Don't have a source, and things may be different in different parts of the world, but I've always considered a dissertation to be:

  A long monograph submitted in partial completion of the requirements for a PhD

Dissertations are generally submitted by grad students as they complete their PhDs -- other academics might publish long monographs, but that wouldn't be considered a dissertation.
Certainly I don't think there is a well-defined standard for how significant a contribution has to be to merit a dissertation -- it's whatever the committee will accept (though in principle, it should have some new advance, not merely a survey or report).
Some institutions may allow you to staple together your papers to produce a dissertation; most require a separate document that re-hashes work that may (or may not) have been published elsewhere.


Explaining Temporary Voluntary or Medical Leave from Prestigious PhD on CV?

I recommend you list your PhD studies on your CV. Industry is full of people who have left a PhD program for one reason or another! It's also unlikely anyone will look down on you for your poor grades in one semester.

There are two issues I would give some thought to: (1) how will you describe your reasons for leaving the programme (temporarily), and (2) will you tell them about your intention to return to the PhD programme. It's best if you can describe (1) in a way that won't give potential employers concern that you might not be able to handle the job. Being honest about (2) may discourage some employers from hiring you if they want a long-term employee, but others may be willing to gamble that you'll change your mind and stick around.


What the difference in CVs between "submitted to" and "to appear in"?

For those papers that have not been accepted, some people write "submitted to" in their CV and some others use "to appear in".

Does anyone really use "to appear in" to refer to papers that have not been accepted yet?  In my experience (mathematics in the U.S.), "to appear in" means "accepted, but not yet published", and it would be unethical to use it to describe papers that have not yet been accepted.  It might occasionally happen, since not everyone acts ethically, but you wouldn't want to get caught doing that.

I can't rule out the possibility that other fields use these terms differently, but I'd strongly recommend sticking with "submitted to".  It describes an objective fact, while "to appear in" is at best a prediction and could be viewed as an intentionally misleading statement.


What are the main practical complications/challenges to using Linux as your full time OS, particularly as faculty in Biology/Ecology?

This question might well be closed as off-topic, but here is my experience as a mathematics professor who has used Linux on his primary desktop machine at work (and on my computer at home and on my personal laptop) for 20 years.  Before that I ran Solaris on Sun workstations.  Before my academic career, I worked as a Unix system administrator in the 1980s, so I had a lot of background.

Your IT department might be unwilling to allow you to run Linux on a university-owned computer and might be unwilling to allow you to connect your personally-owned Linux machine to the campus network.
You may be required to purchase university-owned computers from a particular vendor whose hardware might not work well with Linux.
Your institution might require you to use specific software that only runs on Windows.  For example, earlier versions of the widely used Banner ERP system couldn't be used in Linux. I used to have to authorize purchases that were made with my department's purchasing cards using a Windows only software package (actually a web app that required Internet Explorer 6 and wouldn't work with Firefox or Chrome.)
You may have trouble interchanging MS Word Documents or Excel spreadsheets with Windows users (Libreoffice is pretty good but still not perfect.)
You may not be able to use licensed software (such as SAS, MATLAB, etc.) that the university has site licensed for Windows.
Your students and colleagues will probably be using Windows machines and you won't have an environment that perfectly duplicates their setup.  This can make it difficult to reproduce problems that they have, even with free software.  For example, I recently had an issue using Octave (an open-source MATLAB like language.)  My code ran fine in Octave under Linux but failed in Octave under Windows when a colleague used it.  This turned out to be due to a bug in the math library that was used on the Windows build of Octave.
Your IT department will almost certainly not provide any support for problems that you might have with your Linux system- you'll be on your own to resolve any issues that come up.

I've always made sure to maintain access to a Windows machine for this few times when I really need it, but in recent years that's been extremely rare.   I've got a university-owned Windows laptop that I haven't powered up since July, and I don't miss it.  Despite dealing with many of the issues above, I've had a very good experience using Linux and wouldn't consider switching back.


Earnings generated by open-access papers vs. paywalled papers

For subscription earnings, the most prevalent figure is in the ballpark of $5,000/ per paper. It is obtained by dividing the total revenue of the STM journal subscription market by the number of published paper in the same year. Some sources: this blog post and link therein provide estimate based on precise sources; this STM report (2015) mentions an estimate of £3095 per paper, with a rough decomposition of the cost.

Remember this is an average, I know a publishing house who would typically have prices of the order of $50 per page (in math, so about $1000 per paper) - but hey, they do a much better job than Springer or Elsevier, so of course they are 5 time cheaper. Heu, wait...

For Open Access article, things are way more complicated. First, it is not true that OA means that "researchers/institutions pay when publishing": Green OA is quite independent of journals (authors deposit their postprints in a repository) and many Gold OA journals, including high-standing ones, run on voluntary work or subsidies or both and do not ask for APC (Article Processing Charges, aka publishing fees). Here, it is my duty to introduce Fair Open Access.

Second, there is the case of hybrid journals (some papers are OA, the others are closed to non-subscribers). Figures have to the best of my knowledge not be compiled and publicly available.

Third, even for those Gold OA journal relying on APC, I do not know of a good source to get an average price; I have seen prices from $500 to $5,000, possibly more. But it is true that currently Gold OA seems quite lower priced than subscription on average. However Nature have said that if they where to turn OA, they would "have to" charge several tens of thousands of dollar per article. So one can guess that OA may have developed first in the lower-cost segment of the market, rather than being intrinsically lower-priced.


No specific guideline for the template of first submission

I don't know the rules for this specific journal, but in most venues you're not supposed to tweak the page geometry (margins, headers etc.) of a template, if one is given. To me, it feels dishonest to secretly shrink the margins and squeeze in more content. It may reflect badly on you if the editor notices it.
In any case, I recommend that you contact one of the editors and ask them. That's the only way to get an authoritative answer.


Do journals allow authors to bring their own reviewers

There are some journals that ask authors to suggest reviewers. There is no expectation that these people will necessarily be asked, but it gives the editor a backup at least. There are some journals that ask authors to suggest people who should not be reviewers, though I think that is a bit less common.

Most journals, however, have their own pool of reviewers and the author has no input at all into who will review the paper. Most of those use blind reviewing in which you never learn who reviewed your paper.

But in the case you mention, it is likely that someone other than the author sent the paper to the editor. That may actually be required in some situations. There is no expectation that review is then suspended.


When is applying for a postdoc too early or too late?

Actually, what you described seems very familiar and I'm sure it's the same for a large fraction of Ph.D. candidates. So relax a bit :-)

But - I have to say that, reading between the lines of your post, I'm uncertain that you should even be searching for a post-doc at all:

You express a desire to find employment that sounds at least as significant, if not more so, than your interest to continue your research.
You are not speaking in terms of what you want to do research-wise but where you need to be geographically.

1. First figure out / soul-search whether what you really want is to find a post-doctoral research position.

Are you absolutely sure that you want to pursue a career as an academic researcher, right now? Are you sure a stint in industry (or other non-academia employment) is not something you would find satisfying, interesting, relevant?

(To Op, specifically:) Maybe you are and your motivation and orientation is perfectly sound, but I'm getting a 'vibe' that this might not be the case.

If you're certain that a post-doc is indeed what's right for you to do next, then

2. When the conclusion of your Ph.D. duties is in sight, it is time to start searching for a post-doctoral position.

The research groups / departments with which you'll inquire about open positions are very well aware that prospective availability is sometimes up for change, particularly in your case. Do not hesitate to say "I expect to conclude my Ph.D. in between X and Y months". Now, it's possible that someone might tell you "I need an extra researcher who's willing to start yesterday to get ahead on some funded research project" - and won't accept you on that account. But, well, that's life - and they won't think less of you because you're not done yet; don't drive yourself mad in some impossible race.

3. Sometimes you don't find a suitable post-doc position even if you search diligently and on time. Think about contingencies.

Academia is never very well funded, positions are scarce, and in your particular case there are some tight constraints. I know this is not very encouraging advice, but it's better to recognize this possibility and learn to live with it than spending the last months of your Ph.D. in dread of it being realized. That's really not a good emotional state to be in - and it won't help your work, either.


Use and costs of Creative Commons licenses in scholarly publishing

Even though there is still no complete data set answering my question, I recently found a public data set at least answering my questions for hybrid OA. It's called Hybrid Open Access Monitor. The data and the source code is available on GitHub. It is based on data from Crossref and the Open-APC dataset, also freely available on GitHub. Some more explanation can be found on the About page. As an example, here are the numbers of hybrid articles published by Elsevier split into the different licences.

This figure is licensed under a Creative Commons Attribution 4.0 International License. Author: Najko Jahn (Scholarly Communication Analyst, SUB Göttingen), 2017.

You can also see, how much each country spent (relatively) of the total costs, if you go to the monitor's website.

For Gold Open Access, there is the study already mentioned in the question showing the usage of different CC licences.

Combining both will lead to a data set of the usage of CC licences in Gold and Hybrid Open Access. Nevertheless, regarding the costs, one has to dig even a bit deeper but I'm sure there will be published data soon and I will update this answer accordingly.


If a paper is accepted but not included in the conference proceedings, does organization (IEEE) retain the copyright of the paper?

Restating your conditions,

Copyright form not signed
Conference fee not paid
Paper not in proceedings

This implies that your paper is not published in this conference. Hence by no means can IEEE hold copyright for your manuscript with regard to this conference.

For a conference that requires fees, the respective paper it's published when the sum is paid (although there are exceptions). IEEE conferences seldom require you to sign the copyright form before the payment. They are usually done together. Once, I've noticed that some participants signed the copyright form on the day of the conference since they missed out on attaching the form along with the fee (which was successfully paid).


Grad student protecing ideas in a research paper for futher development

On the face of it this sounds very serious. Of course there may be information that can explain some of the aspects that are unknown to me and also you. So with that in mind.

If you have come up with the idea on your own, the work you have done is certainly yours. Often the basic idea is given by, for example, the adviser, in which case some (how much can differ widely) of the intellectual input is shared. You will, through your work still have some degree of ownership. If the adviser has given a similar basic idea to several students the situation can become really messy. It is not clear from your post if the other students started their work, once they got wind of your success or if they were given earlier input to start along the same lines. In any case, I would argue that the adviser has a responsibility to also protect your possible ownership but unfortunately what is ethically correct and what happens in real life can deviate significantly.

So what can be done? The first thing to do is to talk to the advisor and say you want to work this up to a publication (I have to assume here that you know or have had indications it can be published). In other fields it is possible to post work online to get a time stamp on your work, what possibilities exist for you I will leave to others who may know such possibilities to comment upon.

The comment that "it is for others to use" seems ridiculous. Unless there is a policy or local rule that states that anything produced within a course belongs to the school or course responsible or does not belong to the student, it appears quite unethical to take such a stance. Laws on immaterial rights or intellectual property are usually quite strong. It may therefore be useful to take the matter up with someone in the department who is either there to handle the graduate studies or some form of counsellor at the university level. You must know what structures are in place for possible grievances. the important point is that you need to figure out where you stand based on the details that are known. This is also why a very black or white answer cannot be given here, the information is too weak. But, based on what you have made known the situation sounds problematic from an ethical point of view.


Do applicants have to pay separate fees to apply to two PhD programs at the same school?

I strongly suspect that you would have to file two different applications to apply to two different programs, and each application would likely require a separate fee to file. This is in part because you would have separate essays and letters of recommendations for different programs, each of which would require separate handling and consideration.

If this is a hardship, though, some schools offer an application fee waiver to students who are of limited financial means, but you may have to contact the individual school to inquire about the possibility, because it may not be publicly stated that such an option exists.


What is meant when a job says PhD or equivalent required?

It could also be an equivalent degree from another country. For example, a degree, equivalent of PhD, in Russia is called 'Candidate of science' (https://en.wikipedia.org/wiki/Education_in_Russia)


Time for journal reviewing / referring in mathematics - Is there a recent study?

The American Mathematical Society provides regular (annual, I believe) on journal backlog times. The latest can be found here: https://www.ams.org/journals/notices/201910/rnoti-p1713.pdf
Depending on your subfield it may not contain data on all relevant journals, but it is quite comprehensive. The reports are published in the November issue of the Notices of the AMS, which is also available online.

The data in the report is based on information provided by the journals itself.


Benefit of published papers for grad admissions

Any paper you publish as an undergraduate is a huge benefit to your application. Most grad school applicants do not have any publications, let alone five with some first author ones. You're way ahead of the curve, and it should make a very substantial positive difference in your application.

Of course, this does not constitute a guarantee that you will actually be admitted to the very best places. Other factors go into the consideration as well, but having read several hundred applications, I can tell you that your publications will be seen very positively.


Is it acceptable to be listed as an author based only on technical assitance?

The criteria for authorship may somehow vary by discipline. The International Committee of Medical Journal Editors (ICMJE) stipulates four criteria that must be met if someone is to deserve authorship.

  Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work;
  AND
  Drafting the work or revising it critically for important intellectual content; AND
  Final approval of the version to be published; AND
  Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the
  work are appropriately investigated and resolved.

The ICMJE guideline further states that contributors fulfilling only less than four of the criteria should not be listed as authors but should be acknowledged.

A COPE discussion document about authorship also raises authorship criteria that are considered in different disciplines.

You may decide whether you qualify to be listed as an author based on the different guidelines available, probably based on the one closest to your discipline.


Applying for PhD programs after graduating from a small/unknown college

Things may not be as bad as you fear. I was in a similar situation long ago. One advantage you have is that, at a small place, you probably have good access to your professors and they know your work pretty well.

First, check to see what connections your own professors have to other schools. These could be places that they went to school, or personal contacts at conferences or co-authors of papers. Enlist the help of your profs in promoting your candidacy.

Second, find out if other students from your current place have gone to universities you would find interesting. Find out how they did. If someone before you has set a good example at another university it can work in your favor.

Failing that, write application materials stressing heavily what you can do, mostly by stressing what you have done. Ask your professors to analyze these to see how your projects and performance will be perceived.

And since you have a bit of time, do what you can to do interesting things that others might find impressive.

In general, though, the reputation of your current institution is only one thing among many that will be used in the selection process. I doubt that very many places sort candidates first by the prestige of the applicants undergraduate university.


How to bring up to a future postdoc employer, the point of not asking for recommendation for a specific postdoc employer?

It would be unprofessional to describe your previous employer in anything but positive terms when you are a job applicant.  If you cannot describe them positively, do not describe them at all.  You are showing the future employer how you will describe them in the future.
You could try suggesting an alternate reference, without saying why.
Ask yourself, why would the potential employer make an unusual request for a specific reference if this was not a critical factor in their hiring decision?  Your efforts might be better directed towards a different employer.


How do graduate research methods differ from those learned in undergraduate research?

The biggest difference between undergraduate studies and graduate research is that graduate research very specialized; in many fields, the terms used by graduate (PhD) researchers will not be familiar to most undergraduates.

As to whether the methods are different or fundamentally the same, this is a matter of philosophy. Certainly, the methods in graduate school build on those you learn during your undergraduate, and it is necessary to be an expert on the undergraduate methods before becoming a good PhD student. Depending on the field, that may be basically enough to be competent for graduate research, or, you may have to learn entirely new ways of thinking. For example, in mathematics, graduate research requires thinking at a higher level than the detailed writing of rigorous proofs in undergraduate courses.


Professor dismissed error I found in her work. I need more feedback, but the field is small

In this case, you should consider iterating with you professor again. Perhaps in person, rather through email (the explanation could be lengthy and that might be the reason why your professor was dismissive). You should also consider changing your approach, try to assume that the original research is correct and from that standpoint approach your professor for an explanation (again a situation when a personal approach might be better than an electronic one - the tone of your email might be misunderstood). You can then guide the discussion toward the issues you see.

If all the above fails, I would still hesitate to go to other people (whether in the field or not) with the attitude "My professor made a mistake and refuses to discuss it with me, I need you to confirm for me that I'm right". You course in this case is to learn as much as possible about the area and determine for yourself whether or not there was a mistake. During these actions you can and should ask and discuss your work with as many people as possible.

With original research it is often the case that even experienced researchers need to follow the above path (although their's is shorter than a student's) to state whether or not something is wrong.


TVöD contract E13 (limited contract 2 year) notice period

If you are aiming for a fixed date and are still on good terms with your boss, it is quite common to create an "Aufhebungsvertrag", that is a contract in which you both agree to terminate your contract at a certain date, irrespective a of notice period. After all, you want to leave and your boss likely wants to hire someone new on your position.
You will likely get a call from the "Personalrat" though, as they want to check that you weren't somehow forced by your boss to contravene regulations this way.


Normalizing other people's data on number of significant figures

You are free to choose how many digits to keep, and whether to do it consistently - although you are advised to use as many as it makes sense.

Reporting 1.314 ± 0.287 clearly does not add any useful information to 1.31 ± 0.29 as there is no meaning in the last digit. As a referee I would have requested the original publication to ignore the last digit.

Keeping Doe, J as 1.3 ± 0.1 together with Anon, Y as 1.31 ± 0.29 in a review makes perfect sense, as it shows that Anon's data is actually more precise than Doe's.


How to deal with student with low self-awareness about health condition?

I should not diagnose him

That's correct.  Even if you knew how to, he is not your patient.

I would like him to see a professional

Also correct.  You should tell this student they may benefit from an appointment with the disability office at your university. You can also ask that office for advice.
You should tell your supervisor about the problems with the student's performance.

Should I continue helping him?

If you have tried to help a student several times and made no progress, it is acceptable to give up.  This is particularly justified if the student refuses to follow your advice.  Depending on circumstances, you may also be able to give the student an easier research project.


Is it important to maintain a work-life balance as a PhD student?

It is very important that work-life balance be available to people who need it.  Most PhD students and most scientists need some form of balance but exact needs vary.
You are not obligated to adopt someone else's idea of balance.  There is no evidence that what works for other people will work for you.
Healthy diet and exercise are strongly correlated with better health and longer lifespan.  There is very likely a causal relationship there.  But I don't think that's what you were asking.

Would you consider the cultivation of a field completely unrelated to your own to be an essential component to an academic career?

No.  Common, normal, and fair, but not necessarily essential.

being human in general?

That's more of a religious question than an academic question.


Do professors need to use up their grant money in a fixed period of time?

That depends on where the money comes from, but in general yes, they should use it. Just like everywhere else, budgets are tight. And if the money is not fully used in a year, the funder might assume that this professor can do well with less money, so the next year the funds are decreased. I witnessed a case a few years back where a professor decided it was time to get a fancy notebook for conferences in mid December, because there was still money left...

Another possibility is that some other institute/chair/professor puts his hands on the money if the professor does not keep a tight eye on it. I myself got asked once to "please move to this office for a few months, as if we don't occupy it, it will get redistributed to another institute and we will then never get it back".
Same might go for teaching assignments, e.g. a math chair teaching basic calculus to engineers, economics,... might be a source of income fought for.

These are of course only examples and there might be cases where saving it is possible (so feel free to wait for more answers), but from these experiences I am fairly certain that using the money is the better choice.


Ideal ways of making a call for nominations

Improve the reward. If you're not currently offering money, consider doing it. Other forms of reward I can think of can be:

the opportunity to give a talk at a prestigious venue, to a nice audience
the opportunity to give a talk alongside a famous speaker (say, allowing the awardee to give a 15' talk just before a 1 hour talk by some famous person)
an introduction to some influent people, possibly looking to hire researchers


Joining a group for PhD, how do I judge the atmosphere before I sign?

First off, if the professor is reluctant to have you talk to members of the group, this is a huge red flag.
When you visit, ask if you can sit in on lab meetings or seminars (some group setting) and observe the dynamic. Does everyone seem engaged and happy to be there? Is the mood collaborative and friendly, or authoritarian? Basically, put yourself there and ask yourself if you'd be comfortable.
Ask the professor about their advising style and philosophy. Some like to be very involved, some want their students to be independent. Make sure their answer works for you.
Most important one, in my opinion: contact a few of the other students independently, tell them you are coming to visit, and offer to take them out for a coffee or beer. This is an opportunity to ask them, in a relaxed non-work setting, about what they like and don't like about working in the lab. Do not tell the professor what the students are thinking, in any case.


US usage

A course is generally the main unit of instruction. You will register for a course that lasts a term--which could be a semester or a quarter depending on the university.

There could also be a year-long course but it would actually be two or three courses that you would have to register for each term.

It's also possible to hear the term "course of study" which is the set of courses that you need to take to fulfill requirements for a degree.

The term module is not very common in the US, but it would be a themed subset of a course. I've seen it used in professional development courses.

A lecture is one meeting of a course.

A seminar could be a one-off lecture or meeting but a seminar course or a course using a seminar format would be designed for a small group, likely under 20, with more discussion rather than lecture or every student presenting on various topics over the term.

UK usage

Course is used for the entire set of topics to be covered for the degree, so corresponding to course of study in the US.

A module is a themed subset of the course, what would be called a course in the US.

A lecture has the same meaning as does a seminar.


For letters of recommendation, it's useful to have them written by people with a strong reputation, and by people who have seen you work. These do not need to be the same people. I would base your considerations off how much of this is already covered by your Masters supervisor and your PhD supervisor. There's nothing wrong with getting a letter of recommendation from a postdoc, or from someone you haven't worked with directly. In that vein, may I recommend your department head as a possible reference, if they are acquainted with your work?

Finally, I'd like to mention that I've never heard of three letters of recommendation being better than two. This is in Europe, your mileage in other parts of the world (or different parts of Europe) may vary.


Is regional accreditation important for a masters degree?

The field of game design and development is relatively new and specialized.  The best potential employers are quite likely to know the reputations of institutions that offer suitable degrees.  Therefore, I would say that the reputation of the institution is probably more important than either the exact degree title or the accrediting agency.

You probably have a small number of target employers in mind.  Try to find out where their employees went to school.


Editor indicated that if minor changes are made, paper could be published: what are the chances of publication?

Yes, if you've only been asked to make minor changes, the paper stands a very good job of being published.

Now you've got to work methodically, and be meticulous with the detail.

Go through each required change one by one. If it's not an unacceptable change, make it; and in a new, separate document - a log of the changes = write one or two sentences to describe how you've made the change (sometimes, a word or two, e.g. "spelling corrected" might be sufficient). If it would be an unacceptable change, write a few sentences in your log of changes about the basis on which you're sure it doesn't need changing.

Work through all these with any co-authors.

When you send the changed paper, add a covering note. In that, copy and paste each of their requests for a change, and after each one, add your sentences from your log of changes about either how you've done the revision, or why you haven't. Your editor may have sent you a proforma or template to fill in, that would do the equivalent job: if they have, use it.


Have American universities cut back on H1-B visa sponsorship of new international faculty and F-1 student visa sponsorship for PhD students?

The current ban was stopped by court,
we are waiting if supreme  court of USA will take complaint from Trump administration but that will likely not happen because of the composition of a court.
Regarding American universities, occupations that are related to academia (post-doctoral fellow, research fellow, etc.). You can check referenced link and put desired profession name in search menu and compare rates of awarding H1B by the universities.
Conclusion is honestly that university never awarded so much H1B in a first place, and it is a noticeable trend of declining H1B sponsored by academic institutions ( institutes, universities, hospitals... etc..)
website myvisajobs.com give you opportunity to search and compare different occupation and employees.


What is "academic freedom", when so many professors and post-docs do only the research that is being funded by external agencies?

While it is certainly true that the bulk of university research depends on external funding, and thus requires approval of the external funder, there are a number of ways in which a professor in the United States (and many other nations) can pursue research with almost complete freedom:

Most professors own salaries are supported (at least at a "9 month" level) on the basis of teaching, not from research grants.  A research position, however, often teaches only 1-2 classes per semester, however, leaving significant time for the professor to spend on research, whether or not that research also has external support.
Some undergraduates are willing and able to work on research for course credit or even on a volunteer basis.
Graduate students and postdocs are sometimes supported on fellowships that put no constraint on the subject of their research.
Some institutions also allow professors to "bank" a portion of the research funds that they bring in, which may then be used later as unrestricted funds.
Early career professors often have startup funds and later career professors often have endowed chairs, both of which typically have no constraints on the research they can be used to conduct.
In extremely rare cases, a professor may get a "genius grant" or similar sort of external award that is a significant amount of unrestricted money.

The amount of resources available through such unrestricted routes is typically much smaller than if one can convince an external funder that one's work is worthy, but one can get quite a long way on preliminary work, proofs of concept, and small-scale experiments with rather small amounts of resources.

Combine this with the fact that there is a wide diversity of funders out there with different agendas and preferences, and one can see that academic freedom in research is very real indeed.


Received no confirmation from editor of article receipt

It's the beginning of a semester just now...lots of folks will be navigating very tight schedules.

The answer to your question however depends a lot on the size and publication frequency of your journal, and the nature of your submission.  Put simply, the larger the publication and/or paper, the longer you should give the editor to reply.  Also if it's an infrequent publication schedule, likely the editor doesn't wade through the pile of submissions on a "crisp" pace.

If it's a well-regarded journal, there may simply be too many submissions for an editor to individually acknowledge them all.


Strategies for facing an "impossible" required course for PhD

Your description of your PhD program makes it sound quite unhealthy.  There is a required course that students can only pass by cheating, the faculty have been apprised of this and that "only makes it worse"?  Yikes. If the students don't care about academic integrity and the faculty don't care about the students, then things are dysfunctional to say the least.

It is not reasonable for one required course in a PhD program to take 40 hours a week of a student's time: that's a full work week.  Spending that much time in the course in order to pass it doesn't make sense to me: something else will suffer in your program.  (By the way, you say you also have a full time job, so that's another 40 hours a week.  So you are spending 16 hours a day, Monday through Friday, on your job and this one class, and then whatever else you have to do for your PhD program gets done on the weekend? That's not being a hard worker.  That is dangerously little down time.  Putting yourself in that situation is a very poor investment for your own health, sanity and success.)  To say that you can only pass the course by doing this much work sounds to me like saying you can't pass the course and that you must seek out another option.  If you're not doing that because of "machismo": please be aware that that doesn't actually make any sense.  Neither does a "refusal to fail": what you currently have is a plan that is very likely to lead to failure.  Get a better plan.

I am very concerned that -- apparently, anyway -- everyone else is succeeding in the course by cheating.  That's not acceptable.  You say that it wouldn't help to point this out to the professor.  Unless you have already personally contacted this professor about this issue, I don't see how you could know that.  In my experience, the way that skullduggery like this gets perpetrated is because the people involved think they have "no choice".  Of course you have a choice.  I strongly recommend that you tell everything you've told us to the course instructor.  Yes, there is the possibility that this could "make things worse".  It could even jeopardize your future in the program.  However, your future in your program is by no means secure at the moment, and if all your negative fears come to pass it does not sound like the program is worth your time.

If you approach the faculty with the attitude that the program has to be functional and ethical for you to stay in it, I find it very likely that they will work with you and help you through it.  If they don't, then I think you're better off out of it.  I realize that's a hard answer, but it's what I feel is the correct one.


Advisor unresponsive after agreeing to introduce me - What to do?

The situation doesn't sound promising, but don't lose hope just yet. As C is your advisor and you are nearing completion, you would hopefully have some kind of relationship with him, that if, for example, there were an informal discussion with X and he had changed his mind about offering support, then something might gently have been communicated to you from C to dissuade you from pursuing X.

As to how to proceed, also in reference to the discussion to your previous question, C is likely going to be your best way in. I'm not sure what "spaced out emails" entails, exactly, but if no joy is to be had from email or phone, try visiting. A person physically there is much harder to ignore than not picking up a phone or answering an email. You may get a sense of whether what's happened in paragraph 1 is the case.

In the unfortunate event that C no longer wishes to support, of course you can go with your original plan, but it would be best (as was also previously mentioned) to remove reference to C from any correspondence, as the mention of the name implies some kind of endorsement (or is just name-dropping, which may also be looked on unkindly), and try your luck. It may be a long shot, if X is that big, but if the in-person attempt to bring C on-board doesn't work, no one can be forced to do anything he doesn't want to do. Just suggestions, borrowing from some personal experience, hopefully helpful. Good luck.


Out of school for ten years and letters of recommendation for PhD programs

From what you say it is not clear how your current job is related to the PhD you plan to study. But in general, excellent recommendation letter from your working place might be a good complement to two academic letters. At the end, your work did require technical / analytical skills, and those are the skills that will be useful in academia. Had you been a soccer player or dancer, this would have been a different story. Also, probably you can ask your boss to focus on some aspects that you think are important to emphasize (e.g., technical skills).


How to withdraw a published paper when former boss seems to be raising ethical and data integrity issues with the editor?

The publisher is unlikely to let you withdraw the paper unless you convince them there is an extremely serious problem with it (misconduct or an unfixable mistake).  They have an ethical obligation to make the paper available to the research community, regardless of whether you regret publishing it, and it takes a powerful argument to overcome that obligation.

In particular, if you ask to withdraw the paper, then the publisher will assume that the accusations against you are true.  If you succeed in withdrawing it, then the entire community will assume there was something terribly wrong with the paper (and, if you don't publicly identify errors in the paper, they will assume it was an ethical problem).

In other words, withdrawing the paper is tantamount to admitting guilt.

  I have at least a dozen of emails attesting he knew the study, but I don't know if I can show them to publisher.

Yes, you should certainly make use of any evidence you have that the accusations are not correct.

There should be no problem with the ethics statements.  Presumably you have proof of approval by the appropriate review boards (or, in the worse case scenario, they can confirm their approval).  If you don't have proof, then maybe there really is a problem.

As for the other accusations, hopefully the e-mails from your former boss will help clarify the situation for the editor.


Conferences as publication venues – black and white or is there a grey or third way?

Yes, there's a third type where a single conference uses multiple submission categories, and submissions to one category are thoroughly reviewed and published as papers in the proceedings, whereas submissions to the other category only appear with short abstracts in the conference booklet or similar, and may also be restricted to specific sessions (such as poster sessions).

I know such conferences in mathematical oriented engineering fields. As just one example, I can mention the Vienna International Conference on Mathematical Modelling. If you look at their call for papers, they have a category "Full Contribution", where full papers are solicited, to be published in the formal proceedings after the review and presentation. But they also have categories "Discussion Contribution" and "Student Contribution", where only abstracts are submitted, and there's no formal publication associated with the submission.

There are other conferences in the same field which make this distinction as well within their submission categories.


There is a full-blown, high-quality peer-review process for a thesis: it's called the thesis committee.

If you mean a service where you can get help improve your document before you submit it to your committee, that is something that one's advisor(s) tasks. Maybe you can actually get help from friends, colleagues, or in the most severe cases your advisor's friends, but there is not much.

The thing that may be closely related is that, in some systems (the French one at least), there is a person that is responsible for validating the PhD student's manuscript before it gets sent to the committee. Then, it's that person's responsibility (in theory) to do a basic check of your manuscript and your work, and decide if there is enough to gather a committee. I say “in theory”, because this person will probably get dozens of theses per year (at the very least) and can only perform the most basic checks. In practice, they most often do not check the manuscript content, but its form (does it follow the University's standards), as well as some simple indicators of your research (has the candidate published? how many times? did he attend conferences? that sort of stuff).


How correlated are grades in math courses with potential for research?

Like most things, there is some correlation, but it's not perfect. In other words, good grades are an indicator of future success, but not proof.
This is why most places look at a wide variety of things, not just GPA or individual grades. In the US, letters of recommendation carry quite a lot of weight, for example.
No, a few B grades probably won't hurt (much), especially if they are in a topic that you don't intend to pursue further. Note that true insight into mathematics isn't uniform across sub fields. For example, I had great insight into real analysis and point-set topology, but very little in algebra or even in some other aspects of analysis. But I did fine, since I worked in an area where my insight was deep.
I'll note that when I took the GRE subject test in mathematics I was extremely discouraged when I left the test center. There were so many questions that I had no insight in to at all. But that was really because mathematics is so broad that no one (anymore) can understand all of it (not since the early 20th century, I think). I did well and got into good graduate programs.
However, don't neglect the fact that good programs are very competitive.
The key is to put together a complete application (including letters) through which a reader can have confidence in making a  prediction of your future success. If you get to write a Statement of Purpose (SoP), make it forward looking, not just a recapitulation of what is in the CV. Goals, plans, ...


Working on other stuff (side projects and activities) without permission from the professor and department

I was thinking that is the norm in academia, however in my new lab people seem to work only on their project and don’t do anything else. While I am not prohibited to work on these things, I am uneasy and puzzled to continue, but also I am not sure if bringing this topic to my professor is the best idea.

I agree that the norm in academia is, and should be, that staff on all levels need to have sufficient freedom to pursue their own interests in addition or within the funded project(s). As a postdoc, this is particularly troubling, because you need to use your postdoc time to diversify your research themes, skills, and collaborative network. Basically, if you are a postdoc and sitting in your office all day working on a single project, you are doing it wrong (and hurting your career big time).

I don't think that sneaking a little side project here and there by your professor is sufficient. As a postdoc, you should be able to dedicate significant work time towards progressing your own career. I suggest you bring this up with your professor, and, if they don't appear to understand or accept your concerns, I would start brushing off the CV and get back onto the job market.


How to find GPA distributions for US universities

Stuart Rojstaczer maintains a web page with information about average GPA at many universities in the U.S. The data on that page was last updated in 2009, and is next scheduled to be updated in February 2016 (according to a note from the author on the page.)

At the end of that page, there are links to the historical GPA at each of the schools for which he has data. It also indicates the source of the data, so you can find out whether the school actually publishes the data, or whether the school simply made the data available to the author.

For example, if I click on his link for University of Wisconsin - Madison, I learn that this data was collected from the registrar's website. While the particular link he cites is no longer alive, searching the registrar's site yields this page that allows me to find out grade distributions from any course and term. Similarly, I found out through his page that UCSB publishes this data through its office of institutional research, which led me to this page of reports that include average GPA by major.

You can follow a similar procedure to find grade distribution information for other schools if available, but it may not be available for the schools you are interested in. Universities are not obligated to publish this information.


Struggling to present results from long papers in short time slots

Attempting to fit the material of your paper into a talk is a common mistake: even for shorter papers, there is typically simply too much to include all of the significant details.

Instead, I recommend thinking of your talk as an advertisement for your paper. Your goal is to present enough of the key interesting material to be able to convince somebody that it is worth actually reading your paper.

Once you accept this as your goal, the length of the talk does not actually matter. As an exercise, you might even try making just a single slide for giving a two minute talk (as one might in a "lightning talks" session).

What, then, should you put into whatever time you have available? Think of the story of your work, as opposed to the content.  Your abstract may help you here.  As a starting point, I would suggest this as a general framework suitable for most talks:

Set up the problem, explaining why somebody should care about what you are doing.
Sketch the approach that you are taking, explaining why it is reasonable.
Point out some critical insights that were necessary to make the approach work.
Show your key results and explain why they are significant.
Come all the way back to the set up and explain the progress that has been made on the problem.

Depending on the details of your work, there may be some differences, but this may at least help you get started sketching things out.


How can I deal with a professor with an all-or-nothing grading habit?

This may be almost too obvious to be worth mentioning, but one idea you could consider is to study really really hard for this class in order to make sure you do not end up in the group of people who fail it, large though that group may be. It sounds like it’s not impossible to do well in the class, just more difficult than you are used to. A relevant idea to keep in mind is that you have control over the outcome: the belief that you can adapt your behavior to the situation and achieve a successful outcome is what is known as a growth mindset. It’s a powerful idea and very worth thinking about, both in the current context and for anything else you aim to do in the future.
That being said, it’s possible that the professor is unreasonably harsh in his grading methodology. Failing that many students by setting standards that are so high as to be nearly unattainable does not benefit either the students or the university (or future employers of those students), and results in a waste of resources and a drain on the students’ morale. Certainly preventing students from taking the final exam because of poor performance in the midterm is a rather extreme step, and contradicts much of what I know about best practices in education.
So, at the same time that you are working hard to succeed in the class, it’s completely reasonable to try to get the university to see that there is a problem and put pressure on the professor to change these policies. Some avenues that you can explore are to bring the matter up with the dean, the university ombuds person, your student union, or other types of student advocates that may be available. A local student or town newspaper or news website may also take an interest if this is an issue that affects a large number of students. If you are savvy with social media, you could drum up interest through Facebook or other social media, and attract support for your cause.
Good luck!
Edit: based on the discussion in the comments, many people seem to think my social media idea is a really bad one. I don’t completely understand their objection (the main reasoning given is the idea that social media are a “cesspit”, so it may simply reflect a dislike of social media in general and a belief that you shouldn’t use it for any purpose), but it’s possible they have a point, so keep that in mind. In any case, my suggestion is not meant to be understood as an endorsement of social media in general, only as a suggestion that social media may be useful as an advocacy/campaigning tool in a specific situation like yours.


Short answer

Practice!

Long answer Practice (smart)! The more time you spend being a student (studying, reading, summarizing, asking questions, taking notes, and pursuing answers) the better you will become at being a student. For more specific tips, check out this article by Scott Young. He focuses on methods that allow you to study smarter rather than harder. The key to this is to recognize that all knowledge is interrelated; everything connects to everything else,  and therefore no learning is wasted. I find his tips and hints to be useful, though I cannot learn quite as efficiently as Young claims one should be able to.


In Preparation For The Job Market - On Day 1 of the PhD

Actually the most important thing for you to focus on right now is getting a good research experience and a good relationship with an advisor. Get started on that. Learn to go deep into some subfield of your overall field. Gain expertise in that.

Along the way, if you want to be an academic, a bit of teaching experience will help, but will be more valuable for some positions than others. But without the "gain expertise" part it won't matter much.

And I caution against trying to choose a field strategically based on what is going on this month. You will graduate, in several years, into a completely different job situation and it is impossible to predict how it will go long in advance. As you get closer to graduation, in four years or so in the US, you can start to broaden your skill set depending on the perceived needs at that time.

But some things are valuable in any case. Learning to do research. Learning to write. Learning to collaborate. Building a circle of potential collaborators.

But most of the details you suggest are just distractions at this time. Day 1 is the day you look seriously for the best advisor willing to work with you.


Rules or Laws to guide sectioning and sub-sectioning

Certainly there are no laws on such things. In general the layout depends on the material and the audience.
But it looks like you are writing something as part of a proposal, maybe for a research grant. In that case, the recipient might have requirements for what to include in the application. You need to cover all of those things, of course. And it is often best to include them in your application in the order of the requirements listed. This makes it easier for the reader, who has some power to accept or reject, to quickly check that you have all of the needed elements.
But as a general outline, what you have seems to be reasonable.  As a "working document" is is fine. Tailor it to the requirements of the audience, however.


Resubmission of paper has been "under consideration" for 30 days. Request update?

Journals such as nature and Science and their related publications run on tight schedules. Not hearing from them quickly is usually a good thing since rejections are made quickly. Yes, a month may seem long but for me is too early to worry. It is difficult to say what time frame is reasonable but two months would be on the long side.

Having said that, these journals have professionals working full time with the journal, unlike many others where editors work on the journal along side regular academic work. This means they rarely let any job lie around for very long. Of course, a mistake may happen, but I would not make such an assumption as a first choice. So take it easy for another couple of weeks. If there is any pressure on you for getting advance notice of publication, for, for example, job applications or salary discussions, a mail providing the cause of urgency would always be possible but if it is only pressing anticipation, sending mails to editors early is not a great idea. But in this case, estimating the time frame is more difficult than for regular journals but give it another couple fo weeks at least.


Using copyrighted images for research, not publication

While the key would seem to be to make sure that you cite the use of the images, I would also contact the creator of the images to make sure that they are fine with reusing them.  I did this while working on my dissertation, which not only secured permission, but also served as networking.


Editor gave me five days to revise paper – chance of acceptance?

Unless there are some general reasons to impose a deadline on your paper, such as that it is intended for a special issue, I would strongly guess that your paper is practically accepted and the editor only wanted you to apply some minor changes. I only ever heard of such short deadlines when the only things that needed to be changed were minor and quick to do.

If the editor expected you to present changes and arguments to sway the third referee’s opinion, they would have given you more time. If the editor had decided to follow the third referee’s recommendation, they would have rejected the paper immediately and not further waste your and their time with it.


I would go with:

  P.W.D. Charles, Project Title, (2013), GitHub repository, https://github.com/charlespwd/project-title

Or a bit different, depending on your citation style. Just is is crucial to include: author, title (if style includes it), year and link.

Of course if you do have a publication related to this piece of code (even if only by fact it is your first publication basing on this code), don't forget to cite is as well! (In the current academic system it is all that counts.)

And respective BibTeX entry:

@misc{Charles2013,
  author = {Charles, P.W.D.},
  title = {Project Title},
  year = {2013},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/charlespwd/project-title}},
  commit = {4f57d6a0e4c030202a07a60bc1bb1ed1544bf679}
}

Beware, this above are improvisations (especially the BibTeX entry), not standards.

Even for more established and citable things there are not set standards, see e.g.:

How to cite a sequence from The On-Line Encyclopedia of Integer Sequences (OEIS)? - MathOverflow

See also:

How to cite sourcecode from an svn repository - TeX.SE
How to cite software in LaTeX - SuperUser.SE

EDIT:

See also how to assign DOI to a particular commit in your repository.


Stature vs relationship for recommendation letters

There is more to the story. A weak letter from a "strong" person means very little. If they can't say much about you to support your candidacy, based on what they know, and just send a "form" letter, then it won't have much impact.
On the other hand, a letter from someone who knows you well can read as a much more enthusiastic endorsement.
But, it is the reader who gets to judge. If they actually "know" the writer then it is likely to have more weight, rather than the abstract reputation of the writer.


Postdoctoral Research Fellowship Application Criteria - Functional Responsibility?

It's just boilerplate language, not specific to the post-doc position (or even to academic positions, probably).  All "areas of functional responsibility" means is that it refers to the kinds of things that you will be responsible for doing as part of the job.


How to promote reduction of carbon footprint for conference participation?

Personal, disputable view follows.

Even if you avoid a conference, you save only a few kilograms of carbon. There's millions of other fliers that don't care about it and are travelling at the same time.

The best way to protect the environment is through technological advances: planes that work with eco-friendly fuel, are faster or more effective, better virtual reality technology that allows one to avoid travels, maybe even quantum teleportation and all that kind of stuff.

How do we advance technology? Through scientific research. How do we get it earlier? By advancing scientific knowledge as fast as we can, in the most efficient way. So go to that conference, don't worry about that minor O(1) saving, and do your part to obtain the O(n) or O(n^2) one later on in the history of humanity. Maybe that theorem in homological algebra that you are presenting today is going to be instrumental to quantum teleportation in 100 years.


Google Scholar does sometimes parse citations to codes; here is an example of the R library rvest:

In addition, as MoinMoin implied, many researchers write so-called data papers or software reviews that accompany newly published datasets or softwares. They are submitted to journals and undergo peer-reviews like other kinds of scholarly articles.
Journals increasingly support such data papers or software reviews. I am not only talking about journals that are specifically dedicated to such document types (e.g. Springer Nature's Scientific Data), but also to specified submission guidelines for this kind of documents at other journals (e.g. at PLOS ONE)
Some bibliographic databases capture such documents with a special category. At Web of Science, for instance, you can refine the results to 'data papers', 'database reviews' or 'software reviews':


Although this answer comes too late for OP, it may help others. If it is permitted at your institution, attend defense presentations of others before you must prepare your own.  As others have said in comments or answers, thesis and dissertation defenses are highly variable and depend on the customs of the country, the institution, and even the individual department.  Very best is to attend presentations of students whose committees are chaired by your own committee chair.
If you aren't able to attend a defense or two, try to talk to one or two people who successfully defended recently.
In either case, take notes, plan your defense, then review your plan with your advisor or committee chair.  They'll appreciate that much more than an open-ended "What shall I do?" type question.
A word of comfort: Your advisor or chair should never let you reach the stage of defending unless you are ready.  I know there are exceptions to that general rule, but your advisor wants you to succeed, not only for yourself, but also because an advisor looks bad when students fail.


One thing to consider is do you really need student assignments to be downloaded. I say this because I used to but I recently started using TurnItIn. However, I only use this for plagiarism detection, I do not use it for marking (university policy is that I MUST mark the paper copy...yes I know the dangers there, but that's for another day).

Since you didn't mention the larger issue you are trying to solve, I'll continue just with your direct question about how to download many student assignments without a million clicks.

What I did is simply setup an email account for students to email to (not my main email account). I instruct the students to use specific filenames (StudentID_StudentName_AssignmentName.docx) and they email me. I use a standalone email client (not webmail) so it all downloads to my computer. My client has a preview pane so I simply drag-drop to my assignment folder, move to the next message, drag-drop, repeat. I do this for 200-500 students per assignment per semester and find it does not lend itself to much more automation than this.

In all, it takes me 2 clicks per student (literally) and I end up with all student assignments in one folder. It handles ACK'ing the student on the server (auto-responder) but I could also use read-receipts but those don't usually work with webmail.

If you want to email students who did not submit, that's more complicated. I handle it during the marking process (let's see the file...ooops, they forgot...time to email them...or fail them for not submitting properly). TurnItIn will tell you which students did not submit.

As for students submitting multiple versions, as long as they submit with the proper naming convention, you will overwrite the older with the newer. I'm not sure if that is what you want or not but I would assume so.


How to engage a large class? Teaching strategies that have worked for you

Clicker questions are nice. I use them. They break up the monologue, which is good. The change in mode "wakes the classroom up". They don't "take" much time. They give you feedback on whether something was clear or not. But the amount of active participation from the students is limited; just press A, B, or C. For harder question a lot of students choose not to participate (which is also a sign).

An more intensive method I have used is to give students cards in different colors, and say all red students solve this question, all blue students that question, and all green students such question. After some time, they are asked to form groups of three, each a different color, and explain their answer to the rest. This is much more time intensive (it took about half the lecture), but the students are much more engaged. I was quite happy with the trade-off in that particular situation, but in many cases the cost of time would be just too big.


What is the difference between department and faculty?

The distinction between "faculty," "department," and "school" depends a lot on where you are. As Peter suggests in his answer, a faculty can be a collection of "departments." However, a faculty in Germany (for instance) consists of a number of "chairs," each of which is closer to a professorship in a department than an actual "department." Thus, the faculty is effectively halfway between the American "department" and "faculty" in its function, as it combines some of the hierarchy and responsibilities of each.

The reason for having multiple subdivisions is that there are often many university functions—including personnel and budget decisions, facilities management, teaching, and so on—that can vary widely across the entire university, but significantly less among certain departments that have a similar focus. For these departments, it makes sense to combine these duties in a central administration, rather than duplicate the effort across multiple departments.


Cumulative versus monographic dissertation

If I had had a choice, I would have chosen to write a cumulative thesis.

Results are in the papers. And converting papers into a monograph takes a lot of time with relatively low added value. (When someone asks me about the result I still point to publications.)

One advantage of monographic thesis is when it is on a new field (with publications being very coherent on one topic) - then it can serve as an introduction for the others. (However, it seems that not many theses fit this criterium.)


"The papers I refer to are mostly free PDFs from the internet on various topics" – then it's most likely one or both of:

It is not a peer-reviewed paper published by a reputable journal. Be careful what you read, there are plenty of quack theories out there
You are viewing a preprint, and by finding the article on the journal's website you will find the date. Also, the final version of the article will probably be better formatted, and may be better written and have mistakes corrected (this depends upon the stage of publication at which the preprint was circulated).

Many preprints are circulated prior to publication, so you may not find a better version yet. It's still really poor form for an author not to date a preprint. If a preprint is a few years old and has not yet been published, you have to wonder why.

I can not recall ever seeing a journal that does not put the journal name, date, and issue number on at least the first page. It would be very poor practice not to do this, because taken on its own it is impossible (without further research) to tell where the article came from. It's common even to date every page with the journal name, date, and issue number.

I suspect that if you're seeing this trend in most of the "papers" you read, that you really aren't reading research articles written by legitimate researchers. Ask your advisor or lecturer for the names of the most relevant journals in the field, and start from there.


Accused of cheating by proctor due to information on scrap sheet

I'm sorry, but it looks like it will be impossible to prove your innocence under these conditions.  You refused to follow the instructions of the proctor because you "didn't feel comfortable with handing him [your] papers" (which is not a sufficient explanation), and later failed to control your emotions and ran into the washroom as if you were trying to get rid of some evidence.


Did they do some of the project without telling me?

Yes, it makes sense. No, you didn't do anything wrong. Write up what you did for your thesis along with the necessary supporting material, but avoid complaining about what the institute did.
I think the key misunderstanding here is that they were giving you an opportunity to interact in a real system and that they might be able to take advantage of what you learned, but made no commitment to do so. The opportunity is the important part.
It may be that they used you as a low cost way to make an exploration. I don't see anything wrong with that.
Had they told you at the beginning that they weren't committed to what you were doing it might have lessened your enthusiasm at the time (as it does now). But, even for their own regular developers they don't make a commitment to accept any particular piece of work, especially before it is attempted.
The purpose of the "exercise" was your education, not their system. You did a good job of that ("productive time to research and develop it"), so you learned some things.
I don't have any advice about the "larger system" as there is too little information.


Doing a PhD at a famous football school: how can I ask for time off to attend games?

It’s a tricky situation and you will want to filter any advice given here (including mine offered below) through your own understanding of the details of the situation and the personalities involved.
That being said, my tentative guess as to the best strategy for handling it is to do two things:

Don’t mention to your advisor your football game attendance plans. It’s your private business what you do on weekends. Simply go about your private business as a normal person does. (And for heavens’ sake don’t “ask for Saturdays off”. You don’t ask for what is rightfully yours.*) Any work can wait until after game day festivities are over. You’re a grad student not an indentured servant.

Work hard and be productive and responsive to your advisor during normal work hours/days (including non-game weekend days if you feel like doing work on those days).

If you do the combination of those two things, I suspect (but cannot be certain) you’ll be fine and your advisor will be completely happy with you, perhaps after an initial adjustment period where you might have to deflect some questions from him about why you didn’t answer some email right away on a Saturday. If that happens you can just say you were busy, had an event to go to, or, if sufficient trust has had time to develop between the two of you, simply tell him the truth (but make sure to state this as a statement of fact, not a request for permission or validation, and not stated in an apologetic tone where you volunteer unnecessary details about why you want to attend football games as you sort of did here).
*
If this is a problem, I’m sorry to have to tell you but you’re in an abusive relationship and you likely should be expecting much bigger problems in your relationship with your advisor than a conflict over attending football games.


What to say when a first year PhD student can't handle basic courses?

I suggest having a discussion with the student to see if you can determine together what the issues are and figure out how to address them.  There are many reasons why the student may not be handling her courses well: personal issues, poor preparation, poor study habits, culture shock, etc.  It is also possible that she's not doing worse than other students, but her impression is negative because the courses/material is harder than her undergrad courses.  From what you have said, it's impossible to say whether she'll be able to do fine in the PhD program or not, or how much help she may need, but it certainly sounds like she could use at least some emotional support, if not tactical advice as well.

In addition, as Nate suggest in the comments, it may be helpful to diagnose the issue (for you and/or her) to talk to her instructors to get their impression of her in the courses.  If you have/know some reliable senior grad students, you might also suggest her to talk to them.


Feasibility of obtaining an “individual doctorate” in Germany while working?

Um, I had to google "Individual Doctorate" since I wasn't sure what the German was supposed to be, but apparently this is just the default way to do a PhD in Germany? In which case:

Yes. When I was a PhD student in Germany, the only documents required by the university administration were the B.Sc. and M.Sc. transcripts/diplomas and a letter from my advisor stating "I am supervising this student". There was no selection, everyone who handed those in was enrolled.
Yes, but only if the company agrees. (As @Wolfgang Bangerth notes, many companies will not allow you to divulge details about the work, as they are basically their trade secrets.) Note that in Germany theses have to be officially published, so the "jury is under NDA" workaround that exists in other countries cannot be used.
It is feasible, but the success rate is much lower than for PhD students. I don't know anyone who worked at a private company, but we had close contact with a Fraunhofer institute group, and even for employees of a research institute who had that option explicitly planned for in their employment contact, many of them gave up along the way. The work required for an actual, useful product is very different from research (e.g. there is nothing novel about making sure I/O works correctly for a wide variety of formats, so you are likely to get scooped by some full-time PhD student who is just duct taping five scripts together and copy-pasted the input data into their source file).


How to transition: leaving an EdD before completing to pursue a masters in another area

Finish it off.  Do it as fast and easy as possible.  The doctorate is more impressive than a second masters.  You are half way through.

Note I am extremely skeptical of academia and grad degrees and often tell people to do an MBA instead or just work.  But once you are in it, finish, finish, finish.

And remember, it is pass fail.  Just get through it with the minimum.  ASAP.


Being told a conflict of interest is acceptable for paper review

From an outsider's perspective, both choices are now ethically just. You've declared the potential conflict of interest and been assured that the authority in question doesn't see one ( hopefully you did this through a means which let you keep a record).

So now it pretty much comes down to whether giving the paper a fair review makes you feel uncomfortable. If it does, then get back to the committee as soon as possible, and tell them as clearly as possible that you can't do the review. Otherwise, review the paper, making full use of your deep understanding of the context of the work.

If you're wondering whether the committee member's statement is ethical, then consider whether you, as an obviously knowledgeable person in the field, could think of three other possible reviewers. Of course, if you can, then maybe one answer is to say no, but pass on those names instead.


My paper has not been published because I did not show up for the conference presentation

A conference has a number of limited slots for presentations. When your paper is accepted for a conference, someone else's paper got rejected, because it was slightly worse than yours and slots were limited. In this sense, if you are not going to present your accepted paper, this a huge disservice to the conference (and the related community). As I already said in my comment that annoyed you, if everyone did the same thing (did not show up in the conference to present his paper) there would simply be no conference and this will be a huge waste of everyone's time (reviewers, PC comittees etc..). So, the first step is to understand that such a thing would normally never happen.

On the other hand we are still human and life emergencies happen. You may become sick before travelling to a conference and therefore not beeing able to present there. In this case, this is what emails are for. You should have notified the PC chairs that you were not going to make it and ask for leniency. On the other hand, what you describe is even more far-stretched. Your co-author did go to the conference, was probably paid his expenses from his institution and did not bother to show up at the time to present the paper. Imagine the similar example of some PHD student of going to a conference, partying the night before the presentation and not bothering waking up the next time to present. Have you considered the embarassment of the PC member responsible for your session, when they call out your name and noone shows up to present? And nobody even later this day or even two days later, bothers to send an email to apologize for this? Instead you think the conference organizers are in the wrong, because they are actually doing what they told you they would do (contrary to you). Not publish your paper if you do not show up.

A war with them would only hurt you and not them. Apologize sincerely, ask for permission to publish somewhere else and try to be as nice as possible. Do not upload to arxiv before settling things out. And in the next case, understand that in Academia your word is your currency. Make sure you do not break it for whatever reason and if you do (due to some inevitable emergency) make sure you apologize promptly.


Should I update my arXiv submission after it's been reviewed and published OA in a Springer journal?

Under Springer Open Choice, you retain copyright and the journal releases the published article under a CC-BY license.

So:

By the terms of CC-BY, everyone can make a copy the published paper and redistribute it under the same license, including on Arxiv.
Even better: you, the copyright holder, can relicense the paper to anyone, with the terms you want. As long as you don't give them an "exclusive right to distribute", of course, because you cannot take back the rights you have already granted others.

Some Open Choice journals use CC-BY-NC, though which may make redistribution under the first method trickier, because Arxiv does not have an option for CC-BY-NC. The other method is always ok, though.

Note: I am not a lawyer.


Ethics of Using Victim's Name in Research?

Journalists I have spoken to have emphasized the importance of communicating in private, with ample lead time prior to publication, with multiple people with relevant personal and professional experience. For instance, if it was a suicide, you might want to run a question like this by both professionals in areas related to suicide, and families of people who have committed suicide.

Maybe this is an approach your IRB is already taking, but I see no harm in doing some investigation of your own. If nothing else, it might inform your communication with your IRB.

No "rule of thumb" will cover all situations, and the number of overlapping considerations can make it pretty complex. Communicate with people who have experience and expertise that will make them likely to think of things you might miss.


What is the best way to merge subfigures and convert to a required format for submission to a journal?

I don't know how well this will apply to you because I don't use tikz much. But if you can save them as say a pdf, this might work for you.

I use illustrator (but inkscape is similar and free), and I link in the files so that if there is an update to any component it will update. And I merge them all together.

Then I can just save it as a pdf or svg (or whatever format the journal wants). I found this a little cumbersome to start off with, but now that I'm used to it, I have a hard time reverting.


There aren’t many ways for your to evaluate how your reviews stand against others, but there is at least one. You can keep a tab of the papers you have reviewed, and look for them a year or so after the review. See if your reviews correlate with the publication (or lack thereof) of the papers in the respective journals… if papers you have suggested to reject are frequently accepted by the editor, then you give typically more negative reviews than other reviewers of your community.

Of course, this is a very black-and-white picture (rejection/publication). But, I don't think you can actually do much better, because “negativity” can hardly be measured quantitatively.

PS: I wouldn't call it a reviewing bias. A review is the editor asking you your frankly assessment of a publication. Toning it up or down because you fell that you do not conform to the “mean” of your field would probably diminish your value as a reviewer. If the editor does not think your reviews are helpful to him, he’ll just stop sending you paper to review!

I'll finish with an anecdote: there's a journal for which I have recently given a series of quite negative reviews (well documented, and justified in my eye), and I have actually received some positive feedback about my reviews from the editor.


How to peer-review a conference "Symposium"

This may be a bit late, but I'm a early-stage scholar in a management field that reviews similar proposals for our major conference. Here is how I approach reviewing symposiums (in no particular order):

1- I review them holistically (i.e. as one document), because that is how the final decision is made (accept or reject the entire proposed symposium). To answer your question, you don't need a separate review for each paper and for the introduction. Just write one review of the proposed symposium.

2- I structure my reviews similarly to how I review papers (summarize main points, strengths, areas for improvement, overall recommendation). I also treat them the same in terms of norms (conversational, developmental, includes what the proposed symposium does well, etc.)

3- I also keep in mind that conference papers are qualitatively different than published papers --- and are supposed to in our field! Conferences are where we get feedback on our ideas, get new ideas from conversations and presentations, and, above all, for everyone to learn :-) In short, I'm much more generous and err toward inclusion and look for the golden nugget of a great idea that needs to learn how to shine to guide me in terms of acceptance.

4- My advisor gave me these guiding questions as well to use in my review and these helped me out a great deal:

Does the symposium look interesting?  Are the arguments clear?  Do the presentations fit together well? Do you think there would be an audience for them?  Do the presenters look like they have a good idea of what they are going to say rather than just fluff?  Are the proposed presenters well-published people with something to say?

Hope this helps!


Should peer review invitations be accepted if one is unemployed?

Peer review is not a tax: if it doesn't make sense for somebody to peer review, they shouldn't do it.
Instead, I view peer review as:

an opportunity to contribute to a community that I care about, and
beneficial to me in helping me "keep my tools sharp" on critical thinking, writing skills (even as a reader!), and exposure to authors and ideas I might not otherwise read.

Because responsible peer review takes a significant investment of time, however, I set a budget for myself on how much time is sensible for to contribute over the course of a year, and I refuse assignments that would take me over that budget.
I would thus advise your colleague to consider a sensible budget, given their current situation and how much those motivations make sense to them. Yes, peer review may take time away from job development. On the other hand, peer review may still feel meaningful as a contribution, an intellectual connection, a motivation, etc.
Maybe the budget should be zero.  Certainly the budget shouldn't be 10+ hours per week.  But it may be entirely reasonable to put in a couple of hours of peer review per week if they still enjoy and benefit from it.
Bottom line: the amount to continue peer reviewing is an assessment that your colleague needs to make for themselves based on their personal situation and to periodically reassess as that situation evolves over time.


Advantages of different citation styles?

There exist strong differences in humanities vs. STEM how literature is read, written and therefore cited.

For example, in humanities it is much more important due to e.g. schools of thought who has written something than in STEM. Even in STEM some journals ask you to give the page of a book when citing those, some not.

There is likely no good overview, because in the end the editor should know best, what citation style is the most efficient and useful one for the content, format, author- and readership of that journal.

In STEM many journals don't want all author names in the reference list, rather due to shortness than usefulness imho. To me, personally, it's often much more important to see which last author/group leader conceived an experiment rather than which first author PhD student did most of the exeperimental work with >5 other co-authors which becomes more and more common.

For review articles with >100 references it's often simply not practical to show all co-author names. For letter articles, representing often high importance of the results, the first author et al. often publishs several papers focusing on a dinstinct research question/method/object and deserves more highlighting and fame.

Even withing a single scientific branch like physics you will therefore find very different citation styles serving different purposes for different publishing formats.


Is it legal to withdraw a signed offer letter from grad school?

The following answer only applies for graduate schools in the United States that are members of the Council of Graduate Schools, and have signed on to the CGS Resolution Regarding Graduate Scholars, Fellows, Trainees and Assistants. (Here is a list of these institutions.)

Furthermore, this agreement applies to offers of financial aid, not admission without aid. (Although many schools adopt a similar policy for offers of admission without aid.)

According to the Resolution:

  In those instances in which a student accepts an offer before April 15, and subsequently desires to withdraw that acceptance, the student may submit in writing a resignation of the appointment at any time through April 15. However, an acceptance given or left in force after April 15 commits the student not to accept another offer without first obtaining a written release from the institution to which a commitment has been made.

So the answer is: he can withdraw (in writing) his acceptance of financial assistance offered by School A before April 15 (if School A has signed on to the Resolution).

However, for general reference: you should really refrain from accepting an offer until you hear back from all the schools you are seriously considering.


Cheating among the international students very common in college. What should I do?

As a student there is little you can do other than inform the instructor and maybe the administration that this is rampant. You don't need to mention names, just the fact that you observe a lot of cheating.

The one thing you want to be assured of, however, is that your own position isn't being affected. If grading is competitive in any way this is a serious problem. But otherwise, if you earn the grades you actually get the rest of it is less your concern.

If you were an instructor I'd have different advice as I've seen this myself. I once had a group of students who really wanted to help their friends and it got out of hand. People didn't understand that it wasn't right to help weaker students get good grades if it meant the weaker students weren't really learning anything and would suffer later. We never really had a solution other than to try to convince people that is was counterproductive. Of course, it helps if the course is run in such a way that cheating has little effect, say by minimizing exams. But that is a question for faculty and administration to deal with.

Just make sure that the system treats you fairly and complain if it doesn't.


Some possible ways to respond to a student complaining about not having enough time on exam

When I was a TA for a large artificial intelligence class, we frequently had this complaint from students.  The reason was that, due to the nature of the class, many of the problems could be worked out eventually from first principles (or from the book or notes, since these were often open book as well) by somebody who didn't understand the material, but could only be worked out efficiently by a person who knew the material.  We thus tended to end up with most students finishing well before allotted time, but a noticeably minority who did very bad work right up to the end, and felt "if they'd just had another hour or two" they could have done everything right.

Our response was to explain that the test was looking not just for the ability to solve the problems, but for facility with the problem-solving techniques.  Thus, speed really did count!  This was also borne out by the distributions: it really wasn't a problem for the stronger students.

I would thus recommend first looking at the distribution of the grades: if the strong students mostly finished early, then you probably have a weak student who was trying to work things out from first principles, hazy recollection, or source material (if you're open book).  You can then explain something similar, that you are testing not just the ability to solve problems, but facility with the concepts, and if they are weak with the concepts, it is likely to show up in slow test-taking time.

Now, it is also possible that the student has a medical impairment, such as dyslexia, that genuinely means they cannot work quickly.  If this is the case, then most universities have services that can help to evaluate them and plan appropriate accommodation, which can be communicated to you for application to future exams by the responsible personnel.  Don't just take a Doctor's note, because an M.D. can only detect the existence of a condition, not calibrate an appropriate educational adjustment for it.


Accused of Cheating during an online exam

If you truly did not cheat then there will be a way to prove your innocence because false claims eventually lead to contradictions. The statistics aren't very threatening because it sounds like your accuser is probably assuming that each multiple choice question is a random event to get a ridiculous probability,  but that's nonsense. Exams are written to be answered correctly by those that are prepared. Thus in reality we expect many of those questions to be answered correctly and identically. You can offer to justify your answers to show you answered them on your own.

The identical submission time is concerning, but there is no reason to assume Blackboard is a perfectly coded software. Even programs like Microsoft Excel that are written by experts and probably used by millions have silly bugs in them. If I coordinated with my friends to the best of our abilities we could never click the submit button with identical submission times because we have different response times. If anything the identical submission time better supports there being a bug with blackboard than anything else. You should ask the accuser to explain how the identical times is evidence that you cheated and not that there was a bug with blackboard or any other aspect of online examination. You should also ask your accuser for how long have they been doing examination like this because likely it's new to them and they should be reminded of that.

Good luck.


Should I avoid using footnotes in a statement of purpose?

Personally, I am a big believer of footnotes. They enable additional information to be added, without distracting the reader from the main argument. However, others will not share my position. One test I like to apply before adding a footnote is: can I include the footnote text in the main body? If I can do so without hindering the reader, then I tend to do so.


What is the role of processing editor in a journal submission?

The email clearly says that you will hear from the processing editor's office when the review process is complete, and that the review process will take 2-3 months - so your first interpretation is correct, it will go to the reviewers who are expected to finish reviewing in 2-3 months.
Taking 2-3 months to decide to send the paper to review would be pretty extreme.


I think comments papers are an important (and sadly neglected) part of post-review quality control in academic publication. The fact that someone wants to write a comment paper is suggestive of a problem with the peer review of the paper in question, if only in that it left substantial questions unanswered (or unasked).  As such the journal should not charge either party for the comment paper or the response, if only to show that the journal takes quality control seriously, even if they do make all their money from page fees, I think it is in their long term interest.

Writing comments papers should be incentivized, not discouraged by financial hurdles.


Within normal procedures the best way would be to list the two first authors in alphabetical order and then make a statement in the acknowledgement that the two have contributed equally. In this we assume that the way authorship is distributed in falling order. Many journals now also ask for a specification of contributorship of all authors to distinguish who has done what. One oddity I cam across was a paper by K & H (last name initials) where it was listed in the acknowledgement that both had contributed equally. In this case H was the PhD student of K and so K may have wanted the primary spot to get the full impact of the prestigious publication.

So the way to signal contributions by ordering authors is not without its problems. But, most of the problems come from the fact that first authorship is used without discretion to assign merit. So from this perspective it is a result of a flawed system. Attributing contributorship can even out the playing field to some extent but basically we will have to live with the systems. One should also remember that the most important aspect of the reference for most is the sourcing of information, not who did what. So an example of how a system built for one purpose has been adopted to solve another.


I have to read a paper for my PhD qualifying exams but I don't understand any of it. Does that mean I fail?

If you are unsure of your ability to complete the task, you should go immediately to your advisor and/or the other committee members to get as much help as they can give you.

That is not much of an answer, but I want to supplement it with this: in this case, asking for help on the internet is potentially problematic.  Being assigned a paper and asked to read and understand it in three weeks sounds like a situation which is close to a "take-home exam".  (Maybe it isn't, and maybe you are not understanding the assignment.  Find out.) If so, getting help on the internet on your exam may not be kosher.

Anyway, most graduate students in most graduate programs in most fields do not automatically or easily understand cutting edge papers.  The whole point of the graduate programs is to give them the help and training they need to do this.  So you should be doing what you can to get that help and training, not worrying about whether you are worthy in some cosmic sense.

Good luck.

Added: For those who are confused by the discrepancy between the answer and my comment above: the original version of the question included a lot of content-related information, including the title and author of the paper itself.  I was worried that could lead to getting content-related help from the internet.  The current version of the question is totally unproblematic in that regard.


Am I reading enough of the scientific literature? Should I read for breadth or depth?

My experience is almost exclusively with mathematics papers, and applies little or not at all to other fields.

Much of eykanal's post applies to math as well, but one big difference is that math papers are much more varied in their structure, not having an actual experiment to tie them together.  A good paper will generally explain its organization in the introduction, however.

One point worth emphasizing is that reading a paper from front to back, trying to understand everything at each step, is usually inefficient.  The most common instance is that a paper often starts with definitions which may be hard to make sense of without understanding the theorems they're used in.  It's generally more effective to skim the paper several times, trying to understand more and more with each pass.

Relatedly, you'll eventually pick up the skill of picking out the most interesting ideas from a paper without reading the whole thing.  Early on, though, it's probably better to read things carefully; it's very easy to fool yourself into thinking you've understood something.

As to your main question, about breadth versus depth, your first priority has to be depth, because that's what you'll ultimately need to be able to do your own research and get your degree.  But if you're learning enough to do that, you want as much breadth as possible.  It actually gets harder and harder to learn completely new things as you get on in your career, even when there may be direct benefits to your research to do doing so.  Laying the foundations of a broad understanding of your field while in graduate school will pay off later.