How do I choose the right papers to write a review paper?

If there was an easy algorithm to determine, which papers are important for a topic and which are not, we would not need review articles. A list of Q1 articles with short descriptions can be automatically generated from a citation database and the paper's abstracts. There would be no need to put it into a separate publication. Your primary job as author of a review article is that of curation. You should consider all (or at least as many as possible) papers on a topic, select the important ones and put them into a coherent thread based on their content alone.

It will likely be skewed towards the highly cited, because they are highly cited for a reason. But the point is, if a paper is good and advances the topic, I want a review article to tell me about it even if it only ever appeared as a preprint and hasn't really been cited by anyone. Equally, if it appeared in the best journal, is cited by hundreds, but is only tangentially related and doesn't really offer any new insight into the topic, I don't want to waste my time looking it up just because it was mentioned indiscriminately with the others.


Can the peer-review process be "emulated" in class?

As Nate Eldredge says in the comments, peer feedback is an accepted teaching practice, and "simulating" peer review is one way to implement it.

This method is very effective in facilitating deep learning, developing critical thinking skills, encouraging clear writing, and promoting teamwork. It is less effective when the goal is to give some broad overview of a topic.

Some of the difficulties lie in assigning grades (for the outcome? for the review? what if they are not written?) and in overseeing the process.

Moreover, the process may at first seem efficient as it takes some load off the teacher, but this depends on the degree of oversight and steering. It is also quite time-consuming for the students.


Can good grades alone get me into grad school?

I'm interested in going to grad school for a master's in computer science

There are two distinct types of masters degrees in computer science, at least in the US.

One is the professional masters degree, which is entirely course-based. Professional masters are considered terminal degrees; by pursuing such a degree you are cutting off (or at least drastically reducing) any future opportunity to join a PhD program. Also, professional masters students are rarely funded. You pay tuition, you take classes, you get your degree, and you leave, with a higher salary. High grades and test scores can definitely get you into these programs, even in top departments.

The other is the research masters degree, which requires some courses, but also includes a research component ending in a thesis.  Research masters programs are often used as preparation for, or even soft entry into, PhD programs. Thanks to an explosion of undegraduate CS majors, it's become much more common for research masters students to be funded.  Gaining admission to such a program, at least in top departments, usually requires more than just high grades and high test scores. You also need some evidence of research potential (which doesn't necessarily mean actual research experience).


How should I write an email asking about the status of my PhD application?

I wouldn't make too much fuss about it. A simple short and polite email which states that the current state of affairs (letters were sent, you were asked to wait for a week) and inquires whether there were some problems with your application and what its status is.

On the side note, a week waiting is not at all alarming in academia, unless some explicit deadlines are in place. I would wait for at least another 10 days before contacting the professor.

I also agree with RoboKaren, it is highly unusual to apply to a professor. Therefore, another cultural/professional practices may apply in your case. However, a polite email is almost always acceptable (whether or not it is ignored is another question...).


What is the meaning of h-index for a journal?

The h-index for a journal is defined is just the same way that an h-index is defined for a person: the greatest value h for which there are at least h publications with at least h citations each.  Thus, for a journal, if it has published 1000 articles in its history, and 50 of them have received 50 or more citations, it would have an h-index of 50.


How to get honorary academic position in UK universities?

A number of UK universities have their policies on the appointment of Honorary positions on their websites. It appears from a number of them that the appointments are usually made upon the request from for example, the head of a school, within the institution.

It appears (from the University of St Andrews) that appointments are made when it is deemed to be beneficial to both parties.

  An Honorary appointment is an arrangement which allows distinguished individuals from other institutions and organisations to collaborate with academic staff at the University of St Andrews and have access to certain University facilities to further their own research, cooperate on joint research or contribute to the teaching of the University.  It recognises an ongoing association with the University.

In all of the policies it appears that the Head of School makes that application and it is the HR department that makes the final decision on the granting of the Honorary position.

I relation to gaining a Honorary position, I would think that if you are well known in your field of research there is a better chance of gaining one.

Here is a list of links to policies for the following universities.

University of St Andrews
Swansea University
UCL
Cambridge

In Ireland (my home country) I believe they are occasionally awarded. Trinity College Dublin have Honorary positions in their listing of academic titles


Need advice regarding my possibly conflicting research idea

If you have used those preprints to advance your ideas then it would be unethical to try to beat those authors in a race to publication of those ideas.

The problem is twofold. The first is just the possibility of a perception that you are acting improperly. This can be a big negative. But the second is that, seeing the other work, you have been already influenced by it, so it may not be proper to claim "priority".

You should probably do two things.

The first is to continue developing the ideas on your own and see where it takes you. Write them up as best you can.

The second is to wait and see what develops from the papers you studied.

If the final form of the other papers don't match what you have done you are free to publish (of course) and you may have a quick extension. You may even have a paper "ready to go".

But if they do match your results, you can just treat it as feedback that your thinking is sound and that you are developing appropriately as a researcher. Moreover it is evidence that you are approaching the research "frontier" earlier than many are able to do.

Since you are still an undergraduate such training is good, even if it doesn't result in a publication.

You also have an opportunity to contact those authors, now or later, as potential collaborators. Building a circle of people who are interested in the same things you are is a valuable resource.

And, of course, you said that most of your ideas are appearing in print. Don't neglect to follow up on the others.


Quantum information Science PhD position interview

More and less:

Asking personal questions about your motivation to choose the target program.
Asking about any of your potential ideas, as the main subject of the Ph.D. thesis.
Asking about your financial status and any need to support.
Asking technical questions from your undergraduate and M.Sc. level to assess your knowledge.
Talking about any of your stated stuffs within the CV to check their credibility and truthfulness of your claims, e.g. your expertise to work with an specific software (Be on the edge of your sit and just do not mention the case within the CV, in which you're not proficient).
Testing your linguistic capabilities within the interview, especially speaking skill, for devotion of some related positions such as teacher assistantship, based on your presented level of integrity.
...


What's the point of maintaining a CV after tenure?

Upon joining the club of those who've "made it," you find that there are further gradations.  A tenured professor can safely breathe a sigh of relief for at least a year or two, but eventually she will notice (i) that her salary is lower than most of her tenured colleagues and (ii) that she is still being asked to document and defend her productivity across several axes: research, teaching and service.  (Also, in many cases, (iii) She is increasingly pressured to apply for and get major grants.  In many cases, her future salary and promotions depend on this to a large degree.)

The main tool to exhibit your recent accomplishments in research, teaching and service is...your CV, usually.  In fact, "whether they want a good raise or not," most faculty are required to submit annual "activity reports" in which a CV is often a required component.  (When it isn't, it usually means that we manually copy information from our CV into some form or type it into some internal webpage.  So having an updated CV is more or less necessary for
many faculty members.)  Certainly having a carefully groomed CV is necessary when you go up for "promotion to full", apply for an endowed chair or distinguished research position, and so forth.

The bottom line: academia has bureaucratic, competitive and hierarchical aspects all the way through.  Most people who have made it tenure in recent years have learned how to keep reasonably up-to-date CVs without too much trouble or heroic effort -- the CVs do not need to be rewritten from scratch to showcase their skills for some new job, usually, so it is mostly a matter of regular updating -- so honestly, this is not the worst part of the bureaucratic minutiae.


How do I express my disapproval of a marking boycott without damaging relationship with academics?

Before you can understand how to express your disapproval, you need to understand a little bit about how the UCU (the Union organizing the strike) and universities work.

  I have not personally been affected too much yet, but have had one module's continuous assessment removed with no suggestion of replacement.

It is not the responsibility of those on strike to come up with the alternative. It is the responsibility of the University who is collecting your fees to deliver what it has promised.

  The union in question have poorly planned this boycott and there are currently no plans to remove it. We have had no communication about who is striking and what their alternative plans are if this continues and I am very concerned about this.

The marking boycott has been in the works for months now. The universities and union initially had extended discussions, but were not able to reach a resolution. The union then suggested if an agreement could not be reached, that they would recommend a marking boycott. After additional talks failed to reach a resolution, the union brought asked its members to vote on a marking boycott. After the marking boycott was approved by the union members, a final round of discussions were held. After those discussions failed to reach a resolution the marking boycott was initiated. The union is not allowed to contact students. It is the university's responsibility to contact students and tell them what is happening and what the alternative plans are. Issues about lack of communication and alternative plans should be addressed to the University.

  I want to express my disapproval with their methods as I disagree entirely with the boycott as I believe using students as pawns is never acceptable. For example they have been told "Examination of dissertations and theses at postgraduate level, as well as vivas, are included in the action." which is much too far. I don't want to damage the relationships I have with my lecturers as I plan on staying in academia, but seeing these actions is making me question my desire to stay in academia.

This is something that should be directed at the union. The union chose what they are boycotting. The union could have used a research boycott, a recruiting boycott, or a teaching boycott, but the union chose to focus on current students.

Your student union may be able to help you voice your concerns to both the university and the union. It is possible that your student union is backing either the union or university and will not pass on criticism to either. If you want to contact someone directly, the UCU is suggesting students contact the vice chancellor's office at their university. To contact the UCU you could use anyone on the UCU contacts page.


What's the "proof" of having presented a project results in a conference?

Most of us have some items on our CVs that have no supporting proof.  I recommend checking what can be found on the internet to be sure the information on your CV matches that information.  If there is a big mismatch between your memory and the written record, you should ask for advice on that. However, if there is no listing at all, go ahead and put down the facts as you know them, before you forget them.

The real issues is whether in your field, people generally list presentations by collaborators.  If not, perhaps it is normal to list on-going projects and collaborations.  Or, if you have a short CV, you can buck convention a bit and list what you think is relevant.  You can remove it later on.

The confirmation of many facts on your CV will come from letters of recommendation.  If your "common guide" writes in a letter it will likely mention the collaboration.  Also, most letter writers will ask for a recent CV, and will tell you if you have anything that looks misleading.

By the way, you probably should not list a URL to any paper you get published.  Stick with the formal bibliographic conventions, and perhaps list at DOI.  If you have something like a code repository, you should then put in a URL.

On more thought.  The fact that your guide can validate this work is just one reason to pick that person as a letter writer (referee).  From what you wrote that seems like a good choice, but you need to think about all sorts of facts. (There are Lots of questions on that sort of thing on this site.)  If you have other letter writers who can expound on your research accomplishments and abilities, you might not select this person as a letter writer.  It still could be fine to list this item on a CV.


How can I provide proof that my paper has been proofread by a native speaker?

This seems like an unreasonable request. Frankly, it does not matter if you paper has been proof-read by a native speaker or not. If, after revision, your English presentation is still bad, the editor won't accept it even if you include proof that it was read by a native speaker.

I would personally be prone to just ignore this request, make sure that the English language is as good as it can be, and resubmit the paper.


Is it okay to submit the revised manuscript well before the due date?

Yes, it is fine to submit revisions early.
The timescale doesn't really come into it. Either the revised paper is good enough for publication, or it is not. The logistics of when you carry out the work and how long it takes are entirely up to you. The important thing is that, in your covering letter, you explain in detail why you have chosen not to follow recommendation 4.

In fact, submitting the revisions early could even benefit you. It will mean that the paper is fresh in the editor's mind, which could mean they are able to make an informed decision more quickly.

Note that if you did want to do number 4, but 45 days was not long enough, it would be very reasonable to contact the editor to explain this and ask for an extension.

(NB I don't quite understand what point 4 is asking, so it's possible there is some subtlety I am missing. This is Okay!! Why didn't you do it? What is "this"/"it" and what is meant by it being "okay"? I presume these are not the exact words that the reviewer used.)


Is it okay to record audio for a lecture?

The legal issues involved will, of course, depend on what legal jurisdiction you are asking about. However, there are some common factors that can be considered.

In the UK many institutions take the interpretation of the Disability Discrimination Act (DDA) that teaching staff cannot prevent students making private recordings (Audio or Video) of any teaching activity. The reasoning is that students are entitled to keep their condition confidential (as it may be a private medical matter) but also must be permitted to receive the appropriate adjustment for their condition. It would be expected, as a courtesy, that the student would inform the staff concerned that recording was taking place, but that this could not be enforced. (*)

Conversely, the Intellectual Property (IP) of the class and the material contained therein would be held by the University and the individual teacher to varying degrees. The recording could not be published or used for any means other than private study as this would then violate the rights of the owner of the IP.

Many aspects of disability discrimination, privacy and intellectual property legislation is common across many EU states, but there are variations in practice. I can imagine how these different statutes might interact in (say) the US, but I suspect it might vary from state to state and not always be a federal matter, and so I decline to speculate.

(*) I have responsibilities for assisting academic staff understand these issues in my department...


Non-academic positions after PhD in computer science

There is a large and active demand for computer science Ph.D. holds outside of academia. Some of the main classes of positions:

Contract R&D organizations like IHMC (near you in Florida) or my own employer, work a lot like soft-money academia.
Government laboratories are much the same, though the money works differently.
Government agencies need Ph.D.-level people to help manage their R&D portfolios, either directly as program managers or via private-sector contractors like Booz-Allen.
Giant companies like Lockheed-Martin, Pfizer, or Ford have high-tech or internal R&D sections that do Ph.D.-level computer science work.
Near any major tech university, you will find lots of startup companies and  consulting firms and other odd niches.
Finance companies and hedge funds will offer you lots of money in exchange for your immortal soul.

These are just a few of the more typical routes: the research ecosystem in the US is actually very complex and has a lot of strange niches; I don't have solid numbers, but I suspect the outside-of-academia R&D world is actually much larger than traditional academia, and that's even before we start counting non-R&D positions like hedge funds.

Some of these sorts of jobs, you can find via ordinary online job listings.  You'll likely do a lot better, though, if you reach out through your professional network and research community.  Your advisor and other faculty are one good place to start: they'll likely have former students and other colleagues to put you in touch with outside of academia.  Another good step is to go to the big conferences in your area, especially those with a more applied flavor, and look for the industry people there.  You'll likely find quite a number of good opportunities, especially if you are a US citizen.


How to deal with disagreement with advisor regarding research proposal and direction?

I have regularly had problems with my supervisor regarding scientific direction. I have always known that I write much better than I speak. About 6 months into my PhD I reached the conclusion that its possible that I am not able to coherently convince my supervisor regarding my ideas and reasoning.

This has in fact been pointed out to me by my PhD advisors and also the examination board. In their words, I have an extremely unstructured, abstract and convoluted line of thought. Although, I may reach at the same conclusion, my process is not easy to understand for other people.

So what did I do?

I adopted the show them before telling them process. So whenever I wanted to introduce new ideas to my supervisor, I would generate data for the same, create a presentation and then speak to them. This mostly meant that my supervisor got the point.

In you case, that may not be possible because your application is due in 5 days.

In that case, I would suggest you write up an alternative draft containing your vision of the proposal. Do this, but also complete the proposal your advisor wants you to write. Before submission, when reviewing the drafts send both proposals to him in a politely worded e-mail asking him to review both.


Is it ethical to use a textbook required for a class that was easily found online?

If you're asking whether this will be seen as ethical by a university administration, the answer is no. The law probably lines up with the ethics that fall into the professional norms of the university admin.
However.
The money that the public pays for textbooks does not flow into the pockets of the people that generated or summarized that knowledge, so the system is far from fair.
I had a professor who actually told us to download his book illegally if we could get it, and when we pointed out he was the author, he said he made negligible returns on the sale.
Which gets us to the professional norms of your field. Some fields are big supporters of free access to knowledge. In these fields, the arxiv and scihub are popular. Downloading anything illegally if it's academic knowledge would generally be accepted as ethical within the professional norms of those fields.
Personally, I believe academic knowledge should be much freer than it is, and everyone should have access to the work we do. I'm not studying physics because I want to get rich. I study this because it's beautiful and it's important, and because these are fundamental questions for humanity, and answers should be shared with humanity. We all benefit from living in a society that's informed about itself and the world around it.


How do I approach my group about dividing up the work?

Your approach is fine, even though I would propose a face-to-face meeting in which the assignments are made.

Tipp: Try to make the work packages independent of other peoples result, especially make sure that noone is idle in the beginning because they have to wait for a result of another one.


I worked at three different Universities in Germany and I can not confirm such a level of disorganization. Of course we are having problems because we are public entities, which means e.g. that we can not freely decide where to invest or to shift money from cost center A (e.g. personal) to cost center B (buildings), or hire as many people as we like, or pay the wages we thing are appropriate, but those problems are minor issues compared to the ones described.

It is correct that many management positions are held by amateurs (like me ;-) ), but this is manly the academic part (research, dean, ...), but our "true" administration is in the hands of professionals lead by the head of administration (in Germany "Kanzler") who usually has a management background and expertise.


Does a post doc at a prestigious university make up for doing a PhD at a lesser ranked university for Mathematics?

Actually, what is better is what you do in whatever circumstances you end up in. If you are productive and publish good research, the institution at which you do it is of little importance. But any institution at which you can find good collaboration resources, such as weekly seminars in field, are valuable. Larger places which larger faculties tend to have these. But even quite small institutions manage it.

One of the reasons that few people are winding up with tenure track positions at R1 universities is that the number of total positions offered in a given year is small compared to the number of potential candidates. So, the competition is fierce, but it doesn't consist of ranking the candidates in the order of the prestige of their institutions.

Go where you will find people with similar interests and who are willing to work with you. Write a lot of good papers. Build an expanding circle of collaboration. The very best faculties are not, in fact, concentrated at only the very most prestigious universities.

Note also that doing mathematics alone without any feedback or synergy is very difficult. So, a group of like minds is very valuable. It is possible to wind up at a prestigious place where there is actually no one to give you any support. It will be difficult to advance from such a situation.


Do you need to know in detail the last papers of your future PI in preparation for a postdoc interview?

The advice "look at the latest..." is good advice. Whether it is necessary to do depends entirely on the views of the PI. They may care deeply, or not at all. Certainly it is better to be as prepared as possible, even if their main concerns are elsewhere.
If the position is competitive, then it is likely that other candidates will be as prepared as they can. Due diligence, I guess.
Even if you only bring questions about those papers to the interview you will be better off than being completely unprepared.


Definitely don't print it before achieving your degree, in case you have to make major corrections (in which case the book would be a wasted expense).

In the UK, at least, it's usual for the final copy of a PhD thesis to be bound as a book - so in some respects, what you say about "ready to go to the print shop immediately" is already surpassed. However, that is not to say that the internal format of the work is that which would be expected for a normal book, and I imagine that this --- as well as perhaps writing to be accessible to a slightly wider audience --- is what is normally involved with somebody publishing their humanities thesis in book form.

The question that you perhaps need to ask yourself (or better explain to us) is: Why do you want to do this?


What are the conventions for indicating programming variables within text?

It is common to typeset code with a monospaced font (a font whose characters have all the same width), like get_config_value.

If you're using LaTeX to write your thesis, you can use the command \texttt for inline code. For clarity and flexibility, it's probably better to define a new command, e.g. \newcommand{\code}[1]{\texttt{#1}}. You can use the listings package for longer pieces of code.

For other typesetting systems or word processors, check their manual.


Is there a generally accepted format for submitting papers to journals?

The policies vary entirely from journal to journal about what is considered acceptable. APS journals, for instance, will accept both MS Word-based documents as well as documents formatted with RevTeX, their modified template system. ACS journals and a number of other publishers also offer their own LaTeX- and Word-specific templates for authors to use. Whether the use of the template is required or merely recommended is also a function of the journal. So, as a general rule, you should always check the homepage of a journal before you start preparing an article for submission to that journal.

To some extent, I prefer working with LaTeX in preparing manuscripts, for the simple reason that their plain-text document format makes it a lot less painful to switch back and forth between different templates, compared to a word-processing format like Word or LibreOffice or Pages.


Is there anything inherently wrong with publishing in a bad journal?

It probably won't hurt, but this is the sort of thing you should discuss with your adviser.  Since the journal doesn't have fees, it is unlikely that it is an outright predatory journal but that doesn't mean it is worth responding to. Is this in a field where responses are a normal thing? Other relevant questions: And what do the other papers in the journal look like? Are they absolutely awful or are they just mediocre? That should tell you something about how worthwhile it would be to respond.


My advisor wants me to include a name of someone who has no contribution to the paper

The behaviour of adding non-contributing authors is not considered good practise; quite the opposite. The Vancouver protocol specifies what is needed to be included as (co-)author. See descriptions at ICMJE and BMJ.

The basic points are as follows:

  Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work;

AND

  Drafting the work or revising it critically for important intellectual content;

AND

  Final approval of the version to be published;

AND

  Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Note the "AND".

There are also several posts on the tag authorship here on Academia that can be of use.

For someone to stand up against one's advisers is of course difficult and it is easy to state that one must do so. It is necessary to assess the situation and read up on the recommendations provided by learned societies such as BMJ and use that as part of your case. I strongly recommend this paper for students from APA Science Student Council.


Is a Graduate Performance Diploma considered an academic degree for purposes of PhD admissions or faculty job search?

I did my undergraduate in a large, prestigious music school, which also had (probably still has) a Diploma option.  Before I answer your question, let me tell you something about my degree requirements.

I had to take lots and lots of credits in my performance instrument, and ensembles, large and small.  Then there was lots of music theory, music history, music literature.  A tiny proportion was in other departments -- I took one English, one math, one history, one science, and one social science course, if I remember right.  That's not much for a 4-year degree!  But now, for the Diploma, take out everything except the performance instrument and the ensembles.  Well, apparently at Johns Hopkins, you also do some music theory-type courses as well.

The students that I saw doing the Diploma were typically from another country, were planning to go back after the Diploma, and were there just to further their study of their instrument with a particular teacher, usually a famous name.  It was kind of like a post-doc.  They were soaking up the great person's approach to technique, expanding their repertoire, getting more experience, polishing their performing.

Music schools offer the Diploma because they know there are students who only want to work on their performance instrument.  So they cut out all the extraneous stuff and give the person a Diploma.

This would be good preparation for a performance career (orchestra, chamber music, solo concertizing), and for teaching the instrument in a private studio.  However, it would NOT prepare one for teaching in a public school, community college, college, or university.  However, it would help one prepare for teaching in a conservatory (if the person were a strong enough player -- s/he would have to be extremely strong for this).

If you are from another country and are planning to go back, chances are you are going to do, or you did, some academic work in your home country, and that will fit better with the academic system you plan to seek a job in.

A lot of the Diploma students were astounding musicians, though, who did seem to have a shot at a well-paid performance career.  That I can't be sure of, though, because I don't know what the employment options for classical musicians are in Europe (which is where many of the Diploma students were from).


How to decide what writing sample to include in a phd application?

I think most of the other advice given above is sound. Let me add two things that I've noticed in reading work by first and second year european grad students who are transitioning into the US system.

The paper you send for a writing sample needs to have a clearly identified thesis in the first or second paragraph of the paper. If you can't think of something better write, "In this paper I am arguing that . . . " Many of my european colleagues want the thesis to emerge slowly, reflectively, at the very end of the paper after all the scholarly qualifications and so on have been properly put forward. Don't do that for an American audience. Tell us up front what you are trying to say.

Second, hire a native english speaker to proofread your paper for you and really work on grammar, spelling, idiom, and style. Writing well is really hard and it's the primary job you'll have as an academic. (Your writing in the question is excellent. I'm just saying having somebody who really knows English double-check it.)  Coming from Italy, I don't think most admissions committees are going to hold language against you constantly. It is easy to create a subconscious impression of carelessness with casual mistakes in the language. For something as important as getting into a good grad school it's worth spending some money to get this part right.

Good luck.


Applying in Germany - how far back should the documentary evidence go?

If you did not get an answer from the person in charge, I see two possibilities:

Go all in and send all documents. You have them all ready anyway (you have them, right?) and if they request it, they can have it. If you go for this option, make sure that your CV is well organized and that the whole application document is perfectly ordered as well.
Just attach the most recent ones and add something like "Complete documents can be given if needed". This may save you some time and maybe the committee will not need the documents anyway.

From my experience, these rules often sound more strict than in reality and in reality the committee often does not know the exact rules anyway. But there is always the possibility that some committee member insists on following all rules to the single letter.

Another thing: Often there are two people to ask questions about the ad: The dean and the head of the committee. You may also ask other faculty members at the institution if you happen to know somebody there.

Another remark: As a head of a search committee it is pretty normal to receive phone calls close to the application deadline, so it a question is urgent, rather call than write an email.


If authors leave out diacritics, should I correct them or leave it as written?

In my opinion you shouldn't change the title.

The purpose of your reference is letting your readers find the referenced work, so changing the title (even if it is to correct a mistake) may make this harder or even create inconsistencies in scientific indexing services.


Should I do a group project on my own? If so, how?

A group project in class isn't the same as an assignment at a job.  The teacher doesn't need this project done and isn't paying you to do it.  The project is assigned for your benefit and it was assigned as a group project because not only is course material to be learned but also teamwork skills are to be honed.  Use this opportunity to practice working with a group.  Hone your interpersonal skills and see how good you can make the result in spite of having less skilled teammates.  That's really the point of group projects.


What's the role of colloquiums in academia?

what the speaker is seeking by giving such small talks?

One word: exposition.

As a rule, the more senior a researcher gets, the less of her/his attention is devoted to writing single research papers. It becomes more central to be known for a specific niche, a specific topic where (s)he is the world's foremost expert. One does not become such a figurehead for a specific niche by writing good papers in the area alone (although, clearly, this is still required). One also needs to be an ambassador for the niche. This includes giving keynotes at conferences, as well as giving seminars and colloquia.

  Also, who can give such talks

Everybody who gets invited by somebody. However, typically, one does not give keynote-level talks before senior postdoc or assistant professor level, simply because most PhD students do not have all too much of a vision going beyond their thesis yet. And, frankly, the keynotes of most postdocs also suck. Like most skills in academia, giving good exposition talks is also a skill that comes with training.

(there are exceptions, of course - I can think of at least one outstanding PhD student in software engineering who was regularly invited to give keynote talks at conferences midway through her dissertation)


Since your departure is known to and supported by the head of the department, there is no real issue here: you can talk about your departure in any way that seems most reasonable to you.  I don't think there is any canonically best way to do it.

In my (limited) direct experience, faculty who leave but do not retire often do so without an "official" announcement.  The exceptions have occurred when we want to rehire into the position before the new academic year.  Maybe it would be better in some ways if there were an official announcement.  If you feel that way, I would talk to your chair about it and ask if they would like to make an announcement on your behalf.

  What do you say to students?

That surely depends entirely on what kind of students you have and the nature of your relationship with them, about which I know nothing and you know everything.  I presume that as a PT lecturer you have not been advising graduate students in any kind of official capacity.  But if you know of specific students for which your departure would cause a definite and substantial disruption -- well, sure, I think you should tell them as soon as you know you're leaving.  That seems to be essentially common sense.

Good luck in your new job.


How realistic it is to change to a different field of mathematics after PhD?

I think it's quite misleading to hold up examples of very talented mathematicians or mathematicians from the distant past.  The answer depends heavily on the field you want to switch into, hold closely related it is to the field you wrote your dissertation in, and how talented and hard-working you are.

In the most classical, long-established subfields of mathematics, there is a large amount of background one needs to learn to be able to do significant, original research.  To take the worst example I know, a graduate student who wants to work in the general area of the Langlands program needs about 18 months to 2 years of dedicated study after their second year graduate courses to get to the point where they can tackle some problem of interest to the research community, and this is with an advisor to guide their study and steer them away from pitfalls that would result from having an incomplete knowledge of the field.  (In particular, this means the graduate student likely still has some blind spots in their knowledge that would greatly slow down their research if they didn't have an advisor.)

A graduate student doesn't only have the advantage of an advisor; he or she also has a good deal more time.  Most postdocs and almost all professors have more teaching responsibilities than graduate students, and professors also have service responsibilities which increase as one gets older.  Furthermore, one also has to do enough research to write somewhere between one and two reasonably significant papers a year (depending on subfield) in order to be competitive for jobs that allow time for research and eventually to earn tenure in such a job.  If one wants to switch into a new field, then one presumably has to do this research in their old field while learning the new field.

If someone in representation theory or algebraic geometry or other parts of number theory wants to switch to working on Langlands, then he or she needs to learn the material in one second year graduate course (because they already studied the other two or three that a complete beginner needs) and another 18 months of specialized study.  It's true that some patterns of thought will be familiar, even if the specific ideas are different, so one is going to learn somewhat faster when one learns their second field, but moving into a new field still requires at least a year of dedicated study unless someone is an unusually fast learner or extraordinarily hard working.  Most people don't have the time and energy to fit an extra year of work above their other duties within any reasonable timeframe.  Fifty years ago, one could have given up a couple years of paper-writing to accomplish the switch, but someone trying that today would never get another job that allows significant time for research in today's far more competitive job market.

Most areas of research don't require as much background as Langlands, but unless one is moving into an essentially brand new field requiring minimal background, switching fields requires a substantial amount of time that one simply rarely has after obtaining a PhD.

Lack of an advisor can be an issue, but it is less likely to be one than lack of time.  Many fields do have a significant amount of "folklore" that is well-known to experts but not clearly stated in print anywhere.  These are usually ideas that are too advanced and specialized to appear in a graduate textbook, but at the same time too easy to be the subject of a research paper.  At some point this folklore is used to establish more significant results in a paper, but since "everyone" knows it, it might not be explained very clearly or be easily found by someone who needs it for some other purpose.  However, most fields have experts who are quite friendly and willing to explain the necessary folklore to new entrants to the field, and, at worst, one does things in a clumsy way in his or her first papers in a new field and has some folklore pointed out by a referee.  If one appears talented and capable, then it is not so hard to get some help.
Researchers in countries not connected to the international mathematical community (such as in Africa) generally face much more significant problems with having access to experts than people trying to switch fields.

Is it possible?  Yes, but it's very hard.


Example of educational theory not taken in account in e-learning software?

Moodle and Blackboard & co are learning management systems, not e-learning software that is sometimes (but not always) built into such an LMS. There is indeed a lack of educational theory behind many e-learning units, for example, the learning goals are not clearly defined, the target group is not specified, the evaluation of the learning goals (if stated) does not actually match, etc. And there are many side issues (hidden curricula, usability, etc).


Sabbatical disruption: common annoyance or warning sign?

I work at an R1 institution and we've had a similar, if not more stringent policy in place for at least a decade. I will say that the sabbatical review, like the tenure review, process is different for different disciplines, but I can also say from first-hand committee experience that the policy changes are stemming from what some might call the abuses by the older, tenured faculty, not young tenure-track faculty.

The internal soap opera at many schools right now is around the senior faculty who teach one or two classes a year, advise two or three students a year, and claim their sabbatical every 5 years in order to re-edit a book they published decades previously. Upon completion of their sabbatical, those seniors submit a one-page memo to the Dean declaring the whole experience a success because they updated the footnotes of said book. Meanwhile junior faculty are teaching 500+ freshmen in each of their 3 classes, trying to publish, patent, and mentor.

Honestly, the process of documenting or time-tabling the work of the sabbatical is meant to provide accountability on both sides. If you are a scientist who needs computing time or a laboratory and the department has committed the resource to you during your sabbatical and then fails to deliver, you have proof of the broken deal. Deans and Vice Presidents of Research are starting to take this seriously, and they are starting to notice when some departments systematically fail to deliver.

The assumption that the policy is meant to or might potentially harm researchers is misplaced. If you see hardworking, grant-carrying faculty who want to finish their  NIH R21 and is denied sabbatical, start asking questions. If you see the guy who only ever shows up for the faculty retreat and hasn't published since the 1980s get denied, go kiss your regents.


How and why are PhD programs free in Europe?

I believe what you're talking about is the issue of tuition waivers: that is, are students obligated to pay fees for the tuition, or are those handled by the university.

In many countries in central Europe (including Scandinavia, Benelux, Germany, Switzerland, and Austria) PhD studies are actually paid employee positions, so what tuition charges exist are small, since students normally don't have to take many courses as part of the PhD program (international students may need to register for a few classes to satisfy qualification requirements, but it's not a coursework requirement per se). In other locales, such as as some programs in the US, grants cover tuition charges as well as stipends, preventing students from having to pay those charges. And in many of those countries, the tuition fees amount only to a few hundred euros, not tens of thousands.

It's only where students are expected to do large amounts of coursework and where no arrangements to remit or waive tuition are made that students are responsible for paying large amounts of tuition.


How can a non-native English speaker get assistance in publishing a manuscript in English?

In mathematics, it is entirely reasonable and acceptable to begin by posting a draft on arXiv.  Once it's up online with your name and a date-stamp, you need not fear anybody stealing your ideas, and can work on improving the manuscript, both in content and grammar, with whatever combination of colleagues and collaborators you find best suited for the task.


When is a not updated software considered deprecated in the academic world?

I don't think there is such a standard, certainly not one applicable to all of academia. For your thesis, I would suggest that it might be more useful to talk about "recently updated" / "currently developed" software, rather than labeling the rest as obsolete.

"Deprecated" signals that the creator no longer recommends using the software. I can't think of any real examples for a full software package (i.e. going beyond deprecating part of an API), but I guess it might happen if the software is known to produce bad results.

Software might be "obsolete" if it has been de facto replaced by a better option, but certainly not just because it's old. Even then, the old option might be good enough. Visit a couple of (established) experimental labs in the sciences, and you'll likely see lots of old equipment still running old software. Changing it all out would just be needless overhead, and not be guaranteed to help. There's almost always a better place to spend the money you might have... From another angle, if you consider numerical algorithm implementations and libraries as tools, there's a number of them that have gone decades without updates, yet are still routinely imported and used in new software development.


How do I cite or reference code that has not been officially published?

If it is part of the website or a webpage, simply refer to the webpage in your references. It clearly mentions that you are referring to a code which is published on a website.

Just look at this structure for a Chicago styled reference:

  Last Name, First Name. "Page Title." Website Title. Web Address
  (retrieved Date Accessed).

You can produce your citation like this:

  Code Producer's Last Name, Code Producer's First Name. "Sample computing source code for idea/pattern/code." Website Title. Web Address
  (retrieved Date Accessed).


University I rejected is asking which other one I chose over them; should I tell?

I can't think of any harm in telling them, and in the medium term, this isn't a secret, because it will certainly be clear by the fall where you've gone since your name will probably be put on the department website.  If you're uncomfortable, it's certainly fine to wait a bit until you've finalized things at the school you accepted; you don't even need to tell them you're doing that---just wait a bit before replying to the request.

It may help to know that it's standard for schools to want to know where students who reject them are going, so there's nothing unusual or suspicion raising about the question.  It's useful information because it helps them assess their program and admissions practices.


Why do some reviewers mention their decision explicitly?

Typically I include an explicit recommendation in the report to be shared with the authors when I have a strong opinion, but not necessarily otherwise.  In the former case, the editor can still decide either way (referees make recommendations, not decisions), but if they disagree with me at least the authors will know for sure what the referee thought.

  what is the point of adding the decision statement while the overall evaluation (i.e. on EasyChair system) explicitly says it? is it just the reviewer habit?

It may be habit, and it may reflect uncertainty about what information from the web form will be available to the authors.


Applying for a graduate course not related to my previous research experience

I'd say, go for it! Two reasons:
1) If you stay in academia, you're going to use your creative and imaginative skills a lot. And my experience is that they don't work much if you aren't interested in what you're doing.
2) You will have an interesting edge over other candidates since you come from a close, but not overlapping area.
It will take determination to enter a new area, but I think you're absolutely on the right track in pursuing what you're passionate about; and yes, you're still in time! Don't give up. :)


Delays happen regularly. That is nothing to worry about. Professors often have a high workload.

However, it is expected from a Master's student and especially a PhD student to be able to work independently. A single meeting with a professor should give you at least enough input to start working on the topic. That is, learn the fundamentals in this area, read papers (those of your professors would be a good starting point) and think about your own ideas.

That said, you might not be able to provide a perfect solution for the problem with the input you already have, but it is expected from you that you have at least something at the next meeting. Then approach your professor with something like

  I have read your paper about how you applied method X to problem Y. Do you think it would be a good idea to apply method X to my problem, too? Do you have time for me next week to discuss this?

So, yes, you have to worry if you do not make any progress, especially if you have time constraints. But not being able to talk to your professor is nothing that should prevent you from making any progress in the meantime. At least you can get more familiar with the tools that save you time in the long run, for example LaTeX, Pandas or whatever you will need for your field of research.


When is it most appropriate to transition from first to senior author?

I think in most fields in which author order denotes the relative level of contribution, while people talk about the last author as being the "senior" author, this is more of an artifact of the fact that the PI of the group generally makes the least contribution to the work. I have never heard of some one striving to be senior/last author. Rather, the author order simply reflects the order of contribution.

If I have the highest academic rank, am the oldest, been in academia the longest, have a name that comes last alphabetically, and obtained the funding, but contributed the most to the project, I would want first authorship. More often than not what happens is people in my lab do most of the work and I make contributions through guiding the research. This generally leads me to making the smallest contribution and naturally being the last author even though I have the highest academic rank, am the oldest, been in academia the longest, have a name that comes first alphabetically.

A related question is when do you start structuring your research program such that you make more less "first author" like contributions. This tends to happen naturally as your time for research decreases and the number of projects that you are involved in increases. Typically this means you have enough funding for a small team of research assistants, PhD students and Postdocs.


Recommendation letter from supervisor in this case?

You can definitely ask a recommendation letter to other researchers. Try to get the most experienced of the ones your worked with to write it, if you did a good job, that should be no problem.


Penalties for postdoc passing off students' work as his own?

The sanctions are usually very light. Sanctions depends on institutions' willingness to reprimand the perpetrators.

In the case where this person is copying earlier conference contributions and claiming them as their own, it's a clear case of plagiarism. If the conference contribution is archived in a way, notifying the journal will result in the retraction of the paper. This will hurt the plagiarist's reputation possibly at the cost of a prospective employment opportunity.

In the case where a person "steals work of two graduate students, passes it off as his own" in the absence of publications that shows the work is effectively the students' journals are faced with a "someone's word against someone else's" situation. Often journals defer the responsibility of investigating to the author's institution. This can be a lengthy process with disappointing outcomes for the students.

All of this is off course highly unethical and all reputable journals will want to retract papers if they learn they weren't written by the alleged authors. But it's not illegal per se and "sanctions" range from nothing (the most frequent case) to a few years of publication ban, and in extreme cases: getting fired.

Some reading on the topic:

Arizona prof plagiarizes student’s thesis, gets reprimanded, but keeps her job

Heads up: “Borrowing” your student’s work will earn you a partial retraction — and a five-year publishing ban

If besides being interested in "what are the sanctions" you are wondering what you can do about it, my recommendation would be:

explore all internal reporting routes: report the behavior to this person's adviser, or to the dean.
If all fail (i.e. if they do not ask for the authorship record to be straighten) contact the journal's editors.

In all cases, be prepared to substantiate your claims. You mentioned you have lab notebook, or even conference publications to show that the material is not original. That is good. Don't expect a harsh punishment but at least the papers should be retracted.

(This answer has been adapted to the latest changes in the question)


Do I benefit my professors by publishing papers with them?

Would I be acting out of line asking Professor K to conduct this research with me with hopes of publishing a paper even though he won’t be my adviser and graduate me from my master’s program?

You wouldn't be out of line, but you should check that Professor L is OK with you working with K, too. L's biggest concern is most likely to be whether or not you have time to work on both projects as well as going to classes and doing whatever else is required of you as part of your studies.

If you're not already exceeding expectations on your first project, it's unlikely that you'll be able to make good contributions to two projects simultaneously.  Also, bear in mind that, as a master's student, you almost certainly haven't yet developed an accurate judgement of what would or would not be publishable.

  Are there any benefits for him from working with me, or am I just being selfish by wanting to do both projects? Note that he’s not yet tenured (will this help on his track?).

Yes, there are benefits to everybody. Academics are primarily judged in terms of things like their research output, their ability to attract funding (which, in turn, depends on their research output), and their work with graduate students. Working with you directly helps him on two of those and indirectly on the third, so you're not being selfish at all.

And working with smart, enthusiastic, hard-working people is fun.


Is it ok if I haven't decided my research topic when I first meet with a potential phd advisor?

In most fields in the US, coming to a potential advisor with a proposal isn't necessary. But with an MS, you should have the area you want to study narrowed quite a bit. I don't know specifically about how it works in applied math, but in theoretical math, you generally work out the project details with your advisor given some common interest.

The advisor, if interested in what you are doing can then be more than just someone who looks over you shoulder as you carry on by yourself and can become something of a collaborator. If you are too tightly focused when you first meet, you might hear: "Interesting, but not to me."

But if you want to work at the intersection of, say, analysis and health science, but without anything more specific, then you have a chance to find some common ground with an advisor. The field should be something that you already know about (since you have an MS) and that the potential advisor has previously worked in or has expressed interest in.

If you were a BS graduate instead, very little is actually required (in the US) and you have time to work together with potential advisors in a more general way to develop some common ground for a research problem.

For specifics, just say where you are (intellectually), and what your general interests are. Be prepared to answer about what you have done, and what you have considered.

For completeness, outside the US the answer might be quite different.


How to obtain an evidence of teacher effectiveness when I never was evaluated?

If someone is asking you to teach classes before you've had any experience doing it, then I'm going to guess that they don't expect you to produce a full dossier.  In that case, letters of recommendation from the people that invited you to give guest lectures, or people who saw them, might be sufficient.  You might get some clarification on what's expected by asking the person who's asking you to teach the classes.


How should I style my German doctoral title in English documents?

Don't overthink it. Both "Dr." and "Dr.rer.nat." would be OK, "PhD" would be inaccurate. The key information is the line in your CV where you point out that you have completed your doctoral degree.
(As relevant context: I am a native German speaker and have experiences in Germany both as a selection committee member and as a successful applicant.)


What are possible outcomes when a PhD cannot be completed during the funding period?

When a school makes a funding commitment, it is generally true that the commitment is contingent upon a student making satisfactory progress to the degree, as judged by the department.

What happens when a student can't finish in the stated period depends upon a combination of factors:

Where the funding to continue supporting the student will come from
If the student is, in fact, making adequate progress and will finish in a reasonable period of time
What the regulations of the department or university are with respect to enrollment (that is, is there a limit to how long a student can be enrolled)

So long as a student is making satisfactory progress, and a source (such as PI funding or teaching assistantships) can be found to pay the student, departments are usually not inclined to dismiss a student based on failure to meet an arbitrary timeline. Usually, the student, supervisor, thesis committee, and department will agree on some sort of timeline to finish the degree program as quickly as possible.


How to prove receipt/no receipt of work?

I doubt this will work with 200 students, but the first thing I do when I collect assignments is check to see whose assignment is missing, and send the relevant students a message via the class messaging system. This does two things:

if there was a slipup at either end, this catches it quickly. Most often, the student says that they're turning it in late (I have an automatic submit-late-and-get-deductions policy).
By using the class messaging system, I'm on record as having asked the student about the missing assignment. If they complain a week later that they did turn it in, I can point to the message and ask why they didn't respond to it.


How effective is ResearchGate as an academic selection and recruitment tool?

Some mathematicians I know (me included) appear in Research Gate. Many many others don't. As such, in the areas I'm related to, RG is not a significant source of information. It might be significant with respect to a single person who worked on her/his profile, but not representative of the market. When I click on "related researchers" on RG, the omissions in the list are way more significant than the inclusions.

More specifically to your question, I didn't know that RG had any relation with recruitment. We wouldn't use it because it is not obvious that our target audience is well represented in it.


Do ACS and RSC journals have identical credit in a tenure-track application?

Given reputable venues like these, you should expect a good department that you'd want to be a part of to pay attention to the substance of your work, rather than splitting hairs on whether they like one society better than the other.

Not all departments will do this, of course.  For example, I know of at least one department that discounts all journals except ones published by its favorite society.  Do you really want to be part of such a narrow institution, however?


Lack of team support in post-PhD Mathematics career

This model is extremely common in Europe (for example, one of my coauthors in Germany is in a group with her and another senior professor, two junior mathematicians on essentially very long term second postdocs, and about 7 or 8 young postdocs and 7 or 8 graduate students), but there is no institutional framework for it in the US.  I know of pairs of tenure-line faculty at the same institution who are close enough to essentially run a joint research group, but outside of a few departments, they are unlikely to have more than one postdoc at a time, so "research group" mostly means them and their graduate students.
Not really.  Essentially postdoctoral positions are the only mechanism that exists in the US system for paying people who are not already performing at a pretty high level to do research.  You could still apply to these, though as I think you've already guessed, the odds aren't great this long post-Ph.D.  I think the other possibility would be obtaining a long term, non-tenure-track lectureship at a research university (for example, my department hired someone to such a job this year) where there are senior faculty who might work with you.  There would still be high teaching expectations (though maybe not worse than a TT community college position), and any research involvement would be "on your own time," but presumably that's largely the case now.
I suppose this depends on how you define "career as a research mathematician."  The answer is obviously not "absolutely no," look at Yitang Zhang.  Of course, that's a very extreme example (Zhang didn't even have a teaching position in mathematics for several years), but I think it does show that if you do something undeniably great, at whatever age, the community is open to it.  On the other hand, this is like asking "If I can't get on a Division I college team, does that mean my career as a basketball player is over?"   Obviously, no one can stop you from playing basketball, but if you mean doing so professionally, the odds are slim. If you're really that good, then maybe an NBA team will notice and hire you.  But you're not going to be in the place that they look for potential new players, and you'll be missing out on how most people develop their skills.  So it's a tough row to hoe.

I think in terms of what's realistic: if what you're missing is being around other people doing mathematics, getting ideas, etc. and you're not worried about security then I would look into finding a permanent (or at least renewable) but non-tenure-track teaching position at a larger research department.  It will certainly have some downsides, but I think it's the closest feasible approximation to what you're looking for.


Is there anything special to the CV format for PhD applicants in Germany?

No, there is no special format for an academic CV in Germany. In general, CVs in Germany differ somewhat of Angloamerican CVs (see for example this newspaper article by The Local). It might be the case, that German professors and selection committees expect a more German CV. However, that should not be a boundary, as academia in Germany is internationally oriented. The Career Center of the RWTH Aachen offers an  English information sheet about German CVs that might be helpful. In addition, you could use the European CV from the  European Centre for the Development of Vocational Training as an orientation.


Is there a journal or 'place' to publish poems written by and for other researcher in the same field?

In mathematics, the Mathematical Association of America has several journals aimed at undergraduate students (which many researchers also read): the American Mathematical Monthly, College Mathematics Journal, and Mathematics Magazine.  All of them regularly publish short poems related to math. (Often they appear in the otherwise empty space on the last page of a regular article).


Should the fullstop go inside or outside the brackets for Harvard in-line citations?

Full stops and periods should always go outside parenthetical references. The only time a stop should be "inside" a citation is when you are using superscript references, in which case the numbers normally appear after punctuation marks (at least in US based journals).

The reason is that the punctuation mark is not part of the citation itself. Therefore it should not be buried "inside" the citation.


Differences between cover letter and research plan?

In general, the discussion of research in a cover letter is much briefer than a research plan. The former is generally one or two paragraphs, while the research plan for PhD positions is typically one to two pages.

A good "research plan" (or in this case, more accurately a "statement of purpose") should explain why and how your past and present experiences prepare you to undertake the topic you'd like to study as a PhD student. Note that this is not meant to be a "life story"—we don't care what you did when you were five years old. Instead, tell us about relevant experience: research, professional experience, service work, and so on.


Do you know if there exists a database for the type of data you are interested in? That would be the easiest way: browse the database until you find an interesting data set, and the paper will likely be referenced by the database entry (if it is a serious database).

Here is an analogy with my own field (structural biology): most (if not all) journals require that structural models of biological molecules be deposited in the PDB in order to publish the article describing the structure. Only the model used to be deposited, but nowadays researchers are also encouraged to deposit the data that led to the model. Therefore, if I am looking for the article describing a particular structure, it is often easier to look up the molecule in the PDB, possibly choose between different entries (one of they may have associated data, not only the model) and find the paper from there.


Do I have to make someone coauthor if he/she solves a problem in StackExchange, asked by myself, which is later used in my paper?

I have been in this precise situation. I wrote the manuscript to a reasonably finished state and then contacted the helpful SE person, asking if they want to be a coauthor and whether the attribution is sufficient. The attribution consisted of citing the MO answer and additionally naming them in the acknowledgements.

This approach has the benefit of maintaining or building a good relationship with the helpful person.

Remember that the typical norms of co-authorship include intellectual contribution, as well as writing or critical review of the manuscript, and in any case accepting the final paper. If you see their contribution as relatively minor, you might want to offer them the possibility to extend or otherwise improve the paper if they are interested in co-authorship.

If the contribution does not merit co-authorship, you can still cite it or acknowledge the (possibly anonymous) contributor on SE, if that is warranted. It is polite, but not required, to ask the person how they should be referred to, in any case.


What's the standard text that I should put at the bottom of a handout containing unpublished data, asking people not to cite it?

This is not a situation that calls for subtlety.  I recommend adding large bold capital letters across the top of the first page:

  PRELIMINARY VERSION — DO NOT CITE OR DISTRIBUTE

I would also include a footnote at the bottom of the title page indicating where the final version will be made available.


Which license to choose for article publication?

No license nor lack of a license will permit/allow people to cite your work. Citation isn't affected by copyright or by the license of rights. Not even patent holders can prevent citation. People can cite your work whether it has a permissive or a restrictive or no license at all.

License is a distinct issue that determines what people can do with your work other than writing about it. For example, can your work be incorporated in whole or in part in the work of another? Can it be so incorporated into a work for sale? Can someone take your work and extend it, while including your work within their own? These are the sorts of questions addressed by license.

I've often used an NC (no, commercial) license, but never an ND (no derivations) license. They aren't at all the same. An ND license seems odd to me for scientific publications. But always insist on BY, or you are coming pretty close to putting your work in the public domain (which some wish to do, of course).

But notice, that the various licenses of CC and others depend on you retaining copyright. Otherwise you have no rights to license. If you are transferring your copyright to a journal, then it is up to them to license in, not you. In that case, perhaps they are just letting you suggest what you think is the best course for the work. But only a copyright holder can license copy-rights.


In the medical (and medical devices) field, pubmed is the place to go and the search is free. In most cases the abstracts should give enough hints on whether a paper might be relevant or not.

You should check patent databases (just ask google about "free patent search") as well.


Why do journals reformat your submissions?

I can think of a few different reasons:

Not all authors are able or willing to conform to the formatting style. After all, academics are supposed to be experts in their field of research, which usually isn't typesetting. The journal provides formatting as a service to these (and other) authors, and to ensure a consistent style.
Copy-editing can also fix a number of typos - it doesn't always just introduce errors...
Even if the authors manage to nail the formatting and spelling, chances are that the journal has an extensive style guide that goes way beyond "some additional rules". If you submit papers to more than a single journal, will you really be able to remember which journals insist on capitalizing words like "ansatz" in English?
Additionally, journals may use headers/footers they don't want to make available in public templates, or even unusual page sizes that may require the text to be reflowed.
Publishers may accept manuscripts in several formats, and have to convert at least one of them into their own format of choice.
I don't know how common it is, but the format of choice need not be one of the accepted formats at all. E.g. APS accepts LaTeX and MS Word submissions, but converts both into an XML format. This allows them to generate both PDF and web versions of the papers, and additional versions in the future. There is even work underway on using the XML format to make papers fully available to the blind.

Finally, as long as the author signs over some or all of their copyright, such issues should not be a reason for this. Also note that formatting/editing does not necessarily cost that much, especially compared to carefully checking a submission.


As an undergraduate, is it alright to get help finishing my paper?

For scholarly work, as opposed to classwork, it is fine to ask for help whether you are an undergraduate or a full professor.
However, the nature of the help needs to be considered. For simple editing and phrasing, an acknowledgement of the help within the eventual paper is probably enough. But if it crosses the line to the point where the "helpers" are contributing ideas, then they become collaborators and co-authors.
Some publishers will provide technical copy-editors if that is all you need, but I think this is more likely for books than papers. It might even be that most of the editing you need can be done by a general text-editor as long as you vet what they suggest. Sometimes they will get it wrong and you need to be able to see and correct that. But such services are likely more available than someone with experience in your field.
After submission, some reviewers will suggest rephrasing as needed. But there is no guarantee of it. Telling an editor of a journal that you need a bit of help with the language might be worth the effort, but, again, no guarantees.
And, no, having collaborators and co-authors doesn't degrade the work. Collaborations with the right people can enhance it. But if you originated the key ideas you want to assure that you get credit for that. In some fields it is being the "first author". In others it is just a short paragraph describing contributions. But at such an early stage, any publication will help you along. There aren't a lot of people who achieve that.


Can published papers outweigh average marks when applying to top institutions for MS?

Your entry into a Master's program is based on your grades/GPA - these programs stipulate a minimum GPA (or specific grades for certain subject, as was my case). So, it is imperative on you to pay more attention to your grades and improve your overall standing so that you meet this requirement (the requirements can be found on the target institution website).

Published papers, particularly if they are in high-level journals certainly won't hurt, but can not take the place of the grade/GPA level required by the graduate school.

Think of it this way, your grades are a reflection of your ability to master and apply the necessary knowledge and skills required as a foundation, at least, for any graduate program - the expectation is that this evidence of your abilities are at a certain level. Journal articles do show some application of skills and knowledge, but not of all the topics covered in your undergraduate studies.


Does mentoring an undergrad give an edge on job or grant applications?

Assuming the mentoring has a measurable successful outcome (student goes to grad school, student writes paper), the NSF would definitely look kindly on such mentoring. Whether the time spent doing this will (minute for minute) be a better value than writing an impactful paper - probably not. But that reasoning is of course flawed - you don't know ahead of time whether the time you spend writing that paper will pay off :).

As with most other things, do it if you care about the mentoring process and enjoy working with undergraduates. Don't do it if the primary goal is to get the bullet on your CV.


Research on pedagogical benefit of lab reports at the graduate level?

There is research to graduate student's teaching skill:

Graduate Students’ Teaching Experiences Improve Their Methodological
Research Skills (link)

And research to lab reports, evaluating the reports and how reports are viewed:

Using the Science Writing Heuristic in the General Chemistry Laboratory To Improve Students' Academic Performance (link)
Development of a ‘universal’ rubric for assessing undergraduates’ scientific reasoning skills using scientific writing (link)
“As You're Writing, You Have these Epiphanies” - What College Students Say about Writing and Learning in their Majors (link)
The Laboratory Report: A Pedagogical Tool in College Science Courses (link)
Writing-To-Teach: A New Pedagogical Approach To Elicit Explanative Writing from Undergraduate Chemistry Students (link)

If a paper you found is interesting, use Google Scholar to search for that title and click 'Cited by' to see other papers that refer that paper. Then you might find more interesting papers. For example, for papers that cite item 3 probably use this rubric or relate to the use of lab reports: (link).

I'm not in this area of research, so it's hard for me to find the right papers and I'm not 100% sure what you look for. Some of the links above require university access to read the full paper.


Persistent URL for each DOI pointing to open access papers when available

I'm not completely sure what you mean by "maintains a persistent URL for each DOI" - the point of a DOI is that it is the persistent identifier and the underlying resource can be shifted around as needed.

But answering the question...

Why, yes, there is - doai.io

This takes the DOI, looks for an OA version (loosely defined), redirects to that if found, and falls back on the original DOI target URL if nothing is available.

Two examples from a randomly chosen issue of Nature last year:

doi:10.1038/nature14178 > http://doai.io/10.1038/nature14178 - no OA version so falls back on Nature, the original DOI target

doi:10.1038/nature14260 > http://doai.io/10.1038/nature14260 - OA version available on PMC, so directs the reader there


Letter of recommendation for grad. school application source

I would ask mentor #1 (with a master's degree) to write a letter to the PhD research scientist #2, and have the latter (#2) submit a letter for your application. Thus, the recommendation letter is received from a prestigious source, is based on current experience of your work habits and character, but can also incorporate quotes/details from the more junior person. This is not an unusual pattern in my experience.


How often do authors actually perform and publish the work they indicate as the future work they plan to undertake in a publication?

It depends on two factors: how well the researchers are organized and funding. I would say less than half of the research groups I know in Computer Science manage to follow their future work plans. The ones that do manage to follow their plans, have clear areas in which they are active and write their projects after half the work was done :)

Funding has repercussions on what you do at work: most of the time you will have to do the tasks related to your funding as opposed to what you would like to do (future work of your favorite article). The problem is funding stops at some point and then you take another project without getting to the future work from your previous article.

If you had worked well in a field, had some articles, there is no reason to abandon that work just because the funding ended, but you will have to follow it between the funded tasks and in your free time.

There is also the alternative that you write a follow-up research project and get to do a part of this future work in the second project.

I have gone through all these phases:

I have future work that was never done
I have future work that was done in the follow-up project (precisely a sequel project)
I have future work that was done in projects that were not related
I have also seen future work from some of our articles implemented as commercial project at a start-up by some of the co-authors of the papers

If you work around the clock and if you like the field you're working in, you will definitely find a way to integrate your long-term research goals with the current project goals or with the next project goals.

EDIT:
At least in CS there is no survey/study/article about such a thing, as far as I know. There are though articles that look at how often a certain technology gets into a new company.


Tasteful way to indicate large funding in job application

The (main) reason you can't just blurt that out in your CV is that it's not necessarily relevant:

  Company X partnered with my university in a Billion-dollar-funded research project and I'm one of the Ph.D. candidates in it.

Suppose I said that. Well, so what if it was a Billion-dollar collaboration? Did I broker the deal? Did I propose the project? Was I in charge of coordination? If not then it really doesn't matter.

In your case, if you actually had a contribution to the collaboration other than being selected to do a Ph.D. - write a few sentences about what you actually did. Those sentences could at the same time illustrate the large scale (inn terms of people, organizational commitment, impact, time etc.) of the project and why you deserve some credit for it.


In the textbox, just say 'See attachment'.  On the page where you upload your revised paper, there is usually an option to upload other files.  Use the option to upload your responses to the reviewers. Just double check that the compiled pdf include your responses as well as the revised paper.
Same cover letter, but you may want to add '..revised paper'.


Can I, as a reviewer, tell authors to get a native English speaker to proofread their paper?

It's obviously appropriate and constructive to comment on writing issues that significantly affect the quality of the paper. The only question is how to do it as constructively as possible.

Personally, I prefer to suggest that "the authors get editing help from someone with full professional proficiency in English" rather than asking for "a native English speaker." I see other reviewers write the latter, so it's not uncommon, but I feel like it sounds a little bit like I'm "punishing" the authors for not having been born in an English-speaking country. There are plenty of academics who are not native English speakers, and don't have the same proficiency as native English speakers, but are still perfectly capable of high-quality academic writing.


What are the disadvantages and advantages for a senior graduate student to restart after 6 years' study?

It is very common to be beset by self-doubt at this point -- just when you are poised to begin writing.  (It's best if you can write as you go along, but sometimes the nature of the project does not permit that....)

(There are questions with good answers on this site about how to keep up your nerve during this final stage.  Helpful reading!)

In your case, these self-doubts are complicated by some weaknesses in your department and some frustrations you've had along the way.

Let me draw an analogy from parenting.  Most of the time, a parent will do best if he is really tuned into his baby or his small child, and his antennae are set to pick up subtle vibes from the child, so as to be as responsive as possible.

But there are situations in which this is actually counter-productive, and you have to detach yourself, and care for the child more or less on auto-pilot.  For example, if your child is the non-responsive type, and you are getting frustrated.  In this case, you have to back off emotionally, so as not to overwhelm the child.  It's okay, it won't be forever.  You just need to let the child's brain mature a bit more, and then try again, in small steps.

In your case, the thing you're going to have to train yourself to ignore, on a temporary basis, is the niggling voice in your head that makes the negative remarks and the probing, self-doubting questions.

You are very close, just keep plugging away!  Crank out an imperfect dissertation and move on with life.  You are not the only talented person to have attended a school that has some weaknesses.  Think of the Third World!  I once attended an agronomy class, "Farm Machinery", that was taught with posters the instructor had made on his kitchen table.  An actual tractor was not brought in until the last day of class, and then we did not even practice changing the oil.

For your postdoc, forget about rank -- look for a position where you will have comfortable, fruitful collaborations.


Should I put a theorem statement with a lot of hypotheses and notation in the introduction?

Generally, I feel that the common approach is to sweep the details under the rug, and present a high level version of the theorem. For example:

  And finally, we prove that under certain assumptions about the automorphism group of a graph, G, that either G is “essentially” a Johnson graph or it has what we call the Splitting Property. This allows us to construct a new proof of Babai’s proof that GI is in quasipolynomial time that doesn’t rely on the classification theorem of finite groups.

What is meant by “”essentially” as Johnson graph,” or what the “Splitting Property” is will be defined later, but they need not be explained in the introduction. The important thing is to give a gloss explains why someone would want to keep reading.
For another example,

  We then define a particular distance metric on circle and prove that, under certain modality assumptions, that this distance metric captures the intuitive concept of roundness.

You can also provide pointers to later in the paper where words like “a particular distance metric” or “the Splitting property” is defined.


Problems in making a submitted paper available to interested fellow researchers

I don't see any problem with sending the paper to interested colleagues. This actually a good thing and if you then mention that this is still work in progress and might occur changes in the final text, it is no problem. Additionally why do you want to indicate that they should not circulate your paper? It is still your own text and research and I guess, you want that as many people as possible can read your paper?! But by saying that they should not circulate the paper to other colleagues, this sounds strange to me (and probably, they do it anyway to some extent ;)  You can state in your CV or on your homepage that you have presented your work at conference X and that your paper Y is under review in Journal A and if your work get published, you can send the persons who got your previous version of the paper the link to the final version of journal article.  EDIT: my take on the argument above by  darij grinberg: Even if you send your earlier draft to the respective reviewer, it is not your fault and thus, not your problem that you should worry about. She/He could either indicate a conflict or interests because he or she knows you or he/she just observes the improvements of your paper and will give you further feedback.


Is it ethical to TA in another university?

Based on the other comments & answer, there appears to be significant regional variation regarding this topic.

TAing in another university is certainly not uncommon eg. in Northern Europe, and in fact universities regularly cross-post TA advertisements to other universities, especially for lower-level courses that don't need special expertise and need a lot of TAs.

There are generally not a lot of volunteer TAs. Based on the other answer, my guess is that this might have something to do with the lack of tuition fees in this area.


Publishing Unpublished undergraduate research after a decade

You have a lot of questions to answer before you proceed.
If you intend to patent, you should start with that, or at least note that if you publish first, then in some places (US) a clock starts and you need to file a patent within a fixed time period or you work could become "prior art". You also need to know if the university is the proper party to file the patent. They may have rules about that, which you implicitly agreed to earlier. And patenting can be an expensive proposition, require advice from a patent attorney.
If you intend to publish, you need to determine whether others should be co-authors, and, if so, get them involved. Be careful of issues of plagiarism here if others contributed.
As to the required quality for publishing, the editor and reviewers of a journal will give you that information after you submit your work.


My department has changed its favorite fields of research. What are the consequences?

I'm afraid I find the question rather vague.  You write

  When I was hired to a math department (in the US) my field was among the favorite directions in the department.

I have spent my entire professional life in math departments in the US, and I was not aware that they (we?) have "favorite directions."  Even the smallest departments I know have at least four different research areas represented, and the general attitude / expectation is that everyone should be collegial and helpful with each other while feeling that their own area is the "favorite" and promoting accordingly.

It is true that often different research groups have different sizes or different profiles.  In my department for instance the number theory group has been larger than the analysis group (and had more students, offered more courses, organized more conferences and so forth...) in the time I've been there.  But there is no explicit, systemic way in which number theory is promoted over analysis in my department: in fact we have hired in both groups in recent years.

  Few years later the department decided to put more attention on some other areas of math.

Again, what does that mean?  Do you mean in terms of hiring initiatives?  If so, maybe you have nothing to worry about: hiring initiatives are very often cyclic: departments target areas where the ranks have shrunk in recent years.  I have never in my life heard of a hiring initiative whose express purpose is to deemphasize or somehow lessen in any way the stature of faculty who are already there.  Why in the world would a department agree to that?  Even if a "lessening" of a current research area was in the best interest of the majority of the current members, faculty have more solidarity and longsighted worries than that: first they came for the analysts...

  E.g. whether my research will be considered to be less important for the department from some point of view? Will I get more administrative duties? Will it be harder to get grants for my research? Any other consequences?

Again, it seems really impossible for us to answer these questions.  The first one is excruciatingly vague. Everyone's research may be considered to be less important for the department from some point of view: if it's too theoretical then how is it contributing to the world really, and if it's overly applied then it's, you know, not as cool to pure mathematicians.  Will you get more administrative duties is certainly a question to ask the other members of your department.  I don't really understand why this would affect your ability to get external grants, but then I don't really understand what you're talking about.

In general this is something that as a tenured professor you absolutely need to discuss with your colleagues.  Honestly, you sound like you don't understand the whole thing very well.  I urge you to get a clue by talking to your colleagues, repeatedly and protractedly if necessary.  Being tenured means your colleagues need to listen and address all your questions and concerns.  It's time for you to use that power.