How do I explain my failed career decision to a potential postdoctoral/academic manager/employer, when I'm almost seven years past my PhD?

I think the answer you have now isn't so bad. But you could be painting yourself in better light. Rather than saying jobs in academia in the pay range and stability you aspired to were too competitive, say you preferred the higher pay and stability you could access in industry. It's the same sentiment but doesn't point to you somehow failing. Many good people get bad luck and don't make it to tenure, and we all know industry offers a wider range of people a better material life in many aspects.
So for example I would tweak this to:
"Initially I wanted to move into industry for (better reasons to reference: higher pay and a more stable lifestyle, choosing where you get to live, etc). So I moved to industry. In R&D and I thought I'd be doing almost fundamental research; but I was wrong - the industry mindset and environment I found to be very different than the academic one, and hence I'm realizing my mistake only now, and trace my way back into academia."
And then maybe say that you've realized it's important to you to be doing fundamental research, so important that the pros of getting back on the academic track now outweigh the cons for you.
Caveat: I'm not in mathematics but in my field your publication record doesn't justify looking for a permanent position, and that would be immediately known to people interviewing you for a postdoc. They may instead phrase this question more like "what have you been up to?" Or maybe even directly ask, "why did you leave industry?"


Soft money tenured profs in schools of medicine

For soft money position, especially NIH funded one, there are a number of things working in your favor. You might be PI on 2 or 3 grants and CI on another 1 or 2 which means that no grant has more than 30 percent of your salary. Since NIH grants are generally 5 years long, it means you write a new grant every year.

The amount of time between getting an NIH grant and starting it can be 12 months. This means you have lead time before you run out of money. The NIH also allows you to get a no cost extension, which allows you to stretch what money you have.

Universities also will often allow you to either front pay or back pay your salary while you wait for a grant that has been awarded to start. This again allows you to cover gaps.


Present tense or past tense for presenting someone else's paper?

It depends on your sentence construction. Use the past tense when talking about what Mendel did, since he did it 150 years ago; use the present tense when talking about what the paper says, since the paper still says that now.  For example, "Mendel did experiments on pea plants. His paper describes the results."


I want to be a guest speaker at a university

Find out who organizes the relevant seminar. Often there is a website listing talks and a contact person. If you can't find this information, just pick someone from the faculty who is likely to be interested in your talk.
Either email that person yourself, or get someone (e.g. your advisor) to introduce you. Introduce yourself; say you are interested in visiting the department and/or giving a talk; indicate what you would like to talk about; and specify what dates work for you. The following email is a good start.

  Dear So-and-so,

  I am visiting Madeuptown the week of Sextember 47th and would be interested in visiting the University of Madeuptown underwater basket weaving department.
  I am currently a PhD student in underwater basket weaving at Fictitious University advised by John Namedrop and I have been working on the use of new wicker weaving materials, which may be of interest to the students in your department.
  Please let me know if you would be interested in arranging something.

  Best,

  Das

I have been the organizer of a computer science group seminar (in the US) and I regularly received such emails. Indeed many of them were much more direct than this.

Most likely, you'll be invited to speak. However, it is possible that they are unable to schedule something suitable at the time you specify. (If you don't get a positive response, then leave it at that. I.e., don't pester them.)

It's worth a try if you are interested in giving a talk. The worst thing that could happen is that your email is ignored.

If you are lucky, they may offer to cover some of your expenses. However, don't bet on it if you are "self-inviting."


Passion is good, but passion alone does not make a successful student. You also need to talk about your academic achievements and interests in a realistic manner, and emphasise how your qualifications and aims make you a good fit for the particular MSc you're applying to.

Emotive statements which use time honoured clichés such as "I've been interested in physics ever since I took my first trembling steps into the subject" should definitely be avoided.

Academic writing should be crisp and clear and ultimately there is little room for sentiment. If you can convey your motivations in that style your statement will likely be much better received than an incoherent or overly emotional letter.

Note: the answer to this may be somewhat dependent on the local academic culture (you don't specify where in Europe you're applying) but I think it's broadly true that too much emotional writing will have a negative effect.


How important is the "major" of the PhD?

It depends more on the aspect of your research. If you have a physical chemistry degree but do research more in the realm of physics, it is possible that you could be hired in physics or chemistry, even hold a joint position in both.

The limiting factor that your PhD major will be in that it is the general area where you are more trained in, that is, you can probably teach courses in your major better than those in the other department. Sometimes hiring decisions do take this into account.


Is it possible to also change the title?

Yes, you can change the title when submitting a revision.  You'll be presented with the same web page on which you originally entered the title, and you can edit it (or anything else) there.

  Another solution would be to start a new submission with the new title, but it would probably generate some arXiv overlap warnings, besides not looking too professional.

The arXiv would certainly not allow this if they noticed (when I think they would), and you are right that it would look unprofessional.


What is a good method to assign topics to students?

I have seen instructors/advisors assign the topics by random chance, followed by a brief 'trading session'. Students pick the topic out of a hat, but they then have the option to trade with other students. Of course, some students may be stuck with a topic that they didn't really want, but they should also have the option to work with you to tweak the assignment into something that they can be passionate about. Since you say that you will have more topics than students, you could also have the option to put their draw back into the hat and try again (after everyone else has drawn at least once). This method seems most likely to avoid the problem of a student feeling as though they were forced to take a 'very much not wanted' topic.


Accurately Documenting Dates of Attendance at Previous Institutions for Ph.D. Applications

The format on most applications is: "Date Attended: From-- to--" without the option of listing several date ranges.

Just put your earliest attended date to your latest, unless it specifically asks for dates related to your AA. Don't overthink it!

  Because of this, it is also a bit confusing as to whether I should list my GPA from institution X at the degree confer date, or to list my cumulative GPA

Again, unless it specifically asks for your AA GPA, I would list your cumulative (I assume it's not much different in any case).

Details of your associate's degree are not going to be a deciding factor in your PhD admissions. Plus, it's likely your transcript lists your AA and cumulative GPA separately anyway (mine from my four-year undergraduate university does), if they truly care.


What is an angry email? All caps, curse words, sarcasm? You must have this conversation with him. It sounds like he has been pretty helpful, so it would be very appropriate to ask him what he would like to see. He has been with you for two years, and he must know your current time restraints. His requirements should be workable, if you know them. We can discern from your current position that you are not afraid of work.


What to do when untrusted claims are made in an extended abstract of which the full version hasn't appeared

The obvious place to look for either a substantiation or a retraction of the extended abstract's claim wold be on the arXiv. Also, since the author is still active, you or your adviser could write to him and ask about the algorithm and its running time.  If you still can't get the information you need, then I think you can publish your work and include, in a "Related Work" section of your paper, a citation of the extended abstract and a statement to the effect that you have been unable to find the details in the literature or to reproduce them yourself.  Of course, if you manage to contradict the claim in the extended abstract (or to show that it would imply implausible things like P=NP), then you should say that.


Sign research contracts in a private university or create a "ghost" company

The situation you describe is fairly typical of research contracts—if you are employed at a university, then normally the university is the one that negotiates contracts on your behalf. This is usually for legal reasons, although it does, as you indicate, usually come at the cost of having to give the university some of the money in the contract as "overhead."

As you also indicated, however, it is possible to form a start-up company; there's nothing wrong with doing so in most countries, and such companies can engage in contract work with private firms. However, there are often restrictions on receiving government research awards unless they're partnered with universities or other approved non-profit organizations.

Some points to consider:

How much of your business leads are the result of the identification of your group with your host university?
Will you have enough outside business to support your staff through this outside research income?
It is quite likely that much of what you save in overhead payments to your university may go out to your government in the form of taxes as well as to pay for other business expenses you have.

You cannot expect to run a company while on-campus, using university resources. If this is discovered, you can almost certainly expect to be terminated for misuse of university resources (and worse, possibly public resources as well, depending on what country you're in). At a minimum, you would expect to have to have off-campus resources, and employ your contract employees separately, if you want to maintain this arrangement.


Should I put my supervisor as coauthor of a paper?

This entire situation is an ethical quagmire that both you and your advisor are responsible for.

The reason why I say that you share in the creation of this situation is the following. Let's replace your advisor with an external collaborator. The sequence of events, as you have outlined here, runs as follows:

The two of you collaborated on an initial version of the paper.
You had a conflict on some issue (seemingly related to this paper)
You then proceeded to go behind the collaborator's back, redo the analysis, rewrite the paper, and submit it without informing her.

Under such circumstances, it is clear that you would bear a large percentage of the blame for the situation. The fact that it's your advisor instead of an external collaborator doesn't change the ethical considerations here.

Your advisor probably feels that because you were previously working on the problem together, you have cut him out of the loop without his consent. You should have showed him the preliminary results of your new analysis and let him decide if he wanted to collaborate further. If he was to be an author on the original paper, he was entitled to at least that much.

Of course, at this stage, it's hard to say what to do—your advisor has also complicated the situation by asserting his author rights on a paper he allegedly has never seen, which is also wrong. I would follow JeffE's advice here and take the path of least resistance. Getting out of this mess of a relationship is the critical step right now.


Etiquette when continuing work on a research direction without involving former collaborators

If you have a feeling that you will disappoint them then, by all means, let them know! And indeed, you should let them know that you've continued this line of research independently.

You can phrase your invitation in a way that it hints that you would like to go on alone. Something like

  Lately, I was working independently on extensions regarding our previous work and I went pretty far and I have such-and-such results. I believe that these results are interesting enough to make a publication. I would like your opinion about this and about potential venues that would accept this paper.

By this, you make clear that this is your work, you acknowledge their expertise and definitely you give them a heads up. This is actually quite common and I expect them to either ignore it (if they are busy) or be happy that you were able to generalize it and give you valuable hints/advice.


The name of the document which prove my studies at the university

I once had to acquire a "Certificate of Matriculation" or "Confirmation of Matriculation," similar to what is described here: http://www.ed.ac.uk/student-administration/order-documents/matric-certificate.


Is there any difference between these two kind of researchers?

Some physicists teach more mathematics.  Some physicists teach more applications.  It's just a matter of university, teacher, and student preference.  Yes, the way you are taught will influence your career.
I do not think these preferences have anything to do with the country.  A large portion of physicists have experience with multiple countries.  And within a country, you will find quite a range of opinions about how to do things.


Is there a tool to visualize the academic citation network around a researcher?

You might want to have a look at the Web of Science (formerly known as ISI Web of Knowledge). When I started my PhD back in 2008, I used it particularly for visualizing citation networks relevant to my research. I think some time later it became a subscription based service, so the access is not as easy anymore, but a lot of scientific institutions or libraries may provide you the access. I haven't used the Web of Science any more in recent time, so I am not really aware of their capabilities today -- but the description still reads similar to what I remember.


How to immediately show group answers onscreen?

We have the Moodle online teaching tool, another is Blackboard.

On moodle one of the possible activities is "feedback" where you set the questions and make it anonymous as you wish... This may meet what you are looking for.

This does mean that all the students must get a moodle account etc.

I have seen other sites that do this interactive survey type activity but can't think of their names off-hand, but they still need the students to log-in...

A quick google search gave this article : https://www.educatorstechnology.com/2018/09/some-of-best-tools-for-creating-surveys.html

The first 4 of their list (as links can fail) Google-forms, Plickers, Kahoot and Socrative...

I use the quiz activity on moodle a lot!


How to reconcile with an old mentor after (unintentional) plagiarism accusations

Nobody is going to mention that the OP's old mentor put undergraduate work directly into a publication (i) without checking that it met professional-level standards of academic honesty and (ii) without informing the undergraduate that this was being done or that he was being added as a coauthor?  In my view, these transgressions are equally bad or a bit worse than including a few sentences without quotation marks from sources that have been cited in a survey paper.

In my opinion there is a good chance that the mentor is embarrassed that these lapses of his own have been exposed, which complicates the OP's situation.  I am surprised that other answers seem determined to pin this all on the OP.  @Scott Seidman suggests that the OP contact the editor:

  I think an email to the editor involved, cc'ed to your mentor, taking responsibility (without qualifiers) and stating that none of the other authors were in a position to recognize or correct this prior submission,

In my view the mentor was in the position to recognize and correct academic cultural errors made by his undergraduate mentee, and since the OP was not involved in the preparation or submission of the manuscript in any way, the responsibility for this clearly lies at least partially (and I would argue, primarily) with the mentor.  Sending such an email to the editor could just call attention to his poor mentorship and supervision: i.e., it could actually make it worse.  (Pro tip: don't contact an editor about something unless you're sure all your coauthors are on board.  If there is any real doubt, clear it with them explicitly.  If someone is not returning your emails, you can't do this.)

The OP is not blameless in the situation: he made a mistake, and a mistake involving what sounds like a borderline instance of academic dishonesty.  He should apologize to his old mentor -- which he has done -- and move on.  I would recommend that the OP continue to treat his mentor like an old mentor: i.e., send him occasional emails keeping him up to date on his current academic life.  I would certainly not assume that someone never wants to hear from me again based on a single unanswered email.  But ultimately the mentor should know that he made mistakes as well, from a position of far more experience and responsibility.  It does not fall on the OP to take any kind of heroic or (especially) self-abnegating measures to remedy the situation.  One hopes that eventually these two people can move past one negative interaction amid many other good ones.


Is it good practice to share pre-print of PhD thesis?

I think that question can only be answered by your University and your advisor. It is conceivable that they have some rule prohibiting it. I think that is unlikely, but you should learn first. Even if it is not forbidden, your advisor can give you feedback on whether it is advisable in your case.

If you were submitting to a formal publication, on the other hand, their rules might also be important to consider.


Is it a good idea to contact professors before applying to grad schools?

This really only works as a strategy if you have something truly meaningful to say. If you have to force yourself to do it and struggle to come up with something to say in your email, you're not helping yourself. Faculty get tons of email all the time and every year - as you say - get emails from prospective students, many of whom will not be admitted and in whom they invest no effort. So, if you genuinely think you're a good fit for a program/lab and have solid questions in mind to ask the faculty/PI of that lab that will communicate your quality and fit, this may be viable. But, I would definitely not recommend it as a general strategy.


Grad school hasn't responded to me two months after the results are supposed to be out

It seems like a long time beyond their own deadline, but things driven by committee in universities get delayed. It is possible, though unlikely, that your application has been lost. And, it is usually the case that you hear earlier about a rejection than you will about acceptance.

It is also possible that some communication has gone astray somehow.

Don't despair yet about acceptance, but you are due some sort of explanation. If you are close enough to visit you can do that and talk to the head of the department or an admissions officer. If you can't visit, but can make a phone call, do that. You will be hard to ignore. Call any of the people with whom you communicated, but the professor would probably be a good choice.

If you have to resort to email, let them know that you have other decisions pending and need feedback.

But if they truly have lost your application, you should be able to request your application fees. But that seems the least likely scenario to me. The most likely is just the slow turning of the academic wheels.


Bad experiences with the production of an accepted manuscript

It doesn't matter whether you paid an APC or whether the publisher is getting money from subscribers for seeing your article.
There are journals that have very significant production backlogs, so that accepted papers are not produced for months or even years.  A long production backlog is not really cause for serious complaint, though undoubtedly both you and the editors of the journal are not happy about it.  Note that frequently the only way to fix a production backlog is to stop accepting papers (or accept very few papers) for some period of time.  (In particular, back when people mostly read papers by going to their physical library, there was no reason for the production backlog to be any better than the publication backlog, and some publishers still think this way.)
However, the number of errors in the production process and the amount of time and number of iterations it has so far required to fix them is completely unheard of in my experience.  I have had some production issues twice in 20+ papers (both times with the same publisher but different journals), but they were nowhere near what you are describing.
At this point, you should let the editors know what has happened and ask them to complain strongly on your behalf.  (Of course, you should be nice and understanding about it, since it's not their fault in any way.  But they have leverage that you don't.)  They are on your side.  They can see you have been treated badly, and they know that incidents like this are very bad for their journal.  This should be a serious issue, to the extent that, if these kinds of production issues are a common occurrence, the editorial board might try to switch publishers (if they own the name of the journal) or resign.  (You don't know if your case is a one-off or common, so you can't very well ask them to do this, but they should want to know and should take this seriously.)
Finally, I think you are well within your rights to not submit to a journal run by this publisher until you have some indication they have improved their processes, and you should quietly let anyone who asks you for journal advice know about what you have gone through.  (If someone reads this question, figures out who you are, and e-mails you, you should let them know who this publisher is.)


Most German students coming out of an BSc program will not have any publications at all. Most of our BSc programs are 3 year programs with a 3 to 6 months thesis at the end, which is not enough to get publishable research. And it's just plain not enough time to get something published if you are directly applying for a MSc. Getting a paper written and accepted on top of writing a thesis takes months. This is of course a generalization - but from the about 70 students that graduated with me (Biology), none had a publication at the end.

Teaching experience is also usually not necessary. MSc students only rarely have to teach anything, that's for PhD students/postdocs /professors.

MSc programs are also usually more general than you seem used to. The first year is taking courses, the second year is doing research and writing a thesis with a group you got to know in that first year. There is no need to get in contact with a specific professor before applying and they might not be able to help you have a successful application anyway. You might of course want to look around already so that you know there's a few groups you'd be interested in working with at the university you choose.

Publications and research and teaching experience are of course not a bad thing, on the contrary, they give you an advantage when applying and you emphasize them in your application . They are just not required because German students often don't have publications when graduating from their BSc programs. Grades are very important for universities here, in fact, when I applied for my MSc (which was 9 years ago, though, when Germany was just starting to switch to the Bachelor/Master model), they were really the only thing the admissions comitee looked at. The university website should tell you a bit more about what they expect, though.


Pursuing research before applying to grad schools

EXACTLY   HOW do to define " research  experience"?
 You may have  more  research  experience  than  you  thin,k. Bow many  term papers Din;t  you do ANY LIBRARY RESEARCH  for term  papers  during  middle  school,  high school  or  college,  no matter   what  your  major  was  in  college?  Library  research IS RESEARCH. I learned  how  to  write   term papers  with  footnotes   and  reference  lists  in  7th  and  8th  grade  more  than  50  years ago.   There  was  section  of  "how  to  use  the  library  in  English class in  both  grade  school   and  the  (th  grade.  That  i went  to private  college  prepatory  schools  in  the  United  states  is  NOT  that  unique,  "how  to use'  the  library  was  also   taught  in public  schools.  in  the  USA.
Apparently  how  to use   a  search  engine  is  not  being  taught  at  all.  I've  been using  Google  since  1993  or  1994,  but  i went  to  back  to  college  in 1992  just  as  the  internet  was  taking  off    in higher  education.

"...Undergraduate research experiences help students understand a particular topic or phenomenon in a field while simultaneously strengthening their comprehension of research and research methods. Undergraduate research is inquiry-based learning that involves practicing a discipline, not just being told about it...."
https://serc.carleton.edu/introgeo/studentresearch/What.html

You probably DO  have  research  experience  and  do not  realize  because  your  haven't  bothered   to look up   the  definition   of  "research  experience."  I LOVE  doing  library  research,   but  i know  most  people   think  library  research  is  waste  of  time    and  is  boring  and  tedious  until  they  get  stuck   and HAVE  to  review  the professional  literature   and KEEP UP   with  it    g  for the  REQUIREMENTS  for  specific  college  degree   and  have  to  either  numerous  term papers  or  senior  thesis  which  requires   library  research,  possible  lab   research  compiling  data.   and  even  Field  work   to  father  more  data  or  field  truthingt  and  verification like  i   did  for  my  master's  thsis,  that  what  is  in  ssatellite  image  and  geological  maps  really IS  there  on  the  ground   and  is  real  and  is  accurate..

Part of  the point  of    going  to  college  these  days  is  to    teach you HOW TO THINK  critically , logically,  analytically  and  objectively  AND     so you   acquire  the  research  skills  to KEEP  doing your  own  research  AND   contribute  original knowledge  to  society.

You probably DO have   research   experience.

I  am  still  getting  used  to how  stack  exchanges  work  too. I  am  AMAZED  at  how much research i  can  do  online    these   without  having  to  get  anywhere  near  a  brick  and  mortar  library.


How should I handle students who ask questions that are "beyond the scope of the course" as a TA

"This is beyond the scope of the course" is not a great answer without further clarification or commentary.  As you say, the ethos of the university is that your instructor is someone whose qualifications and expertise lie far beyond the scope of any undergraduate course.  The answer is justified for a student who asks a certain kind of question in class, because class time is limited and one must exercise judgment about what to say and cover in that limited time.  Going off on a lengthy digression that is likely to be of interest to only one student and perhaps not even well understood by her is not a good use of class time.  So I would expect an instructor to say "Come talk to me after class if you are interested in that."

If a student comes to talk to you in your office hours or your spare time, I think that she deserves some kind of answer.  The answer may in fact be that the question lies beyond your expertise (and there is nothing inherently wrong with that; there is a lot of stuff out there...), but in that case you should still spend at least a little while trying to direct the student elsewhere, either to the appropriate reading materials or to some other faculty member who can better help them out.

If you do feel that you know the answer to the question -- or at least, enough of the answer to the question -- then, sure, take a crack at answering it.  It takes a lot of expertise -- subject expertise, pedagogical expertise, and practice -- to be able to give answers to such questions which occupy a reasonable amount of time and are at least somewhat meaningful to the student.  This may involve for instance asking some quick questions of your own, trying to understand the student's background and the true direction and depth of their interest.  One mistake that even seasoned pros make is to open up the gates and flood the student with information of a quantity, density and sophistication that is beyond what they can be expected to process in the moment.  If someone asks you about the example of a conservative vector field on the punctured plane which is not a gradient field that you discussed in class, you should probably not respond by giving them a half hour lecture on DeRham cohomology.  (At least not at first.  One of the amazing things about teaching is that the chance that a multivariable calculus student really is looking for a lecture on DeRham cohomology in answer to their question is very, very small...but it is positive!)

  How should I handle students who are interested but asks question beyond the course in the sense it requires an additional course or two to truly appreciate its importance or at least to see how the actual calculations are performed.

You take a shot at it.  Make your first shot very brief: just drop some terminology and try to give a sentence or two expressing one of the main ideas in broadest terms.  In the above case, you might say "Whether every conservative field is a gradient field depends on the domain.  We saw that this is the case when the vector field is defined on the entire plane [or all of three-dimensional space...].  It is also true if the domain is something like an open disk or ball.  It turns out though that 'holes in the domain' lead to conservative vector fields which are not gradient fields."  (By the way, I first wrote more and then deleted some of it!  Restraint is truly hard.)

  I could tell them the answer but sometimes it can lead a student down a rabbit hole which can be devastating given how busy first year students are.

I'm not really sure what you mean by this.  The type of personality that is going to be "devastated" by learning that things go deeper than they currently know does not seem well suited to higher education.  If anything I feel exactly the opposite way: as an educator at any level, showing students the rabbit hole is one of the most important things that you can do.  Especially, getting an undergraduate degree is all about learning just enough to get an awareness of the true depth of knowledge and acquiring a sound foundation upon which more knowledge can be built.

  Further, I don't want to disrupt their "natural course" by saying something that may prevent independent self discovery.

Again, I don't really buy into this.  Students who want to be sufficiently well insulated from being taught things by other people do not belong in a university.  Self discovery is a wonderful and important thing, but it is enriched and reinforced by prior knowledge and coursework, not ruined by it.  There are plenty of things to discover for oneself, and anyway you are only telling them a little.  It seems very likely that such a conversation would if anything trigger the student's independent learning and self discovery, not inhibit it.

  Lastly, I don't want to say something which could be misconstrued as a test topic.

This is why it's best to address such questions outside of the classroom, or at least outside of the class session, and ideally with only the students who are explicitly interested.  It should then be much clearer that what you are telling them is not a test topic.  If there is any ambiguity about that then you should resolve it.  For instance, maybe the question actually is closely related to a test topic but comes from a direction in which the student does not see that.  In that case you should point out the connection to them.


What are some good writing tablets for taking notes that are heavy on math/physics?

I believe the limitation is more on the software that you are using, rather than the tablet itself. So, if you are using an iPad, you can use UPad, whereas android tablets users should be looking at something like Repligo or ezPdf Reader.


I need some code that was made available by a student 15 years ago, but is no longer online. How can I contact someone in the group to get the code?

PhD students come and move on, so if you are looking for code that isn't exactly brand new then contacting the responsible professor is usually your best bet. That being said, I would not get my hopes up too much that you get your code "urgently". There is a good chance that even the responsible professor will need to do some good ol' digging before (s)he unearths this material, if at all (and then there is still a good chance that nobody knows anymore how to make it work, or that it does not run anymore on today's platforms). Assume that this is going to be a bit of a project on its own.


There are no absolute rules, but I think the most natural policy is to use title capitalization for major labels (plot title, axis identification, elements in the legend).  You may then reserve lower case names for additional minor labeling (like specific, localized features in a figure), although it would not hurt to use title capitalization for everything.  Don't use all caps; it looks like you are shouting.


Opening of applications for PhD in computer science at UCL,King's College London

Generally speaking you should see applications for the upcoming year open in mid to late October in the UK. This allows the admissions offices and administration offices to deal with the students who have made a September or October start before the floodgates open again.

Regarding University-specific scholarships, you will gave to talk directly to the universities in question.


Is it bad practice to study or reference the work of an academic who has fallen from grace?

No, it's generally not a bad practice.  For a closely related question, see How does it affect the treatment of a mathematician's results, if that mathematician was a Nazi?.

  Should individuals publishing work in his field avoid referencing his texts or published research?

His published research: for sure no, not avoid references to his research; the linked question covers this well.

As for his textbooks: Most often one is not forced to reference any particular text, as there are other texts that do the same.  (Perhaps "there are other texts that do the same" ought to be the definition of a text rather than a research article or monograph, but there are exceptions to this definition.)  I think personal preferences can and do come in when choosing which text to reference: for instance, I would be happier to reference a text that is freely available online, or if I don't like (academically speaking) a text generally then I might try to replace a citation to it by a citation somewhere else, even if that's a little trouble.  (I remember doing that recently in a joint paper: a coauthor cited a text I didn't like.  I got him to (find and) cite another one instead!) But if Dr. Fallen's text is the unique source for something, you must cite it, and if you unambiguously feel that it's the best source, you probably should cite it.

As for your studying: I see no argument whatsoever against studying the good text of a bad person.  In fact, "bad person" is a kind of reification.  Everyone does good things and bad things; when we say someone is a "bad person," we mean that our evaluation of their actions (that we know of) is weighted towards the bad.  But avoiding or trying to nullify the good actions of a bad person is...bad.  We should encourage, reward and make use of the good behavior in everyone, right?

I do have one proviso: you may not want to financially support Dr. Fallen, for instance if you suspect that financial support would somehow abet his reprehensible activities.  So you may well not want to buy his book if you haven't already.  If you feel that citing Dr. Fallen's text in a situation where you could also cite another (both are secondary sources) could induce others to financially support him, then maybe that's an ethical reason for choosing a different citation even if you personally think Dr. Fallen's text explains it better: this is a bit of an unlikely edge case, I think.


Making conferences accessible for people with anxiety

Since the interpretation of the question changed I'll add an answer for the new one, leaving the old one in place in case it helps an individual.

Some conferences have two simple features that might be adapted to your needs. The first is a "newcomers/first-timers session" early on the first day of the conference in which people will learn about what to expect in various kinds of sessions. This can, perhaps, be used to put people at ease with only minor changes.

The second thing is that many conferences also have student volunteers who help out with various things but are also allowed to attend any sessions without fee. Some student presenters are also volunteers, lowering the cost of attendance. But one of the uses of the volunteers is to be an assistant to any presenter who requests it, handling unforeseen issues so that the presenter can concentrate on what they want to say. This might be reassuring to some people that "bad things" are less likely to happen.

An additional advantage for the volunteer is that they, themselves, become more familiar and hopefully comfortable with what to expect at a professional conference  so that later they don't have first-timer anxiety themselves.


What exactly should I add in an extended and revised version of my research paper?

In my experience, extended versions most typically contain three classes of new information:

More extensive prose and examples to explain, discuss, and otherwise clarify the material presented in the original paper.  Conference papers are sometimes rather haiku'ed due to page limits.
Important details omitted from the original paper due to length.  For example, a discussion of the key points of an algorithm may become a full presentation of its details, and a proof sketch may become a proof.
Extension work, either enhancing evaluation or extending the set of material studied, as suggested by the original paper's future work, feedback from the reviewers, questions raised in the conference talk, etc.

Some combination of these is almost certainly the right sort of material for your extended paper, but which combination exactly is something that only you, your collaborators, and your advisors are in a good position to determine.


How to cite a newspaper article with no author in APA style using MS Word?

First, I must always advise that you speak to your professor and/or your university librarian as to what the accepted form would be at your University. Both as professors and Universities can vary slightly on the specifics of APA rules and due to the fact that what they say will be accepted. As far as APA 6th is concerned

  Title of article. (Year, month day). Title of publication, p. [or pp.]

So:

  Zarif: We’ve never claimed nuclear deal only favors Iran. (2015, July 22). Tehran Times, p. 1.

would be the correct Biblio (provided one correctly indents it).

While In-text

  "First few words of the title", year, p. [or pp.]

So: ("Zarif: We've never claimed", 2015, p.1)

As confirmed at the University of Melborune, EasyBib, and APAstyle.org

One of those variance, by college and professor, is in-text citations and the use of page numbers. As some schools only require one to cite page numbers on direct quotes while others requires one to add page numbers in all instances

Another variance is with online articles, as online articles may not reference a page number (depends on format) but use the paragraph number or section title in the citation. Further, you would include a "Retrieved from full url here" at the end. (pp.171-172, APA Manual, 6th ed.)


When bidding for papers on softconf.com as a reviewer, does it make any difference between answering no or not bidding for a paper?

I can't answer specifically for this service, but in general it can make a small difference if some papers fail to get bids. For some CS conferences, if you answer no for a paper you are unlikely to be asked again if a second round of bids is needed. If you don't answer at all, then not answering will be likely treated as more like "maybe" than "no".
But, while not especially rare, it only happens at the margins.
But it is even possible that a desperate program chair will come back and beg even "no" voters for reviews in a future "ask". Even less likely though.


I'm also on a saga to look for this tool, hopefully the answers in this thread can end all the search. Here is what I know.
There used to be a software called RefViz that does what you exactly want. It was released by Thomson at a price of about US$295. Unfortunately, the response wasn't too good and it seems the product has been discontinued for more than five years. I used to use this software quite often to generate some themes from the literature pool. Since it was discontinued I have moved away from this type of relational analysis.
Instem has another product OmniViz, which remains in the market. OmniViz is like RefViz on steroids, and is much more capable. The price is also higher, reaching about US$1000 for an educational copy. Apart from literature relation, it can also be applied to genomics and that perhaps explains the high price. Instem has also produced a text-specific version of Omniviz, Txtviz that is designed specifically to support people wading through large volumes of textual documents to find specific themes and areas of interest.
If you're tight on budget, try Google "citation map software" and you should be able to find other cheaper alternatives, like SciMAT, which is free.
Thomson has also hosted an online citation map, which does not hook up to your literature library, but if you click on any indexed article on Web of Science, you can get a network consisted of the cited and citing articles. If you'd like to see how much impact a certain article has, it's a good tool as well.
A more rudimentary way is to make the network yourself using mind mapping software. I have been using the brainstorming function in Qiqqa and it's not too shabby as a thought generator.
Last but not least, I'd also like to advocate for a large piece of A3 size paper, a good black or sepia felt tip pen, a box of color pencil, and some fun attitude to draw your own. I got the most out of this method, to be honest. When using the online tool or software I feel I am just producing a thing, but when I use my hands to make a network of articles that I feel important, I am also thinking. I guess person-to-person it's different.
Just remember whatever software we use, the relevance is based on algorithm. It's just like data mining, there will be false positives and negatives. Be mindful when analyzing the so-called literature gaps that the software found, sometimes it could be a gap, sometimes it could just be a void and does not deserve attention. Strong discretion along the process is necessary.


How do I approach a supervisor who seems to be unconcerned with my projected end date?

It sounds like it may be time for you to lay all this out to the director of graduate studies in your department.  Here are some suggestions in case you decide to do so:

You can take a friend with you for moral support if you wish.
Make an appointment. If someone asks you for a reason, you can say something brief, such as "ask advice about my graduation timeline."  (That's to get you a foot in the door.)
Speak calmly.  Just explain your experience so far, and leave out the part about your fears and how long you've been working on it.  Leave out your conjectures about your advisor's possible motivations.
The administrator may ask you some questions about your timeline and you may, of course, answer them.
If the administrator makes a suggestion or advises you to do something you've already tried, don't nod and say you'll try that.  Tell him or her calmly what has occurred when you have tried that.
Ask him or her if s/he can get back to you by (name the date that comes up in 6 days).  That way, if you have to go up the chain of command, you'll be able to say, "I met with Prof. YY a week ago."
Document the conversation by sending a thank-you email that same day.  E.g. "Thank you for meeting with me today to discuss etc." and include a bulleted list of the points covered in the meeting.
If the administrator does not commit to getting back to you, you may jump to the next level without waiting.

I think that in most departments a five or ten-minute conversation with the director of grad studies will do the trick and either your advisor will start moving, or the department will find some other way of getting you out the door.


What valid reason can I give for my low CGPA to a prospective PhD advisor?

Honestly I don't have any valid reason, I did not pay attention earlier to my academic studies.  But I think I can't mention that.  What can be some possible reasons that I can tell him?

On the contrary, if you think that was the cause, then that's exactly what you should say.  Prospective supervisors are interested in a lot of aspects of candidates, and one of the important aspects we are interested in is the capacity for students to objectively review their present deficiencies, or deficiencies in their past work.  It is possible to assist a candidate with lower level grades to improve their work, but it is much harder to deal with a student who is not honest about their own work, or unwilling to be honest with their supervisor.  Thus, demonstrating the capacity for self-reflection and self-criticism may be viewed positively, even if it involves admitting you slacked off.  (Academics are humans too --- we know that there are other fun things in life for young people to do besides studying hard.)
Setting aside whether that will assist your application or not, you need to grow some character --- start to make a habit of being candid with people about your actions regardless of whether this will advantage you personally.  Deficiencies in your work can be fixed over time, but getting into the habit of searching for false excuses is a deficiency that will damage a lot more than a PhD application.
Reframing your question, there is no "valid" reason or "invalid" reason for your lower grades --- there is just the truth, and not the truth.


Mistake in uploaded file type after revision

Mistakes can happen.
You should email the editor or they might notice it and ask you to upload the correct one.

"One more question: how long should we wait for the status change from "with journal" to "with editor" or "under review" for the revised manuscript? "
It depends on the journal, you should check the journal website for more information or ask directly the editor.


Is it easy to find a job in industry in a different area?

Yes it is possible to find a job in a different area than your field. But you need to gain experience. In my point of view.. follow these steps..
1. Take courses of your interest. (Online or from institute)
2.Gain experience (Paid or unpaid internship)
3. Find a real job based on your experience.

I am electrical engineer and working as software engineer.


I quit a master’s program for a PhD program. How do I list this on my CV?

I would suggest something like "left to pursue PhD" rather than "quit" or "abandoned". The explicit meaning is the same, but there is an implicit negativity in quitting or abandoning something.

PhD student, Dept of Rocket Science, University A, 2016 to present (expected Spring 2032)
MA student, University B, 2015-2016 (left to pursue PhD)
B.Sc. Physics, University B, 2015

(I'd also probably add the program name/degree titles and anticipated graduation date)
In your case, it's a short enough window that you could also probably leave it off without any notice, especially if you are applying to industry positions.
One time to definitely not leave it off is anything asking for your full academic record - the cases where this typically applies are in graduate admissions (which likely longer apply to you) and some grant applications (which still could).


Can a professor accuse a student of cheating on an exam without witnessing it firsthand?

Generally speaking, the answer to your question is "Yes."

If there is a strong similarity in answers that is highly unlikely if the students worked independently, it can raise suspicions of cheating.

For example, in Reilly v. Daly,

  At the conclusion of the exam period, the professors held the exam papers of Reilly and the neighboring student in order to determine whether their answers matched. A comparison of the exams revealed that the first seven pages, which included twenty-seven multiple choice and matching questions, were identical.

  ...

  Taking the conservative approach of comparing only wrong answers on only the multiple choice questions, the professors were advised by a statistician that there was a one in 200,000 probability that such a match of wrong answers on the multiple choice questions would occur by chance.

  ...

  Reilly also presented her own statistical analysis of the exam and brought to the professors' attention the possibility of "lure" questions on the exam which would heighten the probability of the match occurring by chance. The professors thereafter obtained a new statistical analysis taking into account "lure" questions on the exam. This analysis demonstrated a one in 500 to one in 5000 probability of the match occurring by chance.

Whether this kind of evidence is enough to initiate disciplinary proceedings, and what the consequences could be, depends entirely on the detailed specifics of the scenario and the university policy.

For example, in Papelino v. Albany College of Pharmacy vs Union University, while similar statistical evidence raised suspicions, it was not considered sufficient to conclude that the students had cheated.


Authorship dispute on a paper that came out of a final report of a course?

While it's impossible to judge contribution from outside, I generally recommend erring on the side of inclusion when it comes to authorship.  If there's a reasonable argument that somebody contributed, it doesn't really cost you anything to have them on the paper.

Furthermore, there are many ways to contribute to a paper (see, for example, the CRediT taxonomy), and many journals even require a contributions section in which you can explain who exactly did what. In this case, it sounds like you wrote the paper, designed the system, built the system, and both of you ran experiments. You can't ethically "undo" somebody's experimental work by redoing it yourself.

What you should never do is to drop somebody from authorship without consulting them. You had a draft with this person on it as an author, and even if they never got back to you, for all they know they're still a co-author. Probably it doesn't matter to them very much (or else they'd likely have gotten back to you), but it's still unethical to remove somebody from authorship without their consent. It is also unethical to submit a paper without the consent of all of the authors, so that's also a potential problem in this situation, where you're just kinda doing what you feel like without consulting with anybody else.

In fact, the basic problem I see here is that you seem to be operating without any advice from somebody who can help you navigate these questions (as well as the issue of quality, which I won't touch otherwise). Your advisor is likely a good source of such advice, and even if you don't like/trust your advisor, you should be able to find somebody who knows the scientific world well who can be a mentor for you.


Where can I find a collection of past exams w/ answers on various subjects?

MIT's Open Courseware project has a lot of material of this sort.  Here is a link to the Course Finder, with courses organized by topic.  The depth of the offering will vary from course to course. Some have only syllabi, others have complete video lectures, homework assignments, exams, solutions, etc.  The coverage is quite broad and includes courses in all of the specific classes you have listed.


When is Research Assistant/Associate/Fellow a correct title for a PhD student?

How about "PhD student"?

Since you also asked about Germany: in German you can call yourself "Doktorand" or "Promovend". But also in Germany, "PhD student" would be perfectly fine.

If you want to leave out the "student" part, you might call yourself "PhD candidate".

Be careful to avoid calling yourself something you are not (e.g. "Dr."), since particularly in Germany that might be illegal.


What does “temporary faculty pool” mean?

Looking up a few such postings, it appears to be another name for "adjunct faculty".  In other words, temp work for academia.


Editor wants to change Full Article to Short Communication

Handle this the same way you handle any other dispute: you tell the editor you think the article should be a "Full Article" instead of "Short Communication", giving your reasons. If the editor agrees, problem solved. If editor doesn't agree, it's up to you how much you care how your paper is classified. If you really, really want it to be a full article, you can dig in your heels and withdraw the manuscript if the editor still doesn't agree.

I wouldn't worry about exceeding the word limit for short communications. After all, if the editor didn't ask you to shorten the manuscript, presumably he's going to break the rules in this instance.


Etiquette Question - Professor asked if I could meet after X time on Y day. I emailed to confirm a specific time but he has not responded

No, it would not be rude to knock on his door. He's already said the time is OK! However, I would not have worded the email asking him if [time] is OK - I'd simply say something like "alright, I'll be there at [time]", which saves him from having to respond.

If he indeed rethought the offer, it'd be quite unethical of him not to tell you before you visit him. But you knocking on his door won't hurt anyway: the worst that can happen is that he tells you then that he's rethought the offer.


What should I do if I discover a paper I rejected because of methodological flaws has been published in another journal?

Two things are unclear about your question Is there anything I can do that doesn't violate the confidentiality of the peer review process to address the problem?:

What is the goal of any intervention?
Why do you think that anything should be done?

If, for example, you aim for retraction, I guess this could be difficult. You may go for this on the ground that you can prove that the authors were aware of the flaws you pointed out and submitted the paper knowing that there was something wrong. The journal may have some rule that the authors have to certify that the results are true to the best of their knowledge. If this really is so, you may have some angle of attack. If you aim for correction by the authors, it could also be difficult. However, you could consider writing a letter to the editor, pointing out what is wrong and then ask if the journal would publish such a letter. Some journals I know have such formats. You could also do follow-up research on the same topic and write a paper yourself where you refer to the paper with flaws and describe what wrong there.

For the second question, it sounds like you feel that "What's published and peer-reviewed should be true." While this resonates with me, it's not something that is close to true now and probably never will be. Mistakes happen. You may then trust in the scientific community that the flawed paper will be perceived as such in the long run and find peace with this particular paper.

Finally, the premise that confidentiality of the peer review process may permit some actions is not totally clear. As I wrote in a comment, I asked a question about this on MO and got very different responses.


What is the cost of an endowed chair in a medical school?

For a fully endowed position, multiply the expected salary, benefits, and research funds by 20x to get an approximation.

If the researcher is making $250,000 in salary and benefits and $250,000 in funding for their lab, then you would want around $10,000,000 endowment minimum (salary and lab numbers chosen for ease of calculation rather than proximity to reality).

This assumes a 5% per annum draw on the endowment, which is both conservative and average. A university with better fund managers could draw 8-10%; a very conservative institution or a place that wants to grow the endowment endogenously might only draw 3-5%.

And as @Dawn notes, for some positions not all position costs are paid entirely out of the endowment, and thus may require a smaller investment. For example, some endowed chairs might only receive 30% of their salary from the named endowment and the rest from general funds. If that were the case in the above example, the endowment would only have to be at the $3 million level.


How to include industrial research experience legally?

So, is there any way (or is it legal) I can include the project, in my CV without giving many details?

If supplying this information is prohibited by a nondisclosure agreement you signed with your employer, then there's nothing you can do.  It won't help your case at all to say "I did something really interesting, but I can't tell you anything about it, so you'll just have to believe me."

Assuming your employer doesn't object to providing this information, you can say anything you like in your CV, as long as it's true.

  Problem is, the project I was working on (in this company) though completed, may not have my name as author. As per company policy, as I am leaving before it is getting published.

This is indeed the problem.  By academic standards, leaving the company before a completed project is published should have no impact whatsoever on authorship.  If you won't be an author, then either you are being treated unfairly/unethically, or you never deserved to be an author in the first place.  That's a tricky situation that readers won't be able to sort out without more information.

So although you can include such a project on your CV, just listing it there probably won't help you much because nobody will know what to make of it.  If the project really matters for your application, then you'll need to explain in much more detail in your statement of purpose.


What does "contributed paper session" mean?

A contributed paper session is a session where anyone can submit a talk (rather than having to be specially invited).  The criteria for approval are usually not selective and mostly just involve a check that your topic is appropriate for the session / conference.

  If I register for a contributed paper session, can I register with the paper that has already been published before in a journal (I am the author of the paper)?

Yes, it is fine to give a talk on work that is already published.  You should include a citation of your paper in your presentation.

  Can I use my paper that has not been published yet?

Yes, this is also fine.  If you have a preprint that is publicly available (e.g. on arXiv), it would be good to give a link in your presentation.  You can even give a talk on work for which the paper is not yet finished, but this  is a bit risky, as someone in the audience may decide to work on it, and get their paper submitted before yours.

  Does the title/abstract of such a talk need to be the same as the title/abstract of the paper the talk is based on?

Not necessarily, but it's a good idea if the titles are similar.  That way, someone who attends the talk or sees the abstract will have an easier time finding the corresponding paper.  For the abstract, your abstract should describe what you will actually speak about, and so the abstract from your paper may not be directly suitable.  For instance, your paper probably contains lots of details that you won't have time to address in your talk.

  If I am not the only author of the paper, but I am the only speaker at the conference, should I list only myself as the author of the abstract?

For the Joint Meetings, all the authors of the paper should be listed as authors in the abstract.  (For projects not yet published, list everyone who is expected to be an author of the paper when it is finished.) There is an option to indicate which author is actually giving the talk.

Other conferences might have different practices.  If coauthors are not listed explicitly as authors, they should be acknowledged within the abstract, i.e. "This is joint work with Name and Name."


A very complicated F1 visa administrative processing issue... What are my chances if I reapply?

Visa questions are best asked in expatriates.se but here's an abbreviated answer.

Visa application voluntary withdrawals are normally without prejudice towards future applications, however you showed a great deal of emotional immaturity in writing the letter the way you did.  This might have been noted in your file.

The only way you can know is to try again. Note that trying to game the system by applying from another country may actually result in greater scrutiny of your file than if you simply reapplied from your home country.

Returning to questions of academia. If I was your future advisor, I would certainly consider this a negative indication of your maturity and readiness to engage in a PhD program.


How can I explain my grades?

Clearly, and with references: You have done a reasonable job in this post of giving us a basic run-down of how the grading system at your university works.  If you are trying to explain it to a university where you are an applicant, it would be useful to set out a document giving a brief but clear description of this system, and showing what rules correspond to the courses you did.  Explain this as clearly and simply as you can, and try not to make it too long.  Try to think like you are the person receiving this information, and ask what you would want to know to make it as clear as possible.

Also, remember that the university will not accept your word for this, so you should make proper references to the policies of the university where the grades were awarded.  Your university in India should have policy or grading documents that set out this information, so the relevant sections of those document should be included as an annexure, and you should make reference to them whenever you make an assertion about the grading rules in your courses.  Try to make it as easy as possible for the person reviewing your application.


Late letter of recommendation for grad schools

I'm sorry about this situation. I suggest that you find someone else who is willing to write you a letter within a short timespan.

Talk to the programs to which you have applied to understand how they will consider a late letter of recommendation. Many programs are very lax as to when a letter of recommendation arrives, but will begin sorting and analyzing candidates the day after the deadline (some even before!). Tell the programs, either by phone or by e-mail, that your reference has just recently informed you that something personal has occurred and that it is unlikely they will be able to provide you with a letter, but that you have already arranged with another person to submit it. Ask about how and if your late recommendation will be considered, and whether your application will suffer from it. Also ask how you can include an additional reference in the system if it is not directly available through the system.

I know that some programs will look into candidates even if their file is incomplete. However, they will only officially admit you once all documents are in place. Some will reach to you to let you know that you are missing a document, but the best way to know is to ask them directly.

If you don't ask someone else to submit a letter, the worst case scenario is that your application won't be considered at all. If someone else submits a letter, the worst case scenario is that you may be competing with a lukewarm letter, which is still better than not competing at all. If the original reference submits their letter, you will have four letters, which is better than two strong and one lukewarm, but not much worse than three strong, and significantly better than just the two.


What should an unpaid research fellow do when they thought they would be writing papers but are instead writing grants?

I think the answer to this is pretty field and country dependent since there is variation on the frequency of unpaid post docs. In terms of ethics, I am going to ignore the big issue of whether it is ethical for you to be doing an unpaid post doc and focus on the grants/papers issue.

Despite how it may seem, most PIs do not go out of their way to take advantage of people. The PI probably thinks it is in your best interest to be writing grants and not running experiments or writing papers. One reason for this might be that getting if the PI, or one of the PIs collaborators, gets a grant, then they could pay you. There does not seem to be anything unethical about trying to get an unpaid person into a paid position as quickly as possible.

As for what you should do, you need to talk to the PI. Make sure he understands where you are trying to get to. Then work with him on an approach that gets you there. It might be writing more grants or maybe you need to switch to papers.


Am I allowed to give a gift to a fellow student for helping me in a very direct way?

A low-value gift card doesn't adequately compensate the work, so there's no perception of paying someone to do [your] schoolwork. (I can't comment on whether it is against your university's policies, that's off-topic here anyhow.)


The importance of having a "big name" as your thesis advisor

I'm surely not the most qualified person on this site to answer, but I have been on a postdoc hiring committee in pure mathematics and I quite disagree with the existing answers. The single most important factor is going to be your letters of recommendation (with second on the list being your publications and preprints). I think having a famous advisor is going to be of minor importance in comparison; most people understand that also great mathematicians sometimes have students that are just mediocre, so that it's no great predictor of future success. In fact I heard in a sense the opposite argument being made, that if an applicant from a smaller university with a less famous advisor has strong letters from big names, then this is more impressive than if a student at a "top" university had the exact same letters.


Maybe they just mean: "At which institute (or lab, if applicable) do you plan to implement the project?" And the answer could be "Institute of ... at the University of Vienna" or whatever?


How do you make connections to faculty outside your department?

I organized a beer night for tenure-track profs in our department (and this was later expanded to related departments). the basic rules were: it's once a month, anyone is welcome, and it happens even if I'm the only one at the bar :).

Do you have one person from a different department you can start this up with ? set up a mailing list and ask around to get maybe another 1-2 people involved. Start doing this regularly, and never lose a chance to mention this when talking to professors.

Word will spread. Tenure-track profs need support groups. Our beer night is very popular :).


About solving research papers involving complex Mathematics

I would start with e-mailing the authors, or perhaps other experts in your area that you are close to and asking for help from them. I've found that a lot of researchers, even big names, are happy to discuss details about their work (or at least they seem to respond to questions of this nature more frequently than you would expect).

Keep in mind however, that in some fields of physics and engineering (I am not sure if this is true of yours) mathematical rigor isn't a high priority, and so it can be impossible to verify the mathematical reasoning in the paper, even for expert mathematicians working in your area. As a mathematician I find this frustrating, but my understanding is that researchers in physics/engineering are more concerned with the big-picture ideas than making sure all the mathematical details are correct, and perhaps you can take that attitude too.

As an example, my collaborators and I were trying to understand this physics paper (from a top physics journal, written by a distinguished physicist), and we found it impossible to understand the mathematics- there was a step in the calculation where they had an infinite sum that clearly diverged! We emailed the author, and he acknowledged that the sum diverged and the calculations in the paper were not correct, but the idea was still valid. This is a fairly typical point of view in physics and engineering from my experience. So it might be good to adjust your expectations on to what extent you can recreate the mathematics in a physics or engineering paper.


Contacting a paper author: best way to address an engineer

Default to "Dear Mr. [last name]" (assuming you're sure the person is male).  If you're not sure the person is male, use "Dear [first name] [last name]".  Don't worry about other titles unless the person specifically uses "PEng." or other professional association designation after their name, in which case include that.


Is it normal for my masters advisor to ask me not to share code from my masters work with my PhD advisor, and not to continue with the same topic?

II don't know anything about the law in your country, but I think that the request of Professor A has a weak justification:

As lang as you wrote the code in the course of your master
program, your advisor has no right. The algorithms should be considered as public domain (unless you've
signed an NDA). It is different, if (parts of) the code are done by
others.
Being a master student does not constitue an employment relation. There is simply no base for any restriction to your further academic career.

Beside of this, I consider the behaviour of Prof. A (given you've presented all facts) as a bad academic style. Knowledge exchange, a.o. by exchange of people is a well established academic method. To answer your direct questions:

While conflicting loyalty may be a typical problem, I've never heard that a colleague of mine issued such request. Your course of actions depends (of course) on practical issues, too: Is there any danger that Prof. A prevent you from getting the master degree? If so, explain the situation to Prof. B and try to reach an agreement that you "officially" apply after you get your degree.
As I explain above: IMHO no. I would be a waste academic
resources, i.e. your knowledge and abilities. (Beside of this, it is
always a good advice to at least widen your area of expertise as
well as include at least few topics that are totally new for you: It
make you a better researcher)


How, if and where to submit a paper when former co-author cannot be contacted

The most important question is whether anyone else should be a coauthor.  From your description, it's unclear whether the professor you were initially talking with should be one (the others do not sound like coauthors at this point).  The fact that you describe it as "completing a paper that I had started with initial discussions with a professor" suggests that maybe he should be.  The key issue is whether he contributed anything significant to the paper's content.  If so, then you need to discuss the authorship issue with him and cannot make a unilateral decision.  If he did not contribute anything, then there is no ethical barrier to submitting the paper to the arXiv or a journal if you choose to do so.  However, you should be careful with this decision, since it is a major problem if the two of you disagree about coauthorship (especially if you find out after you have already submitted the paper without him).  If you think the situation might be ambiguous, then you need to discuss it with him before submission.

When I say there would be no ethical barrier to submission if you have no coauthor, I mean submitting it would not be a form of academic dishonesty.  You might still offend people, if they feel you are not taking their advice seriously or giving them a sufficient chance to respond.  I'd recommend giving everyone plenty of warning before submitting the paper.  For example, you could send an e-mail saying something along the lines of "I'm just about done with the paper on topic X.  I'm planning to submit it for publication in a month, after I do some final polishing, and I would greatly appreciate any feedback or suggestions you may have."  (But don't say it this way unless you are sure nobody else could have a case to be a coauthor.)


Appropriate to write to the head of a department to ask about potential openings?

You certainly could.It's a low-risk action with the following responses in roughly descending order of probability (assuming you're looking for a tenure-track job, and not just an adjunct/visiting position):

1) The e-mail is ignored. Chairs get many strange e-mails about things that are unanswerable. This goes into the e-mail folder labelled "To respond to when I have much more time than I do now"

2) The Chair writes back with a polite letter thanking you for your interest but that there's nothing in the immediate future, promises to write to you if there is, and then promptly forgets about your e-mail which gets archived along with the other people who wrote the same.

3) The Chair writes back saying that there's an opening for exactly someone with your specific research interests, teaching background, and desired seniority. They were going to have an open search and advertise this on all of the usual sites, but because you're such a perfect fit, they're skipping straight to hiring you.

I should add that #1 and #2 combined represent about 99.99% probability and #3 only happens once in a millennium. But again, the risk is so low that you could do it and buy a PowerBall lottery ticket at the same time and see what happens.

On a more serious note, many job sites have 'alert' functions that will let you know when a job that meets your criteria pops up. I'd subscribe to those. In the meanwhile, I'd become chummy with that department if possible so that you can hear about any gossip about spots. Or try to impress them so much that they decide to do a targeted hire with you in the spotlight.


Why is the date left out of some academic papers?

There is often a substantial delay between when the author finishes a paper and when the paper is actually published. The author may not be totally aware of the publishing date. This is why the authors do not include the date.

The date is generally found in/on the book/proceedings that the paper is published in. This is the date that should be used for referencing a paper.


Using images with CC-BY-SA license in slides or a thesis

Including CC-licensed images as discrete elements in your work does not require the overall work to be CC-licensed. Reasoning 2 is correct here.

(See a similar discussion on opendata.se)

The BY-SA license works in terms of "collective works" and "derivative works":

  1a. "Collective Work" means a work, such as a periodical issue,
  anthology or encyclopedia, in which the Work in its entirety in
  unmodified form, along with one or more other contributions,
  constituting separate and independent works in themselves, are
  assembled into a collective whole. A work that constitutes a
  Collective Work will not be considered a Derivative Work (as defined
  below) for the purposes of this License.

  1c. "Derivative Work" means a work based upon the Work or upon the
  Work and other pre-existing works, such as a translation, musical
  arrangement, dramatization, fictionalization, motion picture version,
  sound recording, art reproduction, abridgment, condensation, or any
  other form in which the Work may be recast, transformed, or adapted,
  except that a work that constitutes a Collective Work will not be
  considered a Derivative Work for the purpose of this License. (...)

An image reproduced as part of a larger document ("see Figure 17...") falls under 1a as a collective work. You have to comply with the formalities of the licensing (4a, identify the license, 4c, identify the author), but section 4b is explicit that it "...does not require the Collective Work apart from the Work itself to be made subject to the terms of this License."

If you do modify the image (eg by adding a new element to a chart, making a composite of two photos, etc), then you have to release that new image as CC-BY-SA, but you can still incorporate it into your non-SA book as a single collective-work element.

Having said all that, 1a could certainly do with some broader examples of what constitutes a collective work, to avoid ambiguity...

Edit (October 2015): a US district court has recently discussed a similar issue (a CC-BY-SA image being used as the cover of a book) and held that that situation clearly constitutes a "collective work":

  Because this 112-page book of maps is not in any way "based upon"” the Photograph, and because defendant did not "recast, transform[], or adapt[]" the Photograph when it used it as the cover art for the Atlas, see License § 1(b), the Court finds that neither the Atlas nor its cover constitutes a derivative work subject to the ShareAlike requirement. Rather, the Atlas is more akin to a collective work, because the Photograph was placed "in its entirety in unmodified form" alongside "other contributions, constituting separate and independent works" – that is, the maps."


look at the link below.
http://www.business-school-pgsm.com/delocalized-programs.html

for delocalized institutions….understand them as partner institutions.

Oxford Dictionary:delocalize
verb
[with object]
detach or remove (something) from a particular place or location, or from local limitations:
(as adjective delocalized)

Merriam-Webster: Delocalize:
to free from the limitations of locality; specifically :  to remove (a charge or charge carrier) from a particular position

Definitions aside:

Some smaller institutions/colleges have partnerships with big colleges/universities to confer degrees. For instance if you attended an institute that offers degrees with a bigger universities' name, then Yes your diplomas were obtained from a delocalized campus.

I attended a university with more than 7 campuses.
So if you attended any of the six campuses apart from the main campus or if you took your studies online; then Yes, your bachelors/masters degrees were obtained from a delocalized campus.


How to publish thesis as a book after getting most of the thesis published as research articles

This depends on the copyright license or transfer you signed with the journals. These range all over the place: they may own copyright, you may own copyright, or somewhere in between. If you transferred copyright to the publishers and they did not grant back any rights, you cannot republish without their permission. (Moral for the future: DON'T TRANSFER COPYRIGHT if it is avoidable, which it often is.)

I suspect you will also have to spin this very carefully (and honestly) with book publishers; many will not want reconstituted journal articles.


Retaking GRE during gap year from PhD to improve pre-doctoral fellowship award chances

The return of investment on a GRE score is much less than other activities. If your score is horrid, then go for it. I wouldn't spend more than 2 weeks prepping, though. Squeezing out every point from that GRE is not worh the effort. I would wager that the score is only to determine the seriousness of your application, and that it would not be a major deciding factor otherwise.


What does it meant " assignment of paper with decision in prosess " in the same time?

It means that the editorial board is in the process of making the final decision about your paper.


What's the best way to find where a paper is mentioned in a paper that cites it?

scite does a great job at that.
Additionally, It's able to show you where in the paper to find such statements.
"...uses deep learning to classify citation statements in three categories: those that provide disputing or supporting evidence, and others, which mention the cited study without providing evidence for its validity."


Communication with a student pursuing the bachelor's thesis

Giving your personal phone number to a Bachelor's Thesis student will allow the student to contact you at inconvenient hours or during your free time. This is the main reason why people do not give their private phone numbers at work (neither to students nor to their boss).

If you are fine with this, there is probably not going to be any other major consequence. The student is not going to think less of you (on the contrary, they will appreciate it), and others (colleagues, boss...) will probably be indifferent. In the end, it is your choice how you want to communicate with your students.


Exam requires self-imposing a time limit: what should I do when others are likely to use more time?

You’re in an unenviable position and I don’t have clear suggestions how to proceed. But at the very least, it’s worth calling attention to the fact that

your instructor is neglecting their duty to maintain an acceptable level of academic integrity, and

this may rise to the level of being more than just a “feeling” but an actual violation of university policy.

For example, at my university, our guidelines about faculty responsibilities in connection with academic honesty state (emphasis mine):

Academic honesty is an integral part of the University's educational mission. According to the UC Davis Code of Academic Conduct, all members of the academic community are responsible for the academic integrity of the UC Davis campus.
[...]
Faculty are encouraged to promote an atmosphere of honesty in the classroom. For example.
[...]

Use exam and assignment formats that discourage academic misconduct.

Now, to be clear, I’m not suggesting that this is grounds for an official complaint or to ask for the instructor to be punished or anything like that. But the point is, if and when you choose to complain either to the instructor or to other campus authorities (department chair, office of academic integrity etc), citing relevant university guidelines or policies can be a good way of strengthening your case and reminding people that academic honesty is a two-way street in which both students and teachers have responsibilities. When the teachers are neglecting their own responsibiltiies by creating such obvious opportunities for a “thought crime” form of cheating that cannot possibly be detected, they can’t very well expect students to fulfill their side of the bargain.
Good luck! Sorry you have to deal with this nonsense.


Is it normal/okay if my professor grades me lower "in comparison to my peers"?

Sounds like you're in a course which is grading on a curve. The idea here is that everyone's score is going to fit a Bell curve with a predetermined mean. This means there won't be any "Christmas-comes-early" results where everyone scores A's, but also no "what-the-hell-everyone-is-failing" panic attacks either. Grade inflation is unlikely in a class that's grading on a curve, because there'll only be so many students who get A's.

If you're in a class which is grading on a curve, then yes: it's normal to "deduct points" because someone wrote better than you. "Deduct points" in inverted commas because you don't actually lose points, you just get a lower grade.

If you want to score well in such a class, you'll need to outperform your classmates.


Can I cite email communication in my thesis/paper?

The exact manner of how you should cite the communication may vary from style to style (often the date is included), but it's entirely reasonable to cite such a communication in a paper or thesis. Typically this is referred to as a Personal Communication. Obviously, wherever possible, you should look for information in published sources, but where this is not possible citing such a personal communication will suffice.

From memory, I think there might be one in my own thesis. A specific detail of an experimental method used in a published article was not discussed, but I thought it relevant to my argument so I contacted the author to get the information I needed.

Edit: Typically personal communications should not be included in the reference list as they are not evidence that can be readily recovered by anybody reading your work. This is made explicit in several prominent styles (e.g., Harvard, Chicago, APA).


I lost my students' quizzes due to a theft, what should I do?

Report it to the police. Report it to the department.

You don't have anything that requires making up to the students. Of course you should be fair to them and not let this hurt them (e.g., no grade for this quiz, but allow students to take an optional alternative assignment to take its place).


Should I ask the Editor for a third Referee when the answer of first two Referees do not agree?

The situation you are describing is not uncommon at all. Acceptance of an article in the prestigious Physical Review Letters is a big deal, and that is also the popular perception regarding it, primarily because of the high reviewing standards. Having personally attended a talk about this issue from one of the journal editors, I point out the technical correctness of work is not sufficient to guarantee publication in PRL - how much captivating is it for the Physics community is also a big factor. (Some part of this is hinted at, in the Acceptance Criteria of the journal.) Unless both the referees strongly recommend that the article qualifies to be a PRL on all eligibility counts, the decision is generally unfavorable. It is important to note that not all articles rejected by the journal are necessarily incorrect - some can rejected only because they were not deemed to be interesting enough!
In your situation, you can definitely appeal. This has been treated in the journal's Editorial Policies and Practices, under a separate tab of Appeals, from where I quote:

Authors may appeal a rejection of their paper by the editors. In the case of a formal appeal, the paper and all relevant information, including the identities of the referees, will be sent to a Divisional Associate Editor (DAE). The DAE may review the case on the existing record or may seek additional expert opinion. The DAE will present an advisory opinion to the editors, which will be sent to authors and/or referees with the DAE's name.
Authors may suggest those DAEs they feel are appropriate (or not appropriate) to conduct the review, but the editors are not bound by such suggestions. If there is no suitable DAE available, the editors may appoint an appropriate scientist to consider a paper under appeal as an ad hoc DAE.
The author of a paper that has been rejected subsequent to a DAE review may request that the case be reviewed by the Editor in Chief of the American Physical Society. This request should be addressed to the Editors, who will review the file and, if appropriate, forward the entire file to the Editor in Chief. Such appeals must be based on the fairness of the procedures followed, and must not be a request for another scientific review. The questions to be answered in this review are: Were our procedures followed appropriately and did the paper receive a fair hearing? A decision by the Editor in Chief is the final level of review.

Please note that the above form of appeal is more of a fairness measure from the point of view of the journal - just in case the authors feel they haven't got a fair review. You must note that the official statement here is "In the case of a formal appeal, the paper and all relevant information, including the identities of the referees, will be sent to a DAE". So, the report by the second referee (as well as info as to who this guy is) shall also be sent to the DAE. Thus, he can also uphold the second referee's verdict if he considers it appropriate, i.e. if the reasons appear genuine. But, of course, he may also rule otherwise.
Quite obviously, this appealing does not guarantee that the paper makes the cut in the journal, it is only like a half shot more at it. It may also happen that the DAE may not feel that it makes a very strong case for a letter, even though there may not be any fundamental flaw with the results. If that happens, and even otherwise, don't feel very bad about missing out on a PRL. It is much more important that the contents of the article are correct, and the Rapid Communications section of Physical Review A/B/C/D/E might be a safe bet too. And of course, you can always opt for other letter journals. But if you think it makes a strong case, PRL does offer you a procedure for appealing too. Avail it if you wish.


What ratio of PhD graduates in STEM fields ultimately end up as (tenured) professors?

It's a shiny info-gram, but I think there is a lot wrong with it:

It transports the (common) misconception that the 53% leaving to industry after their PhD are sort of failed professors. At least in CS, and probably a lot of other STEM fields as well, many PhD students start with the full intention of leaving academia sometime. Hence, the better question the diagram should be asking is How many of those that want to become professors actually do?. Basically, I could come up with similar low percentages for every field. Let's say less than 1% of all working population of a city works in supermarkets. Does that mean that supermarket jobs are horribly hard to break into? No, because most people do not have the career goal of working in a supermarket in the first place.
Similarly for the 17% non-university research. In CS, good industry labs (like the ones at IBM or Microsoft) are preferable options for many researchers, so they would not take a professorship even if offered.
As already stated by commenters above, the title professor means different things in different places. In Austria, for instance, many high school teachers are officially "professors" (tenured even), despite not having a PhD or ever doing research. In Great Britain, very few people are professors (most are lecturers or senior lecturers). In Madrid I know an academic research lab (not affiliated with a university) that calls their staff members research professors. Job titles are almost never clear-cut.

That being said, I do think that there is a problem. If we assume a reasonably stable system (number of professors in a discipline stays more or less constant), then every tenured professor is in average allowed to see one of her/his students through to also become a tenured professor. Given that many tenured professors (at least here in Europe) maintain groups of 15+ PhD students at a time, I is pretty obvious even without digging into the data too much that the job market for professors is insanely competitive (which, incidentally, captures my personal experience hunting for tenure-track positions pretty well).


Question asked in phd application form - How you intend to fund your studies

For PhD studies in the UK, funding and admission to the program are usually separate steps. Funding opportunities will generally marked explicitly as such, and many of them are only available to UK/EU citizens resident in the country. If you are just applying for admission to a PhD program, there is an expectation that funding is taken care of separately.

The "ideal" answer for such the question regarding the funding source in a UK PhD application takes the form "I have been awarded the following competetive scholarship which will cover all my funding requirements". Other good typical cases are "My employer (company or government agency) really wants me to do a PhD and will foot the bill". These answers strengthen the application, because they show that someone else is sufficiently convinced of the whole PhD thingie to put a significant amount of money behind it.

"Neutral" answers are "I/my parents are rich and we can just afford this" or "I'm getting student loan from XY". Be prepared to provide evidence of claims like this! These answers mean that funding is taken care of, but don't add to the application beyond that.

"I'll get a part-time job" is NOT a good answer. University regulations typically restrict how much work PhD students are allowed to do, and with that number of hours it is probably not even feasible to cover cost of living, not to mention university fees. Anyone who needs a student visa to come to the UK is subject to even stricter regulation, which will actually be enforced. For the universities, the rationale is that PhD students who spend a lot of time working for a living, and a lot of energy worrying about how to make ends meet are far more likely to underperform or even fail than PhD students focused on research.


Buying Internet hosting from an academic institution

Within the United States, universities help startups in many different ways. This includes "internal" startups that are created by students and faculty as well as "external" startups that are created by university outsiders but receive support from a University.

Google initially had an "exclusive licensing partnership" with Stanford. As noted in a Wall Street Journal Article, this deal paid off well for Stanford.
Academic researchers and students can be encouraged to do technology transfers and "commercialization" of research. This can be within the University or outside of the University. For example the Wisconsin Alumni Research Foundation got started because the University did not want to help support a professor's efforts to sell his research. As another example, Texas Tech has an Office of Research Commercialization to help within the university.
Universities can also have incubators such as Univeristy Research Park in Madison, WI. Incubators such as these can help startups overcome the hurdles you mention.


How did German universities outperform the US's and the UK's, before the 1930s?

Prior to the 1930s, Germany had some of the world's oldest and best universities. This is largely a due to historical reasons discussed in this article

But what changed in the 1930s? Rather than ask why German Universities out performed US universities before the 1930s, perhaps a better question would be "Why did US universities out perform German universities after the 1930s?"

I would answer that by saying the two events caused the change. First, the influx of refuge scientists prior to World War II boosted US Science (e.g., this article). Probably the most famous scientist to flee Germany to the US was Albert Einstein.

Second, the US funded science much better than Germany after World War II.  This extra funding was partially done out of fear of Soviet science and partially an artifact that the US economy was the only one not destroyed or heavily damaged by the war. (This article talks about US Science funding and provides more insight into this specific topic)

Also during the post-war period, many scientists choose to come to the US because of research opportunities. As described in the book Moon Shot, Wernher von Braun chose to surrender to the US because he knew only the US and Russia would have the resources for a space program (he surrender was part of Operation Paperclip). He chose the US because he would rather live here.

Similarly, many scientist immigrants continue to chose the US because of opportunities not available in their homelands. The NSF describes this here.


can I submit in a new journal after submission in a predatory journal who force to pay in order to withdraw?

Could you provide some more details? In which country are you based? Where is the journal based? Is the journal WOS-listed?

Here are some basic orientations:

If you are certain that the given journal is a predatory journal, you can certainly retract the publication. Predatory journals are designed to maximise income and minimise expenditure. Accordingly, these journals are certainly not interested in a lawsuit (especially an international lawsuit). Emails are a matter of empty threats in that case.
If you are uncertain about the degree of predatory-ness, simply retract the publication based on the most relevant limition/flaw of your study. State explicitly that you feel that the quality of work does not fit their criteria of "high-quality, peer-reviewed science" (quote whatever the described on the webpage). Write the email in a manner, which puts them in "double bind" dilemma (https://en.wikipedia.org/wiki/Double_bind). Force them to either agree with the retraction at no cost, or to openly have to admit dishonesty regarding their "high-quality" peer-review process.
If it is just a low-quality but not predatory journal, be fair and go along with the submission this time and stay away from the journal in future.


Identical projects by students at two different colleges: still plagiarism?

The fact of being at different/same colleges or different/same universities has zero bearing on whether it is considered plagiarism or not.

If you submit a project that includes someone else's work, without making it clear what is your own work and what is not (and crediting the other contributor/s properly), this is plagiarism. This is true whether the other contributor is at the same college, same university, someone not in college at all, etc...