How can faculty best telegraph work-life balance challenges under COVID to our administration?

Let me suggest two things. First, the administration is probably acutely aware of the challenges you face and have many of the same issues themselves. Losing some of the "best people" is, itself, a wake-up for administrators.
One of the problems is that large universities (especially) move very slowly and have a lot of inertia. But this sounds like a problem that should be addressed in a bottom up fashion, rather than asking for a top down solution.
Meet with other faculty in your own and other departments. Perhaps there is a faculty association of some kind or even a union. List the problems you face and come up with sensible solutions for them. Try to think of more than one solution, some of which have minimal effect on overall finances, though they might require reapportioning funds.
If appropriate, get department heads involved in this and even deans. Discuss among yourselves how you think it ought to be and then work on those issues, probably one at a time. The long term viability of the institution may be at stake as times change and there is no clear end point to the current difficulties. For state-funded institutions you may even need to enter the political arena to obtain changes, especially additional funding.
If you first get public/open recognition of the problems from administrators you have a better chance of pushing proposals for solutions.
Don't neglect working with other departments. There is a lot of expertise in solving problems among the faculty generally. Some of those people are experts in proposing solutions to social problems and dealing with inertia and opposition.
Small-scale short-term solutions may not be sufficient. There are no guarantees that the university will return to what it was a year or so ago. Think and plan for the future. The universities that do this best will have the best chance to succeed.


How can I invite open comments or reviews of my published papers?

Okay, this is totally not an answer to your specific question, but I think it is an interesting answer to the broader question of getting comments and feedback on your published papers…

Go to conferences, present your work (either at oral or poster presentations), and make sure you stick around and are welcoming enough so people will ask questions, give you feedback, engage in discussion about your methods and results, etc. I have received tons of insightful comments on my own work in conferences, and still find them an extraordinary tool to gather feedback on your published work.

Also, do not hesitate to engage with other researchers with research interests close to yours, and after you get to know them, ask them clearly what they think about it. I mean, if you discuss with top-notch people in the same area, they will have read your paper (unless it's really very recent); I have started very insightful conversations with lines like:

  Hello, professor Smith, it's nice to meet you. Since the 2011 conference, when we last met, I saw your nice paper on X in Flagship journal of your field. It was really an improvement over existing methods. Actually, there was a question I wanted to ask: you may have seen that we published a different approach with the same goal last year in International journal of our field, and we are getting slightly different convergence properties. I haven't had yet the opportunity of asking you what you thought of our approach and the way it may prevent the issue of Y…

Just remember, that's not a conversation everyone is willing to have. So, if it looks like they are trying to bail out, help them get out easily! Manners, always :)


Is it OK to publish a book as an undergraduate?

Go for it, and see whether you can get one of your professors to do a technical review.  That technical review, acknowledged in the preface, will lend weight to your book.  If you have professors who speak your language, think about co-authors.

Do not, however, expect to make money.  Only blockbuster textbooks make significant money for their authors.  Also, beware vanity publishing, where you pay the publisher rather than the reverse.

If you write the book, Amazon will let you make it available free or very cheap.  (That's true for English language books; you'll need to check about other languages.)


Is having a master's thesis important for US PhD applications in linguistics?

Ph.D. student in linguistics here.

I'd say "probably not," especially if you and your educational background are both American as well. Stand-alone MA programs in linguistics in the U.S. are difficult to find. Where they exist, they tend to be focused on applied linguistics and education. Most domestic applicants will have only undergraduate degrees. Focus on demonstrating that your research interests are well-defined, that you have a good sense of how to pursue them, and that you have a rock-solid understanding of why the University of X would be a great match for you. Don't worry too much about the writing sample; mine was just a small course paper that the professor liked.

That being said, it can't hurt to have an MA from a reputable school, and aiming for that might make sense as a backup plan. I've seen several people move to Canada or Europe to do an MA in theoretical/quantitative linguistics, then come back to the U.S. for a Ph.D. One of these ended up saying that their MA experience north of the border was something they'd wholeheartedly suggest to people having trouble getting admitted to Ph.D. programs in the U.S. I've heard that there are even a few schools up there that provide funding for international MA students in linguistics, though I'm not sure which ones they are. Worth looking into, though!


Am I eligible for a fellowship doing interdisciplinary work?

You sound like a perfect candidate, given your major and your further plans. Many social scientists like to understand problems more than fight about academic boundaries--at least if they are at an institute that describes itself as concerning the "Social Sciences" rather than a particular discipline.

Do look carefully at the guidelines to see if they specify which programs they will support. If they are vague, you may want to ask the program officer for the fellowship about whether it is designed to fund such cross-disciplinary study, and/or if there are "computational social science", etc. programs to apply to that would be purely in scope. (You can look at lists of past awards to see the variation so far.)

If you have a strong start in computer engineering and you can convincingly convey your dedication to use it for the social science purpose you mention, as well as show that the degree program will let you, then you could be a strong candidate. (Unless the fellowship is specifically toward master's degrees, you may face tough competition from doctoral students, though not because you are on the wrong track.) Good luck!


Do postdocs in the United States generally get annual raises?

From my experience in the US, it is typical for a postdoc to be on a fixed "short term" contract where there are certainly no "promotion" raises, but might or might not provide cost-of-living increases.

A one-year contract will almost certainly contain no salary increase; for a 2- or 3-year contract, they will be minimal at best.


Possessive case when there are post nominal letters

You could go with:

Dr. Smith's student

and

Dr. Green's clinic


Activities for welcome event for incoming PhD students?

At the risk of making this event too serious, I would suggest that you have several speakers who talk about their personal experience concerning how they survived grad school, in this department/school or in others.

There is no more valuable information for incoming grad students than information about the personal side of grad school and how to avoid the pitfalls.  And there no better way for them to feel connected to the professors and students in the department than through personal and meaningful stories -- both the highs and the lows.

I offer this suggestion because, personally, I find such meet-and-greet events to be dull, boring, and worthless, no matter how much alcohol is on offer.  I realize that many academics have meager social skills and that standing around with drinks in hand can sometimes get conversation started.  But I still find it a waste of time.

Likewise, "welcome" speeches are typically vapid and cosmetic.  You will never here any new graduate student (or new employee of any kind) say:

  "I didn't feel comfortable starting at X, but  then I heard that amazing welcome speech by the Department chair."


Graduate Admissions and Earlier Programs

First of all, I'm sorry for your painful experiences. To answer your question:

Based on my extensive experience directing a graduate program at a leading public R1 university, your initial experience in the initial program will have very little bearing on your chances of admission. I say this for a number of reasons:

We are concerned with trajectory even more than overall grade point. I am relatively unconcerned by someone who gets C grades during freshman year, so long as I'm seeing A and high B grades by junior and senior years.
When a student goes to school for a couple of years, then does something else for a few years, and then returns to school, I consider the grades subsequent to return almost exclusively. In most cases, unlike yours, this is because the student needed time to grow up. But I'm happy to accept that he or she (frankly, it's usually a "he" that fits this pattern) has grown up and to accept the high marks after the return to school as ample proof. I don't care what somewhat was like as a 19-year-old, I care what that person will be like in my program.
You can and should explain the switch of programs in a graduate application. Having a letter-of-reference writer explain it as well would be a wise move. Once an admissions committee sees the highly valid reasons, there is little chance that they would hold your record at the first institution against you.
Everywhere I've been, if grade points are used to prune or order applicants, only the gradepoint at the final undergraduate institution is used. This may not be universal, but frankly I find it unlikely that most graduate admissions programs would go to the trouble to compute the proper weighted average across programs, even if they did care about your earlier performance.

I hope this is helpful and perhaps even encouraging.


What does it mean if a committee chair asks if I applied to many similar jobs and if I plan to fly back and forth?

Unfortunately there are budget constraints at all institutions, and interviewing faculty can be an expensive affair.  Most likely, this is a polite way of trying to figure out whether you'll already be state side during a date range they'd want to interview you. No reason to have you hop the pond repeatedly if the timing works out.

No, you should not preempt the question and ask other schools about sharing airfare.

I am tempted to think this school is reluctant to spend the money to bring people from abroad over.  It is somewhat strange they would have you research airfare. In my experience, there is staff that takes care of that. I, for one, would mark this in the 'con' column, because if they skimp on airfare for desirable faculty, what else might they skimp on?


"1 year with possibility of extension" - what does this mean?

I'd probably read it this way:

  I have funding for one year for sure, and hopefully for additional years, but it might depend on the success of future grant proposals, so I can't make any promises.  But assuming that my funding is successful, and the postdoc is continuing to do a good job, I'd be happy to keep them for 2-3 years.

In some cases, postdocs might be funded by "hard money" coming from within the university; this is common in math, and such positions often have names like "Famous Person Assistant Professor".  In this case, funding can be assumed to continue (barring a financial catastrophe for the university) and it means more like "2-3 years assuming you do a good job".


The importance of finding potential mentor before applying for a postdoc

It is in general a good idea, not just for your chances but to ensure you will find a productive or at least welcoming group to work with.

The impact on your success chance I think depends on the country of choice: in some countries (e.g. Italy), postdoc calls are advertised as a public competition with a committee that should judge your CV impartially.
In other countries, a professor may hire a postdoc on his personal funds and choose the candidate of his own will. In the latter case having at least some prior contact may be strictly necessary.


Disclaimer: The opinions I'm about to express are based on my experience in mechanical engineering, as an undergraduate research assistant, a master's student, and currently a PhD student. I'm quite confident that what I'm about to say should apply to Computer Science as well, but if I am incorrect, then I apologize in advance.

First of all, it is good to see that you are motivated about research. You seem to be interested in fields that are very active today (I know quite a few colleagues that are working on machine learning for instance). Your curiosity and interest in advanced fields are admirable.

Now what you need to know, is that most professors (in my experience), hire undergraduate level research assistants with the prospect that they'll pursue graduate studies afterwards. The reason being, most fields of research are far fetched compared to the knowledge typically available at 2nd - 3rd year level, so you have to spend quite a bit of time reading literature, and your supervising professor will need to dedicate a lot of his time guiding you through it. Moreover, research methodology is very heuristic, and requires experience, because you have to solve open-ended problems. That means there is no solution in a book somewhere that you can look up. So the whole exercise is to train your mind to see a possible path to a solution that you might arrive at after months of work, with occasional milestones that tell you that you're on the right track. So this means that after months, your supervisor may have dedicated long hours of his time supervising you and have nothing to show for in return. The only consolation is if a student plans to stick around for a master's, then it makes sense to invest the time required, because you will have learnt a lot out of this process.

As a community college student, it may not be clear to the people you're contacting that this is your aim. This is due to the fact that most people view community college training as job training, not so much education that could lead to a field of research. As a matter of fact not even undergraduate studies train you for research, which would make the prospective supervisor even more hesitant. You may need to prove to them that you have a path in mind such that you can satisfy the university's admissions requirements for graduate students if it comes to that.

From what you've said in your OP, I can infer that you feel insulted because you are offering free work, and yet nobody seems to be interested. That is noble of you, but for the reasons I stated above, as far as they're concerned, statistically speaking you're likely to be more effort that benefit.

Another aspect that I'd like to touch on is the fact that your grammar is not adequate based on what is expected in academia. I'm making this assumption based on your original post, so I may be wrong if you simply wrote it in a hurry, but if your contact e-mails with the researchers were anything like it, it suggests that they'll have a difficult time communicating with you, and that is another headache for them. A big part of research is being able to communicate your work to people who are from your field, from other fields, and requires nuanced language to express subtleties that exist in most advanced scientific and technological fields. I know it doesn't seem important, but it truly is. You're expected to leave some sort of record of your methodology, present it at conferences, submit to scientific journals, and write grant proposals for which grammar and format is an easy way to dismiss applications at a time when research budgets are getting tighter.


There are several major websites on which jobs in mathematics, including postdocs, tend to be posted.  Most importantly (in the US) mathjobs.org, but also the AMS's service and others.  (See this mathoverflow question for many more.)  Postdoc positions can take a while to sort out, since many of them are filled (or even created) in response to what happened earlier in the hiring season, so there may still be opportunities, especially if you're willing to look outside the US.


What are the benefits of organizing a science conference for a company?

There are a couple of reasons that companies sponsor major conferences (rather than directly organizing them). First is that they get name recognition among the attendees and also, to a lesser extend, among the public. More important, however, is that they also have an opportunity to meet and interact with leaders in research in which they have an interest.

A company doesn't have to organize the conference to do this, and organizing a new conference may not be the best way as it takes some time for it to be well known enough that those researchers want to attend (or submit papers).

Some companies just do this as fulfillment of what they see as an obligation to the research community on which they depend for both ideas and employees.

Companies, of course, have other ways to reach these researchers, but providing an environment in which some collaboration can be initiated is valuable to some of them.


Research schedule for postdoc application in mathematics

I have never served on a grant committee, but I have experience as an applicant. Even though you obviously do not have any experiments or data collection planned, you surely have some idea of what you want to do, and how you want to approach that. And you know how many years you have available. By estimating the relative difficulties in each step, you should be able to come up with a rough idea of a timeline. What I believe they want to see is that you are able to give a realistic estimate of how difficult your proposed research is and how much time it will cost. You also might have different somewhat indepdendent projects in mind. Are you going to do the sequentially, or in parallel? Maybe you plan a research visit to another university. Answering such questions gives you a rough schedule that you can include in your proposal. I don't think it has to be very long or detailed.

Clearly during the course of the research it might be necessary to change the plan, because things did not work out as anticipated. But that is no different in other disciplines I am sure, and the reviewers are surely aware of that.

In short, the main goal in my opinion is that you should be able to show that you have a realistic assesment of how your proposed research can be completed in the alloted timeframe.


Value of contributions to Wikipedia when applying for academic jobs

I have never heard of any weight given to contributing to Wikipedia for any aspects of academic evaluation. I personally wouldn't attach any weight to it either, especially given that many articles have a long history of edits and figuring out exactly who contributed what can be difficult.

If you want to include this on your CV or similar, I would mention it under "Misc." or "Other" or something like that. If you have made significant contributions to other similar sites (e.g. stackoverflow) I would put that into the same paragraph. I would definitely avoid trying to make it appear as one of the major things you have done. Wikipedia is regarded rather suspiciously in general because it can be an unreliable source. While contributing to it could be a bonus, it won't be a significant one.


Is it difficult to get admission to a phd in stem cell biology in Europe?

As aid before, the process is very different from country to country. I personally have experience in Germany, Austria, and Switzerland.

More and more institutions move to PhD programs. Sometimes it is the only way to do a PhD, and Professors are discouraged to hire students without them going through the initial assessment of the PhD program committee. Usually, these programs are easily to find on the web. See e.g. here http://www.vbcphdprogramme.at, or here http://www.biozentrum.unibas.ch/education/phd/overview/
Look for job advertisements at dedicated portals like ResearchGate (http://www.researchgate.net) or http://www.eth-gethired.ch in Switzerland.
Contacting Professors out of the blue might work in some cases/disciplines. In fields or countries were industry pays much, much more than academia, Professors have problems in recruiting talented PhD students, e.g. computer science or generally in Switzerland. They are glad if they can finally put a qualified person who does the work on the grant they already got month ago.


Grounds for an ethics complaint? UK math prof. publicly misrepresenting results from an unrelated discipline

First, and foremost, be very cautious about taking this issue outside of the scientific realm of argument.  If you start to file ethics charges or libel lawsuits, then you are likely to be casting yourself in the role of censorious scientific villain, and it is likely to not go well for you.

Instead, if you feel that your work really is scientifically defensible, I recommend that you stick entirely to the evidence to defend it.  If you cannot do so, then that is a serious problem --- having not read your thesis, I have no idea whether you or your critic has a better case.  Do note, however, that being in a different discipline does not immunize you from a person's criticism: a critic need not have any credential at all to point out a potential flaw in your work, and the nature of science is that if you cannot defend against criticism, your work cannot stand.

Finally, I would strongly recommend talking to your advisor before you take any further steps and strongly heeding their advice.  Your advisor is likely to know better than you whether to take your critic seriously, given the state of your work and the field, as well as what types of response are likely to be wise or foolish.


Contacting my undergraduate supervisor after an extended period of time to ask for help?

Just send email.  Ask him to "remind" you of the names of faculty he knows at your proposed institution and ask whether he would be able to write a "strong recommendation."  It'll be OK.


Use of future tense to refer to following sections

I think that this is pretty field dependent. The first two sentences don't strike me as odd, though J-Kun strongly disagrees in the comments. In particular, I would say that the phrase "in this paper we will show" is common in the papers I read. I have first hand experience that the future tense used in this way is common in mathematics, computer science, and philosophy.
I also have very strong opinions about the fact that papers should not be dry. The fact that some researchers praise dry writing is fundamentally misguided in my mind. Papers are written by humans to be read by humans, and should be enjoyable to read. In my field (theoretical computer science), historical anecdotes, philosophical interludes, jokes, and amusing names are commonplace in academic writing. I strongly discourage you from aiming for dryness in any portion of your paper.
Given the field-dependent nature of stylistic issues like this, consulting the editorial guidelines of the journal or journals you hope to publish this paper in / have published in in the past would likely be your best option. Even if they don’t have specific style guidelines, you can usually in for what is preferred by reading other papers published by these journals.
EDIT: In your edit, you specify that you're in computer science. In my experience, computer science writing is far more conversational, and computer science culture is far more casual, than most other fields. I doubt anyone would bat an eye at either of the first two phrases. In fact, the paper I currently have open on the Arthur-Merlin Protocols says:

In Section 3 we will also use the representation of Boolean functions by polynomials with real polynomials (p. 5)
We will show that this
protocol needs communication at least Ω(√na), which implies the theorem. (p6)

and has similar constructions in at least four other places. IIRC, Babai's original paper introducing the A-M protocols had the first four pages entirely in the form of a faux mythological story about King Arthur.


What is the difference between TV-L E13 and TV-L E14 positions? Is it negotiable?

The key difference between a TVL E13 and E14 position would be the job responsibilities and required qualifications. In an academic context, E13 positions are for researchers at graduate or post-graduate level working under supervision. E14 positions have a higher responsibility in the sense that these would typically include project leadership and / or supervision tasks. Typical academic roles that should be filled at the level of an E14 position would be group leaders, principal investigators of projects, research lab managers, or just someone supervising graduate or other post-graduate researchers. Nevertheless, someone working in these roles may still get only E13 due to budget reasons.

If the position you have an offer for includes tasks at E14 level, then it certainly is something that can be asked for. Whether or not it will be possible to make it E14 will mostly depend on how the position is being funded. It may be that this was specifically budgeted as an E13 position, and then it will be difficult to change that through negotiations from your side. If the position was announced specifically as E13 then it may be a high administrative hurdle to change that. However, if the funding is just a bunch of money without detailed budget plan, it may be easier to get it as an E14 position. Especially if it is only for few years, the total salary spent need not be much higher in E14 compared to E13 because you would likely start in a lower grade (Stufe).

Regarding the grade I think that indeed with more than 8 years of research experience you should definitely get Stufe 3 in E13. The number of years could even be enough for Stufe 4, but I've heard that new hires will usually get Stufe 3 at most. However, if you get an E14 position, then I guess that you can just get Stufe 1 or maybe 2, depending on whether you have some prior experience with the E14 type of tasks I mentioned above.

As a side note, there is also the possibility to start in E13 and then being promoted to E14 if job responsibilities are accordingly and the budget is available. In that case, one would get the lowest grade in E14 where the salary is still at least as high as in the most recent E13 grade one has achieved.


4 Years in PhD. No publications and adviser keep changing my research

Change your adviser. Probably time to cut your losses and leave, your time is more valuable


Can I back out a tenure track faculty offer?

There's no way to do this gracefully. You call school A and tell them that you will not be joining them after all. Afterwards you deal with the fallout.
Before doing so you may want to estimate exactly how bad the fallout will be and whether it might affect your ability to do your job at school B.


How can I best prepare myself to keep the option for academia open, after leaving for industry?

In Germany there are actually quite a lot of such positions at the so-called Fachhochschulen. To be a professor there, it is actually expected to have worked in Industry for at least 3 years (or so, depending on the state) and share your industry experience for a more applied education of students. Of course, an excellent PhD is also necessary. And usually one needs to have some form of achievements while being in industry; e.g. papers, presentations, patents, rise to leadership positions, cooperations with academia, or similar; such that continued applied reseach can be expected.
This is in addition to the comments of @user2768 and @A rural reader.


Whether to complete revise and resubmit that requires major changes or submit to lower impact factor journal?

General Issues

Presumably this depends on your perceptions of:

The time and resources required to make the major changes
The probability of acceptance should you make the major changes
The degree to which the paper will be improved by the changes and the value you place on that improvement
The probability of acceptance in another journal were you to not make the changes (or just the minor changes), and how much work any future journal might request from you as part of making changes, and any cost assigned to the delay in publication that this may involve
How much lower impact the alternate journals are  (and how much you care about impact factors and rankings)?

General advice

If I get a revise and resubmit from a high ranking journal, I would almost always try to make the changes requested. There is a little bit of luck involved with publishing in good journals. If you go on to submit elsewhere, these other journals may reject, or they may have equally onerous edits. However, once you get a revise and resubmit, if you do a good job of implementing the requested changes, then the editor will typically accept the manuscript. Furthermore, at least in my world, publishing in prestigious high-impact journals has many broader benefits (e.g., increased exposure for your idea, and improved cv which helps for grants, promotions, job security, etc.).

That said, I can think of a few exceptions where I might not make the changes.

The editor says something about liking the broad topic, but is basically requesting a whole new study (e.g., collecting a whole new dataset with a bigger sample, better measures, different design, etc.). In particular, this is often combined by comments suggesting that the editor would be happy to consider such a study: i.e., not really offering a commitment to publish even if such a study was implemented well.
Sometimes, I'm working on a paper that is not my core focus: e.g., perhaps converting a student thesis for publication, or helping out a colleague. The paper might be fine as is. I understand that it could be even better were we to collect whole new datasets or invest substantial time in some other respect. But in such a case, this time and these resources may feel like a distraction from my core program of research.

Ultimately, it's up to you to weigh the issues up. But I would assign a high-value to publishing in high impact journals and taking advantage of the opportunity that you have been given to make revisions.


COVID-19 - Is it okay to send emails this time for post-doc position?

Yes, by all means keep looking for a position. The future is unknown. Things may settle down or not, but it would be a mistake to wait until they do before you even begin a search. But email responses may be slower than usual and people may need to be more tentative. Expect that.

I suspect things will be hard for a while, but no one expects it to be permanent.

You can't win the game if you don't play.


MS thesis defense equivalent to publishing as a MS student?

No, a defense is not equivalent to a publication. A defense may just be something required by university rules and takes some of the responsibility and guidance from the advisor and gives it to others. Some such theses are available in, say, the university library, but that isn't the same as journal (or conference) publication which is more public by definition.

The defense is usually a closed system within a department, thought there could be external members of the committee. But a publication has been vetted by independent referees and an editor and it is done in competition with other papers.

And if a defense is required there is no reason that you can't also do a paper if the results are good. It might not be the thesis itself, but could be based on the work.

A publication is almost certainly better if you plan a career as an academic, but possibly not by a tremendous amount. The admissions committee may actually do some (probably minor) evaluation of the work in either case. But having a publication in a reputable place will relieve them of some of the burden of judgement.


How long after first contact, where editor says "manuscript is still under review", is it okay to enquire again about status of manuscript?

As an editor of a number of mathematics journals, I would be pretty irritated to receive two queries from an author within two months. What exactly is achieved by emailing a journal to ask for an update in the first place? Mostly, it helps on the (perhaps not so rare) occasion where the paper has fallen through the cracks, as happens when someone agrees to review the paper but then forgets about it. What would be achieved by emailing the journal twice in two months? It's hard to imagine it resulting in your paper being reviewed any sooner, and easy to imagine it annoying the editor. I would wait six months between queries.


At what point is it OK to claim that you review for a journal in a job application?

I am not sure how this would be considered in a PhD application, but I think it would strengthen my profile, given that this will be the second most prestigious journal to which I will have provided a review.

While it doesn't influence the when, I am not sure your premise is correct. There is something important about an editor asking you to review for a journal since it demonstrates that someone (specifically a respected someone) thinks you have a thorough understanding of a field and are capable of independent critical thought. The act of reviewing is not really worth much.

As for when you can disclose it, I think this is a little messy. I would probably wait until the editor sends a decision letter to the author. At that point, you have clearly reviewed for a journal. Prior to that, I might mention that I have agreed to review for Editor X at Journal Y.


I'm still not sure that I understand the entire scenario, so this will be a bit hypothetical.
If you write something but it isn't published in any form then, later, you can simply copy and publish any part of it without citation or further comment. It isn't self plagiarism to use your own unpublished work.
Assignments in a course might, however, follow some rules beyond those generally accepted in scholarship. If the thesis is at the same institution as the earlier coursework, then, for purposes of keeping the faculty happy, it would probably be wise to mention that some of what you write was written earlier for a course.
But normally, student work for course assignments isn't really published, though it is shared in a limited way (with the professor). There can be exceptions, of course.
A way to be safe with all sorts of plagiarism, including self plagiarism is to cite if there is any doubt at all. Over citation will not, generally, be a problem. Under citation can be.


Replying to potential professor about my position

You could easily reply now and say you are looking for a position and have made some applications. Just start the conversation. It may be that by the time you get a reply from him you will know more about your other prospects.

Perhaps the first mail need not be very detailed, but you could ask about the possibility of working with him if you haven't done that already.

It might be valuable to keep in touch even if you wind up with the other position. Nothing is forever and a circle of collaborators is valuable.

And you might get a reply around the time that you hear about the other position and can make some decisions or follow up more seriously.


Precarious employment in academia: Why is there no labor union in academia?

Why is there no labor union in academia?

Some universities have unions, others do not.  The scope of the unions varies.

  Why is there no movement inside academia trying to change this?

Many people support changing academia, so the premise of this question is wrong.  The reality is that change is hard, especially when the old system obtains lots of cheap labor.

  how successful have they been in the past?

Unionization usually results in an increase in pay and job security, but the change is small.

For problems 1-5, the solution is simple:  Don't get a PhD.  As long as many people try to get PhDs, economic forces will encourage these problems to persist.


Doctoral admissions in the United States is usually done at the departmental level. Departments convene admissions committees and these usually utilize one of the following strategies for selection:

Candidates are chosen who are presumed will work with one particular faculty member (or a small group of faculty) who will serve as their advisors or project leaders.
Candidates are chosen without faculty assignments and are expected to find an advisor / project group in the first one or two years

This is very discipline and department/university specific.

In the case of type #1, yes it helps to contact a POI (professor of interest) who will be your presumed advisor.  In the case of type #2, there's no real advantage to contacting faculty.

However, you should note that even in the case of #1-type departments, faculty do not respond to cold-call e-mails for all sorts of reasons, so one cannot read too much into non-communication.  Also, in many #1-type departments, the decision is still ultimately made by the admission committee and not by the individual faculty member, which is why they may tell you that the decision is out of their hands.

I suggest writing to graduate students in the department whose interests best align with your own. They can give a sense of which type of selection committee the department utilizes, and which faculty generally respond positively and promptly to e-mail.


how to bring into full play what was prepared during faculty interviews

Don't overthink it.

In a skype interview, you're right, it is mostly their questions. Answer them directly, and maybe keep 2 points in mind that you really want to make when they give you a chance to lead the conversation for a few minutes.

For on-site interviews, it's a long day or two, and you'll have plenty of opportunities to say the things you want to say.

I suggest you trust that the important things will come to light during the interview. If you forget one or two things you wanted to say, that omission is very unlikely to determine the success or failure of your interview. The overall picture that the department gets of you is much more important -- is your research strong? does it fit well with the department? will you be a good teacher? a good colleague? I suspect that the "rehearsed lines" will be less important, in the scheme of things.


What is the approximate composition of a statement of purpose in Mathematics?

When I review graduate applications, the statement serves three purposes:

If you are not a native English speaker, it may tell me something about your English proficiency.  However, it cannot be relied upon too heavily since you may have gotten at least editorial help from a friend or even a professional.
More importantly, it is an opportunity to demonstrate that you know something about a research area that interests you.  This is more important for PhD applications than for MS applications, obviously.  If you have already done some research, hopefully your recommendation letters speak about that.  Your statement can sometimes be useful in showing that you keep up with some research area even though you haven't yet contributed to it.
Finally, your statement can address issues in your application, like a period of low grades related to something in your personal life, a gap in your schooling/employment, etc.

There is in my opinion no correct ratio of personal versus research components; it depends on the individual.


Is patenting based on theoretical findings possible?

The relevant concept here is "reduction to practice," which means that a concept has been sufficiently realized to make it believable.  Where, exactly, this bar lies depends on which field and which country you are dealing with.

The United States, for example, used to have much stronger requirements for working models, but has recently introduced a notion of "preliminary filing" which lets one start the patent process before demonstrating a working model.  In some cases, particularly mechanical devices, the device (fortunately) might never actually have to be demonstrated in action.  In others, such as many types of biological invention, the science is considered so unpredictable that you cannot be considered to have reduced the idea to practice unless you have an actual working example.

For your particular question of computational material design, I do not know where the boundary of "reduction to practice" currently lies.  It is likely to be field-dependent (e.g., is this a mechanical macrostructure like a fabric, a simple atomic structure like a new alloy of steel, or a complex organic structure like a protein agglomerate), will depend on jurisdiction, and is likely to move again in the future as patent offices slowly come to accept the validity of more classes of models.  Thus, the overall answer is "it depends" and "talk to a patent lawyer."


Would graduate committee be more favorable to a barely passed grad course or no grad course at all while undergrad

The big question that both your recommenders and the admissions committee will wonder about is what this experience predicts for you in graduate school.  If you do poorly when taking a grad class now, will you be able to do well in grad school?

One factor may be preparation.  Maybe you were enthusiastic but overly ambitious, and in another year you'll have the experience and preparation needed to do well.  This is the reassuring scenario.

Another possibility is that you're just not used to be challenged by courses, since the undergraduate program was not very demanding.  Now that you know what you face, you'll take it more seriously and do better.  It's entirely possible, but this scenario is more worrisome.  Lots of people say "oh, next time I'll work harder," but this is easier said than done.

And there are even more worrisome possibilities.  For example, maybe you just didn't like the material and couldn't bring yourself to engage deeply with it.  This could be a symptom of lack of preparation, or it could be a sign that this field is not a good fit for you.

I'd recommend dropping the course.  In grad school there's no value in barely passing a course: if you need to learn something, then you need to really learn it well, not just avoid failing.  This means a bad grade on a transcript won't impress admissions committees, and it means you're going to have to go back and learn this material properly in the future anyway.  Probably you should take this course in grad school.  If you don't take it, then you'll need to put in some serious effort to master the material on your own.

Meanwhile, you should think about what went wrong and how to explain it to your recommenders, so that you reassure them regarding your future in grad school.


Situations where changes in advisor/lab interests makes you feel lost

The desirability of such a situation varies from person to person. Some people, but I doubt many, would love the independence. But others (most?) need more guidance, especially at the start and possibly near the end.

But if you need more guidance then you need to find a way to get it. A co-advisor? A different advisor? Something.

But just going along as you are is probably counterproductive.

An outside possibility is that, provided the advisors "business" interest has research potential, that you could get involved with that as a source of ideas and research opportunities. I don't know if this is actually possible or desirable, of course.


APA citation: book versus electronic book

Do not take it for granted that different versions of a book are identical.

Either cite the version you've used, or use the version you want to cite.


How do I demonstrate that I read and understood a professor's paper to the professor?

That is why I have decided that I will read some papers of the professors to convince him that I am well prepared to work under him.

I disagree with this advice. I would rather see applicants (especially those with an MS) demonstrate their ability to do research, usually through a publication or a strong thesis. As long as their topic is somewhat related to my research, that would be a stronger demonstration of their potential to succeed in a PhD program. Being familiar with specific papers that I have written is not necessary or expected (you can always read such papers if you are accepted).
If your only option is to study the papers of professors, my advice is to implement the methods discussed in those papers numerically, i.e. repeating the results, or possibly even conducting some trivial yet new extensions (like repeating the experiments on a different dataset). That would be far more impressive than simply reading a paper (where your depth of understanding is not clear).


How to transition from MBA in Finance to PhD in Financial Economics?

PhD programs exist to produce researchers, so an admissions committee would like to see that you will be able to produce original research. (In economics, that means journal articles.) So, what would help immensely would be to gain actual research experience. The best way to do that would be to work as a research assistant for someone who is actively publishing research.

It would be fantastic, of course, if you could co-author a paper and get it published in a top journal. But don't worry so much about that. What you're looking for is a chance to work with someone who can then write a letter of recommendation that says they are confident that you will go on to produce quality research of your own, and whose opinion will matter because they have a good track record of publishing their own work.

Add some statistics coursework to your programming experience and you'll be well-positioned to work as an RA. (Even without a stats background, being able to wield Perl or R or some other tool to collect and clean data is valuable.) Or find someone working with agent-based modelling who needs a code jockey. Then, of course, work hard and ask lots of questions.


Getting proper credit for a paper: author order

I suppose the alphabetical order is in favour of the supervisor. Unfortunately, if the excuse is indeed valid for the field you cannot do much. You can try and challenge it based on the practices of target journals, but you should be prepared for some confrontation.

An informal convention in many fields is that the PhD student gets to be the first author and the supervisors follow. It is within the power of the supervisor to uphold it but it is also violated both in favour of an undeserving student and to the detriment of a deserving one. Field conventions do vary, but as long as first authorship has weight and there is not a very good reason I am thoroughly in favour of first authorship going to the PhD student. I can only express my sympathy.

In my experience, a standard situation for publications stemming from a PhD is that the major bulk of the workload falls on the PhD student and supervisors undertake some rewriting (introduction/ conclusion/ discussion), polishing and getting the paper published. In that context, it is natural for the student to undertake as it is part of the learning process of the PhD.


How do professors and lecturers learn to teach?

This answer is based on my experience in Germany, and in an engineering field.

For interested teachers, universities usually have a central department that offers training, workshops, brochures, and plenty of information about how to teach. For example, here, here, and here.
Many lecturers do not take advantage of these possibilities and still learn on the fly. Doctoral students often have recently attended master courses and observed how teaching was done there. In many cases, the professor gives the lectures and the doctoral student teaches the corresponding tutorial, which consists of doing practice exercises on the board. This is easier to do than teaching concepts, and provides an opportunity for the doctoral student to become confident in teaching.
Evaluation by the students also plays a role. The students are asked to give anonymous feedback on the lectures and tutorials approximately at the middle of the semester. The teacher can then learn what they can improve in their method of teaching.


Impact of student suicide on PhD advisor’s tenure prospects

To get the elephant out of the room first:

If you are contemplating suicide and wondering whether you will hurt the tenure case of your advisor by this, stop this thought right there and get counselling. The tenure case really is of no concern in this question. I am sure your advisor would also agree to this.

Now, assuming that this is a hypothetical question, or it concerns a suicide that already happened.

A suicide of a student will very likely not hurt a tenure case directly. No educated person in her/his right mind would react like "he killed this guy, he must be the worst teacher ever!" I would rather expect a wave of sympathy and compassion about the loss. Of course, whenever a student leaves (for whatever reason), the tenure case is indirectly hurt a little, simply because the advisor needs to start from ground up with a new student, who is likely not going to be very productive for some time.


What is the difference between an academic CV in the US and an academic CV in France?

Off the top of my head: The European CVs I've seen typically include a photograph of the person; that is more the exception than the rule in US-style CVs.


Citing Blogposts from official governing authorities

You can cite blog-posts, and whatever citation style you are using will explain the right format. Citation styles are written to be all-encompassing, not just for citing papers. I suggest including an archive link of the page, because blog posts can easily disappear from the internet and then the citation becomes invalid. I actually saw a case where the person cited an article and a few weeks later it was gone, I couldn't even find it by googling.

Keep in mind that blogs are not peer reviewed, and are not afforded the same authority on facts that papers would be. So you should be careful about using the blog as support for your claims. Generally, taking what is said in a blog post at face value and accepting it as fact would be foolish in an academic text. People can write anything they please in their blog, it doesn't make it true. However, the fact that a person has chosen to write that, is a fact. That fact may be interesting by itself. For example, if a senior official claims a certain thing, they may or may not be right, but the fact that they claim it is enough to suspect that they will try to exert their influence to make the claim true. That part is significant.

In the text I would also make it clear that you are talking about a non-peer reviewed source, instead of simply citing it as you would a paper. I find it very annoying when you see a very interesting and cited claim, excitedly go to the reference list, only to discover that the citation is really just some blog so the claim is effectively pulled out of thin air - the citation only proves that the pulling was done by a third party, rather than the citing author.


How to search for a PhD student opening in Japan?

The best option if you can get accepted is through a MEXT scolarship. Usually, the application process is detailed on the website of the Japanese embassy of your country. Of course there are other scholarships but this one is the most advantageous.
If you can self-finance, you may want to try to enroll as a "Kenkyusei" (research student) for 1/2 years. Being a kenkyusei allows you to do some research under the supervision of a professor (ideally the one who would advise you as a Phd), taking Japanese classes and more broadly getting adjusted to your new environment while preparing for the university's Phd entrance exam. The application process for kenkyusei should be detailed on universitys' website.


No you should not drop out of grad school. The words "grad school dropout" doesn't fare well on any freshman CV. But, it must also be noted that after the initial slog, it also doesn't matter as much.

I have been told this statement many number of times by professionals who are at much better positions than me (a newly graduated PhD) in terms of both earnings and academic positions.

There is a real dearth of hard-working professionals in every profession.

I know it comes across as a bit philosophical, but I take it as a ground reality after having observed the same. Notice that I do not say talent, because talent seldom makes a person successful, hard work on the other hand almost always does. Also, a freshman with a degree always has more value than one with none.

Having said that, If you are worried about covering your debt after school, you should ponder these thoughts

Are you in a graduate course which makes for high employability?
If not, can you transfer to a course which offers high employability? CS and Informatics, are some examples of fields that offer very high employability.
Can you learn skills or enroll in courses which may increase your value in the job market?
Maybe try enrolling in one of the many free courses available online through portals like Udemy and Coursera to increase your value?

Invest as much time as possible towards learning as much as you can with employability being the focus. Furthermore, only learn that which you would love to do yourself because to get ahead in any field you need mostly determination and perseverance. You can only muster these two things if you love what you do. I do not make any mention of money here, because money generally follows people who get ahead in their respective fields.


How much do grades from beginning of bachelors impact PhD admission?

This may depend on the country as well as university/institute. You should have a look at the corresponding websites, as most information regarding PhD admission can be found online.

For example, the TU Munich website [1] states:

  Results are considered to be above average if studies were completed
  with an average grade of at least 2.5, or at a minimum passed with a
  grade of “good.” In exceptional cases, your above-average
  qualifications can also be proven through academic work (e.g.
  publications) completed after your course of study.

This means that your bachelor or earlier grades to not affect PhD admission as a hard citerion. However, when you hand in your application the professor will have a look at ALL your grades. It is his/her finial decision whether to accept you, so all your grades might have an influence on the outcome.

Personally, I have experienced that having publications beforehand helps a lot. Thereby you prove that you have at least a basic understanding of scientific work. This may give you an advantage compared to other applicants.

[1] https://www.gs.tum.de/en/applicants/application/requirements/


Should I take a Certificate for University Teaching while doing a postdoc?

I would recommend you to take the certificate now. The reasons are the following:

Although research excellence still remain to be the most important criteria for early-career faculty members, it is rarely a single criteria candidates are compared on. In the UK it is increasingly common that new faculty members are expected to teach from their first day in the Division; an evidenced skill and knowledge of the process can give you an advantage over other candidates, excellent in research and research only. I don't know what is the situation in other countries, but I have a gut feeling that academia across the globe is becoming more dependent on student fees, and hence the emphasis on teaching skills will increase.
You seem to do really well on research front now, having your own fellowship funds, etc. You are clearly appreciated and valued in your current Division. However, you will need to establish yourself in the new place in the new role of young but fully capable faculty member. This could include a lot of teaching, plus a lot of administrative work you're not familiar with now. Transition from research-only postdoc to a faculty is not a smooth one. It is quite important to be prepared to the faculty role as much as you can, before you take it. So, it is worth spending 200 hours now rather than later on top of other commitments.
It is not uncommon for people to move between countries and departments and having their certificates recognised. Commonly, HRs would need some evidence, but as soon as they can read the document, they are likely to accept it.


Is it wise to ask a PhD supervisor about the quality of my work?

Yes, it is appropriate to ask her what is going on. This is your PhD and she has no right to delay it in the way that she is currently doing. As a supervisor, she is supposed to support you in finishing your thesis, and if she is not doing that, you have a good reason to complain about it.

I do not think that it is even important what she is thinking of your work. If she thinks that your work is bad, that would make it even more important to give you this kind of feedback. So that is not a good reason to not give you feedback, and I also think it's highly unlikely that this is the actual reason why.

I would simply argue with the facts. After 5 years of doing your PhD, you want to be finished soon. In order to do that, you need her to give feedback on the manuscripts. If she says "why the hurry" again, there are several things you can point out, for example:

Postdoc positions usually start in autumn, so in order to get one of
those it would be good to have the PhD rather sooner than later,
since there is a lot of work to do for applications etc. beforehand.
You feel that you cannot use the additional time productively, since
you have done all the work that you wanted to do and do not need to
delay any further.

But actually, the question is beside the point, because it is your decision, not hers, and that is not why you are talking to her. If she really tries to derail the conversation in this way, I would call her out on it. "I feel like you are avoiding the actual issue I am addressing here. I have waited for your feedback for 1.5 years now. I think this is clearly too long, and now that I am ready to finish my PhD, I really need that feedback. I can understand that you are busy, but I have the feeling that you are frequently giving my work a low priority. I do not know why you are doing this, but it is frustrating. I currently do not feel appropriately supervised by you."

Well okay, I might have a slightly confrontational nature, so take this with a grain of salt. But I think in such a case it is adequate to criticize her for the lack of supervision that you have experienced throughout your PhD.

A last tip would be to give her deadlines. Usually people prioritize things where they get a clear deadline, even if the deadline is arbitrary. In the best case scenario, you can tie the deadline to an actual milestone of your final phase of the PhD - like maybe you want to say that by the end of March, you want to be done with the actual research and only focus on structure and design of the thesis, so that the deadline for her would be somewhere in March.


How to cite a paper that looking for a journal for publication

You can submit the first paper to a pre-print sever such as arxiv. Once, it appears in arxiv as a pre-print, you will get a citation information, which can then be used in the second paper.

I don't see any other way of doing it unless it appears somewhere as a pre-print or a published article.

Further, if you are citing a small portion (such as a method or a result) of first paper, you can replicate the same thing in the second paper with a note saying

  The initial approach of this method is to appear in the article entitled 'ABC Approach for ZYZ Analysis [draft]'.


Quantity vs Quality of Publication during PhD

I don't know what publication rates are typical in computer science, but in mathematics it is true that quality is more important than quantity, when it comes to getting postdocs and competitive research positions.

This does not mean quantity is irrelevant. But postdocs are partially given based on your promise as a researcher. To that end, one truly excellent paper may be enough to land a job (along with good references), because it suggests you have the potential to produce more excellent papers. On the other hand, 10 truly mediocre papers is not likely to be as impressive, because it only shows you can publish lots of mediocre papers.


Is it a normal process if all changes by "Track Change" function in Word of my revised manuscript are visible after being built in Elsevier?

I think the comments and changes should have been accepted and then sent to the reviewers for them to appraise as necessary.


Are there other cities in the world like Boston where a large number of good postsecondary institutions are located?

So, "good postsecondary institutions" is a bit hard to define. University rankings are probably about the only thing less meaningful than impact factors, but they'll do to give us a basic idea here - do any cities have a large number of universities that are rated higher than the lowest one in your set?

The US News & World Report has a handy list searchable by city. Annoyingly it doesn't quite work for the US (it defines city strictly) but it's a good approximation. Brandeis is rated #280 (making it fifth in the Boston area, if you include Northeastern).

On the US News & World Report ranking, and plugging in a few likely candidates, there are

six London universities ranked higher than Brandeis.
five NYC universities ranked higher than Brandeis.
four Paris universities ranked higher than Brandeis.

So that's one higher, one equal, one close. In the specific case of London, Wikipedia has a handy table of universities by ranking. Depending on which metric you want to use, it has either five, six, or eleven (!) institutions ranked higher than Brandeis.

So with these admittedly flawed tools, it looks like London is likely to be an answer, but there are a couple more close contenders. There may be other concentrations in the US depending on how generously you define the city areas - I would guess the Bay Area around San Francisco is a likely candidate, for example.


Solliciting letter of recommendation from student for tenure paquet

If a university highly values teaching then such letters can be helpful and can be solicited ethically as long as there are certain considerations met.
A former student, with whom you no longer have any supervisory (or grading) relationship is fine. Such letters should be sent independently and their sender's identity and content not revealed to you. Both conditions should be met.
Alternatively, simply announcing that you are up for tenure and any student who wants to comment can send a letter to the committee is welcome to would be fine, as long as student anonymity is maintained.
A student who has graduated and with whom you will no longer have any possibility of a supervisory relationship is fine, even if not anonymous.
But everyone needs to be assured that there was (and can be) no pressure applied, nor any bribery possible.
And, yes, I think it is common enough in teaching colleges and some others. Probably more common is for a candidate to supply a list of names of students that the committee can contact independently.
However, if you contemplate doing this, I suggest that you discuss it with the department head and/or the dean before you act to assure that it is acceptable at your place as well as any additional restrictions. In particular, including letters that you have actually seen might not be allowed, or even proper.


Posting what I learn and notes from my classes moral dilemma

I think in general that what you are doing is without moral implications. You are certainly free to post your own thoughts or your interpretations of what a professor has said in class.

However, it would also be good to talk to your professor and get his/her advice. If you post problems or exam questions you might be, inadvertently, helping others to cheat, which would be unfortunate. The professor might request that you not do that.

Whether you cross over into copyright infringement or not depends on a lot of things. I will guess, but you should verify, that even the professor's notes would be permitted by some, even though they are copyrighted.

But for your own thoughts and words, you are certainly on solid ethical/moral ground. Even if other students find them, it isn't infringing for them to use your thoughts to help mold their own.

As a professor, I put a lot of things online for students to use. I also had mailing lists to which students could share their thoughts and help one another, with few limitations. Making it public/open to all makes it useful and avoids some ethical concerns that might occur (if rarely).

Nor is it unethical for you to simply help fellow students learn through conversations, etc. as long as you don't abet actual cheating. But I see no issues of that in what you describe.


H18 stands for Hiver 2018 (Winter 2018), that is, the current semester.

Similarly, E18 is Été 2018 (Summer 2018) and A18 is Automne 2018 (Fall 2018).

Source: I'm from Québec, and I recognize my former University software in this screen capture.


Replacing tech reports: can we put good undergrad dissertations in arxiv?

Yes.

Any research writing (paper, report, monograph, dissertation, preprint, etc.) approaching publishable quality is welcome on ArXiv, whether its'written by tenured faculty, postdocs, graduate students, undergraduates, high school students, or hamsters.

(I am the ArXiv moderator for cs.DM and cs.CG.  I have not, as far as I know, accepted a paper from a hamster.)


Don't convert it. Most places I applied to only required that you submit your grades based on how your institution provided you. For your case, that would be 4.33/7. Do not manually convert the scale unless being explicitly told to do so by the university you're applying to.


You are not very specific: on the one hand, there is more than one kind of mathematical writing; on the other hand, you write "I am concerned this may tarnish my reputation" and that depends (a little bit, at least) on who you are.

I will assume that you are a junior mathematical writer, i.e., that you have not yet published many (or any) mathematical papers.  (If you have already written a few dozen papers, you have not only a lot of experience but have gotten a lot of feedback, so you know what kinds of writing variations referees, editors and other careful readers will pay attention to.)

Let me begin with some (unfortunately rather conservative, but still inherently sound) advice for the journeyman writer in any academic field:

  Don't try to be innovative or different in your writing style in your first papers or first years of writing papers.  First learn how to write acceptably -- or better, well -- according to the most standard norms of your discipline.

It takes a while to master the standard conventions of academic writing.  When I look back at some of my earliest papers, I see some weird stuff.  In a few cases I was trying to be innovative, but most of the time I just didn't know what the standard convention was.  About 50 papers in, I am still learning new things about the standard mathematical style.

What's so great about standard mathematical style?  Nothing inherent.  But as a culture, we're used to it.

  The cardinal goals of mathematical writing are precision and clarity.  After that, the next goal is unobtrusiveness: good mathematical writing does not call attention to itself, because attention that is diverted to the writing is diverted away from the mathematical ideas and reasoning.

Again, what is unobtrusive depends on the culture.  For instance, there are some mathematical turns of phrase that would be pretty weird in ordinary writing but are not weird in mathematical writing because they have been done so many times before.  Examples include: "in the sequel," "by abuse of notation," "a trivial case"...And of course the best example is the use of "we" in mathematical writing.  It looks pretty weird the first N times you see it...and then it doesn't.  It is an entirely standard convention of mathematical writing, as can be seen by its approved use in virtually every mathematical style guide but even more strongly by its almost universal use in published papers.  You don't have to use "we" in mathematical writing -- e.g. this style guide contains some tips from Paul Halmos on avoiding it -- but I can think of no good reason to avoid it.

Every mathematical style guide known to me denigrates the passive voice in mathematical writing in the majority of instances.  So for a journeyman mathematical writer to insist on using the passive voice would be a violation of both of the above pieces of advice: on the one hand you are not learning to write in the standard way, and on the other hand you are writing in a nonstandard way that a lot of your readers are going to notice, get mildly distracted by, and therefore in some cases get moderately annoyed at you for writing in this way.  Why do you want to risk this?  You say:

  "I am interested in using the passive voice in mathematical proofs as I feel that this reinforces the objectiveness and universality of the proof as opposed to the specific instance of the proof or my own self."

Honestly, I am very unsure what you mean by that.  In case you are suggesting that there is some logical or ontological difference between

  We will show first that A implies B and then that B does not imply A

and

  It will be shown that A implies B and then that B does not imply A

I can assure you that there is not.  More to the point, readers of math papers are not going to be critiquing the proofs for "objectiveness": I don't even know what it would mean for an otherwise satisfactory mathematical argument to lack objectiveness.

Moreover, what are you actually trying to accomplish by using the passive voice in your math papers?  It can't be to make your work easier and more pleasant to read...as you seem to understand already.  You write

  "Would it be looked upon negatively to intentionally employ a writing style uncommon in my field to express what I see as key values in the field?"

What "key value" is expressed by using the passive voice?  I don't think there is one.  But if people get wind of the idea that you feel like you, as a junior person, are in personal possession of a clearer understanding of the "key values in the field"...Well, since you asked for feedback, my honest appraisal is that you sound a little nutty and a lot inexperienced.  So it is a bit of a negative, yes.  Of course, all mathematicians start out a lot inexperienced, and many, many of us are a little nutty, so your eccentric-sounding ideas about writing and mathematical values will not be a major sticking point in your career.

The largest issue I see, honestly, is the impediment to learning good writing that you've placed on yourself.  Without meaning to be harsh: parts of your question remain obscure to me after repeated readings.  The comments show that other readers feel the same way.  This is a real example of your writing not being properly understood by others, perhaps to the point of your overall message getting lost.  That's the risk you incur by not placing a premium on clarity.  It's a big one.


Citing an accepted manuscript that hasn't yet been published

How can I cite a conference paper that has been accepted but not published?

Cite the paper as if it were published (albeit without page numbers, etc.) and add to appear at the end of the citation.


How much do budgets affect likelihood of grant funding?

A badly written budget could put your proposal out of contention, but a well written budget that scrimps on costs isn't likely to help you get funded (what are the odds that your project is "on the bubble" for funding and just fits within the total funds available?)

In your proposal you should ask for what you need to get the research project done and to support the "broader impact" of the proposal.  Don't load up the budget with unnecessary expenses just so that you can get a larger award.  On the other hand, don't prepare a low-ball budget that doesn't include adequate funding for travel, students, etc.  Being too extreme in either direction can hurt the reviews of your proposal.

Be aware of your institution's overhead rate and if it is higher than normal, don't be surprised if your budget is larger than average for the program that you're applying to.  If your institution has a relatively low overhead rate, than don't be surprised if your budget comes out on the low side of average. A lot of the variation in budgets is due to differences in overhead rates (along with PI salaries and the cost of students.)

Also, work with your "restricted funds" office to make sure that your budget conforms to your institution's regulations as well as the applicable federal regulations.

In my experience, the likelihood of getting funded seems to have little connection to the size of the budget, as long as the budget is within the normal range for the program, the expenditures make sense for the project, and there aren't any very expensive looking items.

For a grant in mathematics you really should have a very a simple budget and it shouldn't be hard to justify the budget.  Compare this with some grants I've worked on with earth scientists that included international travel to places like Peru and Tibet, shipping boxes of rocks internationally, expensive laboratory tests, etc.


PhD.-Application; How to deal with reference-letter requests when being out of academia for 2 years?

I suggest asking your old writers or others at the institution for new letters. Treat it as a chance to catch up with old professors which is a good thing to do for any prospective academic.

The old letters have less relevance and new ones, while still dealing mostly with what you were like two years ago can give some assurance that you've been active in the interim.

Two years isn't that long. But if the gap gets much wider people will start to forget you. This is a good time to renew old ties.


How to address strange author order of a collaborative paper within "equal distribution" section?

Go with your supervisor's advice, talk to the Computer Science student and ask him/her, in a very gentle manner, why the authors were ordered the way they were rather than alphabetic in both sections.  This is the norm for equal distributions.  Can't imagine what reason the other student would have to go a difference way.  If he/she does not have a very good reason, ask them to reorder the names in alphabetical order.  If they do not comply, you can always ask them, again, in an email copied to the supervisors.  At all times, exercise grace and patience - being firm but gentle gets results much more often and burns bridges much less often.
PS: be very careful if you ask that student in an email.  Written communication on what could be a negative issue, will by default come across as confrontational.  Even if you are not trying to, they will usually see it as you confronting them on something they did that was non-kosher.  So if you do email him/her, make extra efforts to explicitly communicate a non-confrontational tone.  Maybe start by thanking them for their work in the paper and telling them how much you appreciated the opportunity to work on it as well.  Make your question about author order very light, do not point out his/her name came first, just that it was not in alphabetical order and you are wondering why that is, especially since you note the advisors are ordered alphabetically.


Is it possible to submit a thesis to a univeristy without having been enrolled while writing it?

Probably not without meeting some minimum requirements.  At my university a student must be enrolled for a min of two years full time.  There are exceptions but require an extensive justification to be put forth that is then review by a committee.  Also any parts already submitted for the award of any degree cannot be reused.


Do students in taught programs need to go to their professors before publishing?

I know that graduate research students should not publish works without their professor's permission.

It's a little more complicated than that.  Nobody needs permission to publish anything that they did entirely on their own.  If you work collaboratively or as part of a team, then it's not 100% your work and you need your collaborators' permission.  If you do not collaborate but work under someone else's supervision, then it's still polite to ask for advice/permission.  (They might see it as more of a collaboration than you do, and in any case your submission may reflect on their supervision so it is reasonable to get their feedback first.)

  Is this rule relevant to students in taught programs?

If you have no collaborators or supervisors in the research, then you can publish it however you'd like.

  Can I submit my paper for credit in a course, without giving up ownership of the paper?

I don't know of any case where you give up rights to a paper by submitting it in a course, so ownership is probably not the relevant issue here.  In the universities I'm familiar with, you can certainly submit for publication an essay that was written for a class assignment (most such papers would not be accepted for publication, but a few could be).  On the other hand, you cannot get class credit for a paper that you previously wrote for another purpose.  The precise rules in your case may differ, but if you plan to use this paper for a class you should investigate your university's rules.


How should disallowed collaboration on a freshman homework set be handled by a TA?

I personally follow the rule "once is nothing, twice is a habit". I think a warning would be a good way to start. I do, however, think that it is still a good idea to run this by the instructor. I assume he/she is responsible for the course and the decision is up to him/her. You can explain your point of view and perhaps get some feedback on the matter. In addition, by taking up the discussion the problem is in th eopen and it makes it easier to catch repeat offenders. If you keep it secret, the culprits, in the worst case, can get by repeated cheating for each new teacher they encounter.

Cheating is an abomination but I think people are allowed to make mistakes. I also think most people learn from mistakes and will not easily do it again. But, it is necessary to make sure they understand their attempt has put them under scrutiny, that is probably "punishment" enough.


I wouldn't refer to the specific editor, just because if there was a change in the role before your paper is seen (uncommon, but happens), it wouldn't be nice. The editor-in-chief is a safer choice.


Advisor professor asking me for the source code of my dissertation in order to be used by another student

You developed the code as part of your curriculum. It's quite possible that therefore, the source code belongs to the university anyway. This does depend on the laws of the country your university is in.

Also, I don't see what you should be concerned about. Someone else building on your work is exactly how science is supposed to proceed. If I were you, I'd take the request as a compliment.


COVID-19 anxiety's impact to my output: any strategies for mitigation?

I expect research output overall to be down this year into next. Surely some people will cope better than others, and different types of research are more or less directly impacted (e.g., that requiring solo work at a computer, versus that requiring access to shared facilities that may be/have been closed, versus that requiring face-to-face contact with human subjects). Others will have additional direct challenges to their time: childcare may be closed and children may be learning from home rather than school, for example.
@paulgarrett's comment is exactly what I was thinking of as an answer:

A small point: forgive yourself (as opposed to judging...) in this situation. It is crazy. To accidentally pretend that things are not crazy will obvs make you more crazy. My advice would be "cope with the bad current state, and wait to think about things later..."

...except I think this is the main point rather than a small one.
Besides that, it sounds like you're trying all the right things (eh, maybe not the booze, but if it does help you relax and if it's in moderation and not purely as medication then there's little harm).
I think the most "solvable" problem you have (or, at least, one I can provide some advice on) is this part:

Compounding all this, I accepted several large projects in January which are now past due. (...) Writing, especially, is very difficult, which puts me further behind, which leads to more anxiety.

You're probably best off doing some prioritization (from @avid's comment: "What actually needs to be done by when? Can projects be reorganised to be more achievable? Can deadlines/deliverables be re-negotiated? Try and focus on completing one task/project at a time") and scheduling. There is no way you can make up for weeks of reduced productivity in an instant. Instead of worrying about everything you need to do (a circumstance I find myself in often; not new to COVID for me), set an immediate-term schedule for yourself.
The granularity might be something you experiment with, but try to set specific, achieveable goals for the next week, the next day, or the next hour. Do your best to meet them, but don't beat yourself up if you don't. Reevaluate your progress the next time you set goals. Try to focus on what you've accomplished.
It may be helpful to tier your short-term goals into:

Things you will accomplish (today/this week) no matter what (except emergency, of course)

Things you reasonably expect to accomplish

Goals to aim for in an ideal world

Probably the things you slot into "3" might look like a normal week for you pre-pandemic, or even far less than normal, and that's fine. Focus on making bits of progress on your projects that you can feel good about. Be prepared to have days and weeks where you only accomplish the tasks under (1), then forgive yourself for not doing more, remind yourself you've at least achieved your personal minimum, and move on.
In closing, though, and echoing Paul: forgive yourself, you're under a lot of very understandable stress in a crazy time.


Do I owe potential collaborators an explanation for late follow-up?

You would be wise to bring them up to date and apologize for your absence. If you value the collaboration then you don't want the other person to think you just gave up on it.

The explanation could be minimal or not, depending on your personal relationship to the other person. "Going through a divorce" or "Time consuming personal situation". You judge, but definitely stay in the game.

Also, if the situation is expected to continue, you can warn the other person that your time, but not your commitment is limited in the short term.


PhD - How dependent are public universities on funding from the US Government?

As Nate explained, these cuts aren't relevant to whether a school is public or private; the factors are much more complicated than that.  Public schools in many states have gotten serious funding cuts in recent years, but that's not a decision that's made by the president, but by the governor and legislature of those states.  You can research whether they've been doing so at the public institution you're looking at, but of course, the situation could easily change after the next election.  I think this is just too complicated to really try to game out how things will be impacted; I think probably the best source of information is talking to other students at the institutions and the precise financial details in your offer.


Professor not giving solutions to exams and assignments that I need to grade

I can't tell quite what your concern is, so I'll address both.

Is it OK for a non-professor to write solutions and design a rubric?

In my experience (large US universities, STEM), this is extremely common. I disagree a bit with others saying that only professors can make such determinations (though of course the instructor of record can make such determinations if they are inclined to do so).

Is this abusive toward the TA?

How are you being paid?

If it is hourly, then there is no issue; you should solve the problems and make a rubric however you see fit, and then bill for that time as normal.
If it is a set stipend, then there is usually a nominal time requirement (in my university it was 20 hrs/week for grad students). If making solutions will put you way over this, it's fine to raise the issue with the professor and/or with the administration (in fact, you may technically be required to do so)

One other tip -- you might consider taking the top-performing students' solutions and using them as a starting place for your own solutions. Of course, you'll have to be sure you're grading those students fairly and catching any errors. But I've found that the I can often create a solution set just by mixing and matching solutions from the top ~3 students and adding a few expository details.


Journal rejected my paper because contents of paper are in PhD thesis

Email the editor, explain that their automated plagiarism detection system has seemingly gone awry, inadvertently flagging your PhD thesis.


Web of Science; any way to get the "Published Items in Each Year" numeric data?

I don't think this is possible in WoS without pulling each paper's citation data and assembling it manually, and I don't think you want to do that!

It is possible to do this with Scopus, however:

select all search results
"view cited by"
filter by year

Note, however, that citation numbers in Web of Science and Scopus are not directly comparable, as Scopus indexes many more items. So if you were to use this, you'd want to make sure all your data came from the same source.


Since you indicated that you are focusing on oncology, it seems likely that a PhD will enhance your oncology practice. This thread on The Student Doctor Network explores the pros and cons of an MD-PhD in Radiation Oncology. The general consensus is that it is worthwhile if you plan to be active in research as an MD, otherwise it may be a waste of time, money, and energy.

As Shion mentioned in a comment, most MD-PhD's become medical research professors, while it sounds as though you will be in active medical practice. There is a possibility that having a PhD may exclude you from consideration by the hiring boards at non-research-focused institutions. At research-intensive insitutions, the PhD will probably help your case, and certainly can't hurt. It appears that many practicing physicians at top US cancer centers are MD-PhD's. See here, here, and here.


It seems to me that this question is less about the arxiv per se and more about how to navigate doing research in a very fast moving academic field.

  I get the impression that arXiv is more than just putting something on a personal website.

It's certainly different.  The main differences are:

(i) Many more people will see your paper.
(ii) Your paper will indeed be archived, essentially permanently.  (Withdrawing a paper from the arxiv has the effect of uploading a new, empty version.  Older versions are still there!)  On your own website, you can take things down at least as quickly and easily as you can put them up.
(iii) Some (very obnoxious) journals may regard posting on the arxiv as "prior publication".  (This is strictly unheard of in my field, mathematics.  My guess is that CS is close enough to math so that it is at least very rare in yours.)
(iv) Minimum standards of completeness and professionalism are enforced on the arxiv.  These are enumerated on the site itself, but the gist of it is that they are looking for manuscripts at the last step before conference/journal submission or later.  They are not looking for early drafts.

Of  these points, probably the last is most relevant to you.  If it is standard in your subfield to include 25% experimental data [you say that is standard in "CS", but that is certainly not true across the entire field], then a paper uploaded to the arxiv without that would probably look to many in your field to be incomplete, which is against the spirit and perhaps the rules of the arxiv.  So I wouldn't recommend it.

But the situation doesn't fundamentally change for papers that you or others post on your own website.  The phrasing in your question suggests that you feel that you might not have to "be responsive" in the academic sense to papers that you find on people's webpages (only).  That's not true.  As an academic you have to be responsive to others' work wherever you find it.

In terms of the prospect of people uploading "the bare minimum to arXiv in order to get credit for the idea": is this an actual problem for you or just something you are wondering might be a problem?  I have never encountered this problem in my work.  That you are wondering whether it might be a problem makes me think you may be a quite new researcher and haven't fully grasped the way the academic community works.  (Which is fine, and you have only to look forward to understanding it better.  But you should talk to others, including advisors and mentors, to try to get a better idea.)  Academia places a great privilege on completed work for exactly this reason.  If you put out a manuscript which, say, modifies an algorithm and hints that it could be faster in some situations, the most likely reaction you'll get is "Go on..."

This question may finally have made me understand what people on this site are on about when they say things like "An idea is worthless".  An idea is certainly not worthless, but a vague and unimplemented idea is of highly uncertain value, to the point where rushing to publish "only the vague idea" would be a very poor, um, idea.

By the way, you don't have to immediately drop something because someone else had "the same idea" and put out a paper before you.  Much -- perhaps most -- important academic work overlaps with other work and even more of it refines and extends the ideas of others.  How to respond to seeing "your idea" in another paper is a topic for a different answer.

Finally, let me say: if what you've done, are doing or want to do has real value, then it is unlikely to be received with thunderous applause this week and totally ignored next week.  If you're living in fear that someone else will say what you want to say, maybe slow down and find more to say.


Citing a passage which includes added words by the translator?

The bracketed annotation is a gloss to support readability. When you quote this translation, verbatim, just cite the quote and have the bibliographic entry identify the translation (rather than allowing the reader to conclude that you did the job).


Can I write my whole SOP about machine learning for graduate school admissions?

Writing statements of purpose (SOP's) can be challenging. If you make the statement too general, it may come across like you don't have a solid reason for attending a graduate program. On the other hand, if your SOP is too specific, you may unnecessarily restrict your chances of admission—for instance, if you only talk about working with one or two professors, and they're not taking new students, you may not be admitted.

That said, you are free to write your statement of purpose however you choose. Just keep in mind that in formal application processes, you are generally writing to an entire department, not just one or two professors.


How do academics change their area of research in the middle of their academic career?

There are two parts to this. The first is easy. If you are tenured then you just make the change, either immediately or gradually. Tenure gives you the freedom to do that. If you are untenured then you make the change and worry a lot about whether you will get tenured.

There is, however, one scenario in which it is advantageous for even an untenured person to change. If you are the new hire in a department in which there is no one to collaborate with then it might be an advantage, even if you are untenured, to join a research group and move toward their interests. It could, perhaps, enhance tenure possibilities.

The second part is a bit more complex, assuming you want to behave ethically. You can't really advise students very well if you have no knowledge, though a surprising amount can be accomplished. It is, in theory, possible to teach things that you don't know yourself, but you have to do it carefully, putting the student on a learning path that you haven't followed yourself. This is possible if you know about research and how to conduct it and are sophisticated enough to follow the arguments put forth by the student, just as you would the arguments of any colleague. I'll note that research groups actually do this - exploring a path that no one has followed.

But if you change fields gradually then you can also work into the advising role gradually, perhaps by being a co-advisor of a few students - even if informally until you get the required background.

I'll note that advising students outside your expertise, while possible, is risky and so the methodology used needs to remove risk for the student. A student, on the other hand, is best advised to choose an advisor who already has sufficient expertise in the direction to be followed in the research.

Note also that at the end of doctoral research the student is actually expected to know more about the specific research area than the advisor, unless the student has brought the advisor along on the journey to the end. If the opposite were true we would never advance, with each student being somehow less than the advisor.

Note that I've assumed here that the change is to a field that has similar research methodologies, such as changing subfields within a larger field. It is harder otherwise, of course. But the way we do mathematics or computer science is pretty similar within most subfields. Similar for chemistry, say. But to switch from math to history is a bigger challenge as the research methodologies are (I assume) much different.


From an author's point of view, what would you consider as negative peer reviewer comments?

When reading reviewer feedback, I generally divide things up into five mental categories (sorted from best to worst):

Praise: It feels really good when a reviewer "gets" a paper.
Little stuff: Anything that can be cleaned up easily, like typos and grammar failures, dropped minus signs, mislabeled figures.
Suggestions for improvement: Things that are legitimate issues, but are reasonable to push off to future work if necessary.
Legitimate complaints:  This is where a reviewer points out actual significant problems with one's work.  If you were unaware of them before, or thought they were less important than the reviewer explains them to be, then this can really sting, but it's a reasonable judgement.
Nasty, unfair reviewer #3: This is the stuff that really burns, when a reviewer seems to have an personal agenda or grudge and is taking it out on your paper.  A recent example I encountered included the phrase: "All the hard questions are systematically discarded."

What's very difficult, as an author, is distinguishing between suggestions for improvement, legitimate complaints, and unfair reviewing.  This is particularly true when things are presented harshly: I find a major difference between directness (which raises a clear issue about the science) and harshness (which might or might not be clear, but is presented with a side-dish of personal attack).

However, especially when it comes to things where you have feelings like "but it's obvious!" or "but we already addressed that!" or "they must not have read the paper carefully!", there is usually a legitimate difference of viewpoint, which it's important to figure out how to overcome.

That's why I always read feedback more than once, at at least a couple of days separation.  The first reading lets you see how much the review is praise vs. little stuff vs. the other three categories.  At that point, though, you're generally too emotionally involved and reacting (particularly if you got a rejection) to distinguish which category the issues raised by the reviewers actually fall into.  A couple of days distance, though, and I find it much more possible to parse out the different strands of negativity, figuring out which are legitimate, which are unfair, and which are more appropriate to push off to address other papers.


Is it possible to be accepted to a Communications Engineering PhD program without a Masters degree?

In Europe it's very uncommon to start a PhD program without finishing your MSc. However, it might be possible in some countries / programs to start a research project as a part of your masters, and finish this in a 3-year PhD program. You barely even started your MSc (you probably did the self-study for the easiest/fastest 30%), so it might be an option to switch to a university where you can do one big research project for your MSc and PhD.