Conference and journal papers in physics

I have seen, at various times, deliveries at conferences that discuss papers which:

have been published,
papers that have been submitted and accepted for publication,
papers that have been submitted and are in the review process, and
papers which are still being prepared for submission (including papers which have not yet been written).

Sometimes a conference paper is also prepared and published as conference proceedings, as a summary, lead-in or discussion of preliminary results which are then published in detail in a journal.

It is expected that the paper submitted to the journal will be different enough to the conference paper to be suitable for publishing as a separate article without infringing on the "not submitted elsewhere" condition, and you will probably also need to either cite the conference paper or the journal paper in the other to avoid plagiarism.


Why is the concept of self plagiarism in coursework not manifestly absurd?

That's not that easy to answer because it really depends in my opinion on what is plagiarised and why and what's the impact.

For example we submitted a paper and the publisher found a plagiat in our introduction. Turned out we had written the same sentence in one of our other papers on a very similar topic. We had around 15 papers in that field and well, the introduction is always basically the same so sooner or later you will write down the same sentence. It's just stupid to forcefully rewrite the same introduction over and over again and it has nothing to do with the actual scientific work.

And while I feel it's unethical to use previous work in university courses the even more interesting question is: why? Why would I reuse my previous work for classes at university rather than learning something new/training my skills. Why would I study, if I'm not interested in the subject.

You really should take courses at university as an opportunity to learn something, rather than an annoying obstacle on your way to your degree, which you want to avoid/manage with the lowest effort possible


Changing due date for a student suddenly

It's unlikely you can do this.

Unless you have a statement in your class syllabus that:

explicitly bans the use of cell phones in class and
specifies that you can make students turn work in early,

this is probably going too far beyond your actual authority and in principle could be overturned were the students to appeal.

If you're going to have students working on homework assignments in-class then it is probably best to institute a "participation" component to the grade, which you would then be certainly entitled to lower on account of their lack of participation during class. But unless that's already built in, there's not much you can really do here.


Seeking Your Advice on Preparing for Mathematics Graduate Programs

No, undergraduate research is not a very important factor for graduate admissions in mathematics.  It's nice if you have it, and if by any chance you publish a solo author paper in a respectable journal that's fantastic, but that kind of fantastic stuff is done by people who would assured of admissions to top programs anyway.  Since every letter ever written about a math student's undergraduate research is positive, admissions committees just don't get enough information to use in tough admissions choices.

  I am a rising college junior (five-years tract) in US with a major in mathematics and an aspiring mathematician in the fields of theoretical computing and cryptography. I apologize for this sudden interruption but I wrote this post to seek your advice on preparing for the mathematics graduate programs; I am currently attracted to the applied mathematics. Through introduction to the computational biology, I found my true passion and love toward the mathematics,

You have named at least four different fields in one introductory paragraph.  This is a bit disconcerting to a potential admitter.  We might worry that you have not managed to settle down on any one thing for long enough to study it in any depth.  Maybe that worry is totally groundless, but you should do what you can to allay it.

  Does Putnam score also play an important factor? I am interested in preparing for the Putnam Competition as it has many interesting problems on algebra and number theory (topics of my interest) and I have been preparing vigorously with the problem-solving-strategy books as I never participated in any mathematical competition before.

Similar answer to the last one but more extreme.  If you score in the Top XX, that looks good, but it would be very rare for that to be the breakthrough good thing about your application.  Moreover, whereas one must admit that undergraduate research in mathematics is becoming increasingly popular and viewed increasingly seriously over the years, the same cannot be said about the Putnam: if you never take it, no one cares.  If you got a zero every single time, no one cares.  (I took it in my freshman year only, honestly don't remember my score but suspect it might have been in the single digits, and I got into every program I applied to, including the top three.)  I was never excited about contest math so I need to ensure that my own proclivities don't creep into my answer, but quite soberly: studying for the Putnam (or any university math contest) might be fun and it might be educational, but it is not much of an investment in your future.  If you like algebra and number theory, great (OMG! me too) -- study algebra and number theory.  Working Putnam problems would teach you more of that than watching Game of Thrones, but it's still quite indirect.

  About my current course schedule, should I take the Abstract Algebra I with other courses? At my university, the AAI hs the pre-requisite of linear algebra, but I was granted a special permission for enrollment since my research advisers strongly recommend me to take the abstract algebra for the theoretical computing and computer security. I am currently studying the abstract algebra and linear algebra to prepare for the courses and upcoming undergraduate research.

This type of question needs to be answered by someone who is familiar with you and with your department's program.  We're not.  It's exactly the sort of question you should ask your faculty advisor.  If you don't have a faculty advisor yet, no problem: this is an excellent opportunity to get one.

One final comment: based on your writing, I suspect you are not a native speaker of English.  Good English language and writing skills are important for an American PhD program in mathematics: a low enough GRE verbal score can kill an application.  (Conversely, in my program, in order to be competitive for the top drawer internal fellowships you have to have a high "academic index", which is some weighted numerical measure of your GRE quantitative, your GRE verbal and your GPA.  So it's serious.)  Shoring up shaky English skills is more of a priority than studying for the Putnam exam, if you ask me.


Open Source Software and Reproducibility in Computer Science

Computer science is a particularly friendly environment for releasing material in advance of publication.  In fact, there are a number of methods for doing so that provide a clear archival time-stamp on your work, including university technical reports, arXiv, and big repository sites like github and bitbucket.  Moreover, unlike many other disciplines, such pre-release almost never impairs your ability to build conference and journal publications on top of your released material.  In fact, you can typically release not just your code, but also your draft paper through the same mechanisms.

If you do such pre-release, you are essentially immune to plagiarism, because anybody who pirates your results will look like a fool with date-stamps marking their guilt for all to see.  It may not stop bottom-feeders from trying, but it will mean that nobody you care about (including reviewers) should take such an attempt seriously.

The only likely problem that you can run into is double-blind reviewing, as discussed in this question.  If that's not a major concern for you, or if you can use one of the mechanisms suggested in that question, then I see no likely downside in computer science publication.

On a side note, however: just because the code is available doesn't mean it's reproducible, as anybody who's spent significant time having a dependency-fight with poorly-document open source projects can attest.


Can a research statement contain research interests which are not concrete?

If a statement does not sound right to you, it is highly likely not to sound right to other people. So you might have as well just leave it out of your statement.

Focus on what you know and what you know you are in a position to focus on as part of your further research.

If you are selected, you will have plenty of opportunities to nurture your thoughts and ideas with stimulating colleagues.


Is it appropriate to give your supervisor an early thesis draft that has informal self-addressed notes?

I would suggest that yes, you should feel comfortable doing that, particularly if this is an early draft. My rationale is simply that, with large documents like this one, the more feedback you can get, the better. The notes show that you've given thought to what should be where and recognize that it's not complete, and will demonstrate that you're thinking that sort of thing through. To that extent point, your own recommendation is spot on; add as many "diagram X should be here" notes as you can, simply to save him from having to add that comment himself.

That said, if your advisor is a very finicky person who wants the drafts to be picture-perfect (yes, those people definitely exist), then don't do this, as you'll just make him annoyed.

Post-edit addition: I would suggest this is entirely dependent on the temperament of your advisor. Personally, I love humor, so as long as you mentioned in your email that the comments are tongue-in-cheek, I would find that entertaining. If he's a stick-in-the-mud, he won't like it. Its really just dependent on his sense of humor.


I have some (possibly) original results and advisor cannot help, how should I proceed?

Cold emails are very common in this situation, and not at all a bad idea. Indeed, I know of many cold emails that have turned into coauthored papers.


Going back to university after suspension, how do I move past the shame?

The university suspended you, which is a signal that it is still willing to have you as a student after serving your suspension.  (If it wasn't, you'd have been expelled.)  Therefore, upon your return, this professor (and every other professor) has the same professional obligations towards you that she would to any other student: to accept you in her classes, to treat you with courtesy and respect, to help you learn the material, to grade you fairly based on your work and the standards of the course.  It is possible that your assignments may face extra scrutiny for plagiarism, but hopefully that is irrelevant as you're not going to do it again.

It's possible that relations may be strained between you, but I think this may be more on your side than hers.  Speaking for myself, I certainly find it disappointing when a student cheats, but it's not as if I'm going to declare a personal vendetta against them and seethe with fury every time I pass them in the hall.  That would be unprofessional, and not worth the emotional energy anyway.  We go through the disciplinary process, I hope that they learn their lesson, and it's back to business as usual.  If they are able to turn things around and show genuine interest in and dedication to their studies, for me that's ultimately uplifting.

So if you want to take her class at a later date, by all means do so.  You might find it helpful to talk with her first: express your regret over the incident, as well as your continued interest in your subject and in completing your degree.  I think it's very likely this will help clear the air for both of you.  It would be wise for you to be extra diligent about quotations, citing sources, etc, and to consult your professor if you have the slightest question about any such issues.

Maybe she won't invite you to dinner, and she probably won't be the best person to write you a letter of recommendation.  (Even if you get to be on better terms, which I hope you will, she might still feel it's her duty to mention the cheating incident in any letter she writes, which is probably not good for you.)  But I don't see any reason you can't have the same basic educational experience as any other student.


Publication- rejection with advising to resubmit

While a reviewer has mentioned "major revision", is this decision advising for resubmit after revising the paper? Does this mean "Reject and resubmit"?

Yes, this means your manuscript is rejected, but you are free to submit a new version once you addressed the mentioned problems.

Note that whether one of the reviewers voted for Major Revision rather than Reject is completely irrelevant - it's the editor's decision that counts.


Is there an increase in papers authored by undergraduates?

Has there really been an increase in papers co-authored by undergraduates?

These facts can be established:

There has been an increase in the number of undergraduates, except for recently in a few areas that have falling birth rates.
There has been an increase in the number of papers published.
The average number of authors per paper has increased.
For most papers, it is impossible to tell if an undergraduate is an author without asking the authors.

On balance, I think that there has been an increase in papers authored or coauthored by undergraduates, but that it is impossible to tell how big that increase is because nobody is collecting the data.

This pressure is at the back of my mind every time I am working on my research, and is preventing me from enjoying its process.

As a PhD student in STEM, you will be assessed primarily on your research publications.  If you particularly dislike being assessed that way, do not get a PhD in STEM.

Does this mean that publishing a paper does not carry the same level of significance as it used to in graduate admissions?

The number of PhD students is also increasing and admissions practices are slow to change, so I doubt there has been or will be much change.


Is it a good idea to take a break from studying a mathematics PhD and revisit academia at a later stage?

Is it a good idea to take a break from studies if wanting to continue them at a later date, especially for mathematics?

That's a tricky question.  There are probably some people for whom this is a good idea, but I wouldn't say it's generally one.  If it's possible in your current situation to essentially hit the "pause button" on your studies and be guaranteed the ability to come back (I think this is possible at many US universities), it might not be so bad, but otherwise you're taking a pretty big risk.  Also, in even as short a time as 6 months or a year, you risk forgetting a lot.  Certainly this is something a lot of other people I know who've taken breaks (say between undergraduate and graduate degrees) have mentioned.

I would think about trying to arrange a shorter vacation (maybe 1 month) first, and see how that feels.  Taking a whole year is a genie that will be hard to get back in the bottle, and you don't know how you will feel, say, two months in.

  Would it hurt any opportunities later on down the line to take up a PhD a year or so from now?

It certainly might.

  Would my department or supervisor think badly of me for wanting to terminate my studies - and (generally speaking) would I not have to pay back the studentship instalments that I've been paid so far? (I've been funded solely by the University, not by a funding body such as the EPSRC).

I can't speak to them (or speak about the financial aspects), but probably it will not look great.  You should be prepared for everyone in the department to assume this means you are dropping out, no matter what you say about coming back.

  What would be some worthwhile things to consider doing during a break from academia?
  Has anyone else on here had experiences of a PhD (particularly maths) not going too well and feeling like they have had to stop or recharge their batteries?

I do know of one situation where this worked out a very well.  A friend of mine in grad school took a year off (after 3 years in the program) to teach in an inner city school.  I think at the time he started he was not so sure he wanted to finish, but the experience motivated him very effectively to go back and complete his degree, since he realized teaching middle school was definitely not for him.


How to increase the odds of becoming an invited speaker at science conferences?

Give some colloquia (departmental seminars or lab-specific talks) in the departments of organizers of conferences. You can sometimes invite yourself by writing to the organizer of their seminar series and offering yourself as a speaker but better might be having your phd advisor write and recommend you.

This will increase your name recognition with the critical people and can give you a reputation for giving good talks. Organizers are unlikely to take a chance on someone that is junior and none of them have heard speak. If you can give a talk somewhere that will be videoed and posted online, that would also help with this issue.

Finally, if you work with a more famous friend (or phd advisor) in the same area who is frequently invited to give talks, you could mention to them that you are trying to do this and they may recommend you for talks they have to decline.


arXiv is running out of IDs -- is their solution known?

The format presumed in the question is incorrect. The format is YYMM.NNNN, rather than YYYY.NNNN. Shortening the year to YY and including the month as MM gives a factor of 12 increase in the number of available IDs. Version numbers are appended to the ID, as v1, v2, and so on. That said, it is still a problem, but arxiv have thought about it.

  NNNN is a zero-padded sequence number starting at 0001 and permitting up to 9999 submissions per month. If current growth rates
  continue, we expect to change the sequence number to 5-digits NNNNN in
  10 to 15 years. We will do this in a uniform fashion so that, likely
  starting on some year boundary, all subsequent identifiers are
  zero-padded to 5-digits. We cannot currently anticipate extension
  beyond that although extension to 6-digits would be possible.

This was posted in 2007 so we are 6 or so years into their 10-15 year window. Submissions of multiple versions might grant some extra headroom, however it does appear that we could run into problems in about two years. It looks like they underestimated their growth a little bit!

Status change in 2015. arXiv.org switched to 5-digit IDs in January 2015. The format is now YYMM.NNNNN or YYMM.NNNNNvV.


Google scholar "sort by date" returns articles from last year only?

First, you should realize that Google Scholar is not the same thing as a "free" equivalent of a commercial scholarly database (e.g. EBSCO or ProQuest). Although it's great for finding grey literature and relatively obscure topics (not to mention tracking citation counts), it has some serious limitations for general literature reviews. In particular, it does not permit you to do many of the focused searches that commercial scholarly databases. I suspect that this is for copyright reasons, rather than technical reasons--the journal publishers probably wouldn't permit Google to search their copyrighted articles in depth without paying for it.

What this means for your purposes is that, in general, you cannot do a title-abstract-keyword search on Google Scholar. The exception is that you can search for abstracts only, but only for articles added to Google Scholar in the last year. That's what you get when you click on "Sort by Date"--it's not obvious, but that means "Sort articles added in the last year by date". This is only useful to find what's new, but is useless for any general search on what exists in the literature.

The solution is to search in a commercial scholarly database (e.g. EBSCO or ProQuest). Your library pays them for the right to access them, they pay the journals, and so the journals authorize this kind of search.


How to Remain Competitive at a Mediocre University?

Read as many mathematics books, lecture-notes, and published articles as possible. Not just "textbooks". Not just "undergraduate textbooks" as these contain very little substantive mathematics.

Even if your faculty people are not stellar mathematicians, they surely know some advanced mathematics and can give you guidance about what to read. Uninformed self-study can be a huge time-waster so you will want some direction to be productive and your mathematics faculty will be the best & most available people to provide you with productive guidance.

Definitely talk to faculty to get guidance! This can be done officially through a "reading course" or "directed study." It can also be done informally through frequent check-ins with interesting questions. Either way this will enable those faculty members to write excellent letters of recommendation about your interest and motivation based on your capacity to appreciate the things you will have read and your perceptive questions.

It's not so much whether you (as a novice) can handle random questions, which novices rarely can, but whether your sensibilities are heading in the right direction, which would be manifest in your reaction to substantial mathematics.


In Moodle, how to submit student evaluation without assignments

You can grade assignments even if students have not submitted anything:

Can I grade work that’s been done offline outside of Moodle?
Yes. Just untick all submission types when setting up the assignment and just use it for grading.

The quickest way to do this is, unexpectedly, to use Quick Grading. When you enable this, you will have input forms directly in the grading table. Just enter the grade in front of each students and click on the button at the bottom of the page to save.
(If you want to get complicated you can use CSV imports and whatnot as explained in Solar Mike's answer using Offline marking, but honestly why make it complicated when you can make it simple...)

Another, maybe simpler possibility, is to simply add Grade items and then edit them directly into the Gradebook. For something so simple it probably doesn't make much sense using the full-blown Assignment activity, unless you want to add material each day like grade sheets, solution sets etc. So you first add Grade items as explained in the doc, and then edit them in the Grader report. It can be done very quickly.


Releasing all lecture materials at once vs. releasing materials lecture by lecture

As a CS student, I experienced both types. In my opinion, there are many practical disadvantages and psychological effects to consider when releasing everything at the beginning of the semester.

However, it is very nice to be able to view the materials from previous years in full, and almost none of the disadvantages listed below apply for this case.

Practical considerations:

If everything is available at the beginning of semester, students might deem it not necessary to check the course website during the semester, as they already know that "everything is there". They will miss announcements and updates to the website.
If the lecture materials are changed or revised during the semester, students might miss these updates if they downloaded everything at the beginning of the semester.

Psychological effects:

Information overload: Students may think that the course will be too difficult if they take a look at later slides at the beginning of the semester and thus might drop the course.
Frustration: Eager students may try to understand the contents of later slides (e.g. a few weeks in advance), but get frustrated if the slides are not completely self-contained and there is information missing (that would have been given in the lectures).
Lazyness: If everything is there at the beginning of the semester, students may not feel the need to keep up with homework/reading week by week, as there is less of a weekly reminder that things have changed (the page is static and does not change every week). If the materials are released weekly, there is more of a motivation to not fall too far behind, as students are reminded every week of how far behind they are. Also, students might not be motivated to go to the lecture if they already know that all the material has been released.
Inattentiveness: Students that have already read the slides of the coming weeks may be bored or inattentive during the lectures. This may be important if the slides "give away" too much of the thought process if students read ahead. In some lectures, homework is only mentally stimulating if the slides of next weeks' lecture are not available in advance.
Students may also get the impression that the professor is just "phoning it in" for this year, even if that is not the case. If slides are released every week, this gives more of an impression that the lecture was tailored to this specific year, and to the questions asked during this year's lectures.


Should I include my MSc admission in my CV?

I think it depends on where you are applying.  If you are applying to career-type positions, potential employers may be hesitant to hire someone they know will be leaving in a year, or less.  In that case, I would leave it off.

On the other hand, if you are looking for an internship, or a research assistant position, adding it may help build bridges between organizations.  For example, if you have the opportunity to work with someone who has a connection to the MSc program, this is a great way to start building a network.  This was the case when I worked in a lab between undergrad and grad school.


I'm surprised that you have found any reasons to stay. I don't predict that you can have any happy future if you stay in this situation. There is clearly a lack of respect, maybe both ways.

I can't think of any path to success whatever if you stay. Even if you can force better behavior, the resentment will come back to hurt you when you are ready to move on. I wouldn't expect any decent letters of recommendation.

None of what you describe is proper. I hope it is uncommon.

Find a better situation, even if you need to change universities. The head's lack of interest may make staying also impossible.

Unfortunately, this advice comes with a heavy cost since moving will be difficult and you may not be able to take your research with you. The less developed it is, probably the easier it is to carry it away and continue. But you need a supportive advisor.


My advisor has only met with me twice in the past year. Is this enough cause for me to change advisors?

Yes. You are early on in the program and you should begin to work on changing advisors if you are not thriving under this advisor. When talking to new potential advisors, you can ask how they would handle the question of evaluating your performance given the switch. They can help to “go to bat” for you with their colleagues if questions come up about your performance. They may ask you to wait until after comps to officially switch if there is a chance that the switch could affect your passing. Usually, provided you pass comps, your performance is evaluated mainly by your advisor so this should not be a big issue.


Since this is an "internal" application, the recommendation letters are really a formality.  The department wants to know whether you're likely to succeed in their program.  Since they already know you, they have a good idea what sort of student you are.

In my opinion, your real problem is that they know that you're that type of student who bites off more than he can chew.  That sort of student is not likely to be successful.  (I don't know why, but that sort of student annoys me deeply.  It pushes some button deep in my psyche.)  You expend lots of effort but you don't master anything.  All these graduate profs have had you sitting in their classes, thereby soaking up some of their effort and for no results.  Meanwhile you dogged your undergrad classes, and wasted the efforts of those professors.

My advice, if you want to get into their program, is to go on a mission to convince the faculty that you've learned your lesson, that you know you need to focus and master today's learning today.  That you won't, in the future, be distracted by every shiny object that arises.  Yes, lots of different bits of mathematics are interesting to the point of being seductive, but you can't learn them all at once.  The moral of the story is that joke about the old bull and the young bull looking down the hill at a herd of cows.


How to justify not using a certain program or API or framework because it is not free

Most of the reasons you gave in your post seems justifiable enough. I'll just list them to make it clear.

You have sufficiently abled tools to solve your objective without the proprietary tool.
You don't have a funding to cover the expense of certain proprietary tools.
You are able to use limited licensing to cover up most of the commercial options.

Apart from the good excuses, you could at least request the tool provider to see of they would sponsor you with a temporary research/student licence (or a similar sort) by stating your objectives.


My research is on specific publications and their publishers. Should I include all articles mentioned in the bibliography?

Generally speaking
If you are referring to particular content of particular issues, you should cite them.
If you have a database of the contents of the magazines and you work with that, then ideally you publish the database, or in any case explain how you created the database and what was included. In that case you would cite the database, if published, or otherwise refer to it, but you would not cite specific articles unless you use their particular contents, as per the first paragraph.
What are the notes?
In your question you mention that individual articles have been referenced in the notes. Are these notes a part of the dissertation or something distinct?
If you dissertation is a collection of articles and these notes are the articles, for example, then you are presumably writing an introduction that ties them together. Then the introduction would cite whatever it mentions, but likely not very many individual magazine articles, as the details would be left to the research publications.
If you mean some kind of notes you have written for yourself and not to be published in any way, then they don't matter for the question of what to cite in the dissertation itself. The dissertation should stand by itself, without needing private information.


PhD interview - how to explain why I left a previous PhD?

I'm not sure that explaining why you left is the most important thing. Questions might be phrased that way, but people really want to know what is different now so that they can predict that you will be a success this time. You can't avoid giving some direct response to the question, of course, but you also need to be able to point to things you have done since then that make your success more possible and more likely.

Perhaps "loss of interest" was a result of lack of support or burnout. Both of those are easier to account for than lack of interest, I think. You needn't give every reason you can think of, but reasons that are fairly common and that have obvious corrective actions are easier to account for than others.

Don't avoid the direct answer, but focus on what is now different.


How to organize course component when there are a lot of students?

However, due to the similarity of question, students from Tuesday, Wednesday and Thursday classes can obtain quiz questions and keep practising them. In the end, these students excel while students from Monday do averagely or poorly.

Give all of the students sample questions similar to the quiz questions ahead of time, so that seeing Monday's questions does not become an advantage, and all students can practice the problems and do well. (That's what you want, right?)

You can also set about 80% of the quiz questions to be the same "type" of question across all of the sections, and vary the last 20%. That way the quizzes remain similar in difficulty, but students still have to prepare everything in order to do well, even if they know what was on Monday's quiz.


How will this departmental restructuring plan affect students and faculty?

One of my former PhD students works in the CISE department at UF, so my opinion is not exactly objective.  But here it is:

Will the quality of education in the CISE department be the same after this restructuring?  Absolutely not.  Teaching computer science well requires serious manpower.  Unless CS courses are limited to a very small number of students, which seems incredibly unlikely for a flagship state university, educational quality will plummet.  The near-certain increase in faculty teaching loads only makes this worse.  If nothing else, with less individual attention on students and more automated grading, cheating will increase dramatically.  (Also, in the longer term, educational quality will suffer because the instructors are not themselves active researchers.  Computer science changes fast; if the faculty aren't leading that change, they'll fall behind.  Obviously.  But in the short run, the removal of TA support is a much bigger issue.)
Can [CS] research take place in [an ECE] department?  Maybe, but probably not at existing levels.  If faculty treat the incoming CISE faculty as anything less than full-fledged intellectual peers who should be judged by the standards of their own research communities (as opposed to ECE community standards), then no.  Most recent CS-EE mergers have failed for precisely this reason.  This has far less to do with the distinction between "software" and "hardware" than cultural differences about intellectual values, publication standards (conferences vs. journals), funding, intellectual property, entrepreneurship, and the like.
Do you think [teaching] professors will remain at UF given the circumstances?  I expect some faculty will stay, either because they prefer teaching anyway (or even support the restructuring), or because they have eternal constraints that make moving impossible, or because they are close enough to retirement that they're willing hold their nose for a few years, or perhaps because their recent research records are not strong enough for them to land a tenure-track position in a comparable department.  But I would expect most CISE faculty—including the research faculty forced into other departments—to leave at their earliest opportunity.
Will the teaching-only CISE department be able to attract quality professors?  Not as easily, and not as long as the current political players are in power.  Setting aside the common assumption that quality is correlated strongly with active research, I expect most strong teaching faculty would have trouble accepting a position from a college with such blatant disregard for academic freedom and shared governance.
Top students?  Undergrads, yes, although probably in smaller numbers.  Because UF is a flagship state school, it attracts a significant fraction of the top high school graduates in the state (at least by STEM standards).  The number of such incoming students is unlikely to change very much, but many of those students who would have studied computer science will go into other majors instead.  Graduate students, probably not, for the same reasons as faculty.

And one question you didn't ask:

Will employers value a UF CISE degree as much as they do now?  I doubt the restructuring would have a significant effect on the job prospects of current CISE majors, except possibly if some of the software companies who've recently announced plans to open offices in Gainesville change their mind.  But if the quality of education (and the strength of incoming majors) suffer as I expect they will, then a UF CISE degree will be less valuable than it is now, even for the best students.

The flagship state university where I work has attempted a few similar restructuring efforts, and currently faces similarly severe budgetary constraints.  Some of the resructuring attempts were successful (for example, our Theoretical and Applied Mechanics department was recently merged into Mechanical Engineering); others were not (for example, our Nuclear Engineering Department survived a proposed closure).  In the years leading up to the TAM closure, a significant majority of the TAM faculty moved or retired.  Although TAM survives as a degree program within our MSE department, it attracts considerably fewer students and faculty than it did as an independent department.


What are the common productivity measures of a scientist, like h-index?

The h-index is common (and the g-index, which corrects for self-citation), as is the Journal Impact Factor. Johan Bollen has a good review of the various metrics.

However, it's important to point out that all those measures are just different ways of counting citations. They don't account for things like code you've written or talks you've given and they can't address systematic bias in citation practices such as coercive citation or citation mutation. Also, any citation-counting metric will penalize younger researchers simply due to the time it takes to publish one paper and for other papers to get published citing yours. In order to keep academics from having to publish a paper just to describe some code they've written or a dataset they've accumulated, aggregators have been built to pull in these various metrics and consolidate them. Total Impact is a good example of such a system. The general field of study looking at incorporating these broader metrics is called #altmetrics, and you can find a collection of research on the topic here.


Is writing to prospective PIs during admissions season a good idea?

It's usually better to contact a potential PI than to not contact them... but you're timing is a little awkward.  The thing about contacting them is that you want to be pointed in what you're communicating.  Although asking if they are accepting students is relevant, it seems a little late for that because you've already applied.

In other words, you can't just send the typical email because it doesn't seem as relevant, even so here a couple of ways of reworking the typical approach:

Briefly discuss your interests and why you're a good fit for the lab. Then simply state that you want to alert them to your application. ...If they are interested, they will look up your application.
The other thing that comes to mind is for if you are offered an interview, which should be happening around now. You can email the professors you are interested in at that point in time and briefly discuss your interests and why you're a good fit for the lab, then say that you're excited about interviews and you hope you have a chance to meet with them at that time.

Yes, professors are busy, and you may not get a response, but I don't think writing an email could lead someone to throw out your application which they otherwise would have considered. In other words, if your email is polite and nothing weird, then I don't see how it could have a negative impact.

Hope this helps and best of luck.


What is meant by rewarding No-Grades when one's adviser remained satisfied towards one's research?

Before jumping to conclusions, first review your university's grading policy. There may have been changes to the classification system.

If, after reviewing it, you find that the grade is indeed "negative," then you need to have a conversation with your advisor. Do not come with an accusatory tone, as that will end badly for everyone. I would ask something like:

  "I'm a little confused about my thesis grade. I thought I was making satisfactory progress this semester. Could you explain what I need to do to improve?"

This will give your advisor an "out" if there was just an administrative mixup (for example, if it's a bubble form that was improperly filled out) or some other problem. On the other hand, if there's something serious, then you'll know. But usually a good advisor will level with you if there's serious issues in your work.


First, negative results are useful too: for instance if you can show that the method is inapplicable by trying every reasonable option to make it work, this is a result by itself and it might be worth publication. Since your intuition is that this method cannot work, why not try to prove it? It doesn't really matter that your supervisor doesn't share this intuition.

It's not very surprising that your supervisor insists on continuing in this direction since it was what you agreed to at the start. Now if this is not something you want to do, then you have no choice: you need to talk to them about switching to a different topic. Mind that it's not always feasible to switch to a completely different topic during the course of a research internship.

Without knowing the details, my impression is that it's probably in your interest to finish the work that has been started rather than restart something from scratch (I assume that it's only for a few months). The important lesson here is: don't accept a topic that you don't like in the first place. Keep this in mind if you choose to do a PhD later ;)


Are there universities with policies that default intellectual property decisions to faculty?

The University of Illinois (where I am a faculty member) classifies most written faculty work as "traditional academic copyrightable works", and by explicit policy all such works are owned by their authors.  If their creation requires university resources "over and above those usually and customarily provided", then by default the university gets a royalty-free non-exclusive license, but even that requirement is routinely waived.
My university also supports faculty releasing their software under open-source licenses.  In principle, any code developed with the support of a research grant requires university approval before it can be released, but in practice, faculty routinely publish their research code without prior approval (or censure) from the university.  I can see the possibility of a dispute arising if a piece of code were patentable, but the last time I remember the university wielding that particular hammer with any force, the NCSA Mosaic authors left (middle fingers high in the air) to found Netscape.
I have never felt any pressure to ask anyone's permission to publish an algorithm or source code.  (My first-order research area is algorithms.)


IF you're already a data scientist, then many US firms are crying out for your skills, and willing to pay really good salaries. I'd have a look at coming across to the US in employment as a data scientist with a good company that will probably be willing to invest in management training. The danger with the MBA route (assuming you mean full time at a good business school) is high cost outlay together with a period with no income - but then again only you know your financial position!


As first author, what should be included in the first formal communication [email] with other coathours

Just don't sweat it.  They are colleagues just be friendly and share the info you want to share.

I get the sense that you are not a professor.  Maybe you're still a grad student.  I remember feeling like this but the professors are (hopefully) looking at you as kind of colleague in the making not an undergrad who needs to make some show of respecting their authority and position.  Just be friendly and make sure you communicate everything they need to know and, if you are unsure if something is ok say so and ask, e.g., don't try and dictate the author order.

Of course, I'm a mathematician so I'm not in public health but if you are talking about United States academic culture and you're a genuine part of that (e.g. grad student) don't sweat the formality so much.  Of course, cultures differ so your mileage may vary if you are working with foreign professors who weren't educated in the US.


Goal for 20min. presentation at math conference

If you have one very interesting result, then I would go with focussing the talk around that. The alternative of trying to cram multiple topics into a 20 minute would be very difficult because that's not a lot of time. Your talk is more likely to be remembered if you present one very interesting result.


Do researchers at schools that publish good journals get priority in publishing in those journals?

The answer is certainly not - not officially anyhow - except insofar as being a well known mathematician (which someone who is at a place like Princeton typically is) makes it easier to get one's paper accepted to a fancy journal. That effect is likely real (though of a magnitude that would be difficult or impossible to measure, and hopefully not too large), but it typically applies on a more global level rather than a journal-locale-based level.


Should I accept the job offers before having the results for my grad schoold admissions?

Are the jobs and Master's programs in the same city? Many graduate programs are designed around the idea that many participants have 9-5 jobs. It may be possible to do work towards a Master's while employed. If you think that would be too difficult,  you might be able to ask your employer whether you can drop down to part-time status. Another option is to look into delaying the start of the Master's program for a semester or two, so you're not leaving the job right after starting.


Graduate Admissions - applying math phd without outside experience

REUs probably don't matter all that much. Presenting textbook chapters will not count as research experience, although depending on the material it might count as evidence that you can learn advanced material on your own. So definitely get a letter from that prof if you do a good job.

From what little you've said, you're probably only semi-competitive for a top 25 school, and probably not competitive at all for a top ten school even with stellar GREs. But there are a lot of factors in play. For example, not having taken grad-level courses is OK if you have a good undergrad math major. And outstanding letters go a long way.

As far as going to a top 25 school is concerned, people get way too obsessed with rankings. There are about fifty R1 programs in the US, and whether you go to the 20th or the 50th matters a lot less than what kind of work you do once you're there. The ranking is also not a reflection at all of the quality of the education you'll get, it only tells you in a very rough sense about the research quality of the faculty and the average talent level of the students. But the important word there is "rough."


In STEM fields, are ten-year, funded PhDs an exceptional case or more common than we think?

In the United States, long PhDs (taking more than 10 years) are a minority of STEM PhDs, but not exactly "exceptional" either. See image below, which shows percentage of 2006-10 doctorate recipients taking six years or less and more than ten years to complete their degree (via data collected in the Survey of Earned Doctorates):

(Image via MLA Office of Research blog)

In many US departments, if a student is making progress towards the degree (not just wasting resources), is a contributing member of the department, and funding is available, there is no general reason why the advisor can't continue funding if the degree takes longer than expected. Without funding, the student is much less likely to complete the PhD, which is an undesirable outcome for both the student, the advisor, and the department.

(In some parts of the world, there may be regulations that make it impossible to keep funding a PhD student for that long. Even in the US, some departments may set a time limit on PhDs, and/or on eligibility for some sources of funding.)


An inteview with another live offer out!

Has anyone heard of such things happening? Getting a backup lined up outside of the first round of invites to campus interviews after an offer has already been put out?

It's not usual, but I have heard of such things here in Europe. And why not? If the search committee already knows that, or at least has the strong impression that, their originally preferred candidates are not going to work out, why not immediately line up backup interviews? I should also note that they seem to be playing with unusually open cards towards you, so I would certainly count this as a positive.

If I understand you correctly, your main problem seems to be that you already have an offer that you cannot delay until you will get a decision from this school. Note that it isn't only about whether the preferred candidate will work out or not - even if the preferred candidate cancels, you still need to ace your own interview and do better than the other backup candidates (typically, if a search commission goes through the trouble of inviting backup candidates, they will invite more than just one person!).

At the end of the day, your options are likely as follows:

Try to delay your standing offer, and/or convince the school where you are interviewing to hurry up. Some schools seem to be fairly flexible with timing (I have heard from TT offers to be delayed for many months), others are not. There is only one way to find out.
Cancel your standing offer, and take the risk with the interview.
Cancel your interview, and take the TT offer.
Accept your standing offer, go to the interview regardless, and back out of your earlier acceptance if you get the second job. You certainly can do that, but you should expect some backlash. I would not recommend that, even if it may appear like the approach with the highest short-term profit for you personally.

If you need to decide right now (option 2 or 3), you should ask yourself (a) how much better the second job is than the first one, and (b) how disastrous it would be for you if you ended up with no offer at all. Oftentimes, when making such decisions, it is better to take the offer that you already have than a slightly better offer that you may or may not get, but at the end of the day the decision is yours to make.


Word limit for paper after addressing reviewer's comments

I can now provide an answer to my own question (I hope this is alright): I recently submitted a revised article that was about 15% longer than the word limit to a small biomedical journal. The original version of the article kept to the word limit. In the rebuttal letter, I explained that the article had become longer due to the reviewers' question. This article was accepted without further comment from the editor.

So it seems that at least some editors do not see a problems with longer articles, as long as the original submission keeps to the limit. I suspect that the rules may vary greatly between disciplines and journals and that no journal will ever explicitly state "we do not care about length for revised submissions". My PI was very confident that the article would be accepted, so it may be advisable to ask an experienced colleague in the field for their opinion.


What is a final undergraduate paper called in English?

In my experience, in Mathematics, in the U.S., (where "senior year" is typically the last year of an undergraduate degree), things done beyond literal coursework can be called "senior project", "senior thesis", "honors thesis", "senior writing project", or nearly anything similar, with no precise sense from university to university or even from student to student. That is, sometimes "honors thesis" has some actual requirement beyond "senior thesis", but not reliably so...


How "submitted", "to appear", "accepted" papers are evaluated in a CV?

It's a tiered system:

Peer-reviewed published articles. Published means published in any form, so it includes papers in all states published online on the journal's website, including “in print”, “ASAP papers”, “just accepted papers”, etc.

That's top notch: it demonstrates your ability to perform research, write it up and publish it. Those are key requirements for the job.

1b. Peer-reviewed accepted papers. All search committees I know will assume good faith, and accepted papers not yet published (thus without proof) are considered as good as published papers. If you want to (and the application format allows for it), you can actually join a copy of the manuscript (not as proof, but for committee members who may want to read your paper to judge its quality).
Submitted papers, non peer-reviewed papers. This has some value, as an indication of your recent activity. It is especially useful to the committee if you have few papers (junior researcher) or have not published much recently (so that it is clear you are still active). Again, you may want to join manuscript(s) to your application, or give a link to arXiv if you deposited it there.
In preparation, in writing, … There is no clear standard on threshold for what is a paper “in preparation”, so these are usually worthless on a CV. The only exception is if you have very very few (or no) published papers: applying for a PhD position, or early application for post-doc position, with 1 or 2 published papers. Otherwise, my advice is simply not to mention manuscripts you have not finished writing.


Is the phrase "We can see that ..." appropriate in research papers?

The goal of scientific writing is to transfer knowledge and information with high degree of clarity, precision, conciseness, and a reasonably natural tone. When editing written work, a quick litmus test is to slash away each phrase then evaluate if the sentence can do without it. "We can see that..." is a very popular candidate to be slashed because in 99% of the cases, the sentence's meaning wouldn't change:

  "We can see in Table 1 that the average age is 56 years old with a standard
  deviation of 7 years."

  "The average age is 56 years old with a standard deviation of 7
  years (Table 1)."

When describing graphs or illustration, we tend to see "We can see that..." a lot more frequently than in other plain text; most of these can also be deleted:

  "In Figure 1, we can see that females are the majority (67%)."

  "Females are the majority (67%, Figure 1)."

... or replaced by the graphical components on which that the viewers should focus.

  "In Figure 2, we can see that the sales of graphic novel have been
  steadily increasing since 2011."

  "The sales of graphic novel have been steadily increasing since 2011,
  as indicated by the dotted line in Figure 2." OR

  "The sales of graphic novel (dotted line in Figure 2) have been
  steadily increasing since 2011"

And a few random thoughts from also an ESL:

I tend to focus on how efficient the sentence is rather than how formal the sentence is. I will, on any day, take a PhD candidate who writes clearly than one who writes formally. "Formal" bad writing scratches the inside of my cranium.
When it comes to writing, I tend to gear away from pragmatic advices that say "You always have to..." or "You never should..." Languages and usages change along time; it's more important to be able to tell my ideas to the current crowd, than to be able to write an ancient script. Beginning learners should feel free to stick to a handful of "rules of thumb," but as the learning progresses they should develop their own judgment and some flexibility.
A journal is only as formal as the editors of that journal go. Check the guideline to authors, read the specified style manual, and read a few current issues for an overall landscape, and then write. Leave all other "formal this" and "formal that" behind.


I'm from India, planning to do Phd in Marketing Management. Can I pursue it with my job thats 5 days a week 10 hours a day?

Anything is possibly, but a PhD is a full-time occupation, so holding a job that demands fifty hours on-top seems infeasible. Even for a part-time PhD, you'd be working a lot of hours.
(Assuming a part-time PhD plus a full-time job is equivalent to a full-time job with fifty percent more in overtime is a fallacy in my mind. As is assuming two part-time jobs are equivalent to one full-time job.)


How to determine which textbook problems are the most useful when studying?

Some books list problems that increase in difficulty, so do the first one, the last one and one or two from the middle...


Is it good to compare universities in motivation letter for student visa?

If I were you, I would just write why I want to study at TU Darmstadt. Have a look at their web pages, name a few courses you find interesting and a few professors you'd like to study with. I think that may be sufficient.


How can I write a paper that will convince the reviewers that the results are non-trivial?

In the end, the significance of a scientific advance is determined not by how complicated it is or how much hard work was put in, but by comparison with what was known / possible before.

It sounds to me like you need to have a much clearer and stronger comparison with the prior state of the art, particularly emphasizing why the new result makes a difference to larger or deeper issues.  Depending on the nature of your work, this might mean anything from a little improvement on the prior work section to introducing new sections with explicit comparisons.

For example, if you were able to mathematically compute the Nash equilibrium for preference of donuts vs. muffins, that's a nifty little result, but it might seem obvious or insignificant.  If you can explain that this was something impossible with prior methods, because nobody had previously been able to deal with the breakfast uncertainty principle, then that is surprising and interesting.  If you can show that your result accurately predicts sales in major chain stores, then that is also surprising and interesting.  In either case, you are showing how your result has implications outside of just being a result.

Now, you could probably also make your work appear harder and more significant by obfuscating the mathematics, and that might "work" for purposes of getting this paper accepted.  I personally, however, consider that to be scientifically dishonest, and would strongly recommend against that.  Remember, that your colleagues are not stupid, and sooner or later, people will realize that you are fluffing up your results, to your detriment.


Professor said we should meet again, but never answered my email

Based on my experience with professors, he's probably just overloaded with emails and either missed your messages or hasn't had the time or energy to reply, since it's probably not high on the list of priorities for him.

Assuming he's a professor at the university you attend, you could try just stopping by his office and hoping to catch him there. I did a similar thing once or twice during university and it was generally successful if the professor happened to be in. (If he's in a fancy office with a receptionist you could even ask the receptionist what hours he tends to be in the office, or ask them to pass along a note.)


Will this be a case of self plagiarism or will it annoy the referee?

I have two choices:

  1) Do the small step in (P2) by merely citing the statement of the result from my recently uploaded arXiv paper (P1).

Yes, do that.

  But as I mentioned before, the step for which I need this result is a rather small one.

I'm not sure exactly what "small" means here.  If you mean that it would be easy to get around this step by doing something else, then sure: definitely consider doing that.  But given that you're contemplating attaching three pages of text, it seems that can't be right.  If you mean that this part of your argument takes only a small amount of space in your latter paper: so what?  If you mean that this step only contributes a small part to the result, then perhaps you might want to state the weaker result which does not use this step and then follow with a remark that using your other work the result can be improved.

  Would it really annoy the referee (eventually when I submit this paper) if he/she is referred to 5 pages in a long paper on arXiv merely to justify a small step?

I don't see why that would be annoying at all.  Virtually all significant contemporary mathematical work builds critically on past work.  Referring to the arxiv is ideal in one sense because everyone can access it: it is so much better than referring to your unpublished PhD thesis for the proof of a "technical lemma" (which happens frequently, by the way).  It would be easier for the referee if the other paper had already been published, but so what: things can move quickly, and most people do not wait for their past papers to be published in order to use those
results.  Because so many other people -- including leading people, whose work receives a lot of attention and is probably going to be essentially correct most of the time -- engage in this practice, by not doing so you would be slowing yourself down in a big way.

A conscientious referee would want to indicate whether or not she has read and vouches for the extra five pages or vouches for the result conditionally on the other paper.  What to do depends a lot on the situation: if in those five pages you claim to prove the Riemann Hypothesis then she will really want to take a look.  But reading five pages more is just business as usual for a referee.

  2) Copy down the entire proof of the required result from (P1), probably in slightly abridged format. But even then, this is likely to add at least 3 pages to the current paper and so it feels unethical (like self plagiarism / salami slicing or something like that).

Although I don't recommend the practice, I don't think it's unethical in the slightest, so long as you refer to the other paper.  Having your work be self-contained is a good thing.  Having everything you want the referee to read placed under one roof is also a good thing.  In this case I don't think that duplicating the material really saves anyone any time so I recommend against it, but you're not trying to gain any unfair advantage by doing it, so I have no ethical qualms about it.

  Ideally, I would have liked to keep the papers disjoint,

Why?

Anyway, are you by any chance a student or junior researcher with a supervisor?  This is a good question to talk to your supervisor about: there may be norms within your community or subfield that should inform your choice.


Paper review: The editor is from the same university as the first author and asking for a meeting

Being from the same university may or may not be an issue (it's hard to judge without knowing more details).  Asking to discuss a manuscript in person, however, is a huge red flag.

Communication about manuscripts should pretty much always go through official channels only, thus keeping an accessible record of the complete decision-making process.  Only in dealing with exceptional situations (e.g., plagiarism, negotiating transfer to another journal) is there likely to be any communication outside of these channels, and even then it should be written down.  This is to protect both the integrity of the process and also everybody involved---authors, reviewers, editors, publisher---since both acceptance and rejection are capable of ending up quite contentious.

The fact that this editor is asking to talk with you in person before you've even written your review sounds extremely dubious to me, and would cause me to decline to review for reasons of unprofessionalism.  There may or may not be anything incorrect going on, but it's at least evidence of a rather callous sloppiness that I would not like to be involved with in any way.


Submitting future research plan when intending to leave

Think about the worst case that can happen if you do/do not tell them. If you do tell them and none of your interviews results in a job offer, you're seen as someone who won't be around for long, in whom it is a waste of time and money to invest, etc. It's going to be detrimental to your continued career if you tell them that you're thinking of leaving unless you are certain that you will. On the other hand, if you don't tell them now and leave later, you're certainly going to annoy people in your current department and you may burn bridges, but by then these will be your former colleagues who will not be able to influence your career any more at that point.

So, if I were in your position, I would wait.


How to demonstrate the ability to represent your university at international meetings? (postdoc application form)

Your ideas about what is being asked seem to be correct. But rather than being repetitive, perhaps it is enough to just refactor the entire application, moving some statements from other sections into this one.
But the section need not be long if you say something like "As I wrote in my SoP, my experience and commitment to ..."
Don't leave it blank, of course, in case someone is mostly just interested in that section, but don't be boring. Think of the application as a whole and not as just a bunch of parts.


Citing a result due to a single author that appears in a paper with multiple authors

I would just cite it as "Jones and Smith" and not worry about it.  The standard in math is to cite papers by their authors.  If Smith wanted to be cited alone, she should have published the result herself.

I think this situation has some precedent in other fields.  I might be wrong, but think some journals such as Nature (see http://www.nature.com/nature/authors/gta/#a5.5 "author contributions") make the authors disclose who did what.  It does not mean that the paper needs to be cited differently depending on what part of it is used.


What are effective ways to deal with burn-out while working full-time during a PhD program?

Doing PhD studies isn't a trivial activity - there's a reason why most PhD students are full-time students. Unfortunately, that means you cannot easily both do a PhD and hold a separate full-time job. That would be equivalent to doing two jobs at the same time. No wonder you're burned out.

Options:

Switch to a part-time PhD. You'll take longer to graduate, and you'll still be working 1.5 full-time jobs, but if you're willing to work hard this could still work out.
Put your PhD on official hold (or perhaps even quit it if you can't put it on hold), get on a more secure footing financially, and then go back to finish the PhD. You'll take even longer to graduate, but you'll only be working one job at a time.

Personally, I'd prefer #2, because I've found that working >1 job at a time is really hard and imposes a heavy cost. It's bearable if the period is only a few weeks, but if it'll take years (a part-time PhD could easily take 8+ years to finish), I'll likely burn out anyway.


Are there any research careers except professorship for a person holding PhD in pure mathematics?

I can speak from personal experience. I have a math Ph.D. on a topic with absolutely no real world applications, I work in industry, and my job title is actually "Senior Research Expert". So yes, there are research careers in industry. And while I won't get rich off it, I can't complain about the remuneration.

However, (almost) nobody in industry will pay you for thinking about stuff, going to conferences and writing papers. My research is extremely applied, and I am very much constrained by a) what customers will pay for and b) what is feasible given our code base and software architecture. I simply can't go off on a tangent and argue that a particular algorithm is very elegant, if it is not implementable in a reasonable amount of time or nobody will buy it.

Depending on your Ph.D. topic, be prepared to change fields. I used to do something like discrete optimization - now I do statistics and time series analysis.

While I personally don't code (which the developers are very happy about), I work closely with the developers that actually turn what I thought up into software. Interpersonal skills and the ability to fit into a team and a software development process (Scrum) are much more important here than in academia.

Research mathematicians are rare, and few people understand what I do and why I'm paid. It took a long time and some very fortuitous circumstances for me to demonstrate that I do add value to the company, and I was lucky to keep my research job when my company was acquired - my new employer really doesn't have research positions as such, so I had to justify why I should keep my niche.

Finally, there are about five other originally pure mathematicians in the team I work with, two of them with Ph.D.s. None of them do anything that could be called "research". They develop software or do analytics.

Summarizing: yes, there are math research careers in industry. They are few and far between. Be prepared for an uphill battle, to change fields, to do what needs to be done.


Criteria of experience recognition for "TV-L 13" position

Since universities are governed by state law, it matters which state this is in. In general, you should be hired at Stufe 2 if

you have been employed (i.e., not receiving a stipend or contracted to provide a specific service)
for at least a full year (this can be on multiple contracts, though)
in a similar capacity as the position for which you are to be hired (i.e., after your PhD at a German university, research institute, or comparable institution)
within 18 months (i.e., there should not have been a cumulated break of more than 18 months between these employments, including ineligible forms such as stipends and service contracts).

(If you have more than three years of eligible employment, you are entitled to Stufe 3, but that is usually hard to get.)

Things are a bit more complicated since there is a wider catalog of förderliche Zeiten ("beneficial time") which the university may recognize (but usually don't to save money, sometimes categorically as in Berlin). This includes the more prestigious stipends or scholarships such as DAAD or Humboldt fellowships. This is not something you can argue for, though, but the hiring person needs to apply for with the administration if they believe they have to offer it in order to attract a specific desirable candidate.


Is there an international taxonomy of academic titles/ranks?

In general, the answer is negative.

Not only there are different systems in different countries (and same-spelled degrees may have different requirements), but even if a degree seems to be the same, it is not necessary  considered equivalent.

Often universities and institutes have some freedom in the interpretation of degrees earned in other countries. Common sense can be a good guide but in case of doubt you need to check if university (or institute) X accepts a foreign academic title Y instead of their Z.

For example, when I obtained degrees licencjat (3 years undergraduate, 180ECTS) and magister (5 years undergraduate, 300ECTS) from a Polish university, they refused to translate it into anything else (stating explicitly that it is not equivalent to anything else). However, some other Polish universities do translate it into Bachelor of Science and Master of Science, respectively. Nevertheless, my new institute didn't have problem to find them qualifying me for their PhD program.


What does "awaiting reviewer reply" mean?

It means reviewers have been invited but have not responded to the invitation.

It's not necessarily the same as 'under review' and 'awaiting reviewer scores'. The latter is a clear term that means reviewers have agreed to review the article, but have not provided a report yet. The former is a vague term that could mean anything: reviewer has been invited, reviewer has agreed to review, maybe even reviewer has submitted a review but there're other reviewers who have not yet completed their reviews.

In any case, there's nothing to do except wait.


As a post-doc applicant, should I address a professor by their first name in email after they addressed me that way?

Continue to use the surname until explicitly given permission to do otherwise. One way for her to give that permission, actually, would be to sign a mail with only her first name.

There is a power imbalance between you. She is probably not being entirely correct in assuming she can use your first name, but it is common for people in authority to take some liberties.

But I'd recommend keeping it a bit formal until that obviously no longer works. And my full name is "Bobby Buffy" then I'd never be Professor Bobby. It would either be Professor Buffy or just Bobby. (For the record, though, I'm not Bobby.)

Note that this answer may not apply everywhere. It has a US perspective.


"Cold-calling" for a post-doc position in a group that cites you

If the group is already positively citing your first-author works, then I would say that it's not really a cold call.  You may not have met, but when you get in contact, they will have some reason to distinguish you from the constant barrage of random people who email them asking for postdocs.

I would thus recommend getting in touch by noting your shared interests directly, including the fact that you've noticed their citations of your work, and being very straight-forward about your interest: you're going on the postdoc market, you've noticed the shared interests, and want to get in touch to see if there are good opportunities---either for postdoc or otherwise.  This way, it's primarily about the professional relationship, not the job application, which is what's best for you as well.  If they really do like your work and have funding available, they may jump to hire you.  If not, it is likely to still help build future collaborations and other opportunities.

If they are negatively citing you or if you're Nth author on the works they cite, however, then it's effectively just a cold call, and you should follow the conventions of your field there.


What does "engineering experience" entail

The form was asking if you knew how to do those things, not saying "you better know how to do this or else!". A little preparation in those areas may be nice, but judging from the situation, you don't need to spend all your time coding.

Here's my thoughts on it: if you're going to do an "experience and learn" type thing, you want to be in a position to get the most out of it, right? For example, I'm in an engineering internship right now (I'm a little younger than you, and my situation is kind of odd, but what I'm doing is pretty similar to what you'll be doing, sounds like).

If I didn't know some math and programming, and some bare basics about electronics, it'd be pretty miserable for everyone involved. But nobody expects me to win a Noble Prize in my first week. Everyone expects that, hey, I'm learning, and I'm probably going to need guidance to solve a problem, and I might need instruction in how to use such and such program, or whatever.

So what I'd do if I were you: brush up on programming, trying to understand the basics. You don't know what language they're using, and you have some Java/C syntax experience, so maybe try a different, easier language like Python that's quicker to write (or do whatever language you're most comfortable with; I just happen to be a Python fan) and try solving some of the Euler problems online (not problems written by Euler; they're just called that) using programs you write. That's a good way to practice if you know what you're doing to some extent, but need practice.

(Don't be afraid to google "finding length of list in [language]" or "doing [thingamajig] in [language]". I feel like, especially when starting out, a lot of programming means: run into problem, google error, google function used to solve error, type into program and adjust for situation.)

You can also review math (algebra II should be sufficient; I assume you've already taken it) and a little of the physics you've done if you want. If you've ever used a CAD program, you can review using that; if you haven't, maybe try downloading Autodesk Inventor - it's free for the non-pro edition, or something like that - and go through some tutorials with it so you get an idea how to use it.

Maybe look up some stuff about electronics, or about circuit board layout programs (I think there's one called Autodesk Eagle that might be free like Inventor). I don't know what all your thing will cover, but you get the idea. If you think something'll be covered, try to get a cursory knowledge of that thing, so you know what questions to ask and you're confident in your ability to, at the very minimum, figure things out going into it.

In the end, it sounds like you're going to learn a lot. "The forum sounds intimidating." That means there's a lot of cool people and topics that you don't know about yet that you're going to learn about! That's pretty cool.

Also, feel free to ping me in chat or in the comments if you want any specific advice on resources for different things.


Applying PhD during the last year of master studies

You can definitely apply. If not now, then when?
The number of publications doesn't matter that much because the number is just a number; it doesn't reflect the complexity or difficulty of the research you did. I would fully expect that the publication resulting from your Masters studies will be more substantial - i.e., involve more work, with more robust results - than those you did during your Bachelor's.
If it still troubles you, remember there are people who do PhD studies without having published any papers in the past,


How to make a list of potential graduate school?

It sounds like you already have 1) a list of potential schools and 2) some idea what schools you can realistically get into and which you cannot.

So take these schools and split them into three groups: those you should be able to get into (safety schools), those for which you have a 50-50 chance, and those which you would be delighted to get into (like Berkeley and CMU). It doesn't have to be a very scientific split; a rough one based on your intuition or whatever it was that made you think Berkeley and CMU are beyond you suffices. Then apply to some schools from all three groups.


How to know whether my submission to a mathematics journal is significant enough?

"Good enough for journal X" is not a mathematical claim.  Operationally speaking, it is precisely a matter of collective opinion.  Math journals group themselves into rough, approximate equivalence classes (which is also entirely a matter of collective opinion), and you should take this negative referee result as one data point that your paper is not good enough for a journal of that class.  If your prior belief was that the paper was roughly equal or better in quality to other papers published in journals of the same class, you should try at least once more at a different journal of about the same level.

A good referee report reveals something about why the referee thinks the quality of the paper is not sufficient, either in absolute or relative terms.  This may give you something to improve: either actual mathematical improvements or improvements in the exposition to make referees believe your work is more valuable.

In summary: it doesn't necessarily mean much on its own.  Revise if applicable and resubmit.  Good luck.


For applying to math postdocs on mathjobs, does "N Reference Letters" include one for teaching?

In my experience serving on large numbers of pure mathematics search committees at a couple of different research universities, people who read the files are often only dimly aware of what the ad requests.  The vast majority of files will contain 4 research letters and 1 teaching letter.  Even if they only ask for 3 research letters, it is a poor idea to not include a 4th if you have one since most people will have 4.

Some people go overboard and submit a ton of research letters (I've seen 8-9 in a single file).  This can also cause problems: 1. usually when someone has that many letters they are not uniformly strong/informed, and 2. it looks weird, sort of like a violation of implicit social norms.  Probably you won't cause yourself problems if you go as high as 5, but don't exceed that.


What is the purpose of an article repository

I was asked by a publisher to choose a repository where the article to be published will be uploaded to.

I've never heard of that before. Publishers usually want exclusive distribution rights.

  What's the point of this if the article is already available on the
  journal website?

You can update the repository version to make corrections, should they be necessary.

  Can someone please explain what is the purpose of a journal repository such as PubMed, Europe PMC, PMC?

To disseminate research.

  Is it desirable to use more than one?

One suffices. Increasingly it seems that repositories don't want you to upload elsewhere.


What happens if a reviewer withdraws himself from peer review process?

The two main possibilities are:

Find another reviewer.
Make a decision.

If the editor is sufficiently familiar with the field to check your revision himself, then he might go for #2. Otherwise (or if the journal's policies are inflexible) you might be stuck with #1 and have to wait for another round of reviews.


Can someone with only a master's degree promoted to a permanent full-time faculty at a two-year college?

You should take a look at the faculty credentials at this institution and similar ones (in Canada). Their websites should provide this information. You can see whether any permanent faculty have only master's degrees.
After you have taught for a year, and presumably done a good job, you might ask the administration about the possibility of a permanent appointment.


Should I publish a linear programming method despite my advisor's advice?

It is good to have publications. It is also good to follow the advice of your advisor for many reasons. Advisors have some say over your future, of course, so caution is indicated, at least, in every case.

Note first that it has been many years since I was current with the algorithms of integer and linear programming. I suspect you are more current and your advisor more so, so be a bit careful in analyzing what I say below.

The field in general is quite mature and the existing algorithms are very sophisticated. This was true 30 year ago, in fact. If the field has settled down since then there is little urgency in publishing now, as it is unlikely that you would be beaten to publication if you wait. You can make your advisor happy and, indeed, make progress on your main work without abandoning what you have.

However, I think that a real advance should be questioned and you should be the one to question it. In particular, it may be that the reason for such good results is that your specific problem has characteristics that make this possible and your algorithm is nicely tailored to a special case. The possibility of that actually opens a door for your future work. If it is true, then knowing and describing that special case would be very useful, along with the algorithm.

Also, if it is, indeed, a special case and you have tested only with the confines of this case then your results may not apply generally. It would be good to know, before you publish, whether this is true or not. And it would be especially good for you if you are the one to discover this. Fortunately, you can test your algorithm on a wider class of problems found in the literature. Thus, you can, perhaps, rule out the situation in which you have an anomaly. But your primary work should likely come first.


Is listing non-academic interests on academic CVs important?

The convention in an academic CV is not to include information on non-academic hobbies or interests that are not relevant to your professional skills and qualifications.

You will find this view confirmed on sites that give specific advice on the academic CV. (e.g.: this one).

That's not to say there's never a good reason to include this information; there may be, in some cases. (For example, you might mention your time abroad doing unrelated humanitarian work to explain a chronological gap.) But in academic CVs it's not standard.


Is it acceptable to use personal equipment for research?

Another PhD student in my floor asked how to fix a slow system. Here is my supervisor's reply:

  If you need to have a fast desktop, the best is to convince your boss to spend 3 days of your salary to buy a top of the line Linux machine (or a week of salary to buy a Mac).

Anything else is stupid on their part. Note that your cost is not only salary, but is also taxes, work insurance, university fees (where applicable), rent of the office...

Addition: Also, they got a grant to pay you, they need you to publish. The longer time you spend waiting for code to run, the less you will publish, and the less competitive they will be for future grants.

*Note: he was being moderately flippant, don't take the two days and top of the line too literally, but the point still stands.

The problem with bringing your own equipment is that:

It is yours, and  if you wanted to do something else with it, you wouldn't.
If it breaks, and a lab is a moderately risky environment, it is your loss and no one else will pay for it. Also, you may not  get support from the IT department to fix it.
It sets a precedent for other students to do the same. The stipend you get as a PhD student is quite meagre, and buying a computer out of it is a significant investment.
In some institutions research data  is considered confidential, and they forbid for it to live in non-institution owned devices.

This said, I often bring my laptop to work when I need the extra mobility, or my own workstation (a top of the line Linux machine) is overworked, but I don't rely on it.


Poor grades in courses related to my PhD thesis. Is that an indication to my research and future academic career potential?

My advisor says the grades and courses are a formality and I should focus on my research as I will learn more by doing than through any coursework.

Your advisor is right.  Listen to him.  Class in an engineering Ph. D. program mean very little.  Research is more important by an order of magnitude.


Is it okay to keep pdfs of journal articles from my previous university when my current university does not have a subscription?

This is an interesting question -- and yet when you think about it, it's horrifying that we'd have to consider even for an instant the propriety and legality of keeping our own annotated research materials. But, to provide a proper answer:

In principle, this may depend on the terms of the license under which you downloaded these papers. In practice, you are very likely to be in the right, both legally and morally. In general, I believe that the licenses allow you to reproduce (i.e., print or save) the document for research purposes -- without specifying a time limit or maximum duration of their subsequent use. See e.g. JSTOR's terms of service.

If you are asking about the ethical/moral propriety of what you are doing, you are clearly in the right to retain your collection of papers and notes on those papers. In fact, you may even have an ethical obligation to retain those materials if the notes therein are necessary to reproduce any of your present work.

As an analogy, think about what I did many years ago when moving from one university to another. I had an extensive paper collection of reprints, many photocopied from my institution's library and many extensively annotated. I boxed all of these up and brought them with me. No one in their right mind -- nor even most copyright lawyers, I'd imagine -- would have had me go through those files and discard the articles not in volumes held by my new institution.

Disclaimer: I am not a lawyer and this is not legal advice. It does seem to be good common sense, though, and sometimes that can be worth at least as much as anything a lawyer would tell you.


Asking A Colleague for a Letter of Recommendation

In a comment, you noted that this individual is working with you at your current position.
Yes, I think you should have a letter from a colleague at your current institution. Indeed, if you didn't have a letter from a co-worker (ideally, your chair, but I know that's tough for assistants) it would raise red flags. This letter should speak to your expertise in research, teaching, and service but almost more importantly, provide some context as to why you are departing. Search committees will want to have a narrative that you're moving to another university because it's better or for some other germane reason, and not because you're being forced out or are a toxic colleague, if that makes sense.
So not only should you have a letter from a colleague at your current university, I would argue that it's almost always a necessity.


In mathematics there are still regularly published English language translations of Russian language journals. Examples:

St. Petersburg Mathematical Journal
Functional Analysis and its
Applications
Russian Mathematical Surveys
Transactions of the Moscow Mathematical Society

There are quite a few others.

For most (if not all) of these journals it is often now the authors themselves who supply the translation (I believe this was sometimes the case long ago, although various US professional societies organized formal translation programs, sometimes with funding from agencies like the NSF; the issue is that translating research articles requires substantial understanding of the content, and this greatly limits the pool of potential translators).

Here is a Japanese source journal:
Sugaku Expositions


Does taking graduate course as an undergraduate increase chances of getting into graduate school?

Yes, I think most admissions committees would see this as good evidence of your preparation for graduate study.


I want to change my thesis topic (to the extent that the ethos is still in tact) but my advisor does not agree. What can I do?

The problem that you are facing is that your supervisor is not necessarily wrong to say:

  He says that he is an expert in B and his vision of the group is not inclined with me trying other things.

As hard as this sounds, as the head of a research group one needs to make sure that the people in the group follow some sort of unifying theme or vision. Otherwise, it is basically impossible to build any sort of profile. I am personally not a big fan of visions that resolve around a specific tool rather than a problem set or topic, because this often leads to the kind of research that boils down to "we have a hammer, and use it to punch whatever problem we can think of", but unquestionably a lot of research groups work like that. It also makes sense on some level, because in many fields techniques are more difficult to master than learning new problems and application domains, so it makes sense to keep the thing constant that is hard to learn and vary the things that are easier to get into from scratch.

Realistically, if 'B' is actually useless for your project, and your supervisor is adamant that you need to be using 'B', you can either change what you are trying to accomplish (the 'A' in your terminology), or change supervisor. That being said, depending on what you mean with 'preliminary results', this seems far from obvious to me.

  Another query is, is it ethical to collaborate with people outside the university (of course after letting my supervisor know) for my PhD work. My Masters supervisor would be happy to help me out.

Ethical? Sure - but that does not mean that your supervisor needs to be happy about it or let you do it if (s)he perceives that your main work suffers from it. Look around on this site on the topic of side projects - this has been discussed a number of times here.


How do you decide how to categorize a new idea? Patent? Present at a Conference? or Publish in a Journal?

How do you know if it is worth to be filed as a patent, submitted to a journal, or presented at a conference?

To commercialise, file a patent. To disseminate, publish a journal article or a conference paper.*

* Distinctions between journal/conference publication is dealt with elsewhere and, given the context, is seemingly out of scope.

  [Many patent ideas] were merely theoretical, without proving if the concept works flawlessly. So, how does this concept convince the people in the patent office?

US patent law demands usefulness

...an invention is "useful" if it...is capable of use...the doctrine prevents the
patenting of fantastic or hypothetical devices...

and European patent law demands industrial application

...a patent can only be granted...for an invention which can be made...

These requirements should prevent granting patents for theoretical ideas.


How to format a paper accepted to a conference?

Of course you should list a conference paper as part of your CV. Just make sure that, as you suggested, that it’s separate from peer-reviewed publications. Usually, “conference proceedings” or “presentations” or a similar section heading is used, depending on what records are available.

As for format, use whatever is the accepted practice and format in your discipline.


How should I approach this unfinished research that I do not want to do?

Talk to your supervisor when you know how long you will need to finish the publication.

You are currently in the phase of a project where you have to make very sure everything really works. This is usually the least motivating stage, but it is absolutely necessary. So your supervisor will (hopefully) push you to go through this phase and finish the publication, because finishing research projects is something you have to learn as a budding researcher.

Of course, not every project should be finished. If the costs (time invested) of a project outweigh the benefits (results and publication strength), your supervisor may want to abandon the project. It is important to find out how long you still need, and only then (if still applicable - maybe it's a two-week bug fix that doesn't feel like drinking bleach) have a discussion with your supervisor. You can bring up your independent research during that discussion as well - either as an alternative or as a next project.


How long after PhD Major Revisions sign off

I can't answer the question per se (as I guess no other than the assessment committee can). But I can add my personal anecdote :)
At my University there is a general rule of 2 months assessment time (1st handin). But for me after about 1.5 month I got a mail saying that the Ph.D. School of my university forgot to send my thesis to the assessers.

In general I would suggest that revision should not take more than 2 months.


Are there any experiment reproducibility databases?

While not a direct answer, publishing failure to reproduce can be difficult as a standalone activity (think cost, time, and rewards), and where reproducibility information does exist, it may be field or community specific (like blog-syn for organic chemistry).

But there are a few large and well-funded studies that aggregate information simply because their purpose was to replicate big studies- eg the Cancer Biology Reproducibility initiative, and perhaps some of these studies will grow over time.

You may also want to check sites such as Pubmed Commons and PubPeer, which increasingly are gathering discussion of papers.


Who does the pre-copy-edited version of a paper belong to?

The key here is not actually the history of the manuscript but the submission of a copyright transfer that moves the rights in the manuscript from the author to the journal.

If you sign a copyright transfer form (or a co-author does on your behalf), then all of the versions of the manuscript transfer in ownership to the journal. Author-friendly journals will then typically grant back a wide variety of rights, including the right to distribute preprints, and there are interesting interactions with preprint servers, academic networking sites, etc. The fact of ownership, however, is changed, and that typically applies to previous versions of the work as well.

Because of this, it is also true that the journal might publish your work but never actually own it!  For instance, the ACM now allows authors to choose between transferring copyright and retaining it but giving the ACM a license to publish.  There are pluses and minuses to both approaches, and it is still very much a question of evolving practice.


Can I write a paper on a method that is novel but yields similar results compared to existing methods?

As your three-image method takes a new approach, it is novel in the academic sense: It adds to the existing knowledge. Thus you should be able to publish a paper on this, though probably not in a high-ranking journal (unless you blatantly underestimated the advantages of your method). The rationale for this is the following and you may use it to motivate your method in your paper: Your new approaches may inspire other methods which in turn may drastically outperform existing ones or yield entirely new information.

You could write the paper directly in this tone, not focussing on the method you are presenting but on the fact that you can extract the information your method (and the others) yield in a new way. In this context, you may consider not presenting your method primarily as a method, but as a way to verify your approach to extract the existing information.

You might get bonus points, if you actually have suggestions how to improve your method to outperform the existing ones.


If the professor has a personal administrative assistant, try contacting them and even try scheduling the defense or other meetings through them. I have known professors who rarely respond, but their personal administrative assistants are very responsive and can schedule meetings or otherwise remind them of student deadlines.
If not, try contacting the general administrative staff of the department. The professor might be more likely to listen or pay attention to an email from someone they are familiar with.
Either way, don't be accusatory and try to report bad behavior. Simply say that you are trying to get in contact with this professor and have been unable to reach them through email or phone, that you need to schedule a defense, and ask for their help. They will probably forward your email to the professor; keep contacting the administrative staff every few days if you don't get a response from the professor.