you aren't happy with is not good place to be.
If there is any sort of retaliation it would be, I think, short lived and can be overcome. Other than lying, the person has no real way to say you are not suitable for academia.
Everything seems positive about the switch, both personally and professionally.
But, it would be worth the effort, unless you have contrary evidence, to have a conversation with your advisor giving two messages. First that you are happy with their guidance, but have both personal and professional reasons for a move. They may be disappointed, but that seldom results in harmful action. Clean up joint work before you go, of course.


Whether identical make-up exams are fair depends on the circumstances.  The key point is that you can't eliminate all potential for cheating: there are too many ways to cheat, and you can't even try to rule them all out without brutal and expensive oversight.  Ultimately, you have to make a trade-off, in which you take some anti-cheating steps but stop focusing on cheating once you reach the point of diminishing returns.  [For example, if you are really concerned about cheating, then you can't use take-home exams, and you'll have to police restroom visits very carefully for in-class exams.  These steps might be sensible under some circumstances, but counterproductive in others.]

So how does this apply to identical make-up exams?  If you're teaching a required, low-level class to a large group of unenthusiastic students who desperately want good grades, then cheating sounds like a real worry, and giving the same exam twice would be a foolish decision.  If you're teaching an advanced class to a small group of students you know and trust, then there may be no issue at all.  Reasonable people could differ as to where to draw the line between these scenarios, and it depends on their judgment of the likelihood and consequences of cheating.

There's more to this than laziness, although writing a second exam is certainly a pain.  Instead, there's a trade-off between several effects.  If you write a new exam, then you've eliminated the possibility of learning the questions from a classmate.  However, there's no way to calibrate the exams perfectly, so you've introduced the possibility that the make-up exam was inadvertently easier or harder, and the students may feel stress or bitterness over this.  Both the cheating and the differing difficulty are bad, and there's no way to completely eliminate them both, so you have to decide how much they worry you and balance between them.

There are also matters of educational philosophy.  I'm not fond of any approach that tells students I don't trust them or that challenges them to see if they can slip anything by me.  That doesn't mean I won't take countermeasures against cheating, but it means I consider the countermeasures to be problematic in and of themselves, so I try to use them as sparingly as I reasonably can.

In practice, how I design make-up exams differs from course to course.  Sometimes I write a new exam from scratch (while allowing some possibility of overlap with the previous exam, so students can't be sure something won't be on the make-up just because it was on the original exam).  In other cases, I just fiddle with some of the details or replace a few questions, while warning students not to discuss the exam until after the make-up exam.

Regarding outcomes, I find that students who take similar make-up exams rarely do surprisingly well, and on average they do a little worse than I would have expected.  Of course I don't know what's happening behind the scenes, and perhaps cheating saved them from scoring even lower.  However, I'm at least confident that students aren't using this as an opportunity to rack up lots of undeserved points.

  If it's not compromising the integrity of the exam, why not just have the same exam every year and collect the question sheet from students?

It's not a matter of absolutes, but rather of how much the integrity is compromised and what the consequences are.  Re-using the same exams every year offers much more scope and temptation for cheating than a single make-up exam does.  The longer you re-use an exam, the more likely it is that unscrupulous students will piece together and circulate a list of questions, even if you collect the question sheets.  If you do this for all the exams in the course, then the potential benefits of cheating are quite a bit higher than in just one make-up exam.  (If I saw the same student repeatedly requesting make-up exams, I would wonder why and might become suspicious.)  If the ease of cheating in every exam is known, then the course will attract dishonest students who might never have taken it otherwise.  There's a big difference between possibly being able to learn about one exam if you convince someone else to help you cheat, and being able to learn about every exam by downloading a file from the internet.  It's reasonable to draw a distinction between these scenarios.


If you're looking for biomedical reviews, Pubmed allows you to filter reviews after searching for keywords. This option is available in the sidebar, under "Article Types". Depending on your field, there might be other search engines that allow this type of filtering.

On Google Scholar, you can refine your searches by using Google search operators. For example, if you search for insubject:"obstructive lung disease" intext:"review", Google Scholar will return results that have "Obstructive Lung Disease" in the title and the word "review" somewhere in the text.


UG Research Advisor Not Willing to Write LOR to support my transfer application. How to proceed?

It is fine to mention your undergraduate work. You did it and you received graded credit for it. Talk about it! (In a statement of purpose or something).

What did you do?
What did you learn?
How did it inspire you?

True, yes, your undergraduate advisor would not write you a letter of recommendation. There is no need to mention that. If you have other people who are willing to write you a strong letter, you should be fine. When I sit on admissions committees, there are a few things we take into account:

We are only seeing a portion of the student's profile. We don't know the whole story (either way).
Sometimes professors are hard to get along with in regards to grades, authorship, LORs, etc.
Students are going to school while life happens around them. This means that sometimes the circumstances of life will affect their decisions and opportunities relative to school.
We do not expect a masters student to come in on day one and have the skill set of a master's student at the end of his or her degree. We are looking for potential.

Overall, I am more interested in learning about what you, not an advisor, did. If you are competent in explaining your research, that is going to bode better for you than having a LOR from someone who grudgingly has been forced into writing you a LOR.  I would not spend too much time trying to make this donkey (the undergrad advisor) pull the cart (LOR) he does not want to pull.


Can a tenure-track job candidate infer any meaning from the response to an initial contact email?

Don't stress out about the responses, since it's nearly impossible to get reliable information by reading between the lines.  The variation in how people might respond is enormous, and unless you really know the people involved it's hard to know what it means.  For example, suppose someone sends a friendly, encouraging reply.  Maybe it means you have a real shot at the job.  Maybe it means they think you have a real shot, but they could be totally wrong.  (Sometimes people on hiring committees have unrealistic beliefs about how everything will play out.)  Maybe it's just their personality and has nothing to do with your chances.  Maybe they are deliberately saying the same thing to everyone in order to avoid awkwardness.  If you don't know them pretty well, all you can do is guess.  Of course a standoffish reply is equally difficult to interpret.  The net effect is that you'll get replies that look like they may contain information, but you really won't know what, if anything, they mean.  It's best to resign yourself to this now, rather than spending a lot of time worrying over how to interpret replies and not actually learning anything valuable in the process.


For graduate admissions, are difficult classes valued over perfect grades?

I think this is a pretty easy one.

  I know looking at grades in isolation w.r.t. admissions is a questionable thing to do in the first place, but from an admissions perspective, are difficult classes valued over perfect grades?

Yes.

  I guess the example in mind would be, is it better to have a couple of difficult courses + mostly undergrad courses with all As, or a lot of difficult classes but some Bs sprinkled in?

The latter is distinctly better.  I got a B in the first graduate course I took as an undergraduate.  (I then took 8 more graduate courses and got A's.)  This did not stop me from getting into all the math PhD programs to which I applied, including the top three in the US.


Peer shared with me "too much information" for a homework problem

You are overthinking this. You have not cheated, and there is no need to do anything further.
The goal of assignments generally is to make students learn how to independently solve the problems, and assess them on it. This is why directly copying others' work is disallowed while discussion of ideas (to a limited extent) is allowed: discussing ideas helps your learning, while blind copying does not. You still need to understand the ideas, and apply it correctly, and write a coherent answer by yourself. This is also why your instructor provided helpful suggestions, as you mention, to point you in the right direction, while still letting you come up with the solution yourself.
In your case, you did not even use your friend's ideas. From your account, you were careful to stay within the limits of what was permitted for collaboration, so there's no issue. Even if what they shared was too much, you did not cheat as you did not use it in your own submission. It's perfectly fine (in most cases) to discuss solutions after submission; in fact, a good idea since feedback is quite valuable.
The absence of any response to your emails suggests that the instructor either did not read the message or did not see any issue with your behavior. The fact that the final marks have been declared without you hearing about this reinforces this. Sending repeated mails in this situation is a bad idea and quite unnecessary.


Can I accept two offers from universities and decide later on

No.

In principle, you could do that, but it's not advisable, for the simple reason that if either school finds out you've accepted another offer, then both schools could end up rescinding their offers, and would be within their rights to do so. (Programs want to know how many spots they have filled, so that they can accept more people if needed to meet their enrollment targets.)

Basically, you need to commit to one school only. If the offer is conditional, then you should weigh the probability of meeting those conditions before accepting the offer.


How important is it to choose the right editor on journals that require you choose an editor?

The editor is the person responsible for directing your paper to a competent reviewer. Taking that into account, I'd strongly suggest you choose the editor that is most related to your research area, because he will have more contacts of experts in that field. Your advisor's knowledge on some editors can probably help you discover which ones hold this position, but you really should have this information on all of them. E-mail the journal and ask for this information before you do the legwork.


How to make a concise dissertation defence in Math department

I don't think there is a meaningful answer to this question that is helpful across all US math departments and advisors.  There is too much variation in what is expected.  You need to find out what your committee expects.

That said, if I had to answer without knowing your department or committee, I would recommend trying to focus on the big picture but making sure that you spend most of your time explaining your contribution to that big picture.  That's certainly what you'll want to do for job talks, which you're presumably also giving around now.

If the committee is concerned about your understanding of the technical parts of the proofs, they can ask you in the closed exam following the public talk.


Nervous about my thesis results -how to decode my supervisor's email?

"Major problem" is premature. "Potential major problem" though - that's likely, depending on what the examiners are disagreeing about. It's possible your thesis is fatally flawed, but it's also possible one of the examiners is wrong.

Either way you can't do anything right now, so there's nothing to do except wait for the official email.


You're asking for the impossible.  Almost every mathematician with more than a few papers has had the experience of submitting a paper or circulating it as a preprint and having some relevant work they didn't know about (and are not expected to have known about) pointed out to them.
If you are asking about one or two specific narrow questions or equations/formulas, then usually the best thing to do is to figure out who the friendliest expert who might know is, and ask them.  Even if they don't know, they might refer you to another friendly expert.  (Some subsubsubfields have friendlier experts than others, and this difference definitely influences the popularity of the subsubsubfield.)
If you're looking to break into a new subsubsubfield with lots of history without an advisor, then some subsubsubfields have friendly conferences, but, in general, ...uhh... good luck.


Does a full professorship necessarily imply tenure in American Universities?

It depends on the institution whether it is even possible, in principle, to have nontenured full professors.  At some institutions, being a full professor automatically means you have tenure.  At other places, it is merely overwhelmingly likely that a full professor will have tenure.

Any case where somebody is a full professor but does not have tenure is likely to be a bit odd.  In my department, there have been, in the last twenty years, two people who had the title of "professor" without being tenured.  One of them was a senior person who the department hired, but for some reason they could not hire this person directly with tenure.  Instead, they were hired as an untenured full professor, with a two year tenure clock.  They turned in their tenure file after one year and got tenure with no problem.  The other person is a former tenured full professor (and department head), who moved to an entirely soft money position.  He was allowed to keep the title "professor," but he is no longer tenured, with his position coming up for review every three years.


Do professors actively seek postdoctoral students for projects?

In comparing my experience at several places, and my wife's (in a different field), I think there are two radically different models.

Department has X postdoc (or equivalent, under a different name) positions. Open search to fill based on generic criteria, some degree of importance to "this person will have good research fit here". Faculty encouragement limited to encouraging promising new researchers in one's network to apply, speaking up that they are a good fit, and then making the new hire feel "welcome".
As @Buffy wrote, making potential applicants aware, encouraging them to apply is fine, but nothing can be promised, and there is no obligation of the hire to work on any project in particular.

Research lab (Centre, Unit, one professor...) hires postdocs funded by own research funds. While there are generally obligations to evaluate all applicants for the position equitably, a lot more flexibility and expectation for the lab/group to source suitable applicants, and the position criteria may well end up much more targeted to a specific applicant.

By the way, the postdoc transition is -- arguably -- even more of a difficult one that completing a Ph.D., since it is during that period that a researcher becomes truly independent. So the situation that a postdoc has some of the crucial skills for success and not others, and may or may not succeed in developing them, is pretty typical.


Where do researchers get the money to replicate others' work?

In my field (cognitive science), your supposition that replication is primarily pursued by investigators prior to extension is true. For example, I have an idea while reading a paper on learning targeted movements, I first implement the paradigm as described (either an exact replication or a conceptual replication) and then I extend it to test my idea. Thus, the money for this comes from the same places that the money for all research comes from: largely from government allocations and grants, partly from NGOs and industry.

However, there has a been a recent trend--again, in my field, but as part of a larger movement in the social sciences--to improve replicability of results. This has included fostering availability of code for software projects and pursuing independent replications purely for their own merit. Last semester I attended a talk on a set of these replications, which, along with similar attempts from other labs, were pushing to overturn the original result. In these cases, the money to pursue the replication is probably somewhat independent from other projects of the researcher. This means funding agencies would be unlikely to provide a grant entirely for this work, so it is probably going to be supported as a passenger on previously funded work or on University funds (e.g. start up and salaries).


Typically, one writes Ph.D., 2018 (expected).

If you have a short description (e.g., bullet points) after this heading, you can also put the expected graduation/defense month or something to the effect of "thesis submitted 25 May 2018" in this area.


Would students who drop out before they take any exam be blacklisted by the (prestigious) university?

No.  Students drop out of a class or school frequently.  If it was recent - then you are likely still "admitted" and can register next term.

  Or is it normal to be contacted by the university inciting the student to apply again?

I'm not sure they'll ask you to come back - they might, but it is up to you do work on getting back in.

I suggest checking your status on-line, or talk to someone in the registrar's office.
While a very prestigious school has a thousand students lined up behind you to take your place, it is likely that if they admitted you in the first place, they'll be happy to keep you.  If you do it again, then they might think less of you.


Do I have to pay back an Australian IPRS Scholarship, if I decide to quit my PhD?

I would say no.  When you are awarded an IPRS, you will get the conditions that you need to adhere to.  At my university, there is no clause that says you have to pay back anything if you quit.

If I were you, apply first, and if you are successful, look at the conditions carefully.


Using industry productivity tools and techniques for managing student projects

Yes, but don't overdo it.

Using one or two services such as Slack (the one I have the most personal experience with) can be really helpful in the sense that it can facilitate and organize communication. It's easy to share files, and to collaborate and make progress even when everyone can't be in the same place at the same time (an issue with busy students). It's also good to have some kind of central communication system, where any and all meeting times and information are announced, such as goals, deadlines, progress reports, etc.

However, for it to work, everyone has to be fully aware of 1) what service(s) the team is using 2) how to sign up for and access the service (Does it have an app? Does it send alerts? Emails?) and 3) what is expected from them in terms of the service (How often are team members expected to check it? What are they supposed to report on?). Make sure that if you decide to use some service, that you have a meeting where every member of the team gets together, signs up for the service, configures anything necessary, and discusses expectations. If everyone isn't on the same page, then you're not really going to see any benefit from using it.

Also, limit yourself when choosing your tools. There's a lot of cool team management software, and organization tools out there, but for a 2.5 month project, you probably only need one or two that are most essential to the tasks at hand. Make sure that you have some tool for communication, because effective communication between busy team members is what will ultimately keep the project on track.

If you use a tool for a week and find that it's either hindering productivity or not increasing it, then either choose a different one to replace it or just scrap it totally. Don't persist in using something that isn't helping.


Can my age play as an obstacle in my Ph.D. application, and while getting student visa?

No, your age won't be a problem for being admitted as a PhD student and being granted a student visa, but you may find it difficult to avoid tuition fees.and to win a scholarship to cover your living expenses. Even if you meet the eligibility criteria for such a scholarship, the committee may simply prefer younger candidates, and you won't be able to prove you were discriminated against. However, a professor may be able to fund your scholarship from his grants, but, again, professors generally prefer younger students.

Also, it will be hard for you to pursue an academic career in Australia after you complete your PhD. In order to get a permanent position in an Australian university, you will need to win external grants (e.g., ARC grants), and, again, the committees will prefer younger applicants. If you do not win external grants, you will be an eternal postdoc on short-term contracts (1-2 years), and you will be hired only as long as your PI wins external funding to hire you. Once he fails to do so, you will have to look for another professor who has funds to hire you, and it is not easy at all. It is a miserable and stressful career path.

I lived and worked in Australia and know the Australian academic system. An old Australian postdoc told me that he had wanted to write an ARC grant application and that his boss had said that he (the postdoc) had no chance of succeeding because of the age, even despite that the age is not mentioned in the eligibility requirements. I would advise against trying to start pursuing an academic career in Australia at such an age.


Request to referee from obscure journal (physics)

I would recommend you have a look: If the submission is as bad as it looks, you will not have to devote much time to it anyways.  Someone has to do some refereeing else nobody would referee my papers so my rule of thumb is: I referee as many papers in a year as the number of referees needed to review my work that year.


There are a virtually unlimited number of conferences whose title is of the form:

  "[Society] [International] [Conference|Workshop|Symposium] on XYZ"

where "International" is optional and the optional "Society" is a big organization like IEEE, ACM, ACS, etc.

Since there's basically no information in the first part, the organizers and attendees of these conferences will tend to refer to them as the informative "XYZ", ignoring the preamble.  Citations often do the same (e.g., just "XYZ" as venue, and sometimes even just the initials), particularly in page-limited publications such as standard IEEE proceedings.

The "XYZ, IEEE International Conference on" form is then a hybrid compromise that some venues use to put the informative bit up front while still keeping the full title.


Do I need permission from my past supervisor?

If your past supervisor made a significant intellectual contribution to the new paper, then he should be a coauthor.  And then, yes, you need his permission to publish the paper, because publication requires the consent of all coauthors.

If your past supervisor did not make a significant intellectual contribution to the new paper, then he should not be a coauthor.  And then no, you don't need his permission to publish the paper, because he is not a coauthor.

In short: The fact that he is your former supervisor is utterly irrelevant.  (This would also be true if he were your current supervisor.)


What is the promotion rate of professors in United States?

The US National Science Foundation collects a lot of data from surveys of recent doctoral recipients that it publishes on this web page. The precise thing you are looking for (tenure success rate) does not seem to appear, but there is a lot of relevant information. Specific professional societies collect similar information. For instance, the American Mathematical Society publishes an annual survey of information on recent doctoral recipients; it includes data about the salaries and employment situation of recent doctoral recipients in the mathematical sciences.


What is the easiest way to check for plagiarism in student essay papers?

There are plenty of tools out there. The best 'seems' to be TurnItIn. It's costly so if the school won't pay for it, you might not be interested. My school does not so I found other options.

Here is a tool called WCopyFind that is very good at finding plagiarism when one student copies from another but it will not find something online. After collecting papers for several semesters it has been catching more and more and most students take the same easy way out.

There are other options if you search for online plagiarism checking but they are not as robust as this tool above...however to really see the benefits, you need to maintain a library of old papers to compare against. What I like about it (besides being FOSS) is that it is highly configurable (consider a match 6 words in a row, or consider a match 9 words in a row where 70% of the words match). It all runs local (since there's no internet search) so it's quite fast.


Why do some journals ask if there is someone who you do not wish to use as a referee?

This happens when the author (or applicant in the case of a grant) believes that some likely referee might not act fairly for some personal reasons.  In my experience this is usually some history in these disputes. There might also be conflicts of interests.

Often there is guidance on who can be excluded, and the person must provide some measure (sometimes merger) of justification.


Do I need to sign the cover letter to the editor?

No, you don't need to sign it. (At least that's been my experience with every journal I've dealt with.) My cover letters just tend to be PDF files (uploaded to the journal site) that end like

Yours sincerely,
< List of authors (printed names) >


What do universities usually do with a student's graded final exams?

Speaking as a professor, I typically hold on to them for a year or so just in case any student wishes to see them. That said, I can remember this happening only once in about 5000 students taught.

When I was in college, we had the option of providing self-addressed stamped envelopes in which our final exams could be returned to us. Over half of the students availed themselves of this option.

I do not believe that my university has any formal policy, though they could have one that I am unaware of. It would seem foolish for a professor to get rid of the exams before the students have had an opportunity to see their grades and respond if something seems out of line.


How long should I wait for the response of the possible postdoc advisor?

I don't think there is any need at all to communicate further with this PI regarding this matter.

I don't see any point in asking him if he "likes" your CV.  It's a weird request - it's not his job to evaluate your record at your request, or to tell you whether your CV is well-written.  If that is meant to be a way of asking him "What are my chances of getting a postdoc with you?", don't: that's not something he can reasonably evaluate until there is actually a position and he can compare your application with those of all other applicants.
I would not write him back at all, regarding the postdoc specifically.
He doesn't have a position open, so there isn't any action he can take for you in the short term.  If a position appears at some future date, and if he is still interested in you as a candidate: well, he knows how to reach you.  And sometimes "Please send me your CV and I will keep you in mind for a future opening" is a polite way of saying "No."
Definitely do not contact his other postdocs.  The hiring decision is for the PI to make, not the postdocs, so any questions about it should be directed to the PI.  Trying to go behind his back to wheedle out inside information from them would be unprofessional, will annoy the postdocs, and will probably destroy your chances of ever getting hired if the PI should learn of it.

If you have some other bona fide reason to stay in contact with this PI (discussion about research topics of mutual interest, questions about his papers, etc), that could be helpful in keeping yourself in his thoughts for possible future postdoc hiring, as well as general networking.  But they had better be for real - if you come across as making up reasons to contact him just to get his attention, that will seem slimy.


How should I systematically go about looking for bursaries/scholarships for an internship in the UK?

In the UK, there is not much funding for non-UK/EU students. There is not much funding for undergrads. And there is not much funding for internships. On top of this, as a non-EU/UK student, you will need a visa to work/study in the UK and unpaid "internship" is not a category for which you can easily get a visa. Tier 5 visa is perhaps most appropriate, but it requires serious commitment from the sponsor (UK university), which they may hesitate to provide.

To summarise, my advice is to look for a more standard route, e.g. an undergraduate course for which you can probably get a bursary from your own country. You can also apply for a paid work employment (e.g. postdoc) if you qualify.


Is it ethical to blog about your publications to communicate your research without being restricted by the journal?

I think the answer is yes, but you should aim higher: the line you're drawing in the sand is uncomfortably close to you and that's causing more work for you than is necessary.

Namely, trying to put the essential content of your papers on your own website for the purpose of freely disseminating your work seems wrongheaded: instead, you should be putting your own papers on your webpage and/or freely available preprint servers like the arxiv.  In order to do so fully legally (which is not necessarily the same as ethically: it is possible to feel that the law is unethical, in which case the ethical thing to do could be to break the law, but be willing to live with the consequences of that) you need to arrange this as a condition of the publication.  This is absolutely feasible with all of the major scientific publishing companies.  How common the deal is seems to depend on the individual journal and on the standards of the field.  In my field (mathematics), I do not know of a reputable journal which would not allow its authors to post on the arxiv.  (Once I dealt with a journal which initially asked me to remove the copy of the paper from my homepage.  After some back and forth, the editor in chief told me that it was absolutely okay for me to do that and he was surprised that the editorial assistant had said otherwise.  In retrospect, this was a clear warning that I was dealing with a shady journal.)

I gather that in some scientific fields, there are "popular" journals which do not allow authors to put papers on the arxiv (or, alas, there may not be an arxiv or clear equivalent) or -- gasp! -- on their own homepage.  I find this strange, because in my understanding in most scientific fields the majority of journals are owned by Elsevier, Springer, Science Direct... -- i.e., by enormous multinational, multibillion dollar publishing magnates which are not renowned for their generosity or enthusiasm for open access.  But when you publish a paper in (e.g.) mathematics in one of these journals, the copyright notice that you sign allows you to post the paper on the arxiv and your own webpage.  I find it hard to believe that the copyright notices for different journals by the same publisher would be so different on this point.  So the battle has already been won in these hardest places.  If there are trade journals specific to your field which are less generous to authors than the evil empires I've mentioned above: well, if you care about this sort of thing, don't publish there.

In terms of putting copies of published papers on the arxiv, in light of the comments above let me share my understanding.  What you publish should not include any journal-specific formatting: it should not look like a Journal X publication.  As a general practice, most authors upload to the arxiv before submission, and then only upload a new copy if some kind of significant, content-related change was made.  In particular, if an error was pointed out, then it would be good to correct that.  If the journal did copyediting for you -- which is not the same as directing you to do copyediting after acceptance -- then maybe it is best all around not to incorporate those changes in the freely available version: on the one hand, aside from formatting, this is the only place in which the journal itself is contributing to the paper; on the other hand, going back and manually incorporating the copyediting for an entire paper could take some time and effort.

To respond to what was said in the comments: in my opinion, whether your revisions were motivated by a referee report should not have any bearing on whether you want to change the freely available version.  If you are making changes in response to a referee report, then including that information in a "comments" section on the paper would be a classy move.  But as a frequent author and referee, I feel strongly that the changes you made in response to the referee report are not proprietary to the journal in any way (or in any other way from the rest of the content of the paper).

Added: The task of checking out policies of publishers and journals with regard to preprints is not something that an individual researcher needs to address from scratch: there are several online repositories of information about this.  Here is one.


Organizing technical documents and reports

It might help to add a few details to enable specific constructive responses. What is the purpose for organizing the documents: personal use, internal use within your team/department, public but less formal use such as your personal webpage, public and more formal use such as website of your research group, or inclusion in CV?

Each of these uses is aligned with different (though possibly overlapping) audiences, and might imply different approaches for what and how to present, what to highlight or omit, etc. etc.

So, first I recommend to organize your organizing needs/priorities, then address details.

A few general ideas, with regard to organizing in "professional/formal manner":

Personal use: There are tools such as Mendeley that can be helpful for figuring out and experimenting with ways to categorize the documentation. Mendeley can be leveraged for open/public access to materials as well as private use (e.g. uploading citations but not actual attachments).

Research team website: collaborate with your team to determine what might be worth sharing publicly (beyond what has already been made available). For instance, you might collectively decide that adding some previously un-shared white papers/tech reports, or even datasets might "fill out" the public profile of the group's research and allow the team to cite/reference these resources.

Personal website: Regardless of whether you make the material available on a collaborative formal webpage of your department/group, I see no problem with also featuring a few technical reports/white papers that you have authored or co-authored on your personal department page. Technically, if you work for a public university and unless your research is classified, your research output is in the public domain and you should be able to enable public access to it without any negative consequences. (There may be other specific caveats around this in each case, but you need to explore those and use your best judgment).

CV: In my experience, citing technical reports or white papers in your CV is totally acceptable and could serve to boost your research track record. Since tech reports are not typically externally peer reviewed, a safe approach is to place them in a separate dedicated section, e.g. "Technical Reports."

Finally, there are numerous sites out there such as Mendeley, Academia.edu, ResearchGate, etc. The sites differ in functionality, target audiences (e.g. more hard vs. more social sciences) and visibility/uptake within a given discipline. Here is a fairly complete listing as a starting point:
http://connectedresearchers.com/online-tools-for-researchers/. Good luck!


Should someone excited about research but who really wants to earn lots of money do a PhD?

You shouldn't do a Ph.D. if you don't love research.  You also shouldn't do a Ph.D. if you want to get rich now, since it will require a number of years living on a graduate student stipend.

However, most STEM field Ph.D. graduates have ample opportunities to make lots of money, including:

Founding a startup based on technology developed during their Ph.D., or joining somebody else's startup
Selling out, particularly if they have a solid mathematical background: there are any number of hedge funds and such that are desperately hunting for magic dust to give them an edge.
Just about any industry job will pay a well-suited Ph.D. well - not enough to make you rich, but enough to live a very comfortable life-style.

Of course, there is the danger that by the time one finishes a Ph.D., they may have become twisted such that they are no longer quite so interested in money per se, as happens to many of us.


Method of self-assessment of academic potential

The best way to assess your ability to do research is to do research.  It's kind of like figuring out what Tiggers like to eat---there's just no substitute for trying.

Research generally requires intelligence, hard work, and creativity, but whether you have enough of them and whether those talents combine in a way that fits well with research and whether you actually enjoy deploying them in that manner is something you simply will not be able to know until you get involved in some.

One good way to do this would be by enrolling in a Master's program with a research component.  This is only a couple of years commitment, and can give you ample opportunities to try out research in your field of interest.  If you end up deciding that research is a good path for you, it will help you build credentials to get into a good Ph.D. program.  If you ended up deciding otherwise, you'll still have a nice higher degree that may get you a higher paycheck in industry.


Is differentiated instruction permitted by universities?

It would be very unusual, in my experience in the U.S., for one group of students in a class to be given an "easier" exam than other students in the same class.  When the students who took the "harder" exam found out about it, they would have a valid grievance that the faculty member would be unlikely to win.  If a colleague asked me about this, I would strongly discourage giving different exams.

At the same time, it is perfectly reasonable to give individualized instruction before the exam. This is more feasible with small classes than large ones.  At smaller schools, it is common for faculty to meet one-on-one with students, explain background material, and suggest additional problems to help those students self-remediate.

Whether this is possible for you on how much time you have available to do it, and also on whether you can convince the struggling students to put in the extra work that will be necessary for them to succeed. Unfortunately, some students are unable to do that, or choose not to.

I also want to give some more personal remarks, because I empathize with the spirit of the question: not wanting to leave students behind when they arrive underprepared for a class. I also teach at a school where some students have clear potential but were underserved by their high school and don't have the background that is expected when entering college.

The question mentioned being "fair to everyone". This has many meanings. You want to be fair to each student - which means both recognizing where they are currently at, and not sending them forward without the background to succeed in their next class.  You want to be fair to the other students by making the class similar for everyone. And you also want to be fair to future professors, by sending them students who have the appropriate background.

Sometimes, you will be in a position where you can't do all these things. Perhaps a student has real potential but simply can't get to the necessary level by the end of the course. Perhaps the student could get there, but has personal or family obligations that occupy their time. Perhaps a student is just not quite mature enough to put in the work needed.

This can be one of the more difficult situations for a professor. But it is also very common, particularly at institutions that are not extremely selective. If you talk about it with your more experienced colleagues, they will have their own experiences with it, and they will be able to give you advice and support.


MSc Dissertation Tables & Figures Errors submitted

I would go ahead and have it corrected and prepared ready - if they then say "submit a corrected version now or by 4pm" then you have it ready.

However, if they say have it corrected for final submission in 2 weeks then you are still ready.


For Ph.D. theses, some universities (including mine) care about some aspects of the format in minute detail. They should have an office where such things are checked. Find that office and ask.

If the university doesn't care, then ask your adviser whether anyone cares. If your adviser cares, obey. If your adviser doesn't care but thinks someone else (with some authority in the matter) does, then ask that someone else.

If nobody cares, just do whatever looks reasonable to you.


According to SIAM:

  Note: Figures or tables created by someone other than the author or borrowed from a previously published source, even those created by the author him- or herself, must carry an appropriate credit line at the end of the caption. (See section 5.2.5 for additional information.)

Elsevier and IEEE have similar statements, which explicitly include the recreation of the figures.

If you have a source in mind already, it is probably safest just to cite it in the caption. However, if the form of the figure is indisputably widespread, then there is no need to cite it. I would generally follow the same fair use guidelines as does Wikipedia in such cases.

Examples I would not cite (because they are indisputably widespread):

Using circles and lines connecting them to represent a graph, G
A Hasse Diagram to represent all possible bit combinations
The format of a UML diagram (although I would refer to it as such)
A figure where I cannot identify an appropriate source with a reasonable amount of effort

Examples I would cite:

Any figures that I created for a previous paper ("adapted from [2]")
A figure from another paper that demonstrates a specific point, where demonstrating that same point is the reason for recreating the figure
A figure reporting data when I have not added to/modified the underlying data
Any time that I have a source in mind and I am unclear under which category it falls


How can a demoralized research student restore the passion for research?

If you lack motivation in your research because you feel like you lack the resources/knowledge to tackle the problem, then you should probably discuss this with your advisor. It is important that the advisor offers you projects that can be 'broken down' into small, manageable pieces, rather than some monolithic task.

A PhD is often an isolating and depressing experience. You should find a support system of some sort to help you through the process. This can be family, friends, or fellow students. You can consider taking up a hobby (preferably something social, like sports) to give you an outlet that's not research.

I can't comment on what exactly makes some people great thinkers, but I can say that in successful research takes a lot of hard work, vision, and a hearty willingness to fail 90% of the time.

Finally, and I am sorry to say this, but you need to be mentally prepared for the fact that academia is not the right place for you. If it truly depresses you to the point where you don't feel like it's worth it, you should seriously reevaluate your prospects.


How do I write a white paper for a research plan?

The definition of a "white paper" seems rather loose: see here and here, for example. I would check with your supervisor to make sure of what he has in mind, so that you don't write something overly detailed or overly brief. My guess is that the difference between a white paper and a proposal is largely formal: the latter has to be structured and formatted according to the requirements of the institution you are submitting it to; the former gives you a bit more leeway. Regardless, based on my experience and on this book I would structure it as follows:

Abstract - I find it useful to draft it at the beginning, for your own guidance, and re-write it once the rest of the proposal is
completed so that it reflects the proposal best and it really
"pitches" your research project.

Introduction/Background - a summary of the state of the art in your research field, leading to...

Statement of need/Problem - where you define a gap in the existing knowledge that you want to address, or something that is
considered correct but that you want to challenge for whatever reason
(to be stated).

Objectives/Aims/Research questions - your goals, hypothesis to be tested and/or research question(s) to be answered.

Approach/strategy - similar to the "Material and Methods" of a research paper.

Significance/Impact - why you think your question is worth for you to research, or your goal to pursue, and for an institution to finance your effort.


There are widely accepted standard rounding rules: any number greater than or equal to 3.35 should be rounded up to 3.4.  There is no reason to expect that an application would want non-conventional rules for rounding GPAs.


How to answer to this polite, but strange request?

I agree with both previous commenters: publish your algorithm first and then point them to the YouTube video. If you cannot or don't want to go the traditional journal publishing route, at least, consider self-publishing a paper, describing your algorithm, at a preprint or e-print server, such as arXiv. At the same time, I don't see a problem with this request, IF it involves sharing only data, but not the algorithm itself.

If you see the value of and are serious about commercialization of your algorithm, consider filing a provisional patent application with USPTO and/or Swiss patent agency. I'm not sure about possibility and details of applying for provisional patent in Switzerland, therefore, I refer you to this page, which seems to be relevant. It might be easier to skip filing provisional patent application with USPTO and file a standard one in Europe to establish the priority right (for example, see this page). Should you be thinking about going the patent route, I would definitely recommend you to consult a legal professional, specializing in intellectual property (IP) domain.

Disclaimer: I'm not a lawyer and this answer does not represent legal advice.


Abstract-only presentation - How does it work?

You go and present a talk. No paper will be published in the proceedings. If proceedings are published at all for this conference, your abstract will probably be published therein. This is a pretty common conference format in many engineering disciplines. You should take any review feedback, apply it to your article, and find a journal to send it to. If there is a distinction between published papers and abstracts at this conference, you should think about beefing up the paper before you send it to a journal.


Can offers to international students be rescinded if grades received following the application slightly lower their GPA?

As someone with some experience on the other end of math graduate admissions, let me preface this by saying I really doubt that anyone cares; a program like UCLA looks at a lot more than grades (especially for foreign students).  At this point it would be really disruptive for them to drop a student from the program (it's not like there are other students of the same caliber waiting around to be admitted), so they are not looking for reasons to do so.  This is probably hard to imagine after many years of people telling your grades are the most important thing, but for math grad school, they are really actually not.  They are a proxy for the ability to do good research in math, and the people running the program know they are a bad proxy and take them with a grain of salt.

So, the important thing to do here is calm down.  Imagine this from the perspective of the department; all the people making these decisions have a lot of other things to worry about, you are one of many grad students they admitted this year, and these grades are a very small part of why. Your grades are not something they want to expend energy paying attention to.   Even if your offer is conditional, I think this condition would only be used in really dramatic cases; I've never heard of this happening.

Look carefully at your offer letter.  Either it will say the offer is contingent on your grades this semester, or it won't.  (Incidentally, this info should have been in your post; answering questions well on this site is hard enough without people withholding obviously important information).  If it doesn't, and they haven't asked about your grades, then drop the subject from your mind and never speak of it again.  If it does, I would probably still not do anything unless they ask.  If they really want that information they'll ask for it.  If they ask, just write back saying "I got an 8/10 in X and 9/10 in Y.  Looking forward to meeting you in August." Don't try to explain why your grades are not what you expected. Just act as if everything is normal, and I'm sure things will be fine.


Praise tangibles, not intangibles.

Tangibles
Say things like:

I was impressed with the way you were dedicated to completing programming assignments, even when they are difficult.  Other students gave up, or skipped requirements X, Y, and Z.
You did a great job thinking through the logic on the Data Structures assignment.  I'm assuming that you took the time to think it through on paper, or in pseudo-code first -- something that a lot of first year students never do.
Your algorithms are elegant and show that you studied the coursework and theory behind them.  In particular, on the travelling salesman problem, I could tell that you took the time to study the problem, and think through different solutions.  Well done.
You used parts of Java (or C#, C++, whatever) that I didn't teach.  That gets me really excited, because it is the mark of a great programmer that they are inquisitive about better ways to do things, and to learn their tools without waiting to be spoon-fed.

Then you can follow with encouragement related to those tangibles, such as, "based on the skills and work ethic you've demonstrated, along with your willingness to put in the effort to solve problems, I think that you could make a really talented programmer.  If it interests you, I hope to see you in more CS classes in the future."

Intangibles
Avoid generalities like:

You'd make a great programmer!  You should take more programming classes.
You've got a great mind for CS.  It's not for everyone, so it's fun to see talent in such a young student.
If you stick to programming, I know you'll go far.

Intangibles can set people up for failure because they don't help them identify and grow their strengths.  If a student earned an A in your class, it's because they worked hard, and were determined, and stuck to it.  But if you tell them that they are "good" or "talented", without telling them why, it gives them the impression that their success is not because of their hard work, but is because of some unnamed virtue inside of them.  This can lead to a variety of ills:

They may have only taken that class to fulfill a requirement, and may have worked extra-hard because they were nervous about passing it.  If you praise them by saying that they are a "great programmer", it risks pushing them to continue with a field that may not actually interest them.  Worse, it can make them coast in the future.
It can actually hamstring them, because they are afraid of letting you down, but don't know what it is about their work that pleased you.

Your intentions are good, and it's great that you want to encourage these young women to feel empowered to tackle a field traditionally dominated by men.  But when you encourage them, be sure to give them tangible feedback, not just generalities.

Hope that helped!


Is it plagiarism to closely mimic the structure of a table in a publication?

I doubt anyone would consider a table format as plagiarized when used to show new data. It would be akin to saying use of Tukey's box-and-whisker type plots would be plagiarism. The question is understandable, however, since someone could arguably claim some such structure as intellectual property. I think the key here lies in what is being copied. You are copying the structure but not the content. To protect the form would be quite pointless since no-one would buy the rights and it would be simple to make sufficient variations to argue it is not the same form. I am sure this could be discussed at length by lawyers.

Although, not within the scope of your question, most author's will be happy to see something they produce becoming reused and maybe even a standard. I had a figure in a paper that was picked up by IPCC and used to show something different than my original but still unequivocally based on my design.

So in the end, as suggested in comments to your question. you can pay homage to the original by acknowledging the idea of the table in your acknowledgement or by citing the paper and stating the table is based on their table. Which makes most sense, will depend on circumstances in your paper.


Making a short summary before a set of paragraphs?

Ah, it's just LateX's \paragraph{} command.

It's not the most widespread style, but I think it's clearer, too, and I suggest you to go on using it.

What problems could there be? I can only foresee issues with journal articles, if you encounter overzealous copy-editors. A good card to play is "if your house style contains \paragraph{}, I am using it".


My dissertation is linked to arXiv but its citations are not found in Google Scholar!

Google Scholar, unfortunately, makes no particular guarantees about either timeliness or accuracy. I find that it is best understood as a byproduct of Google's business model, rather than a proper fully-supported tool.

As such, it is not surprising that in my experience sometimes documents will take months, or even more than a year, in order to get properly sorted out by Google Scholar.

In the meantime, I would suggest to not worry about it too much: Google Scholar is not a definitive index, and should be used only to get a relative impression of the significance of a body of work, not to seriously evaluate bibliometrics.


Think of a PhD as a funded research post. Its primary purpose isn't to get you a job but to give you a space to do academic research (with the minor caveat that I am not a computer scientist, and I understand that there are some job listings which ask for PhD graduates). Your research will be on an extremely narrow question, and these are usually not directed at an industry-relevant task. It is highly unlikely that the research output will make you any better at your job.
If you want to do the research, and there is a topic that motivates you so much that you could work on it exclusively, even if nobody else really cared about it, for many years, then a PhD may be right for you. Many PhD students discover that this isn't really the case for them, however, and you could be at a high risk of this if you begin without a reasonably specific topic in mind. Sometimes people phrase this in some sort of macho framing, as though PhDs are there to show you are tough - while toughness matters, intrisic motivation towards a potentially extremely obscure research topic is an absolute prerequisite. There is no point doing it for title, bragging rights etc.
I would suggest that if you aren't highly motivated by research in and of itself, you would do a lot better not to do a PhD. Nobody will think the less of you for not being Dr. Crazy Cucumber.
Edit: typo


Internship university asks to give up all intellectual property

Can I do something about it?

There aren't any magical answers here, but aside from the obvious options of either signing the contract and accepting that this is a price you'll have to pay for a really good professional development opportunity, or refusing to sign the contract under any conditions and seeking an alternative internship at a more accommodating institution, I see a third option: negotiate.

There are many possible ways to go about this, but here's one: I assume you were accepted to the internship by a PI/researcher who thought that you had good qualifications and that his/her lab would benefit from your work and talent. This person could be your ally. What I would do is write them a polite email along the following lines:

  Dear Professor Smith,

  Thank you for offering me the internship at your fusion reactor lab. I am excited about this wonderful opportunity and am looking forward to starting in a couple of months, and have even begun doing some background reading on flux capacitor technology to make sure I can be as productive and helpful as possible from day one. I am writing however to express a concern about an issue that came up and that may prevent me from taking on the internship. I was informed by your Office of Research that your university is refusing to accept the standard internship contract my own university advised me to use (see the email I received from them, appended below) and are asking me to agree to a change in the standard intellectual property clause, which in its present form is designed to protect the interests of myself, yourself and both our respective universities, to an alternative version that transfers all IP rights to your institution. I am afraid I don't see this as an acceptable or balanced arrangement from either a moral or practical point of view. I am happy to assign any rights that would allow your lab to exploit and make use of any work I do while at your lab as in my proposed contract, but since among other activities I will be developing code that I may want to use in the future for my thesis research or other legitimate purposes, I do not think it is reasonable to accept the terms offered by your university.

  For this reason, I am asking for your help in resolving this situation. If we cannot reach an agreement, sadly I may be forced to withdraw my acceptance of your internship.

  Best wishes,

  [your name]

The thing to remember is that while you are negotiating with a counterparty that's massively more powerful than you (which is why they feel they can get away with making such demands), you do have a bit of leverage: they want something from you. Whether you will succeed depends on the personalities of the people involved, how badly the PI wants you, how many other talented students are lining up to take your place, how unique are the skills that you have to offer, how rigid the university's bureaucratic machinery is, etc. If the PI is unwilling or unable to help, you will find yourself back where you started, so you'll still have the option of either accepting the terms you're offered, or giving up the internship.


Should a conference paper in a journal be considered a journal article?

To the best of my understanding, the key reason why some conferences publish their proceedings as journal special issues is precisely to enable the papers to be listed as journal papers rather than conference papers.  This is essentially a kludge to get around bureaucrats and people from fields with an "only journals count" prejudice.

As such, I think that it's entirely reasonable to list such papers in either the conference section or the journal section.  The "technically-a-journal" form, however, typically has different citation information than the conference publication, so if you choose to list them in the journal section, be certain to list them with this alternate citation information, as reported by the journal archive site.