Нow to start an academic career if you got your PhD five years ago and didn't do science for these five years?

I don't know what might be available in or near Ukraine, but can offer two possibilities that might be open to you.
The first is a long-term plan that assumes you have sufficient resources (job, money, time) to start some research. To do this efficiently, you might need to be in a place that has one or more local universities where you could make some contacts and start some collaborative activities. But a professor (maybe one you know) might be interested in working with you on some projects of mutual interest. If you can establish yourself as an effective researcher, you might find a way back in to a university. Your old thesis advisor might be able to offer some possibilities for collaboration. But you wouldn't/needn't be either an employee or student to do this. Your status as an "independent researcher" is enough.
The second idea would work in the US and possibly elsewhere, but requires the ability/desire to teach. Here we have a large number of Colleges that are not focused primarily on research but, rather, on undergraduate education. People are expected to do some research, but are expected to excel at teaching. Moving around might raise language issues, of course, for this type of position. If you were teaching at such a college and it were located in a place with other, more research focused, universities, you might be able to establish some collaborations as suggested above. And, the life of a teaching professor can be pretty nice in the right place in any case.
In the internet/covid age, however, things are a bit weird. The internet provides a way to do remote collaboration, but the pandemic makes it harder to make contacts. Attendance at conferences is often a good way to do that.


Had the idea vs. did the work: Who should be the lead author?

The lead author should be the person who carries out the bulk of the research work—including the planning, execution, and writing.

If the student C is the one responsible for carrying out the experiments and writing the paper, then C should be considered the primary agent of the paper.

Who should be the "final" author is a different matter. I would suspect that this really should be professor B, who had the original idea. The role of doctor A is only as research manager, so his role is nominally weaker than that of either B or C in this process. So, ultimately, barring other negotiations and arrangements to the contrary, it should be:

  Student C, Doctor A, Professor B.

If there is some other distribution of roles beyond what is laid out above, it would need to be negotiated between everybody involved.

Note: In fields where lexicographic order is not used, the final author position also carries weight. It usually is the head of the research group or team that originated the project.


How to narrow down focus in humanities/social sciences?

Ultimately it's up to you to decide what you are most interested in. No one can answer that for you. That said, it's very important that you get an idea of what research is like in all of these fields, as it is often very different from what popular conception or even undergraduate coursework is like.

Assuming that you are relatively early in your undergraduate studies:

Take a variety of classes in the fields you are most interested in. Go farther than just what the class requires: go to office hours, talk to your professors, think about and discuss other questions of extensions related to the coursework, dig into any references that are mentioned in lecture, etc.
Find a faculty mentor(s) to talk about these issues with. This might first take some narrowing down of your interests, but a faculty member should be able to give you some guidance on how your interests fit into academia and an idea of what academic work in that field is actually like. This will often be a professor from a class, but many departments also have a designated faculty member that handles the undergraduate program who may be available to talk to. In my experience, most academics will be excited to talk to you if you express interest in further graduate study.
Try to get some actual research experience. This is heavily field-dependent and I am not very familiar with research opportunities in the humanities, but hopefully you will have some faculty members that you can talk to about this. If you are in a field that doesn't often use research assistants, see if you can do a faculty-directed independent study.
Start familiarizing yourself with some of the academic customs in the fields you're most interested in and start reading some actual research. A good place to start is often the webpages of the faculty at your school that you are most interested in. Read up on their latest publications/books/etc. and use that as a starting point to get at least a small idea of what kind of work is being done and what research looks like.
Find some current graduate students at your school and talk to them about what kind of research they are working on, how they go about doing it, and why they chose that field.


Are end-of-term student evaluations taken seriously?

It depends on the university, the class dynamics, and the position of the professor/lecturer (i.e. are they ajuncts or casuals? Or are the tenured/continuing contracts? Are they solely there to teach, or is teaching a small component to their research expectations?)

Short answer: Generally not. Student evaluations are taken with a large cup of salt. This is because the anonymity of evaluations allow for students to provide unhelpful, derogatory and discriminatory comments without repercussions. If there is trouble with a class, the professor/lecturer may have already brought it up with the head of school/faculty prior to the course ending or evaluations coming through.

I would also be careful in claiming that ALL students will complain. You might find that some students are only agreeing with the loud voices who are disgruntled, but may not feel the same. Students also often tend to only provide bad evaluations, students who really enjoy the course do not always tend to indicate as such on student evaluations and this is taken into consideration. We are more likely to provide negative feedback when we are displeased, than we are when we are happy.

Women and individuals of colour/disabilities and so on are more likely to receive bad evaluations based on preconceived biases that students may not even be aware of. These are also taken into consideration when evaluations are received.

Student evaluations can be helpful regarding what the professor can do to improve the course (structure, content and so on) but they are not helpful in assessing the popularity or whether students like a professor. It's not a professor's job to be liked by the students nor is it a popularity contest.

The best teaching evaluations are those where students have carefully considered their responses and provided constructive feedback for improvement. Anything that reads as malicious or aggressive is ignored, and anything that says one thing which can be contradicted with evidence (i.e. a student claiming that a professor didn't spell out expectations, where in fact, there is hard evidence supporting that the professor did) will be ignored as well. If a professor received contradictory evaluations (i.e. one student saying really positive things, others who say exact opposite on the same topic) there is a general assumption that the student who says the negative things did poorly and is frustrated with their grade.


How do I pick good keywords for literature alerts?

One of the biggest problems is that there are, in fact, waaay to many relevant papers coming out; that's because there are lots of articles published each month in many different fields.

The approach I found most useful was threefold:

Set up author-specific alerts for the big names in your field. Read both those articles and the citations. They know the literature and will cite stuff you should be familiar with.
Set up alerts to see when someone cites a seminal paper. In my research, there were certain seminal papers that everyone participating in my tiny subfield would always quote. Find those and set up alerts when someone cites that.
Read the most popular article(s) of the month (most downloaded/shared/read in your journal of choice) to stay on top of interesting stuff that's going on.


I think that the third option is widely accepted. Students will complain about the other two, though different students and for different reasons.
The book is an outline and is a fallback for students. If it has good exercises, then they can get practice. But you will still want your own exercises to supplement in many cases, and certainly for exams. But I think a lot of, maybe most, professors follow the outline of the book even if they don't lecture precisely from it. Their exercises may be a mix of those taken from the book and those they develop themselves.
And, encourage students to take good lecture notes and not depend completely on the book.
And using your own material lets you adapt a bit for your students if they don't fit a standard model.


Grading criteria changed mid-semester. Not fully communicated. What can I do?

You can try, of course, the question of who to depends on your university. I would start with a student advisor for your subject and take it from there. If you combine your efforts with the other students who also have trouble because of that change right now, that might help.
Furthermore, you should not start with officially appealing right away, as this might force people to take a defensive position against you. I would rather explain the situation, the problems that it causes you, etc. and ask the advisor for a solution.
If you formally appeal and try to get a passing grade through that, that might or might not work. But it will surely burn some bridges and, even worse for you, the whole process will take even more time than writing the missing chapter would.


Are doctoral programs in the USA like a Masters leading into a PhD?

The quoted description is pretty standard for how Humanities departments in the US work. Most students entering Humanities PhD programs in the States do not have MA degrees, although a significant proportion of those from the UK do. It would be unlikely that you could skip those first 2-3 years of coursework. Even if you could, it would put you at a serious disadvantage even if you knew in advance what topic you wanted to research. A 1-year UK MA degree, just does not prepare you to the same extent as 2-3 years of coursework.

As for funding, the top students are likely guaranteed funding for some number of years. The funding will likely require some teaching. The teaching maybe in the form as a TA, but is likely to be much more extensive and require you to design and run a large undergraduate lecture class. For those students, the funding will cover tuition and a stipend. Those without guaranteed funding can still get funding for teaching, but you cannot count on it. How tuition is handled depends on the university/department and where you are in the program.

In the Humanities, it is unlikely that any supervisors will have grants that pay for PhD students, but there are grants that you can apply directly for. Some of these cover students in the first few years, but most are for more senior students.

For US PhD programs in the Humanities, unlike in the Sciences, funding should play a huge role in your decision of where to go. In the Sciences, everyone essentially has funding that covers tuition and living expenses and very little teaching. In the Humanities, self funded students and students with with huge teaching requirements are common. There is a huge difference in productivity and happiness between those who have to take out loans, that they will likely never be able to pay back, or teach and those who do not.


Is there a way to finding an author's H-index on Google Scholar if they have not created a profile?

No, finding the H-index from Google Scholar of someone else who does not have a profile does not seem to be possible. While I could not find a source that confirms this, there is no mention of such an option in the help pages of Google Scholar, and the wording strongly suggests that seeing those metrics at an individual author level are one of the benefits of creating a profile.
From this page (emphasis mine):

Google Scholar Citations provide a simple way for authors to keep track of citations to their articles. You can check who is citing your publications, graph citations over time, and compute several citation metrics. You can also make your profile public, so that it may appear in Google Scholar results when people search for your name, e.g., richard feynman.

However, a few relevant notes:

A profile may exist and be public, but may not be searchable. A profile, even if public, needs to have a verified institutional email address added in order to appear in the search results. To account for such a scenario, you could check if you can find a link from elsewhere, such as the researcher's web page, or from the "Co-authors" list in the profile of one of their co-authors.

To just search by author, you can filter your results better by using the author: operator or using Advanced search.


Should a journal ever reveal the name of an anonymous reviewer?

While I think that blind peer review provides useful protection for reviewers, are Academic Editors generally provided anonymity?

In my experience this is rare but not unheard of.  For example, the PNAS submission guidelines specify that the editor handling the paper will remain anonymous until the paper is accepted.  Presumably this is meant to protect editors from retribution over a rejected paper.  I'm not convinced this is necessary, but the existence of these policies indicates that someone must care.

  Further, is there any precedence for when a journal should reveal the name of a reviewer?

I'm not aware of any policy that allows journals to reveal the name of a reviewer without the reviewer's consent.  It could be reasonable in a case like this, but I wouldn't want to be in charge of writing a policy delineating when it is or isn't allowed.


What to do if my undergrad hasn't prepared me well for grad school?

Just a guess, but the guess is that you are uniformly underestimating your own skills and the quality of your education. You say "When an author derives something, I sometimes need a few minutes to make sure that the math is sound." Well, it might take me hours or days.

You are undecided about field and find a lot of interesting things that you might study. This is natural, but could be a block, since doctoral study is all about specialization. So, pick something that seems the most interesting to you and that seems to have some future possibilities. Apply to a program that is good in that field and find an advisor. You will be led toward specialization over a year or so and your research will lead you deeper.

There are two hard parts to research (well, maybe three). You need to find a suitable problem and you need to find a way to resolve it. (The third is, in some fields, coming up with a methodology for the resolution). An advisor can be helpful, especially, in coming up with a problem - or at least suggesting several, or pointing you at places that might be hiding problems.

But you won't know until you get into the thick of it.

And, for all of the "other" cool things that you leave behind by specializing, they aren't closed off from you forever. But first, get a doctorate so that you again have freedom to pursue whatever interests you.

Some people (myself) have changed fields quite drastically for many reasons. Some because of the academic economy at the time, but others (not me) have actually invented new fields. Some just followed their thoughts and branched off into a new area.

As a researcher you are currently unformed. The forming will come through practice and with the (hopefully good) guidance of an advisor.

Narrow your focus a bit. Apply to a good school. Find a good advisor. Work hard. Hopefully success will come, but satisfaction probably will in any case.


Advice on: Quitting your PhD because you dislike the place and the associated project?

I am not international, but understand what you're going through.  In fact, when I was in undergraduate, I had an Italian friend in your exact position who left after a year to go to graduate school in Europe...so it certainly does happen.  A couple pieces of advice:

1) have a plan for where you are going before you leave.  I'm not sure about the Netherlands, but the economy in the US is not completely back to normal and it can take time to find (good work)...even for well educated folks.  As you said, having a funded PhDs is a pro, so don't waste it!  At the very least, use this time to study all of your interests, not just your dissertation topic.  For example, if you want to become a computer programmer, master some languages, contribute to some projects and document your work on (e.g.) GitHub.  This can help out A LOT if you decide to leave.

2) having a good advisor and topic are the most important pros.  I live in a great place (nyc area) with great friends...but my advisor and I have communication issues (I chose poorly) and my topic is not so interesting.  For me, these cons (sort of) cancel out the pros as they make life miserable more often than not.  On the other hand, if you live in the middle of nowhere...I can understand why you'd want to leave...but you may not find such a great advisor and topic elsewhere!

At the end of the day, of course, you have to choose for yourself.  But I would say that if you are currently doing what you want to do and/or this is the kind of work you would like to do after leaving/graduating, then you should stay. At least until something comes along you know would be better for you.  Plus, things could get better for you at school within the next year or so (graduate school is long) and the you would be leaving for no good reason!

Good luck!


Typically, funders require acknowledgement in every article that was supported by their funding.

So, what's actually getting supported by the funding?

If you're a professor or researcher with multiple sources of support, then you are generally expected to account your time to each supporting project separately.  So if you're supported 10% by a project, you only put 10% of your hours on that project, and only the things you actually do with that time get acknowledgement---i.e., publications related to the specific project.
If you're a graduate student or postdoc, however, you'll often have only one source of funding that supports both your work on the project and your continuing professional development in general.  In that case, you put the acknowledgement on everything, because it's all being supported by the same funding, whether or not it has anything to do with the original proposal.

Note that what's really important here is the accounting, not the position or the proposal.  If funding supports you in create a publication, that funding must be credited, whether or not it's within the expected scope of the project.


Citing a project performed in a previous class that was never published?

You could publish it as a preprint. Or if you want to publish some specific section you could use some dedicated service that provides with with a doi, e.g. you can use protocols.io for your protocol or figshare/zenodo for your dataset. This way not only are citable but it will have a unique identifier.


Does the eigenfactor ranking depend on number of articles in a journal?

Wikipedia’s article on the eigenfactor.org ranking of journals answers your question:

  The Eigenfactor score is intended to measure the importance of a journal to the scientific community, by considering the origin of the incoming citations, and is thought to reflect how frequently an average researcher would access content from that journal. However, the Eigenfactor score is influenced by the size of the journal, so that the score doubles when the journal doubles in size (measured as published articles per year).

To give a simple example: the Journal of Physical Chemistry B is the highest-ranked journal in physical chemistry by this criterion… in good part because it carries the largest number of articles. It is a good journal, but under all other metrics it is not at the very top of its field.


Could number of years in Phd affect your chances to get employed in academia?

If you want to do the doctorate, then just do it. Never mind about the rest. While a few people might question the time, I think most realize that there are a lot of reasons that it can take longer than expected. Everything from funding to supervisor issues, to health reasons. Changing universities or programs.

It is what it is. There are so many more things that can effect "employability" that it shouldn't be a consideration. The general state of the economy in the years after you graduate has a much bigger effect, I think.


What to do in case when advisor refuses to provide a reference letter for a postdoc position?

I do not know your exact field but in most fields you could put someone else from the same lab (e.g. a senior postdoc you worked with) stating that this person was the day-to-day supervisor and the official supervisor is too busy.

But apart from this way out you should also clarify why your supervisor does not want to write the letter. No time? Different scientific opinion on some of your results? He thinks you are not good enough for academia (sounds mean but some supervisors have that opinion on some of their students)? You could become a competition as you know key results from the lab? For each of these points solutions can be found but I would need more details ...


Does changing major if you’re not passionate about a good idea or should I accept what I have and live with it?

As a software developer turned college teacher, I advise a lot of students in my Information Technology program and I like to tell my students "begin with the end in mind". If I want to go to my friend's house, do I go outside and start walking/driving and just turn left and right hoping that one day I will get to their house? Or do I ask my friend where they live, and get a map so that I know how to get there?

Why masters and PhD? Does that help you get to where you want to go? Or are those just streets and turns that you just happen to see in front of you?

Students I work with say "I want to get a job as a developer." If that's the case, I work with them to find some job postings, look at what they require, and figure out what knowledge and skills they need to get that job, and work backwards and plan out their degree or coursework.

I recommend you think about "where you want to be". It's a difficult question to answer for many people and sometimes it's worthwhile to talk to people in the field about what they like and don't like about their job and lifestyle and what they would recommend if they were you. Once you have an "end in mind", you can then work backwards and figure out a map as to how to get there.

Hope this helps!


Can you cite articles if you only read the abstract?

1) Do reviewers actually read (or read) articles you cite ?

Sometimes, but not always.  When I review a paper, I'll generally check a random subset of citations to make sure the right paper is linked.  (It's surprisingly common for references to get out of sync, so that citation [12] in the manuscript actually should be citing reference [13] in the bibliography.)  I'm often familiar enough with the literature to know if the authors are citing an appropriate paper for common points, so I'll skim over these to make sure everything I already know makes sense.  In both cases, I don't actually read the papers, just make sure they pass the sanity check.

If something looks odd (they cite an author supporting something that I didn't think she worked on, or a fact seems reversed, or there's some detail I didn't know about) I will often take a look at the referenced paper.  This averages to probably a couple of papers read per paper reviewed, but when I find one oddity I'll often find several, so it's more like some reviews I'll read 4-5 papers, more often I'll just glance at one.

So you shouldn't count on slipping something by reviewers.

As for looking at abstracts only, you can but probably shouldn't. The only time it's relatively safe is when the abstract explicitly states the single point you're using that paper to support ("We found that 72% of Bulgarian tractor repairmen are left-handed"), but even then you may be missing important qualifiers ("We limited our sample to red-haired tractor repairmen with pre-existing arthritis").  As I noted, reviewers may well be familiar enough with the literature to catch these.


Has there ever been a strike of peer reviewers?

Researchers have refused to review for Elsevier, as part of the Cost of Knowledge boycott, which

Objects to exorbitantly high prices; and
Objects to measures that restrict free information.

The initial success of the boycott was summarised in 2014 by Sir Timothy Gowers (Fields Medal recipient):

  A little over two years ago, the Cost of Knowledge boycott of Elsevier
  journals began. Initially, it seemed to be highly successful, with the
  number of signatories rapidly reaching 10,000 and including some very
  high-profile researchers, and Elsevier making a number of concessions,
  such as dropping support for the Research Works Act and making papers
  over four years old from several mathematics journals freely available
  online. It has also contributed to an increased awareness of the
  issues related to high journal prices and the locking up of articles
  behind paywalls.


Inviting a likely reviewer of a rejected manuscript as a co-author

Two points.

It's actually irrelevant, if X was the reviewer of the paper or not. If you want to ask them, do it. It does not matter, if X knows the paper already or not, but assume they don't.
I would appeal more to the professional interests of X in the mail. Like, "this paper focuses on the weight distribution of spherical cows in vacuum. My coauthors and I think the paper might benefit from your expertise on spherical horses in low gravity".


Handling unsolicited proofs of famous mathematical problems

Unfortunately, I think there's little or nothing you can realistically do for most amateurs sending unsolicited manuscripts.  What they don't seem to realize is how common this is and what a bad state most of the manuscripts are in:

I average several amateur e-mails per week (and I shudder to think of how many Andrew Wiles or Terry Tao must get).  If I carefully read each paper and sent comments, that alone would occupy a substantial fraction of my professional activities, so I have to prioritize.
I at least flip through the papers, and most of them are obviously crackpot work.  Occasionally I see one that doesn't look ridiculous, and I try to be encouraging when appropriate, but I have yet to receive a publishable paper from an amateur.  The best I can do is generally to offer encouraging advice, and even that's uncommon.
Some people seem beyond hope (for example, the ones who send word salad), but some could presumably become solid researchers given the right education and mentoring.  However, this is not something I have a lot of time to provide.  I've got plenty of in-person students, some of whom would probably like more interaction, and I wouldn't feel comfortable telling them "Sorry, I'm busy trying to explain to some guy on the internet why his fuzzy understanding of quantum mechanics doesn't actually yield a short proof of Fermat's Last Theorem."  Even if the amateur seems promising, they aren't likely to be dramatically more promising than my students, and mentoring over the internet is less effective, so it's still an awkward trade-off.
Some amateurs react very poorly to feedback.  If you suggest their results are known (while complimenting them on their rediscovery), they angrily suggest that you must not have understood what they meant or are trying to deny them credit for their work.  If you don't believe their results, they accuse you of incompetence or laziness.  If you encourage them to apply to graduate school, they scoff at what academia would have to teach them.  This is of course only a minority of amateurs, but it's just common enough to discourage giving honest feedback: there's too much of a risk of feeling like you wasted time offering feedback to someone who only wanted validation and responded with insults.
Part of the problem is grandiose visions.  When people spend too much time daydreaming about being the next Ramanujan or finding the proof that didn't fit in Fermat's margin, it's really unsatisfying to learn that their story isn't actually as remarkable as they hoped.  It's much easier psychologically to move to the parallel story of the genius oppressed by academia, rather than starting an academic career from scratch.  (And even people who show no sign of grandiosity in their original e-mail sometimes have it hiding below the surface: I imagine that anyone who sends unsolicited accounts of their discoveries to experts is hoping for some degree of acclaim.)

So what to do about this?  In an ideal world, I'd give lots of time and attention to everyone who wrote, but these are scarce resources.  In practice, I handle it this way:

If the paper genuinely engages with my work and shows no signs of craziness (e.g., drawing religious conclusions from mathematics), I give at least a brief reply.  Same thing if I have some other good reason to believe it was sent specifically to me, and not just as one of many recipients.
If the paper looks relatively promising but has nothing specific to do with me, I'll reply if I have time and feel that the reply would be well received.
If the paper is on a topic I particularly know and care about but doesn't involve my work and doesn't seem especially promising, I might reply.
Otherwise, I probably won't reply, and almost certainly not if the paper deals with famous unsolved problems.


Is it ok to mention a research interest with professors outside of your department in a letter of intent?

You don't need to contact the other professors right away, but you could do it now, and at some point before deciding where you're going to go, yes, good idea.

Yes, do check for cross-department affiliation.  Careful with this -- sometimes a department will list Prof. Other-Department on their list of faculty members, but later will hedge that if you try to have Prof. O-D be your official advisor.  If it was just done to inflate your department's faculty list, things could get a little challenging.  This is not necessarily an unresolvable problem, but it could be helpful to ask the department about this sooner rather than later.  Also see if there are one or two faculty members in your target department who could be natural committee members for your thesis committee.

Should you skip all of that and apply to a computer science department instead?  To decide this, consider:

What the PhD exams cover in each department
What teaching assistantships each department has, and what your duties would be
Are there other courses in the target department you'd be interested in taking
Where do you think you'd feel most at home

At the end of this process, you may end up applying for a couple of math or applied math programs and a couple of CS programs.

I looked at your profile and have an additional comment.  A long time ago I was familiar with CS at UW-Madison, which was, and probably still is, strong in theoretical CS, and had lots of TA-ships.  Such a program would have been a reasonable choice, but you would have had to choose one or two additional areas of CS to do an exam in.  That might have been an argument for choosing the math program as your home department.  I'm just mentioning this one as an example of how you might apply the considerations in my proposed list.


I was in your exact position couple of years back, not that the supervisor didn't want to work with me; rather he left the university and I had no supervision!; and I had to finish up and defend my thesis. So here's my advice to you:

Start Your Thesis: You have to start writing your thesis right now! It is a toxic environment when you are 2+ years in and the supervisor is not responsive; and you are still trying to figure things out. So, have a template, and start adding things; and so on. Time is running out and you are responsible for your thesis at the end of the day.
Regular Meetings: Send calendar invite to your supervisor for a weekly meeting. If he is not responsive you must inform the head of research group. If you don't you cant say "well my supervisor is unresponsive for the last 4 years and I need to finish my PhD" they will ask you why you didn't inform them sooner.

You might ask: what about papers? Well, you could take part of your unfinished thesis and turn it into a paper. Ideally we want to make papers and write a thesis about it. But when time is running out and you have no direction by the supervisor, you must start writing your thesis, to see what parts of your work need more focus.

That's it! Two important points to finish up your PhD. Finding a postdoc position is not your problem at the moment! You need to finish off your PhD first. Being a Postdoc is not that different from a PhD, what are you going to do if the supervisor is busy again? You need to develop your skills first. So, finish up your thesis and think about defending it, as soon as you can.


Mediocre/Poor letter of rec from well-known professor vs great letter from not as well-known professor?

Always go for the recommendation from the professor who knows you better. A letter from Albert Einstein that goes "mayradio0508 was never late to class and has nice handwriting" will not carry any weight.

Having said that, it sounds like you underestimate what this professor will be able to say about you. Running simulations and writing programs to handle data is something you do in research! The professor has also said you did a good job, which is a good sign. Besides, of the other three options you mention, it sounds like none of them can comment on your research ability (the third one can, but you've not started doing research with him).

If you're concerned he won't be able to say something good about you, you could always ask him: "Prof so-and-so, will you be able to write me a strong recommendation letter?"


1) If the definition is well-known and everyone uses it in the same way, you don't need a definition. If you use it in a certain way that might differ from others and thus needs to be defined, you should do so in the thesis itself, when the term first appears. Otherwise a reader might come to the wrong conclusions and only later realize that you meant something different by this term. Jumping back and forth to the definitions every time is also not that nice...
So I would suggest that you define the terms where you need them, where they appear in the work, and then add an index of symbols, only stating at which page each term gets defined (and maybe a one-line "name" of it) and no further definition in the index.

2) As you define the terms yourself, just like you need them, it won't be necessary anymore to use the homepage.
However, if you want to take definitions from there, you should say so. If you copy many definitions, you might want to say so at the beginning of the thesis or at the beginning of the chapter where the definitions appear.


How to intervene with a student struggling in the major?

I can tell for you from troubled student student perspective. I have some friends with such kind of problems here at Brazil in Usp and I think the our academic culture have similarities (including eventualy diagnostic tests), maybe my experience can help you to think the approach.

One or another of my troubled colleages have to work a part time job to pay the living on the city where the university resides, some have some psychologic problems triggered by pression of university or self induced pression by a lot of expectatives and a no neglegible number have the three causalities combined in diferent proportions. And I think the culture of my generation (near 22-28 years) agravates that scenario, where people - having growed up with video games, internet and shinny especial effects every where - think to live fast and expect constant and fast feedbacks , what make one guy or another throw things to the air when the progress looks like very slow, even when need to be because the situation - the expected reality and the experience don't match

There are educational sites, like coursera.org, duolingo.com , brilliant.org and even the stackexchange that have adapted for some expectations of new users with fast feedbacks. In the subject, maybe electing some 'landmarks' to people don't resign in the middle of the way can be helpfull if is this kind of problem that ocuring. This can be real, I know a lot of strange examples, but the most intriging for me is the case one friend of mine whom had completed all calculus courses in coursera.org and got stucked for 3 years in calculus 2 ( and now he works as data scientist in a good enterprise )

If the problem is triggered by some kind of anxiosity, I think that if the students can feel they can count on you for a little and sincere talk in the final of some lecture or another, without being harsly judged - because probably they had heard hints for changing the major or something like that , a kind of talk that could be uneasy and even kills the trust - I just can think a good outcome being constructed along the semester

Well, I hope this can help


paper acceptance probability in case of long peer review time for the 1st decision

It is difficult to say so. Usually it means that the journal is having many papers to handle, referees are not responding in a timely manner or cannot find referees that are familiar with the subject of paper. Of course, I am putting aside the possibility that the journal may have a bad review process as it is usually uncommon for well-known and prestigious journals.

As a matter of fact, I had a paper that I had submitted with a prestigious journal. It took one year to have a first decision and the decision was rejection. In this case, the journal editor told me that the review process took a long time because they had difficulty with finding referees that were familiar with the particular subject of my paper.

This question is also somehow related to yours: Editor rejected my paper stating that reviewers had refused to review it long after submission...?


Who is to decide the main idea(s) of research in a PhD Proposal, the student or his/her supervisor?

First, it depends on the country you're in, the type of funding you're applying for, and probably to a smaller extent on your field of research.

In case you already have an agreement with a supervisor, then you should probably look to him for advice on choosing a topic, but make the choice yourself. Given that he sent you papers on these two topics, you can probably assume (absent any evidence to the contrary) that both would make a good and fruitful subject. Thus, choose with your heart: what problem is most exciting to you?


How to write a Ph.D. thesis Introduction chapter?

My thesis, which does happen to be in the area you are writing about, took a somewhat different approach for the introductory chapter:

Motivations—why is this particular problem important
Related efforts—in what context was the work done
A short summary of the main development of the thesis (without a formal hypothesis statement)
An outline of the remainder of the thesis

The following chapter, which was also an "introductory" chapter, but more of a "preliminaries" chapter, defines all the major concepts, tools, and ideas used in the remainder of the thesis (which were derived from my published papers, and therefore somewhat briefer than what is needed for a thesis).


Evidence of adequate funds for U.S. university

From my experience, during the application process, you only need to sign the form that you are responsible and have the necessary funds to cover the tuition and living fees. You will need to have this evidence (scholarships, own funds, RA/TA assistantships) only after the admission and mostly for the F-1 visa application.

I would definitely contact the department you are applying to for additional information. If they actually require the firm evidence, you are limited to the following options (as far as I know):

Applying for a loan in your home country. – In this case, the letter stating that you are approved for XX,XXX USD will be enough. Depending on the regulations within the financial institution, you might only have to cover some fees in case you don't need the loan.
Applying for an education loan in the US financial institution (tricky, but possible).
Borrowing money from friends and family for a short period. Can be the cheapest option; however, it is not a firm evidence of sufficient funds. One might actually require the statements for the three-five months period and it will become obvious that this amount of money is not really natural and probably an instantaneous pump.
In some cases, you might state that you own some property (house) in your country that you will sell in case of admission. It might satisfy the admission committee (though again, asking for financial documents before considering an application is IMHO too much).
Finding a guarantor (preferably in the USA, but maybe in your home country) that states he is responsible for your tuition and living costs. You will have to submit the documents for his financial situation then.

To sum it up, I would definitely confirm with the department the requirements as they seem to be a little harsh. They might also offer some other options, I doubt it's their first case.


Can we ask a journal to assign another reviewer to review our paper if we think that his/her review is not satisfactory?

You can ask.  It's not likely that your request will be granted, but it's not impossible.  Keep in mind that the editor's default assumption will be that you are simply disgruntled by negative reviews -- every single author who receives a rejection is convinced that it's because the reviewer is incompetent -- so you need to show why you're different. You will need to make a strong case that the reviewer is actually incompetent, not merely that you disagree with them.

That means you will need to point to incontrovertibly wrong statements they make. If they say something that 90% of the field disagrees with, that's probably not enough, because it may still be a legitimate minority opinion.  Similarly, if their statements have any qualifiers, the editor is more likely to side with them. And it needs to be central to their review, not a side point.  Basically, you need to leave the editor no room for subjectivity in deciding that the reviewer is incompetent.

It's probably not worth the trouble, unless you have strong reasons for really wanting that particular journal for publication. Keep in mind that the stronger the journal, the more trust an editor typically places in their reviewers, so you'll need to make a really strong case.

That said, I've seen it happen, so it can be done.  Editors make the final decisions. They very often do deprecate one reviewer's opinion. But again, every author believes the same as you do, so you'll need to show objectively why you're the one in a thousand exception.

Edit: From the comments "it is based on the assumption that the review and the editor's decision are negative. It would be great if you could include the other scenario as well, which I am more interested in."

This makes it sound as if you sent in a paper that you suspect is incorrect or incomplete, and you want reviewers to point out the errors that you believe are there.  This seems like an inappropriate use of the peer review system. The peer review system isn't a free editing service for you. It isn't a way to avoid having co-authors, or to get someone to hold your hand and walk you through a field for nothing. If you have doubts about something in the paper, it's your responsibility, not the editors', to find someone who can reliably identify and fix problems.

If the reviewer approved the paper, but you don't think the reviewer was competent and you are concerned that there are still problems with the paper, then you shouldn't ask for another review, you should withdraw the paper and fix it yourself. If you can't do it yourself, then get a co-author who can, or at the very least have a colleague review it for you.

Edit in response to the question being revised. If the review is positive, but the reviewer shows that they are not familiar with the topic to the point that the review is completely useless, I would not request a new review.  The editor is supposed to be familiar enough with the field herself to understand this, and to deprecate the review or calibrate its impact appropriately.  Telling the editor that the review is incompetent and requesting another review would be pretty insulting, telling the editor that they are incompetent themselves.

What might I do in the case of an egregiously terrible review? The same as I do with a good review. Even if the paper is accepted, there's a response-to-reviewers letter, and you can use this to politely and professionally indicate that the reviewer is incompetent.  Just as I said above, be objective, find points that are irrefutable and unambiguous, and show that the reviewer is completely wrong.  I can't overemphasize that you do this professionally.  It's the same thing you do with every response to a reviewer -- show where they're right and where you're right, and why.  You never say that the reviewer is incompetent, because that's unprofessional. You simply show that they are objectively wrong.  The editor should pick up on this and understand that if every point the reviewer made is objectively wrong, they shouldn't use them again.

Finally, get over it.  Bad reviews are a part of the job.  It's hard for editors to find good reviewers.  Almost every paper I've submitted has had at least one bad reviewer. I've seen scores of stupid, inane, missing-the-point comments.  Get annoyed for a few minutes if you want, but don't take it to heart.


This varies so widely by discipline that asking for an average across all disciplines is unlikely to be very helpful.  Most individual disciplines do keep careful records of this statistic, and it should be easy to search for them on (e.g.) google.

However, I would say with some confidence that no American PhD program requires or even expects its students to complete a PhD in less than four years.  In some programs the "party line" is that it is desirable to complete the degree in four years, but in my experience this means that you start to feel the squeeze of increased teaching and/or decreased funding after four years, not that you get ejected from the program or forced to graduate.

I work in a discipline, mathematics, with a high entry cost but for which, once you acquire the necessary background and skills (with which a small minority of students do enter the program), there is no specific reason why you couldn't do all the work for a great thesis and write it up in a rather short amount of time, say on the order of a semester.  Nevertheless I have met very few people who have completed a math PhD in fewer than four years.  When we get to the upper echelons of talent, preparation and work ethic, this surely must mean that the culture of a PhD program strongly encourages students to stay for this amount of time.

To answer your final question: yes, many programs are trying to shorten their average time to degree as funding is being cut.  In my own PhD program (mathematics at UGA) I was involved in an initiative to do just this: up until recently we guaranteed six years of funding to incoming PhD students without master's degrees and five for students with an incoming master's.  We now guarantee five years to all students.  Note that this does not mean that we do not have funded sixth year students: we certainly do.  But it means that students will, throughout their time in the program, have to keep their eye on the five-year mark, which is something that our former arrangement was not doing: even very strong students would often stick around for six years for no especially good reason.

Finally let me also note that we changed (with my involvement) all our requirements to be independent of whether students arrive with master's degrees.  We have found that the difference in the level of preparedness of such students is not significant enough to justify more stringent time-to-degree requirements.


What funding is available for undergraduate research in Japan?

@Kayan and @fkraiem have provided links for general (undergraduate) fellowships in Japan. You'll note that most provide tuition and a living stipend (as well as airfare / language training in some cases).

What these fellowships do not provide is research funding -- if by this you mean equipment and supply costs. They will not provide funds if you want to build a robot, run experiments, or even to buy a laptop/Raspberry PI.

This is because research grants for equipment purchases go to university professor- and researcher-run labs. If you want to do research in robotics, you should write to professors/researchers and ask them if you can study in their lab for a year under the various scholarship/fellowship programs listed by the other respondents.


Clarifying email instructions with advisor

I think you should realize that your advisor is just an overworked human being. He tends to forget things, particularly what you, or other people in the group do because there are just too many things to juggle. It might be that he isn't a great planner and doesn't keep tabs on everyone in the group, but not necessarily.

That being said, imagine you had to do his job. What would your student ideally do to make your life easier and still do good research? I'm not sure about you, but my ideal student would show as much initiative as possible. They would also self-manage themselves. If I ask them to do some work, they would know why I need that work done (preferably from our discussions), how does that fit in their, or our project and would try to do it on time. If they can't do it, for whatever reason, they would let me know as soon as they can so I can think of an alternative.

I personally don't forget what work I assigned, but if I do, I expect my student to remind me that, and the reason I asked for it. No need to redo work. You keep it short, something like:

  Dr. [insert dude's name], I have finished the assignment you asked and sent you an email on [date]. I have attached it again. Regards,

As for you not knowing the rationale for a specific task you get, I think you should try to find out from him when you discuss. Face to face conversation is very valuable because it's easier for him to make himself understood. It's also easier for you to get your information if you are nice and polite.


My professor changed a take-home test to an in-class test with no notice. Can I fight the grade?

I'm a bit perplexed why they choose to do it that way. If one is doing major changes to an exam, then the students need to be informed of that in due time. I'm assuming you are not the only one who was negatively affected by this behavior? Assuming the situation is as you've described it, I would myself had lodged a complaint at the central examination office or whichever unit is responsible for that at your college. The issue is not that the teacher changed things regarding the exam, it's that the students weren't given enough time to prepare for it.


Lecturer with anxiety. How to survive in academia?

Years ago, I gave up on the idea of a career in music when I developed severe performance anxiety. After I gave a terrible performance in front of a large crowd, I decided the thing I was going to do was 'face my fear' by signing up for something even scarier and going through with it. Result: an even more terrible performance in front of an even larger crowd, which I had nightmares about for ages, and I never performed again. So I know the feeling and can tell you that - based on my experience, anyway - throwing yourself off the deep end might be counterproductive. Suggestions instead:

Talk to colleagues about the issue, especially those you're close to and/or those who are openly supportive of mental-health stuff. I get the feeling that this is more common than most academics generally let on. I once watched an absolute legend of a faculty member in my subfield admit to considerable nerves in front of an unfamiliar crowd, which astounded me but shouldn't have.

Professional assistance: As 101010111100 says in a comment, it might be worthwhile to see if you can find a therapist who'll be on your side and work with you to find a way through or around this.

Toastmasters? I watched a former student of mine with major social anxiety gradually work through it with the help of a local group. The student went to a meeting and said nothing, and then went to another meeting and said nothing, and then introduced themself, and then gave a 10-second speech, and little by little practiced low-stakes public speaking until the idea of doing it felt a whole lot less terrifying.

Remind yourself about the 'spotlight effect': Not that I want to sound as if I'm trying to trivialize your feelings, but odds are that your audience paid a whole lot less attention than you did to your embarrassment. In general no one will notice a verbal slip-up or two, and even if you do come across as nervous or choke on water partway through, the audience is likely to be thinking much more about the content of your presentation rather than your delivery and state of mind. I saw a fascinating talk at a conference last spring and at lunchtime congratulated the undergraduate who gave it. The student blushed and admitted to an immense amount of embarrassment over having been so nervous. I said that while I could see some nerves in the presentation, I was thinking so hard about what was being talked about that I didn't care (beyond hoping the presenter remembered to breathe).


Do U.S. PhD students who engage in research during summer or intersession breaks get vacation time?

If your advisor is providing your pay, then you should negotiate vacation with your advisor.  About 2 weeks per year is considered standard in US employment.

If your advisor is not providing you with pay, you should still discuss it with your advisor to make sure they think you are making progress and are committed to your research.  However, your advisor should realize they are not in a position to dictate terms.

Do not be surprised if nobody cares.  But don't abuse it.

I recommend planning your vacations at the same time as everyone else's.  The benefits are that other people will not notice you are gone, and it can be hard to get work done anyway when the people you work with are gone so less is missed.  Typically these times are late December and August.


What exactly the reviewers mean by saying "the contribution/novelty is limited"?

Possibly related xkcd. Please don’t take offence!

I’ve seen some papers in CS which validly improve upon the state-of-the-art on particular datasets. In fact, you might find these where there is an ongoing annual challenge, or a specific dataset that is used. The numbers are good but they essentially glue two existing methods together. Sometimes there are perfectly novel contributions in the "glue": sticking these two methods together only works if you do it in a particular way, but "glue" contributions are smaller than completely novel "method" contributions and this might elicit such a response from a reviewer. Even if gluing these two methods together is novel.

Usually, in these papers, the results are great (they win the challenge/dataset) and I always wonder why the paper hasn’t been cited more. I think the answer to that is that the citations for the "method" contributions will go to the original papers and the "glue" contributions, if novel, might not transfer to other techniques or fields.


Possibility to use PhD Thesis work in another university

Since you're well published, idea coming to mind is PhD by publication.
Re-purpose as much as you can from your PhD thesis to publish in journals, collections, editions, etc. that would be of an acceptable by a global high-ranking university in your field, and that's the trick done.

Basically, it sounds like your original submission was failed, which is very unique and should reflect poorly on the higher-education institution that failed your submission.

PhD by publication would prove that your research is worth being considered, and you would only need to write an overall introductory paper that demonstrates the significance of your contribution to the field, and how the publications brought together contribute a consistent body of knowledge and expertise to the field.


Negotiating for higher compensation TT position

My thinking would be to let your (A) department head know.  "I've gotten an offer to move to B for higher pay.  I am considering it, but wanted to give you a chance to counter."  Then just leave it with him.

If he asks for "what do you want", just say "a counteroffer".  Then let him and A huddle and see what they can do.  (If you get some kerfuffle about "we need to know what you want to put the offer together", say "your best offer".  Don't worry about them possibly having to tweak the offer after extended.  Everything is negotiable and it is easy to change an offer letter.  Just get them moving.

If you get a nice counter, fine.  I have seen departments work to keep young superstars.

If it's halfway there, than at that point, negotiate specifics upwards.  But it's always better to get them moving first, versus telling them what you want exactly (will "converge"...negotiating salary is like buying cars, always make other person go first to name a number--helps get a higher number.  Also gets them psychologically committed, since they've extended themselves.

If they don't counter at all, you probably need to leave.

I'm not sure if salary is the only thing they can offer.  Maybe tenure or teaching load or what have you.  Just let them see what they can do.  You can ask for specifics after they've made an initial counter.

Note:  there are others here with much more experience than I who can advise you.  I just would be careful to make sure it is in your interest, versus "be fair to the department".  It's not like you will have opportunities or leverage like this always.

Also, I'm curious if the B position is post tenure.  If so, then if A feels they can't extend tenure (being fair, following process, etc.) they probably need to do something good on money to make up for the tenure difference.

Note, if B is a significant step down in prestige, the leverage is less, but still credible.  And you need to consider it if B is post tenure.

(Good luck.)


What are the social norms associated with stealing free coffee?

The big difference here is simply whether the meeting is over or not, i.e. whether it would have to be thrown away or not. If those who are supposed to consume it (for which, as others have pointed out, someone paid) clearly have no intent of doing so (because they left), then I think it is fine to consume it.

In fact, in that case, you would even do them a favor because noone has to clean it up. But otherwise, it's stealing. Another indication for this is the group size: With about 100 students, there clearly wouldn't be enough if everyone took some coffee.


Footnote vs reference for API documentation

The Springer instructions for authors for conference proceedings (including LNCS) don't give any guidance on what information should be put in footnotes, so you appear to be free to choose. I would suggest that if you are referring to a document then the easiest thing is to include it in the references as you would with any other document to which you refer.

Including it as a reference also means:

it will be visible on the article webpage even to people who aren't logged in or don't have access to the full paper, and
it will be linked to Crossref, which may benefit people who mine citation data.

If you're using BibTeX, you can use the @manual reference type, but see also this answer on referencing software documentation for options.


Is it normal that a peer reviewer would ask for an executable file in order to check my results?

I don't know if it's normal, but it should be normal for all reviewers to make reasonable efforts to verify that the claims authors make are correct, so to the extent that it's not normal, I can only commend the reviewer for being willing to make an effort that other reviewers don't make. What you sense as "distrust" is the reviewer doing their job, nothing more or less (and it is probably somewhat accurate to say that a reviewer's job is to distrust the author's claims, so I don't see the idea of being distrusted by a reviewer as something to be ashamed of or offended by).

By the way, it should also be normal for authors to make available any software (including source code whenever possible) needed to replicate and verify their results. So if you are unhappy with the reviewer coming back to you with annoying requests that delay the decision on your paper, next time around you can preempt such issues by releasing your source code (or at least submitting it to the journal) alongside your manuscript. I am sure the reviewer would be much happier and ultimately everyone would benefit, including you.


More than one corresponding author for a paper?

Being corresponding author does not primarily concern the journal publishing process. The role of the corresponding author is to handle communications with other researchers once the paper has been published, to respond to questions concerning the research as a whole, methods, results. It is typically the most involved person who takes on this task and in many cases it is implicitly understood it is the first author. So for you to take on the corresponding author task means much more than the communication during the publishing process.

I can see reasons for there to be more than one corresponding author, although I have never encountered it. This would be if the paper contains material where two (or more) authors are experts on separate parts and it is necessary to contact each for specifics on their specialty. As I said, I have never seen it and am not sure it has ever been done. Perhaps we might find out through comments to the answer...


Is it better to list a non academic reference that knows me really well, or an academic reference that is less familiar with my work?

General Answer

This will in part depend on what type of graduate program you are looking at.

If this is for professional school (business, law, medicine, etc.), I would think that a letter of recommendation from non-faculty would be relatively common. Such a letter (such as in the case of an MBA program) could actually be favored over a letter from a pure academic.

Conversely, let's even suppose you are trying to get into a master's program in a purely academic discipline. (For sake of argument, let's say pure maths). You need to have some letters that can speak to your academics and scholastic abilities directly.

However....

If you already have two solid letters from professors who can speak to your academic qualities, a letter from someone in "industry" who can speak to the more non-academic aspects of your profile might add a positive depth to your application that would not be achieved by having three academic references.

Speaking for myself personally, if I was to receive an application from a student who had two academic references and one reference from a CTO, I would likely be more inclined to look at the application with deeper consideration. The non-academic reference could provide a dimension of insight into the applicant that would not be accomplished with three academic references.

Long story short, I would much prefer to have a non-academic letter of recommendation that gives a fuller and more complete picture of an applicant than a letter of recommendation from a professor than does not know a student well.

Situation Specific

Based on some inferred information from your profile, it seems that you are likely trying to get into a program in the computer science fields. If you have a quality letter of recommendation from a well credentialed CTO (i.e. not someone who runs a company worth US$200 from their mother's basement), I would by all means include it in your application. Many programs want students who have connections to industry. It helps them make inroads with their alumni network into new employers and new fields of collaboration.


I am sure opinions and traditions vary concerning this question. For me the quality of the journal (say, impact factor) is the most important, you try to get published in good journals. In some cases, the field may be so narrow that only one or a very few journals may be good. In such cases the selection may result in a single journal.

To publish in a variety of journals seems to be a means by itself for many but I think the reasons still vary. There may be advantages in getting published in many journals to show that the research has wider applications and is accepted more generally. It may be a way to avoid the suspicion that you have a back way into a single journal (not that that would be true). In some cases, you may select different journals because you know your ideas are not favoured by someone in a specific journal's editorial board (strategic reason).

So reasons for spreading the publications may vary quite substantially. The main point for me is, however, still that primarily the quality of the journal will decide. I would not chose a different journal just to get a new journal mentioned in my list of publications.


Should undergraduates add a "course-based research experience" section in their CVs?

Just call it "Research Experience."  The fact that you happened to earn course credit at the same time you did the research is irrelevant to the needs of employers.


A Ph.D. dissertation would often be considered as a final report for the invented methodology and the proved accomplishments.

One of the most common acceptable and routine criteria to assess the denouements of a dissertation would be consideration of the published papers, are which constructed the dissertation's motif. If you present no sign of publication corresponding to your work, the assessment committee may not be convinced, considerably, about the validity of your work, because related peer-reviewed papers, consisting of the research, are expected to be analyzed in a careful way and authentication of dissertation's accomplishments could be, intrinsically and roughly, taken into acocunt with due attention to such papers.

As the Ph.D. studies are long, it is inevitable that one or two papers (corresponding to the last phases of the research) will not be published, up to the defense. So, one could assert that their referencing as "Submitted" would be ok.


Alternative ways to use lecture time when only one quarter of the students can attend?

I would offer an answer which actually works under the assumption that your restriction may not be as hard as you think (should be a comment, but too long).

Live streaming is possible! I can't see under what circumstances it is not possible to do live streaming. Bring a laptop to the lecture (you probably do that anyway) and point the webcam to where you are lecturing and do live-streaming with some platform of your choice (in addition to the recording of the lecture). It's very simple to do, the quality will probably be much worse than the official recording, but some students will still appreciate the live stream (especially if they can watch a high quality recording afterwards).

What is the benefit for students? The students have to rewatch 3 hours of lecture per week! That's a lot of stuff and a lot of time lonely in front of a screen. If they attended a live lecture it's more engaging. If they did not get something in the live stream (e.g. due to low video or audio quality), the can specifically jump to the time in the lecture which is huge time-saver.

Interaction is possible! Create a chat room for the lecture and include a chat window in the live-stream. (You may use a chat where the students may choose to anonymous to lower the bar for questions.) This is also beneficial for student who are present: What can happen is that students ask questions in the chat and other students chime in and answer the question before the lecturer even notice the question.

I have to add: All this above is based on a lecture I held last semester. The benefits have be reported by the students exactly as I described them. The chat worked out perfectly! Student where pretty active there - they did not only ask questions and answer them, but also posted memes they created for the lecture. I was impressed.

Why could live streaming be a problem? I don't know. I would be very surprised if there would be no internet connection (I used our eduroam and this worked fine for streaming in HD).

What about privacy? My university does not offer a streaming server and I would have to use a commercial streaming service. I don't an issue here: The only one recorded would be lecturer, the students in the lecture hall will not be on the video and it should be the case that even the audio of students would not be part of the recording. The chat if both anonymous and also optional. The only thing I could imagine is that some bureaucrat would say that this is forbidden. Frankly, I didn't ask for permission and if somebody would argue I would simply state that this is needed for my concept and I would gladly change to a similar service which is offered by the university.

Other issues? Low quality video was not a big issue. On some days I had problems and had to use a bad webcam (just 720p, weird colors), but no complaints. (Btw. I had lecture note prepared and distributed in advance and I also included in the live stream; so the students knew what I was talking about even if the video was no that great). Bad audio was bigger problem! The mic of the laptop was way too bad and students complained. I ended up using the mic of the lecture hall through the speakers of the lecture hall (which was already an improvement) and recorded this with an external USB mic.


What is a good enough putnam score to include in an application to PhD programs?

I think saying you were among the top "N" participants where N is something like 500, 200, 100, or less would be the right way to phrase the accomplishment.

The (anonymized) scores and rank of all participants are published, so you can find your exact rank.  Very roughly, I'd say top 50ish programs in math would view a top 500 rank favorably, top 20ish would like top 200, top 10 would like top 100, and the most elite would only view Putnam fellow or one of the (next "X") categories as noteworthy.  I think CS theory views math contest ability in a similar manner to pure math programs so that this mostly still applies.


Should I attend a conference even if I don't have a paper accepted there

I work in computational condensed matter and have attended both computational (or theoretical) and experimental-oriented conferences. When you submit an abstract for a conference in this field it usually does not imply that you are committing to publish that work in the conference proceedings or that you thereby refrain from publishing that work in a journal. Top conferences (in this field) will encourage and give you the chance of publishing in their proceedings, but will not require it.

What usually happens, is that if you can get the paper published in a reputable research journal you do that, and either 1) choose not to submit a proceedings paper or, the option that I find most interesting, 2) submit related technical work that, while still sound and rigorous, might not get published in a journal but will get accepted as a conference proceedings paper.


how could I mention sequence of figures in a research paper?

The exact format should be determined by the publication in which you publish your work (assuming this is what you do). You should be able to write Figures 1-4 or alternatively Figures 1 to 4 (although the former is what I am used to seeing). If the format uses abbreviated forms then Figs 1-4 would be the format. There is no need to repeat the word figure before both numbers in a sequence.


Should I list my work as a frequent journal reviewer as a volunteer work in LinkedIn?

I think you should take advantage of being a peer reviewer. You can add it to your LinkedIn account, and create a profile on Publons and ReviewerCredits to be registered as a peer reviewer.


Toxic former PI trying to block me from presenting work after I quit my PhD

Don't be panic.

If everything you said is true, your PI does not deserve to be a co-author, and I would suggest you not to put his/her name in your poster.

  It is clear that (s)he is very appreciated in the field and no lab
  could accept me if (s)he blocks me.

This is not true.

As you already resigned, the worst they can do to you is not writing a letter of reference. Nothing else.

Just think about it, would they ask/email other research groups "Hey, I just want to check if you-never-heard-of Monica is applying to your group, (s)he is very bad blah blah"? If that really happens, it is them to be questioned.

Note that they do not gain anything by badmouthing you. People can question their ability to select students. And if this behaviour is consistent with different students, they will make a bad reputation for themselves.

Updated:

From @CaptainEmacs:

  Sorry, but this is not realising how blacklisting works. If the PI is
  indeed that powerful, they can do a lot of damage. While OP tries to
  continue in the field, the PI can basically make a side dismissive
  comment or explain how difficult a person OP was or - outright false -
  statements about what OP did, including making underhanded claims
  about sabotage or thefts, out of knowledge of OP. The best chance for
  OP is to switch fields where PI doesn't have a reach or name or go to
  some other big shot who is not influenced by PI and try to convince
  them about their qualities, but this is hard.

I've never heard of such things. Do you have a source for it? or is this a rumor that you hear?

"Powerful" in academia just means that somebody does a lot of good research, and has a lot of collaborations. It doesn't mean they can affect the decision of anybody outside their department.

And if somebody is trying to tell me about their bad former student, the first questions come to mind will be: why this guy needs to spend so much effort going after a random student? why does he think I will care? why can't he just move on?


Showing interest / Applying for Phd position that has just opened, before finishing Master studies

If you are currently working on a master's thesis in the group of the professor with whom you'd like to a do a PhD, the best thing to do is set up an appointment and talk to him.

As an advisor, I don't need to have a published paper to see whether someone in my own group is a competent researcher or not. I can see this by interacting with the person, through reading their project updates and emails, and by talking with other the more senior members of the research group (who sometimes will work with the students more closely than I can).

Given that the goal of an advisor is to select people they believe will become excellent researchers rather than simply the "top students," someone who is an "internal" candidate is often a better option than taking a chance on someone whose work the faculty member hasn't been able to observe directly.

[That said, however, I think there is also something to be said for considering going somewhere else for a PhD than the place where you did your bachelor's and master's degrees, when it makes sense to do so.]


Have applied to, and been rejected from, a number of PhD positions; are they really so difficult to get?

As for the question in your title (which originally was: "Is it really that difficult finding a funded PHD position?") the answer is it depends on the field and the country. As an engineer, in countries with a well-developed industry, the job opportunities for graduates outside academia are good, thus diminishing the competition for PhD positions. This being said, a grad student is not just hired to lay bricks because there is a wall to be built. It represents a substantial investment for professors who will thus rather have no student than a not-so-good one.

To the point, previous experience in the specific field of the PhD study is almost never a requirement, so I doubt it's the limiting factor in your case. Your grades might be though, or your written english proficiency, but these are guesses.

I think your strategy might be inefficient. From your text it sounds like you sent a large number of applications and are waiting for someone to bite the bait. A personal interaction with people in the labs you are interested in would be a better approach, for example via an internship or a visit, if you can afford it.

So I would narrow it down to a few places where you really would like to work, gather the reasons why you like them, and start establishing a contact via email, say what you like about their approach or research topic and how you think you could fit in. They will then be able to let you know what is needed to be accepted in the graduate program (note that you will still have to comply to the department, university or graduate school requirements in order to be accepted).


How should I ask for letters of recommendation whose strength is dependent on intended program?

To me, the following progression seems more natural than either of your suggestions:

  I am interested in further studies but I am not sure whether to go to a second masters or a PhD program from here. [Here is my background and here are my career goals.] What are your thoughts?

then

  Do you think you could write a strong letter of recommendation for me for [the kind of program you suggested would be best for me]?

and then, if the answer is yes,

  If I decide to apply to [the other kind of program], do you think you could write as strong a letter of recommendation for me for that program?


How can I get involved in grant proposal reviews as a graduate student?

Reviewing grant proposals as a student is tricky, at least in some fields.  The NSF is highly unlikely to ask a grad student to review proposals (it might theoretically be possible for a brilliant student who is almost done with their Ph.D., but I've never heard of it happening).  Furthermore, faculty are not allowed to show proposals they have been asked to review to their students (it may sometimes happen, but it's breaking explicit rules regarding confidentiality).  Overall, in pure math grad students basically never review grant proposals.  I can't speak for other fields, but I'm skeptical that grad students ever play a major role in reviewing proposals.

Instead, I'd recommend asking your advisor to see the other side of the process.  They could share their own proposals, and perhaps even reviews of those proposals or drafts of upcoming proposals.  They could also ask collaborators whether they had any proposals they would be willing to share.  This isn't quite the same as reviewing proposals yourself, but it could still give you valuable experience with how grant applications work.


What should I do after advisor got upset when I expressed "belief in evolution" and then said he couldn't add me to his research team?

Well, this is clearly not a match made in heaven.  (Sorry, I really didn't intend this as a pun.)  What a shame, you had really bad luck.

There is no need to keep this a secret from the other professors.  It is very unlikely that they are clones of this guy, even if they do have a friendship with him.

Yes, you do need to talk to the dean of graduate studies in your department and let him or her know what happened.

I don't think that particular research team would be a healthy place for you.  The guy behaved badly.  You need an advisor you can trust to act like a mensch.

In terms of the effect on your future studies -- I can't say.  If you can find another advisor you want to work with at your current institution, great; otherwise, you might want to go elsewhere.

By the way, do you mind my asking, why aren't you in a PhD program?  In physics it seems a bit unusual to be in a Master's only program.

(Just so you know, what he did was illegal in the U.S.  I'm sure the dean of graduate studies in your department will know that, and I'm not going to suggest you mention it; but I wanted you to know, so you will see this clearly as THE PROFESSOR'S problem, not yours.)

-- Edited to add: for some info about the illegality of this sort of thing, in the U.S., see the U.S. Department of Justice's intro page: http://www.justice.gov/crt/combating-religious-discrimination-and-protecting-religious-freedom-20


Can scientists be categorized according to temperament and working style?

I started this off as a comment, but I think I'll try to put it in an answer instead.

I categorize researchers into "Could see myself working together with them" and "I don't think our styles mash". Note that this a completely different and independent from my categorization into "I think they are good researchers" and "I don't think they are good researchers". (For one, I would't even consider somebody in terms of potential collaboration if I didn't think they fit my definition of "good researcher".)

Besides a researchers style, each researcher has their own individual strengths (and weaknesses). I mention as I would attribute some of the things you mention to individual's strengths, rather than style. Here, I would count things such as verbal communication skills, written communication skills, admin and bureaucracy skills (it is amazing to have a collaborator that can easily approve an unexpected expense!), industrial contacts (and a related skill of talking about research to people outside of academia). Note that I am making a difference between "having good verbal communication skills" (skill) and "having a communication style that I like" (style).

The point is: there are just too many factors to "categorize" researchers, and besides unnecessarily creating divides and "boxes" for people, even in your head, sounds a bit counter-productive.

Instead - figure out what you like, and which environment suits you best. For all potential collaborators, see how well they fit with your style, and make a separate decision for every person in your professional network. It is rare that a single person will tick all your boxes if you make it a matter of ticking boxes (i.e. the preferred communication style, preferred communication frequency and medium, complementary strengths, personality match, etc) - but if you figure out which "style of collaborator" suits you the best, you can start looking for a person you would enjoy working with (despite their possible shortcomings).


Is it bad to not test the capability of the explainability of the student at the graduate level?

It depends on what you want students to learn.  Use open ended questions for learning critical thinking.  Either approach is good if you want students to learn facts.

Nearly always, at the graduate level, you want students learn "critical thinking" from the analyze/evaluate/create parts of the Bloom Taxonomy of learning.  Frequently this is the case at the lower levels of education as well.

Open-ended questions are necessary to demonstrate the ability to create, and can make it easier to tell if students are analyzing and evaluating.

If your goal is for students to remember a list of facts, then multiple choice questions are an efficient (but not necessarily better) way to test that.

"Understand" or "Apply" are often best addressed with open-ended questions, but could be addressed either way.


Can I include NIST data in my research software which lies on GitHub?

Their copyright page seems fairly clear to me.  It even goes into what to do if you create derivative works based on it.  That said, best practice would be to include the download as part of the code.  Most platforms have the ability to retrieve a url, for example, if the data is available that way.  Also, note that Github is not really intended to store datasets, though it will work for that if the dataset is relatively small.  It can greatly slow down other work on the rep though.
If you're unable to include the download as part of the code, perhaps include a set of "data download instructions" in the readme.md file. That alone would be more than I'm used to seeing - many times when I've seen the code from published research, it's provided as if you already know how to get all the data yourself.


Slightly revised version of submitted paper two days afterwards: will the editor be annoyed?

The more you wait the harder it gets to do that, there could be a pipeline that is already in progress. I suggest you send a nice email asking if there is a possibility to do this, and show that you would appreciate if he/she accepts the slightly updated attached version as the final version.

Do not worry about making the editor mad, he/she took responsibility for taking care of this and should be prepared for and expect to deal with such situations. If you want to maintain a good relationship with this editor (in case you know him/her personally), then maybe you should weight the values of: your relationship with the editor vs the quality of the final version. Personally I would go for the latter, but this is your call.


What will help a master student more a Research or One extra subject?

I would choose extra research over an extra course. The experience you will get out of a research can be invaluable as in analysis, logic, critical thinking, writing and submitting a paper and so on. For me, if you like a course and can't get enroll in it, you can always buy a book or get some notes and read it on your own time. It is much harder to do research in your own as an MS student. Of course the aforementioned points can vary based on your field. From a civil engineering PhD student point of view, research weighs more than courses. PS, you can always attend courses as a listener (for no credits) or take it if you do a PhD.


How can people with debilitating social phobias get through foreign language?

First, social phobia is not a character defect. It is a recognized medical condition. You are not worth less as a human being if you suffer from a phobia.

Next, depending on your school, you may be able to get a medical exemption from certain requirements. You may want to discuss this with your local student services. (By email if meeting people in person is impossible to you.)

However, I would strongly advise against this approach. You will need to interact with people after leaving college, too, so avoiding the problem is not a good strategy in the long run. Instead, I would recommend that you actively work on this issue.

The good news is that social phobia is very amenable to cognitive behavioral therapy (CBT). The accepted form of therapy is a desensitization approach, where you will progressively learn to tolerate being around people.

No, this will not be easy. You will need to work on your disability. You will encounter setbacks. But your student services should again be able to point you towards resources and therapists that can help you. And there is no better time for doing this therapy than now, when you have a more-or-less flexible schedule, and before you hit the job market, where social phobia will be an enormous problem - regardless of which career you want to pursue.

Good luck!


Which form of English (US or UK) should be used for Elsevier journal publication?

Check the journal's guidelines. Different Elsevier journals have different preferences. Some are happy with either American or British English, as long as you are consistent.


What happens to summer salary funds if one has more than three months' support?

Some people can buy off a course from their teaching duties in the non-summer months usually at the rate the department would have to pay to hire an adjunct to teach it. Some agencies will allow you to shift the salaries off yourself and onto a student so that maybe you go to 3 weeks from each of 4 grants rather 4 from each and use the saved money to fund some additional student time. This may or may not require permission from the funding agency, but it can usually be done without it as long as the PI isn't reduced to zero time.

With the NSF in the US, faculty aren't allowed to have more than 2 months of time funded across all NSF grants without explicit permission from NSF. Now, if you have 1 DoE grant covering 2 months and 1 NSF grant covering 2 months, they won't notice.

Some people also finagle this problem when their grants are staggered enough that there's only a short period (say one of three years) where this is an issue by pushing the money off to a future year and then exercising an option for a no-cost extension of one year to spend out the money.


Would it be ok/wise to end my PhD contract after submitting my PhD thesis in order to be able to start a new job at that time?

It is entirely common for students to take on a job before they have formally completed the program, and then do the defense and submit their thesis in the coming months. It happens all the time, and everyone understands that if you have a job offer that you intend to take and can't defer for a couple of months, then you should of course take the job. Employers will also understand if you tell them up front that you will want to take a couple of days of vacation early on in your tenure at the company to travel back to your university to defend your PhD.

So, yes, it is ok to do what you propose.


Does doing a PhD in a small/simple university make sense after getting a Master's from a very prestigious school?

I guess the first question is What do you want to do with your PhD?

If you want to stay in academia, you will have the same problem after graduating all over again (and, speaking from personal experience, as a young postdoc/faculty, one does not generally have the luxury of choosing where one goes next). Further, going to a (presumably) under-funded local university with weak research programme is going to severely reduce the probability of you doing world-class research. While Moriaty is correct in saying that "It's the quality of your individual work that counts.", said quality is definitely strongly correlated to the excellence of your advisors and fellow students and collaborators. Another problem may be funding (e.g., for going to conferences), which may not be plentiful in a small university.

What I am also wondering is whether you actually need to switch university, or should just live off-campus? I work in Zurich, and I have one student who used to live between Zurich and Bern (about a one-hour car drive away), in an area that was pretty much as rural as it gets. He just did a lot of home office, and took the train approximately 3 times a week. Maybe an arrangement like that helps you more than throwing out the baby with the bath water?


About the information on Professors who write Reference Letter

While anything is possible, I think that would not be normal practice. I think it is unlikely.

However, in some smaller fields in which there are fewer professors and they know one another, it is possible that someone will mention a name to another person. But this would only occur, I think, if there was some question raised by a letter of recommendation.


What does non-exclusive publishing rights mean?

I suspect you're seeing "non-exclusive distribution rights", which means the journal gets the right to distribute the paper, but it's not an exclusive one. Other venues, such as arXiv or ResearchGate, can also distribute it.

If you have an open access paper, presumably it uses the CCBYA license, which means any use, distribution and reproduction in any medium is permissible (i.e. you can publish it elsewhere) as long as the original authors are credited. Journal licenses that only allow the authors to self-archive are more restrictive and usually indicate that the paper isn't open access.

This doesn't mean you can publish your article in other journals. Most journals will have policies that all submitted content must be novel, and if you've already published the paper it's no longer novel.


How common is faculty members changing jobs in the US?

The frequency with which faculty members switch departments varies by field. For example, it happens much more frequently in Economics than in Computer Science. I remember lunch-time discussions proposing an informal study aimed at testing the hypothesis that this difference in mobility was partially responsible for the income gap between econ and CS (economists make substantially more money), but looking for it now, I can't find it. Maybe it was never written up...


Citation for quoting a current accepted value in an abstract?

It is typically not necessary to report the currently accepted value of a quantity in the abstract, but, indeed, you should report it in the scientific report (with citation). In the report you should also discuss the compatibility between your result and the currently accepted value.

However, if there is a significant discrepancy between the accepted value and your result, and the main aim of your report is to discuss the cause of this discrepancy, then it can be useful to report the accepted value also in the abstract. In this case, the citation is needed, but take into account that, frequently, citations in abstracts follow different style conventions from those of the main text.

Pay particular attention to the source of the accepted value. For example, for fundamental physical constants, the Committee on Data for Science and Technology (CODATA) publishes around every 4 years a new "adjustment" of the recommended values (here you can find the values of the latest adjustment with references). These recommended values are calculated on the basis of the best available measurements. The CODATA adjustment should be considered the only reliable source for the accepted values of fundamental physical constants (values reported in books are typically outdated). Other official sources exist for values of quantities related to other fields.


Does self-study leads to fast but shallow knowledge acquisition

It largely depends on your approach to self-study. Answer the questions below:

When you self-study, do you often test your understanding? Do you spend time solving exercises from the textbook? Do you apply what you learnt not only yo one problem, but to other similar problems?
Do you summarise what you've learnt and reflect on the learning process and experience? When you are involved in larger and more complex projects, do you break them down to smaller steps and identify how what you've learnt can help you improve the way each particular step is done?
Do you combine different methods you've learnt? Do you adapt them for new problems? When several alternative methods can be applied, do you know how to chose the most appropriate?

If you answered all questions positively, your adopt a deep learning style, and you should not really worry about the problems which come from shallow learning.


How can I overcome the fact that I attend a weak undergraduate institution?

It sounds like you have a good start on the most important thing: take advantage of every opportunity at your current program and excel at all of them. Even from a weak undergraduate program, if you can come out with multiple letters saying that you are the strongest student they've seen in X years and have the credentials to back that up, you'll have a good chance at solid graduate programs.

Your situation means that standardized tests are also even more important. Math is nice because there actually exists a test (math subject GRE) that most schools put significant weight on, so make sure to take it very seriously. Doing well on the math GRE takes away a lot of the uncertainty that admissions committees will have about your application due to the institution.

Assuming that you don't transfer, some other options:

Get to know faculty and spend that extra time doing research. Proven research experience can make up for a lot of coursework, and you'll hopefully get a much stronger recommendation letter as well. This is important to do no matter what kind of institution you're at, but is probably extra important at weaker programs where your application can't rely on reputation and coursework.
Consider graduating early and getting a Master's degree at a strong program. This isn't always financially feasible, but if it is then it's an option to strengthen your coursework and resume. Availability of strong master's programs can depend on the field, but it's worth looking into.
Graduate early and get a job doing research. Again, availability may depend on field (I hear that these aren't common in math), but if you can get the right job it can be a great boon to a resume and help generate another good recommendation. Bonus points if you can find a job near a good university and take a couple classes on the side.


Is it advisable in my case to take a second bachelor's degree?

In almost every circumstance, one bachelor degree is enough. Even if it's from a less-than-ideal program, as long as you can show that you performed well, it will at least count for that.

If you are really that concerned about how your school appears on your academic record, I suggest trying to enroll in a Masters program at a more reputable school. Performing well at this level will allow you to improve your understanding in your field (and potentially fill gaps that were overlooked in your evidently underwhelming bachelors program) and demonstrate your abilities.

If for some reason you are unable to obtain admission to a Masters program, there are always non-credit or non-degree-track courses out there that you can take to bolster your breadth and depth of understanding as well as your credentials. Then, if you're still not satisfied, you can always reapply to those graduate programs.

But moral of the story, a second bachelors is not worth the time and money. Even once you have it, it doesn't say half as much about you as a graduate degree would in the same area. Top performance at the graduate level will allay any concerns about your undergraduate academic experience.