Most graduate programs try to be more transparent and forthright about TA funding than seems to be the case for you. That is, at the outset there would be promises made about number of years of funding, conditional on reasonably good performance in coursework and teaching. Departments are very well aware that grad students will have difficulty surviving (much less paying tuition) without financial support, so do not usually cut support without considerable prior warning, explanation, explanation of terms for reinstatement, or explanation of economic conditions and prognosis for future funding. To do otherwise is irresponsible.

I do have to wonder whether you were paying attention to disclaimers about fragility of funding, though, too. For that matter, do you have a copy of the TA offer letter? It really should spell out what you can expect in terms of funding. For that matter, no one's advisor should be "the last to hear" that their student(s) didn't get TA funding renewed.

Of course, it might be that the central administration at your university "pulled the rug out from under" your department, and the budget changed abruptly and somewhat catastrophically. But, still, I'd think you would hear something about this, an explanation, rather than just a passive non-support situation arising.


Is single parenting compatible with success in academia?

Summary: The older your child is, the easier it is. But by no means it will be easy. Personally, I don't even think it is possible. I present my own observations to support my claim.

I am an early career researcher myself, having just graduated with a PhD in a STEM field. I also got married a year before my dissertation defense and became a parent literally a month before I was to defend and graduate.

First, of course, anything is possible. While I may not personally know of any such success stories, I am sure others here do and I am sure you can google and find a few success stories.

But I will describe what I think is the average case instead of the extreme case, resulting from my own experiences and what I saw around me; friends, colleagues, lab partners, advisors, coauthors, other professors, people I met and got to know in meetings and conferences, people with whom I have interacted during my career...a sample size of 30-ish people.

Grad school is hard. Grad school in a STEM field is really really hard. It is very consuming. It consumes your time, eats into your social life, takes up your mental energy, your physical energy, and your emotional energy. It always has an adverse effect on your mental and physical health unless you are very disciplined and exercise, eat, and sleep regularly.

Likewise, being a parent is hard. Being a good parent is really really hard. Kids demand so much energy and they need so much love and attention. Raising a child is more demanding than going through grad school. If there are two of you, sure it helps. But both parents have to put in a lot in raising a child. Being a single parent is even harder because in a way, you are filling in for both parents.

Now on to hard data! Master's is easier so we will only consider doctoral students and above. These are all in STEM fields. I only know of two cases where they had children before starting doctoral studies. One had three kids, another had one kid. One had already made quite a lot of money on wall street and wanted to come back to school to get a PhD so he didn't worry too much about TAing or financial aid. The other was a typical student. They both did finish successfully but it took them about a year longer than was average in their respective fields. And I want to emphasize that they were both with their partners who were both full-time stay-at-home parents.

Next, I only know of myself and one another student, who had children while in grad school. We both had children very late in our studies, when most of our work was done, a paper or two was published, a paper or two was submitted, the thesis was being written or half done. Every single other person that I know of who wanted to have children, were waiting to graduate or even later to have kids.

I have never known nor heard of (a friend of a friend of a friend) a single case, a single parent who has wanted to start a PhD, or has started a PhD, was/in in a PhD, or has successfully finished a PhD.

In all honestly, I don't think that in your case, you can put up hard boundaries between your personal life and your professional life. How can you separate raising a child as a single parent and work on your computer science PhD? It doesn't matter what hours you decide, nine hours a day or 4 days a week. You will come home and think about your dissertation problem. You will think of your thesis. You will think of the comp sci question you are trying to answer. You will think about big and small inevitable conflicts with your advisor, your lab colleagues, your coauthors, your thesis committee, and whether you'll get a TAship next semester or not. Similarly, how can you stop thinking of your child when at work? What happens when the child is fussy or upset and doesn't want to stay with the babysitter or go to daycare? What if the child gets sick or there is another emergency? You'll run out of your lab without even thinking and there goes your rest of the nine-hour-planned-day out the window.

Furthermore, let's say a miracle happens and you get your nine-hours-a-day workdays. From a 24 hour day, taking out the time for sleep, how much time will you have for yourself? When will you decompress? When will you destress? When will you have time for your physical exercise and mental wanderings and distractions such as your hobbies? How often will you be able to just sit in front of the TV and eat cereal the whole day? When will you relax with your own alone me-time? Without hobbies, exercise, relaxation time, grad school will absolutely kill you. Every single person I know who tried this either dropped out or was an absolute wreck by the time they graduated. And these people were not even parents, much less single parents.

In conclusion, the statistics are against you. Sure, your child's age is a factor which makes it easier the older your child is...but it will still be very hard. You are taking two things which are notoriously difficult and intrude upon every aspect of life, and you want to try them both simultaneously, and hope you can keep them separate and succeed in both. I really wish you the best. Good luck!


Thesis: What are the requirements before saying "There is no research on that" and how to phrase it?

Is the fact that I couldn't find any enough? When do I know that I put enough effort into searching?

Obviously, there is no way to "prove" that something does not exist, so on a fundamental level that you did not find anything has to be enough. Of course, you need to make evident that you searched in a reasonable way. The guidelines of structured literature reviews have some rules on how to do this, but essentially it boils down to (1) searching all reasonable sources, and (2) searching for all the terms that could reasonably be used to describe what you are looking for.

  how to phrase it?

The usual phrase is "to the best of our knowledge, this methodology has not been used before to (...)".


How should I thank my advisors at the end of my program?

Write a nice thank you letter
Keep in touch; send an email every couple of years to let them know about your recent successes
Pay it forward by investing your own time and energy into mentoring others, as time and opportunity permits

My "gratitude role model" is a high school summer research student I had a few years ago.

First, she gave me a card with a nice message at the end of the program.
A year later, she emailed me to let me know that her time in my lab had really meant a lot to her, that she was still pursuing her interest in computer science, and that she was participating in another CS program that summer.
From her next email, a year later, I found out that she had accepted an offer of admission (for undergraduate studies) from a top-20 computer science department.
A couple of months ago, I got an email from my school's K-12 outreach program (which had organized her summer in my lab), informing me that this student had reached out to them to ask if she could volunteer in their programs this summer, while she's back in town.

Working with students can be a thankless task; but the students like the one I described above really keep me going, and make me feel like it is time well spent. I cannot imagine a better way to be thanked.


Can late recommendation letters have a negative impact on grad school application?

Sometimes the deadlines for recommendations are flexible, and the references have some grace time to get them in.  In my department, we are certainly flexible, but we are not exactly inundated with well qualified applicants either.  I think our approach is pretty typical (at least for the sciences and engineering).  However, I have heard of higher ranked schools being more of sticklers for about the deadlines.

However, if the letter is accepted, then when it happened to arrive is totally irrelevant.  The faculty evaluating the applications almost certainly don't even see when the various parts of the application file arrived.  And even if somebody did see that a letter was late, if anyone were to be blamed, it would be the person who sent it in late, not the student who requested it.


Actually, anyone can write you a letter. The best letters are from those who can help a reader evaluate your suitability for a degree and your likelihood of success in it. Usually that is people closest to your studies, but others can also be helpful.

Evaluate what you think each potential writer will say about you. It may actually be good if they say different, but positive, things.

The only letters that might be discounted, I think, are those that might be judged to be biased in your favor for non academic reasons. A letter from one of your parents or siblings, for example.


Test an already existing hypothesis but in a different setting/country?

I think you have a big misconception of what plagiarism is. Passing other people's work as your own is plagiarism; doing something and later discover that it was done before is not. It is not even unethical.

The worst case is that your work is rendered redundant, but this depends on how different your settings and results are.


Is combinatorial novelty without insight useful? Who cares if we're the first to use tool T on problem P?

Is this valuable to science? If so, why?

Because it leads us to understand if tool T works on problem B. How big the "insight" that we gain from this is depends a lot on how different T is to other tools that have already been used on B, or, conversely, how different B is from other problems that T has been applied to.

The range here goes from "it is mind-blowing that T could work on B" all the way to "meh, everybody knew that T would work because we use it all the time for B' anyway" - although I will grant that most works following this schema in practice end up more on the rather incremental side of things.


What are the implications of submitting a paper to be graded and to arxiv preprint on the same day?

No, there are no implications. Professors grading your work don’t care what you submit to arXiv, and the arXiv doesn’t care what you submit for grading. At any university I have ever had experience with, those two things would not affect each other in any way.

But what you did still doesn’t make sense to me. The only type of work that’s suitable for submitting to arXiv is a research paper. And I have never heard of a student submitting a research paper as a class project to be graded - it’s not that that’s not allowed or anything but research papers usually materialize as a result of extended effort that goes outside the scope of work done for a specific class. It would be a bit like submitting a class project that’s, say, five times longer and harder to write than the requirement. You would get an A, surely, but again, for obvious reasons that’s not something you ever see students doing.

(Edit: according to the comments, writing research papers for a class project is not uncommon in some disciplines, or at least may have not been uncommon several decades ago.)

My suspicion is you have some misconception about the benefits of submitting your class paper to arXiv. Perhaps you should rethink whether that’s something that you want to do and/or consult some experienced people about whether it makes sense. But regardless, for your actual question I don’t see any problems for you related specifically to the simultaneous submission to arXiv and to the professor.


Yes you can remove the URL as you have the ISBN number for each book; which is a unique identifier, universally given and searchable.

Note On The Generated URLs by E-Commerce Websites: Also make sure the on the URL you are using. The URL you posted is a generated one from Amazon that has number of variables for marketing purposes.


What reference from current insitution is required/advisable for pre-tenure move?

I don't think any contact with your current department is expected. Generally you are only expected to provide references who will write letters on your behalf, and it's not required that any of them be from your current department. Academic circles are small, and somebody in your department may find out anyway. Hopefully their reaction will be to incentivize you to stay.

When I have been on hiring committees, we never sought a contact within the current department. If you are shortlisted, then the committee thinks you're pretty amazing, so why would they suspect you are being forced out? My experience is with heavily research-focused departments; this might be different, say, at a small liberal arts school.


For a while I was a graduate student in the math department of Portland State University. At Portland State, the Ph.D. program in math requires students to have an "allied area" (field of study other than mathematics). The student's thesis must be related to this allied area, the student must take about 25% percent of their courses in the allied area, and the student must pass a qualifying exam in the allied area. Thus the whole program is designed to be interdisciplinary from the get-go.

(Side note: The actual name of degree is "Ph.D. in Mathematical Sciences", and it definitely differs from the traditional math Ph.D.)


Common for department guidelines/traditions to require tenure track academics rotate courses?

Almost all top research universities also have a teaching mission. Most have an undergraduate teaching mission as well. Some of those have a special faculty track for the lower level courses (Professor of the Practice, say, at Duke), but many also require senior faculty to teach a few courses per year. For some courses it is common for certain faculty to specialize, say the Compiler Course in CS, for example. But, in the absence of specialized track faculty, everyone has to have some contact with undergraduates, even if it is as a coordinator of all the TAs teaching, say, Calculus I.

Eventually junior faculty need to be integrated into this system. Given that the tenure probation period is typically about seven years, only the earliest part of this is likely to be free of teaching responsibilities. But for a new faculty member, it is common enough to get a year without teaching duties and another year or so of teaching easier courses for which a lot of resources already exist. Of course, you can probably request a specialized course as well.

But, in many and I hope most places, the teaching assignments are more or less decided by request and consent rather than being imposed, as long as every course has coverage. An especially collegial place will likely give new faculty first choice (or second,...) of courses, rather than dumping the hard ones on the new faculty after the "plums" are chosen by the senior faculty.

And, of course, in some fields, having extensive external funding can relieve you of the need to teach at all.

But a new faculty member teaching an intro level course will find a bit of shock when they find out there are 500 students in the course and you need to manage 20 or so TAs as well as give lectures.

As to the question of tenure, some places don't care too much about whether you can teach undergraduates effectively provided that you are a superb researcher and can effectively teach grad students and, especially, direct doctoral work. Others will place more emphasis on teaching. Most will also place at least some emphasis on flexibility. How willing are you to "take one for the team" and teach a difficult course? Everyone needs to do this occasionally, of course, and refusing shows lack of collegiality that can lead to problems at tenure time.

But, also, I hope and expect, that most research universities will find ways to "nurture" tenure track faculty and integrate them into the local culture as well as supporting their research goals.


Which is the most accepted measure for an individual's academic productivity?

There is no accepted numerical measure for an individual's academic productivity.  The available measures can sometimes be useful, but they all have serious weaknesses and many detractors.  In particular, there is no widely accepted or safe choice: if you make any public use of a productivity measure, many people will react angrily, no matter which measure you choose (and their anger may well be justified).

Added in edit:  In my experience, citation and publication counts are sometimes mentioned in letters of recommendation, but just as a crude numerical measure, rather than with any serious importance attached to them; most letters do not mention them.  (I've never seen an h-index mentioned in a letter or job application, but perhaps it is more common in physics.)  Hiring committee members occasionally impose minimal numerical standards, but just to rule out inappropriate cases ("we won't consider anyone for a tenure-track job unless they have at least two publications", say).  In the departments I'm familiar with, nobody uses them to choose between serious candidates.  Like Dan C says, they just aren't that useful: they add a small amount of information, with a lot of noise and even systematic bias.


Received an incorrect review from a conference (a review for a different paper). What should I do?

I do not know which AC manages my submission. All I can do is to contact PC.

Therefore...

  Should I contact PC about this before submitting my rebuttal

Yes, or more broadly: use whatever contact information you have for the organizers. There is no point in rebutting an editorial mistake.


Use logo of university in a presentation of work done elsewhere

Remember that the application process is about pitching YOU to the selection committee / other powers-that-be. Part of that pitch is introducing yourself -- and hence using your current uni logo would be appropriate. You should also explain that the work you're discussing was done elsewhere. That is, make sure anyone listening would not walk away with the wrong impression.


Is it immoral to advise PhD students in non-industry-relevant topics in middle-lower ranked universities?

While the question in the title is a good one, your post also makes some assumptions, in some cases dubious, which are really worth investigating first:

But some research fields have little to no industry relevance -- The truth is that almost all PhD research is highly esoteric and specialized, and unlikely to have any direct impact on industry. This is certainly true in my field (computer science), and probably true in many others to a greater or lesser extent. Why, then, do industry hiring managers even care that you got a PhD? Sometimes they don't, but often they value far more the qualities that having a PhD demonstrates, rather than the content of your research. For example: the ability to communicate well and sell ideas, the ability to solve technical problems, and the ability to dive deeply into learning what you do not understand -- these are fundamental skills gained during a PhD that are equally valuable in industry.
What I'm saying is: industry relevance of your PhD research is often not the top criteria for getting a good job; what matters far more is your general knowledge, technical skills, and communication and interpersonal skills.

These PhD students as such often have to switch fields to stuff like data science etc. Data science is a rare case where PhD research in data science appears to be valued in industry; most other PhD fields are not as valued in industry specifically, only generally. Do you suggest that all academics should just start doing data science? I think that would have some positives, but overall be a very sad world only motivated by money, rather than a true pursuit of scientific knowledge.

Many have been better off getting a job right after undergrad and slowly working their way up -- This is absolutely true, unfortunately. But do you also believe that the only good reason to get a PhD is to get a job in industry? That premise is absolutely false. What we can do and should do: raise awareness and encourage people to get a PhD for the right reasons, rather than the wrong ones. If you are thinking of spending 5+ years on a PhD, it should be because you truly want to do it, and you love the research you are doing for its own sake.

To answer your last question:

In such cases, is it immoral to advise these PhD students?

It is immoral to be dishonest: to make the PhD students believe that their research will have direct practical relevance if it does not, or to lead them to expect a particular job in industry when they graduate which may be beyond their expected skillset.
To be sure, some professors are guilty of such dishonesty and immorality.
But no, it is not immoral to advise students in a non-industry-relevant topic, if the expectations are clear and the expected topic is of mutual interest. In fact it is one of the most beautiful and compelling parts of science, that we do not need to be constrained by what is currently practical in industry.


Data Science is still a novel field. Some might dispute whether it actually is a field in ints own right or rather an intersection of statistics, computer science, perhaps linguistics and quantitative methods (quantitative political science, sociology, or finance, econometrics, computational biology...). With the right specialization, enrolling in a program of any of these fields might give you the skills a data scientist needs. There are, however, also new dedicated data science bachelor and master programs popping up left and right. You have to compare several universities' websites to find the one best suited to your needs and interests.


Advisor is unhappy with M.Sc. research results and is showing signs of preventing the student from graduating. What should be done?

This is half of an answer.

Has anybody ever heard of anything similar?

Yes. Conflicts like this unfortunately is not uncommon, judging from what I have observed in only two universities.
Indeed, it appears to be more and more common.

Is there an appeal process that I could take, if I am not allowed to graduate?

Formal appeal process?  Yes. The process varies from department to department. You should be able to find it in your students' handbook.
However, this should be considered as a last resort ---
it is quite unlikely going to work if your goal is to graduate.
Looking at the bigger problem though,
it seems the most straightforward solution is just to work hard and get results that will be sufficient to meet the requirement (publishable). This will certainly solve your problem, and it is likely the most efficient way.
If that's not the kind of solution you are looking for, then first, you need an unbiased assessment of your work to determine if you actually did work that is sufficient for graduation. While you may feel you have done enough, you need to consider the possibility that you are not an expert yet, and your assessment may not be correct.  If you can find another expert who thinks your work is sufficient for graduation, you may have a case, otherwise, I'm afraid there is not much you can do (if your goal is to actually graduate).
I disagree with the first comment, I think it is quite dangerous to start with graduate program director or some kind of ombuds. This would indeed be the official channel, but if you do that, your chance working out a reasonable solution with your advisor will be greatly reduced.


Is it possible to count the citations that a paper has received in a particular country using Web of Science?

WoS allows you to look at all the papers citing a given paper P, and there is a link to "Analyze Results", where country is one of the options. (It defaults to a minimum count of 2; you'll want to drop this to 1)

For a randomly selected paper from a recent search, here's an example:

There are 11 citing papers; of these, seven have at least one US author, two at least one Czech author, etc. This would give a value of 0.64 if your original author was American, or 0.18 if they were Czech.

The obvious downside is that you need to do this for each paper P; you can't do it automatically for a hundred at once. But it's a start...

Edit: you can do this through Scopus as well. Select the paper, find citing papers, "analyse search results", and you get this:

Here, there are a total of three papers citing P, two of which have German author(s), one Austrian, etc.

With Scopus, you can do the analysis for a large group of papers, but it won't help you very much. From your initial search result, select all items using the checkbox, and click "view cited by". Then analyse search results again, and you get the stats for all papers citing one or more of the original search results. However, this won't help answer your question as to %age of papers with overseas citations - they're all bundled together and not segregated by cited paper.


Professor doesn't reply email even after I talked to him?

Wait. As Buffy said, a day is virtually no time at all. The professor may be trying to give others a chance to respond, or may just be busy with other things. While your zeal is admirable, overdoing it will raise red flags. If he invited applications on Monday, I would wait at least until Friday before following up. Depending on the local culture, dropping by his office in person on Friday (or the following week) may be a good idea; otherwise, I would (again on/after Friday) just send a brief e-mail saying that you are still interested and that you hope to discuss the position with him soon.


What are “ad hoc” reviewers/referees for journals?

Ad hoc might be used in the context of conference review where reviews are usually done by the members of a Program Committee and an extra (usually a specialized expert) reviewer is brought in for one or two papers which require careful review beyond the capability or capacity of the PC members. I haven't seen it used in the context of a journal.


Why only medicine lectures are closed to the public?

In the United States, the Health Insurance Portability and Accountability Act (HIPAA) greatly restricts who can see or discuss medical records. While most grand rounds tend to be obscure the patient's identity, there could be an abundance of caution. Note that there is an exemption from HIPAA for grand round presentations -- if the audience are only medical personnel (including students):

The HIPAA Privacy Rule allows physicians and staff to use and disclose PHI [private health information] without a patient's written authorization for purposes related to treatment, payment, and health care operations.  It further defines "heath care operations" to include "to conduct training programs in which students, trainees, or practitioners in areas of health care learn under supervision to practice or improve their skills as health care providers. [Cite]"

The other reason in the United States that grand rounds are often closed is the prevalence of various types of protesters -- e.g. from PETA or from the anti-psychiatry movement.

[That all being said, at my university most of the grand rounds are open unless closed at the request of the speaker or for other reasons. However, they aren't advertised so you would have to be a department member or on the mailing list to know when and where to go. They are also behind the security umbrella of the university, so you would need an ID card to get past the guard at the front door of the building. So whether you call that 'open' is up to you.]


What are the implications of distributing a faculty annual salary over 9 or 12 months?

There may be some confusion here about the difference between 9 and 12 month appointments vs. arranging to have the salary for a 9 month appointment paid out over 12 months.

In the U.S., the typical faculty appointment is a 9 month appointment.  Under this arrangement, a faculty member is required to be present on campus and teaching (and doing research and service) from September through May.  They typically do not have formal vacation or sick leave but in practice can stay home (and cancel classes) if sick.  They can also go on personal travel when classes are not in session.  Faculty don't have to formally request time off as long as they attend to their responsibilities.

In this system faculty do not have to work over the summers, although many faculty do teach summer school or work on research grants and earn additional salary over the summer.  Faculty will also often work on unfunded research projects over the summer.

Many faculty with 9 month appointments choose to have their annual salary paid out over 12 months.  This doesn't create any obligation to work over the summer and has no significant tax consequences, but it is more convenient for household budgeting since summer salary can be quite variable and unpredictable from year to year.

For example, I just learned today that I will be able to earn a month of summer salary teaching a course that starts on June 8.  I'm still waiting to hear if some research funding for this summer will come through.  I've designed my personal budget so that I'm not dependent on summer salary, so I have my 9 month salary paid out over 12 months.

12 month appointments are quite common for academic administrators and some full time researchers.  These typically do accrue sick leave and paid vacation, which has some advantages but also has some disadvantages such as having to explicitly request time off.


What quality do top schools look for, besides normal requirements?

Graduate admissions is very different from undergraduate admissions. A lot of what you may read online about undergraduate admissions does not apply to graduate admissions.

(Traditional) applicants to undergraduate programs are understood to be (generally) young. They haven't had much of a chance to prove themselves yet through meaningful accomplishments. So in undergraduate admissions, it is not uncommon to look for intangible "qualities" that speak to a candidate's ability to be successful in areas that they haven't yet had a chance to prove themselves in. That's just because many highly qualified prospective undergraduate students don't have many tangible achievements (simply due to lack of life experience, not lack of potential.)

In contrast, applicants to graduate programs have more experience, whether academic, life, or professional experience. Prospective graduate students are simply not nearly as "unknown" as prospective undergraduate students. They have had more of a chance to collect some meaningful accomplishments. Thus in graduate admissions, tangible achievements weigh far more heavily.

So while motivation, curiosity, etc. may be useful qualities for a graduate student, admissions committees are interested in what you have done (which may show that you have these qualities). They're not interested in having you tell them what qualities you believe you have.

Sometimes if a candidate lacks academic achievements but has meaningful achievements in other areas (e.g. entrepreneurial), these can help. (That may be what was implied by "you probably have something else in you that's extremely unusual".)


If you have no choice, is it acceptable to translate a recommendation letter for yourself?

Thanks for asking this question.

In light of recent strong comments I have made on closely related issues elsewhere, let me say that I think that getting a letter translated from one language to another is an absolutely kosher academic practice.  The classy thing to do would be to also include the original (e.g. how do you know that the readers will not speak that language?) and also indicate who the translator was.

However, the translator should not be the student.  That is a problem because:

(i) It is an obvious conflict of interest.
(ii) Recommendation letters are often meant to be confidential, and this violates confidentiality.

If you absolutely cannot get anyone other than the student to translate the letter then you should clearly indicate "translated by the student" and expect to have your honesty applauded and the letter largely dismissed.

I must say that my heart opens up for a student who is living in a context where there is no qualified third party to translate a letter into English.  I have been to academic departments in several non-anglophone countries and never encountered such a situation...but of course I have not been everywhere, nor to a random sampling, nor to any academic department in a "third world" country.  That's a tough situation.  Translating the letter yourself does not seem like the best answer.

Let me also say the following: if you are a non-anglophone student whose English skills are far superior to those of the faculty at your university [and assuming that you are applying to anglophone graduate programs, of course!], then you might try to cultivate relationships with anglophone professors elsewhere in the world.  Twenty years ago that would have been preposterous advice, but due to the proliferation of mathematical interaction via the internet, it seems very viable today.  For instance there is a small but positive number of students with whom I have had sufficiently substantial interaction on MathOverflow and (more often) math.SE so that I would be glad to write them a strong recommendation letter.   If you are a math student, you can always try writing to any professor and having mathematical interactions with them.  They are not obligated to respond (I certainly do not always respond...), but they often do (I often do...) especially if you show them something truly promising.

[At some point in the previous paragraph I forgot that I was supposed to be writing for a general academic audience rather than an academic mathematical audience.  But since I am not sure how far my advice extends outside of mathematics, I will leave the m-word in.]

Among US students applying to US graduate programs, it is increasingly frequent for at least one of three recommendation letters to come from the director of a summer undergraduate research experience (REU) than a faculty member at the university.  Such letters are not necessarily the most penetrating -- they read very similarly, perhaps because of the implicit motivation to paint one's summer research experience in a positive light -- but they often get the job done, i.e., they lead to admissions.

Let me also say that a letter of recommendation for graduate admission is not always the most important part of the application.  If I get an application from a university that I have not heard of, and letters from faculty that I have not heard of and whose reputations I do not know, I can only take the letters so seriously no matter what they say.  (And it is quite true that not everyone knows how to write a good "American-style recommendation letter".  This does not necessarily get counted against the student; it just doesn't get counted for them.)  If you are coming from an "obscure program" then your goal is to convince the readers of the applications that your training is equal to (or superior than!) the training that students in more familiar programs get.  So it can be helpful to include very specific information about coursework: e.g. not just the title of the course and the course grade but the textbooks used.  If you wrote a paper which does not make any research contribution but shows a solid understanding of graduate-level material, by all means include that as part of the application.  Also be sure to take all the applicable standardized tests and do your best on them (and don't cheat on them!!).


How will expulsion for physical abuse and sexual misconduct affect a student's future educational career?

This answer assumes the person in question has been convicted of those crimes. If he has not, things will be easier (but not a cakewalk).

The conviction and expulsion will affect him quite significantly, given that some universities require applicants to declare both certain criminal convictions (usually sex, violence, or drug convictions) and any previous expulsions. Trying to hide convictions is a very bad idea.

Sure, you can find a university who does not require a declaration (or will admit the applicant anyway, if the university is sufficiently satisfied that the student has reformed) - the likelihood of such probably varies by country. I suspect life as a graduate student would be very difficult (getting teaching positions may be hard).

This question reminds me of an article I read a while ago. This man was a convicted murderer, and has turned his life around and obtained a PhD in psychology.

Any specific advice would be subject to the laws of his country, the policies of the universities, and more specific details of the conviction (read: off-topic for StackExchange).

There will always be roadblocks, especially with sex and abuse convictions. Repentance and perseverance may clear enough to find a path through, but it wouldn't be easy.


It is not common in my experience (first-language English speaker in the US) to call anyone just "Doctor" unless they are a medical doctor. In non-medical settings, you should always use their surname after the title.

On the other hand, it is OK to use just "Professor", if you are speaking to the person.

So you could ask, "Professor, can I take the exam tomorrow?" But not "Doctor, can I take the exam tomorrow?"

If you are talking to someone else, you should always use the surname, don't just call the person "professor" or "doctor" as if that was a name.


Intellectual Property Assignment Agreements for Ph.D. students - What is normal?

Very roughly, at the US universities I have worked for, the IP policies have been along these general lines:

When you write a paper or book as part of your research, you get to keep the copyright and any royalties.  But the university gets permission to use the work internally, keep a copy in the library, etc.
If, as part of your research, you invent something that's patentable, contact the university's IP office.  They will help you with the patent process.  You and the university will hold the patent together, or some similar arrangement. They have to agree on any licensing agreements, etc (where you sell some company the rights to use your patent), and they get a large share (perhaps half or so) of whatever royalties or fees are earned.

(I'm a pure mathematician, and we never invent anything patentable, so I always skim the patent part and may have got it wrong :-)


How to break this perception that my research trajectory will be almost the same as my research senior’s?

I hate to break it to you, but after a (very) short time in grad school, once you start making a name for yourself, people will predict your trajectory based on how they perceive you are doing right now in grad school, not based on your previous school and certainly not based on a self-assessment of your work ethics. If you have been there for a non-trivial amount of time, and nobody thinks that you will do exceptionally better than everybody before you, consider that this assessment may be more realistic than your rather rosy outlook.

  How to break this perception that my research trajectory will be almost same as my research senior's.

Easy. Achieve substantially more impressive results than your peers in the same career phase. If you can't do this easily, what makes you think you will certainly do much better than them in latter career phases? If you think you have truly impressive results but everybody else in your institution does not agree, your problem is much deeper. Then you are either surrounded by people who can't see your potential and vision, or you are yourself blinded by arrogance and can't see when you are wrong. Both of these options are pretty bad.


Is it possible to do a Masters dissertation at a different university?

You need to consult your university regulations as well as your department for advice on this. My gut instinct would be that it should be possible, but you need to make sure you follow the appropriate rules. I can just about guarantee that you'll need to find someone at your home university who will be willing to act as the "internal" supervisor for your thesis.

However, the possibility of being able to do it and actually surmounting the obstacles and being able to do it are quite different. It can be very hard to get another research group outside of your "home" university to be willing to take you on short term as a master's student—primarily because they probably have no idea who you are, and how reliable a student you will be. Nobody really wants to take a risk on a completely unknown quantity based on a "cold call" email.

So your best bet would be to work with the faculty in your department to find somewhere else to do your research.


What kind of Visa is required to work in Academia in Japan?

This might help or this. Here is the crux of the information:

The period of stay is quoted as 3 years/1 year with the following documents needed:

Passport
One visa application form (nationals of Russia or NIS countries need to submit two visa application forms)
One photograph (nationals of Russia or NIS countries need to submit two photographs)
Certificate of Eligibility (Note) - the original and one copy

This visa applied for Long-term stay for the following occupations:

Working visa: professor, artist, religious activities, journalist, investor/business manager, legal/accounting services, medical services, researcher, instructor, engineer, specialist in humanities/International Services

The algorithm for obtaining the visa is given on the first link I added.


How to improve self-learning as a PhD student?

During my Ph.D. studies I had to do exactly that: balance my time between learning specific examples and learning where and how to find these examples without wasting too much time. In my case, I did not have that much guidance from my supervisor (he let me be pretty independent) and on top of that my topic was interdisciplinary. Due to the latter, there were gaps in my learning that I had to fill, and taking 20 ultra-specialized courses was not an option because of the time constraint (I had to finish my PhD within 4 years and also publish some papers in that time).

From my experience, a top-down approach is the most effective one. It sounds like you started reading a very specialized paper; try reading something more broad about the subject, ideally a tutorial/video/article/book chapter with emphasis on applications (since you mentioned you need to apply a method to your own work) that will give you a good overview in a shorter amount of time. Then, not only you will gain more insight as to which method is the appropriate one to use in your research and can devote more time to it, but you will also have kept in the back of your head the other ones, in case conditions change and you need to switch methods. Online courses (MOOCs) are a good source of information, as you can adjust them to your time schedule and often are not a semester long but rather a few weeks. I am sure you can find something on what you are looking for on www.edx.org and/or www.coursera.com.
Communicate with people around you. This is crucial. If you are not already in an environment where knowledgeable people are available, put in the effort to find one. Look up people and email them; most of the time professors are passionate about helping out students. I was lucky to have an office one door down from a retired professor, who had time to talk and share his expertise and advice - some insights are difficult to find in books.

Try to get creative with your learning - never is one source enough, try to diversify. It is easy to become overwhelmed by the information, so be organized, take notes, and try to be aware of what you are learning and how it fits in your purpose, with a calm mind. Take breaks when you feel overworked (trust me, this comes from experience).

From the organizational viewpoint, I think sketching out objectives every month or week, and then preparing a summary of what you learned and how it applies to your research (like a progress report) helps a lot in seeing the big picture. You don't want to get carried away too much reading about things you won't use. Of course, that's inevitable, as it is part of research - it is part of navigating in the vast realm of knowledge, sometimes you end up sidestepping.


Help! Professor/Advisor Refuses to Publish Any of His Students' Research

First, this is not an unusual situation.  What is unusual here is your interpretation of the situation.

When you have a problem with someone's behavior, it is wise to look for incompetence instead of malice.  It's highly likely the professor intended to keep his promises but failed to do so.  You have given us no evidence otherwise.  Professors commonly break promises to submit papers.  Some of them do so over and over without realizing there is a pattern.

Your best strategy here is to politely remind the professor of the missed deadline and press for a new deadline.  Repeat this process as many times as is needed.


How can you argue that your leading publication venue is important?

I have been told by our head of department that those on the promotions panel will never have heard of FOCS, STOC and SODA and so this will just be compared with the number papers people publish in any other venue.

I find this stance outrageous.  It is the promotion committee's responsibility to understand—at least at a high level—the publication landscape in the fields in which candidates publish.  Moreover, if the committee is outside your department, it is your department chair's responsibility to educate the committee on the publication culture in your field.

Aside from the conference rankings that Henry mentions, there are other less official rankings of CS departments or just theory groups, based on publication output weighted by prestige.  (The rankings themselves should not be taken seriously, but they do provide a window on what the community thinks of the conferences.)

Another method that might be helpful is to gather evidence about where strong theoreticians actually publish.  Select a handful of successful theoretical computer scientists in top CS departments and show the committee where those people publish.  To pick out a few random DBLP pages off the top of my head: Avrim Blum, Chandra Chekuri, Satish Rao, Santosh Vempala.  Choose whatever experts you consider to be your aspirational peers in your subsubfield.

Alternatively, bypass the "prestige" question and argue directly that your work is strong.  I assume you are provide the review committee with a research statement.  That statement should provide direct evidence that your work is important, visible, and highly regarded.  How often is your work cited, and by whom? (Only your subsubsubfield, or a broader set of researchers?)  What followup work has it inspired by other researchers?  What do other people's papers say about your work or the problems it addresses?  Have you received any research awards (for example, Best Papers or an NSF CAREER) or more indirect accolades (for example, invitations to program committees, journal editorial boards, or Dagstuhl workshops)?  Are you in Oded Goldreich's list, or in David Eppstein's annual top 10?

I'd also recommend asking your department head whether the pre-letter evaluation is merely a sanity check, or if it has real teeth.  My university's promotion process includes a preliminary stage, where the Promotions and Tenure Committee decides whether to request recommendation letters, or not to put the case forward at all.  But at least for tenure cases, this stage is essentially pro forma; a decision not to request letters requires a compelling case for failure.

If that's not the case at your institution, I'd strongly recommend pointing the committee to CRA's Best Practice Memo on Evaluating Computer Scientists and Engineers For Promotion and Tenure.  In particular:

  The primary direct means of assessing impact —to document items (a) and (b) above —is by letters of evaluation from peers. Peers understand the contribution as well as its significance.


Would my paper get rejected if the related work section takes up too many pages, and what would the optimal maximum length for this section be?

If the papers were suggested by the reviewers, there are high chances that those papers were from "reviewers" and they wanted to increase their cite count.

In my experience (non IEEE Access), I cited those papers and the paper got accepted. No need to cite additional papers (OTHER THAN THOSE OFFERED BY THE REVIEWERS). I think because the contribution you made was based on your prior study of literature and it should suffice.

If you think that few papers SUGGESTED BY THE REVIEWERS are not under the scope of your research, simply explain politely that "We found paper XYZ to be out-of-scope of our current research and could not fit into our paper. However, paper XYZ-2 did shared some interesting ideas. We have included a detailed discussion on this in Section ABC"... and


The issue here is not "laziness"; the real issue with reusing figures from the literature is that, without appropriate permissions, you do not have the right to do so.

If you reuse a figure in the literature without the appropriate permission from the rights-holders, you are effectively stealing their work, which is not allowed. Therefore, you need to make sure that you have gotten the right to use the figures, and have the proof to back it up if challenged. Normally, for scholarly works such as theses, such rights are routinely granted and cost-free. However, you need to check with the publisher (or author of the paper, if she holds publication rights) before using the figure. Then, next to the figure you are reproducing, you'll need to have a statement such as "Figure reprinted by permission of X," where X is the person or institution authorized to grant reproduction rights.


Postdoc using current university's letterhead for job application cover letter (academic/national lab jobs)?

Yes you should use your current institution's letterhead. It is important to do so because much of academic hiring turns on prestige and snap judgments. Look professional, look serious, look affiliated with a prestigious place. Use the letterhead.

Edit in response to Nate Eldridge in the comments below:

First, letterhead is to be used in correspondence that constitutes official university business. If helping postdocs and PhD students obtain the positions for which the University has trained them doesn't constitute "official university business," I don't know what would. (Certainly I am instructed to send my undergraduates' letters of recommendation on official university letterhead.)

Second, consider two scenarios. Scenario 1, you apply for a position along with 99 other people. You put the cover letter on letterhead and the other 99 applicants don't. Scenario 2 is flipped, the 99 use letterhead and you don't. In both scenarios, you stick out, which is in general bad. However, they aren't equally bad. Scenario 1 is like showing up to a wedding in a Tux when everyone else is wearing suits. You're a little fancier than you need to be, but nobody's going to think you just weren't putting in care or effort in. Scenario 2, on the other hand, is like showing up to a wedding where everyone is wearing a suit in a shirt and flip flops; you look like you just didn't care what the convention was. So, even if both scenarios were equally likely, I'd still say err on the side of using the letterhead. However, it isn't the case that the scenarios are equally likely--the convention (at least in the US, I'll let others comment about the European or other conventions) is to use letterhead. I'll cite Karen Kelskey, the job market consultant, to corroborate this final point.

I'd hope that no department would allow a faculty who was daft enough to hold the use of letterhead against a candidate anywhere near a search committee.


What university affiliation should a retired member of staff use?

One can be affiliated as an independent researcher and acknowledge the usage of university library. One is a retiree of that university.


It is not unheard of. For a journal that I submit regularly to the instructions for authors state

  Given that the Journal has been in existence for over 80 years and has
  published of the order of 35,000 papers on a wide variety of
  acoustical topics over its lifetime, the absence of any references to
  previously published papers in the Journal raises a flag signaling the
  possibility that the paper lies outside the de facto scope of the
  Journal

I think it really is a scope question and not a self citation question. That said, the handling editors of this journal often alert authors during the later stages of review of potentially relevant in press publications within the journal. Most have been relevant and I am happy to add the sentence or two to the background, but I also think of it as a clear attempt at increasing self citation counts.


How much research experience do US grad schools really expect from an undergraduate CS student?

The general answer to your question is, there are no expectations per se. Although your question is phrased in terms of undergraduate research, your explanation focuses mostly on visibility in the form of publications. By parts and based on my own experience:

Undergraduate research: This is highly desirable, importantly because it's the best way to get an in-depth letter of recommendation. Letters are the most underestimated factor in admissions by students. The difference between a letter from someone we know describing at length your qualifications and a letter essentially re-stating that you got an A+ in a large class is very significant. Another reason why undergraduate research may be important is because it may give your statement of purpose more focus. Last but not least, it's always desirable to get a student that knows what he/she is getting into and that can hit the ground running.
Publications: If you have a publication in a top-tier venue, that is of course an excellent thing to have. A publication in a low-tier venue won't count for much by itself; its significance will depend on, you guessed it, what your adviser's letter says about your contribution.

Ultimately, I think the questions you want answered are:

Will someone with undergraduate research experience and a very strong package (including letters of recommendation), but no publications, be competitive in CS? My answer is Yes.
Could such an applicant lose over someone identical but with some low-tier publications? My answer is, these two applicants would probably be considered essentially equally.
Alternatively, could such an applicant lose over someone identical but with one or more publications in top-tier venues? My answer is Yes, IF they are competing for a single spot--which is unlikely. Also, such kind of applicants are not at all the norm in my experience (which could vary by area).

In any case, it probably can't hurt for you to engage in research that aims at publishing at a top-tier venue: When you shoot for the moon, even if you miss it, you often end up among stars.


Would citations in blogs, public materials, arXiv and magazines increase citation count for the author?

Scopus counts only peer-reviewed articles.

What Google scholar counts is less clearly defined. Intuitively, if something looks like an academic source, then its citations are counted. This means that arXiv is definitely in. I've seen slides for talks hosted on academic webpages being counted, but not in a very consistent manner. I would suspect that most blogs don't count. Mathoverflow does not count.


If I accepted an admission and funding offer before April 15th, is it considered unethical to rescind if before April 15th

The Council of Graduate Schools's April 15th resolution clearly lays out the obligations of students, and notes that a decision made prior to April 15th can be rescinded if the student gets a different offer, so long as it is done in writing.

  Students are under no obligation to respond to offers of financial support prior to April 15; earlier deadlines for acceptance of such offers violate the intent of this Resolution. In those instances in which a student accepts an offer before April 15 and subsequently desires to withdraw that acceptance, the student may submit in writing a resignation of the appointment at any time through April 15. However, an acceptance given or left in force after April 15 commits the student not to accept another offer without first obtaining a written release from the institution to which a commitment has been made.


How often do authors send their paper by email upon request?

Cambridge did a limited survey on this, based solely on requests that came via the repository (so not by direct email). They found that:

38% had the author send the paper directly via the repository
4% of requests were explicitly denied by the author

This leaves 56% unknown. A later followup survey of authors who didn't use the repository response function suggested that about a third went on to contact the requestor directly, suggesting an overall success rate comfortably over 50%.

(As an aside: the repository I manage involves us forwarding such requests to researchers, and we have no "click to send a copy" function, so I get cc'ed on a large number of the replies. Counting only the cases where the author is still around, I would estimate that over two-thirds get a copy of the paper, and it's quite common to see replies that amount to "hi, here's the paper, here's also a few others that look relevant to what you're interested in". I don't have solid figures on that, but given that my academics are fairly similar to theirs, it leads me to suspect Cambridge's success rate may be higher than they expect.)

Interestingly, the Cambridge repository data suggests that about half of requests are for material that is simply not available yet - it's listed on the repository on acceptance, but not yet published online by the journal - and so there is the complicating factor that some authors were reluctant to share the paper "before publication". This would of course not be an issue for people contacting the authors of a published article, which by definition is already out there.

There was no data on academic/non-academic email addresses in the Cambridge survey, but purely from anecdotal observations in my own repository, I would say a) academics will often write a more engaging request ("I am doing some work on X and would like to see the data on Y which I think is relevant", rather than just saying "research" or giving no reason at all), which is probably more likely to encourage a response; and b) in a lot of cases, people will state an academic affiliation but use a private (or not-obviously-academic) email address. This is true for both researchers and students.

[edit: I checked today. Of the last twenty requests, 12 used an academic email address, 7 were apparently from academics (or students/researchers) with a non-institutional email address; only one was clearly from a non-academic]

This is all repository-based data. Direct emails to authors may have different response rates, but I suspect this is the most effective wide-scale monitoring approach we have without a (rather invasive) experimental campaign...


Impact of slide quality on student learning

If you're refactoring the course, consider moving away from a mostly lecture-based approach towards more active learning. There is a lot of evidence out there to support the effectiveness of active learning techniques (if used correctly). To paraphrase What Is the Impact of PowerPoint Lectures on Learning? A Brief Review of Research: "PowerPoint or slightly better PowerPoint?" is a less important question than "How can I
adapt my lecture course for active learning?"

Having said that, there is some evidence that slide design based on principles from multimedia learning research can have a positive effect on student learning, compared to slides that violate those principles.

For example, in engineering:

  [We] compared learning
  outcomes in 110 engineering students who viewed a technical presentation in which the slides either integrated or violated
  six multimedia learning principles. The presentation slides that adhered to the six multimedia principles followed the
  assertion-evidence approach, while the presentation slides that violated the six multimedia principles followed commonly
  practiced defaults of PowerPoint. Essay responses from the 110 engineering students revealed superior comprehension and
  fewer misconceptions for the assertion–evidence group as well as lower perceived cognitive load. In addition, stronger
  recall occurred in this assertion–evidence group at delayed post-test. These findings support the use of the assertion–
  evidence structure for presentations in engineering education

Source: Garner, Joanna, and Michael Alley. "How the Design of Presentation Slides Affects Audience Comprehension: A Case for the Assertion–Evidence Approach." International Journal of Engineering Education 29.6 (2013): 1564-1579. (PDF)

Here's another example, from medicine:

  Methods: A pre-test/post-test control group design was used, in which the traditional-learning group received a lecture on shock using traditionally designed slides and the modified-design group received the same lecture using slides modified in accord with Mayer’s principles of multimedia design. Participants included Year 3 medical students at a private, midwestern medical school progressing through their surgery clerkship during the academic year 2009–2010. The medical school divides students into four groups; each group attends the surgery clerkship during one of the four quarters of the academic year. Students in the second and third quarters served as the modified-design group (n = 91) and students in the fourth-quarter clerkship served as the traditional-design group (n = 39).

  Results: Both student cohorts had similar levels of pre-lecture knowledge. Both groups showed significant improvements in retention (p < 0.0001), transfer (p < 0.05) and total scores (p < 0.0001) between the pre- and post-tests. Repeated-measures anova analysis showed statistically significant greater improvements in retention (F = 10.2, p = 0.0016) and total scores (F = 7.13, p = 0.0081) for those students instructed using principles of multimedia design compared with those instructed using the traditional design.

Source: Issa, Nabil, et al. "Applying multimedia design principles enhances learning in medical education." Medical education 45.8 (2011): 818-826. (PDF)

and there were also long-term effects:

  Results:  Findings showed that the modified condition group significantly outscored the traditional condition group on delayed tests of transfer given 1 week (d = 0.83) and 4 weeks (d = 1.17) after instruction, and on delayed tests of retention given 1 week (d = 0.83) and 4 weeks (d = 0.79) after instruction. The modified condition group also significantly outperformed the traditional condition group on immediate tests of retention (d = 1.49) and transfer (d = 0.76).

Source: Issa, Nabil, et al. "Teaching for understanding in medical classrooms using multimedia design principles." Medical education 47.4 (2013): 388-396.

A third example:

  To measure the effect of a multimedia design principle adherent PowerPoint presentation on test item performance, student satisfaction, student confidence in potential exam performance, and classroom dynamics.Two versions of an identical lecture were presented in different formats over subsequent years (2011, 2012, and 2013). One with traditional PowerPoint slides and the other redesigned to comply with multimedia design principles. Student scores on identical exam items were compared and a voluntary student survey was used to evaluate the activity.Students performed statistically better on identical exam items, were very satisfied (mean = 7.4 of 10) with the redesigned PowerPoint format, confident in their potential exam performance, and a majority (66%) wanted to see pictures and narration more often.Students may retain information better when presented in a multimedia design adherent format. Student reaction was positive and indicates that students may prefer this method to traditional PowerPoint slides.

Source: Pate, Adam, and Savannah Posey. "Effects of applying multimedia design principles in PowerPoint lecture redesign." Currents in Pharmacy Teaching and Learning 2.8 (2016): 235-239.


Does PhD acceptance depend on my current MA's completion?

We can't know for sure, though if the letter of acceptance did not state anything to this effect, then you're probably good. Generally, acceptance is predicated on having completed a bachelor's degree, which I take you already have. Having finished a MA is generally considered a plus, but mainly because it allows the selection committee to see your grades at the grad school level -- whether or not you actually complete the degree may in fact be secondary.

The only way you can find out for sure is to write to the graduate director of the school you got accepted at. If they do care, they'll check on your degree completion when you get there and will find out -- so knowing earlier is better for you. If they don't care, then it doesn't matter one way or the other. So I don't see a downside to just asking.


Getting back into academics after an industry stint: what can I do while still in industry to improve my research profile?

I also took roughly 2-3 years "off" from academia to work in industry before starting my PhD (not computer science related). I actually think such stints are useful if you frame them in a certain way. You could talk in your statement of purpose about your journey to applying to the PhD, including why you went into industry after the Master's degree instead of continuing to the PhD. Many students struggle in their statements to convey why they wish to obtain the PhD and/or why they feel that they can ultimately finish the degree. In your case, you can talk about going into industry to figure out whether you truly want to go back into academia (the "if you love it, let it go" approach), and then talk about how what you're doing in industry directly applies to what you wish to study. I think many programs would welcome such an application.

I'm less familiar with what 8.8 means, so I cannot comment on whether this is a detriment or not. Having no publications after completing a Master's degree and 3 years post-Master's degree may be a weak spot that you should address in your application. At least in the U.S., graduate admissions can be influenced--sometimes heavily--by personal connections. To that end, I would recommend contacting potential PhD supervisors very soon to introduce yourself and inquire about any openings s/he may have for PhD students. It does take a non-trivial amount of time, but I do think it's worth it.


Why do faculty use the software "Blackboard"?

Blackboard is used by the university I teach at and I used it at the university I studied at -

Blackboard (BB) is mostly uniform. While you can customize your courses, to an extent, a student moving from one course to another using BB will already know where everything is. BB is simplistic and students have different technical abilities.

Having each instructor learn HTML is a large order. I teach with an 80-year old man who still has a flip phone and can barely use that. Contracting someone to create the webpages would also be an issue because costs and instructors changing the courses that they teach may want to change the webpage.

BB also has (at least where I studied and teach) a copy checker. If a student from Z class uploads the same paper to both Z and Y then when they upload it to Y the instructor is told that there is a paper within the servers (goes back 2-3 years I believe) that is x% similar to a paper submitted in course Z.


How serious of a mistake it is to accidentally addressed a grad school admissions director as Miss instead of Ms?

I doubt it makes a big difference.
In general, the honorifics "Miss" and "Mrs." are considered obsolete in professional and academic settings, as marital status is not considered relevant (besides the sexist aspect that there has never been such a distinction in honorifics for men).  They should not be used unless someone specifically requests them.  "Mr." and "Ms." have been the standard gendered honorifics for some time, and "Mx." is coming into wider use as a gender-neutral alternative.
However, I think people realize that these distinctions may be missed by speakers unfamiliar with the language and culture, so I don't think serious offense is likely to be taken.  If you like, you could write a very brief followup email saying something like "I'm sorry, in my previous email I meant to write 'Ms. X'".
(In general, also note that people who hold a faculty position or a doctoral degree are likely to prefer to be addressed as "Prof." or "Dr." respectively.  When someone has both, there may be local customs preferring one or the other, but either should be acceptable.  English does not use both titles together.)


Should one put their Master's thesis online?

Every document is, in the way you define it, immature. With everything you write your writing improves. Your papers will not be better because you have a degree. They will be better, because you learned something (i.e. made mistakes) before.

However, there might be reasons not to publish your thesis, but it is not so different from normal working papers. Maybe your thesis is just bad, you did not get any meaningful results, you have made significant mistakes, etc.

So if your university allows, publish it online if you want to (or if you think it may be worth reading / you can not think of a good reason not to); everyone knows, it is only a master's thesis and will read it in a different way than they would read a published paper (or not at all).


How to make my research productive when my advisors don't give me constructive feedback?

I'm afraid you may not be perceiving the value your advisors offer in the form of these questions. They are prompting you to resolve ambiguities and to put your project on a solid footing. Rather than telling you what to do, they are providing a more abstract kind of help: identifying matters that you should address. This is no less important to your project.

If they think you are making a poor use of time, then share with them the questions you are actually trying to answer. You just need a consensus on what to work on.


Visualising connections between scientific papers

Not sure if there is a good way to visualize the connection between the references that I am aware of. However, a good way to manage and organize references is using the free tool called Zotero (https://www.zotero.org/) where you can create tags, directories and subdirectories. So, may be using these you can group similar references into one category. It also has plugins for all the popular browsers and also a standalone version, so you can pretty quickly import references and build your library and it also supports all the popular formats for bibliography. There is also an online account that you can create to manage your library over the cloud.


What is a "normal" teaching load for a Lecturer in a UK pre-'92 University?

I can only answer for biological sciences:

Universities will have something along the lines of a "Workload Allocation Model" system for dividing up work. Under our departments accounting you get 3 hours prep time for every formal teaching session you give, plus 20 minutes for every exam script you mark. Tutorials don't count as "formal teaching sessions" and so get no prep time.

For for example a 10 credit module, with 18 lectures,  and 2x 3 hour practicals for 50 students would get you an allocation of 100.5 hours.

A full time contract is ~1600 hours, so a 50% teaching load would be 800 allocated hours. However:

50% teaching load would be unusual - the normal split is 40:40:20 teaching:research:admin
There is generally an (informal) recognition that prep takes longer for new hires than for old hands.

A common load for a lecturer would be very little in the first year, perhaps one module in the second, rising to around 30-40 contact hours a year once you pass probation (about 4 times the above, if you had the same mix of lectures, practicals and tutorials), and then rising again to a "full" load of around 120 contact hours as you become more senior/part of the furniture.

There is obviously a massive variation in this. If your research goes really well you might never rise above the ~40 hour category, while some of us can teach things the department desperately needs, but no one else can teach, and so have to do more.

For example, I was on a full load of 120 hours within three years of arriving (which was unusually large). My experience of this sort of load is that if you do the teaching well, then you are basically a full time teacher during term time. This makes securing the grant you'll need to pass probation difficult to say the least. While semester is in full swing I only really have time to meet each of my mentees once a week (note that supervising postgrad students counts as research not teaching) and run my lab meeting and journal club on top of my teaching and admin duty. I then concentrate on pushing my various research projects along properly during the vacations.


How to stop weird labmate from staring at me doing experiments without damaging work relationship (too much)?

It's more of a comment, but I just want to voice that in my teaching career, I did encounter a couple people with these traits and they do have what we called Autism spectrum disorder (ASD). I am not diagnosing OP's colleague, but I'd like to suggest this possibility, and we should be mindful that it may not be fair to assume the person of question can fully function socially.

After talking to faculty and doing some homework searching for resources, what I found useful was i) talk to the person privately about your expectation, and ii) be direct, don't use social hints. In many ways it's not that different from what other users suggested you to do, but I'd just like to add another point that sometimes some people can appear to be rude because they don't know it's rude, not because they are rude.


Can a Peer-Reviewed Article Claim Novelty in Something Introduced in a Preceding Phd Thesis?

Of course, they can claim novelty -- and of course, this would be not true. It would also not be true if you published e.g., in a blog. (And of course, if they are aware of the thesis, they are not behaving ethically.)
However, if your PhD thesis is not very visible (most thesis are not), it could be that they are not aware of the thesis and the referee is also not. Most likely, you cannot do much then afterwards to change the claim in the paper -- if you are very lucky, the writer posts some kind of erratum on their homepage.
Many peer-reviewed papers were forgotten and ideas rediscovered afterwards. Of course, this could also happen with a PhD thesis.
Wouldn't it be a strange world if it was okay to take theorems out of a PhD thesis and claim them to be one own's theorems?


is it ethical to publish the same paper in a conference proceedings and a journal?

In computer science, the typical rule of thumb is that a conference paper may be 'upgraded' into a journal paper with at least 30% new material.  Certain subfields and other related fields covered by the IEEE may have different standards, however, and ultimately, the standard for this particular conference/special-issue pair is whatever the organizers have decided it is.  Since a 3 page paper is a very short form, though, the full manuscript will almost certainly be reasonable to submit to a journal.

It may not, however, be appropriate to submit to this special issue. Special issues associated with conferences are sometimes open submission (in which case, you can probably submit immediately), sometimes open to extended versions of any accepted papers (in which case, you need to wait to see if your paper is accepted), and sometimes only for a select set of invited papers (in which case, you need to wait to see if you are invited).  The organizers should have posted this information on their site: if they have not, you can email them to ask.


PI puts up a "facade" of great research, but doesn't support real academic work. Is this common? How to recognize this kind of situation?

In this question, I see two separate issues: First, you have the impression that you fell for someone similar to an "academic con-artist". Second, there is a conflict of goals between you and your supervisor. Your question is worded in a way that emphasizes the first issue, but in this answer, I want to make the point that it would be more productive to focus on the second issue.

Let me summarize the situation from my perspective. Your goal is to make an academic career, and for this goal you (reasonably) strive to produce work that gets published at top-level conferences. Your supervisor's goal, however, is to establish a new research direction which may or may not ever pan out to be of interest to top-level conferences. Since these conflicting goals seem impossible to reconcile, it is clear that you need to change your supervisor.

Since you don't want to wind up in the same situation again, you're wise to ask how can avoid that in the future. By focusing on your goals, this question becomes almost self-answering: Choose an advisor whose goals are easier to align with yours. The ideal advisor would be one who lets you work on a topic where he has recently published papers in top-level conferences.


Why do people buying things for UK universities have to pay VAT?

Its not technically true that companies can reclaim VAT. What they can do is offset the VAT they've collected from their customers that they would normally have to send to the government by the amount of VAT they have paid on goods they have bought.

Universities do not sell any VAT chargable goods or services, and so have nothing to offset.

From the HMRC (https://www.gov.uk/vat-businesses, my empahsis:

  VAT-registered businesses:

  must charge VAT on their goods or services
      may reclaim any VAT they’ve paid on business-related goods or services

  If you’re a VAT-registered business you must report to HM Revenue and Customs (HMRC) the amount of VAT you’ve charged and the amount of VAT you’ve paid. This is done through your VAT Return which is usually due every 3 months.

  You may want to appoint an agent to deal with HMRC on your behalf.

  You must account for VAT on the full value of what you sell, even if you:

  receive goods or services instead of money (for example if you take something in part-exchange)
     haven’t charged any VAT to the customer - whatever price you charge is treated as including VAT

  If you’ve charged more VAT than you’ve paid, you have to pay the difference to HMRC. If you’ve paid more VAT than you’ve charged, you can reclaim the difference from HMRC.

As the amount of VAT "you've charged" is zero, no VAT money changes hands either way between government and universities.

There are exemptions for some, but not all charities. Genreally you have to be selling medical or medical reserach supplies, things related to charitable advertising, and goods/services for disabled people to be allowed to not charge VAT.


Why do some US states have multiple universities?

Your question seems to assume the default is for all campuses to be the same, but there's no reason for this to be true.  For example, the UC schools are far more research-oriented than the Cal State schools.  There's nothing wrong with that: California wants to have some public research universities, but that doesn't mean every public university should be a research university.  That would be extremely expensive, and the net result would be either more research than the state wanted to fund or fewer universities.

There are many ways universities can vary (degree of research focus, graduate and professional programs, selectivity and prestige, etc.), and by default they will be different.  This is typical in U.S. states, not just limited to California.

  It'd be easier for the students, as they now wouldn't have to go through a transfer application process just to go to a different state-run campus.

That's not generally true, and indeed you can't easily transfer between UC campuses.  From this perspective, California doesn't have two public universities, but rather dozens of them.  It would require massive changes to make easy transfers work in practice, because some locations are far more popular than others and would be terribly overcrowded if everyone could transfer wherever they liked.


Open Lab Notebook in early postdoc career, advantages vs disadvantages

I really like that you put 'scientific visibility' on top of the list. That is one side of open notebook science (ONS) that is often overlooked. Also, one thing I would like to add to the pros part of the list is how ONS really facilitates collaboration between researchers. If you are going to keep several projects going and collaborate with different groups, then I think you'll find ONS really helpful.


Are there any Books/Guides to developing researching skills for academia

These are things I found useful
I don't have enough reputation for links, but you will be able to find them

Standalone articles/talks/papers/blogposts:

You and Tour Research by Richard Hamming
http://www.cs.virginia.edu/~robins/YouAndYourResearch.html

10 Things You Should Know Before Starting A PhD from Next Scientist
http://www.nextscientist.com/graduate-school-advice-series-starting-phd/
especially the point that your job is to write papers

The care and maintenance of your adviser by  Hugh Kearns and Maria Gardiner

The illustrated guide to a Ph.D.by Matt Might

Advice books for scientist

Advice for a Young Investigator by Ramon Cajal, Old but good and everything written there is still relevant. Mostly about important mindsets, personality traits and skills for success in science. It's good to realize that in 1897 common concern of new grad students were that The most important problems
are already solved.

Crafting Your Research Future: A Guide to Successful Master's and Ph.D. Degrees in Science & Engineering By Ling and Yang, Has very concrete guides for finding a research gaps, branding yourself, reading papers etc

Books not necessarily for scientist

So Good They Can't Ignore You by Call Newport, about developing valuable skills

Valuable blogs

Next scientist

Matt Might

Thesis whisperer

Fumbling Toward Tenure


Use cases of org-mode as a scientific productivity tool for academics without programming needs

I use Org-mode and AUCTeX (Emacs LaTeX package), to do all three tasks
you outline.  I have an Org folder that I sync across machines using
Dropbox, which I find to be a simple solution for someone who does not
use version control on a regular basis.

Organization

I separate my tasks into broad groups with each group getting its own
.org file.  For example, I have .org files for administrative tasks,
journal publications, service, research topics, and any major projects
that I am currently working on.

The structure of an .org file is relatively simple, for example a file to
track journal submissions, revisions, etc. may look something like this:

* Initial Submissions
* Accepted
* Rejected
* Revisions
* Book Chapters

Org-mode uses asterisks to denote levels of headings, and <Tab> to
fold and unfold the headings.  So expanding the revisions heading would
lead to:

* Revisions
** Paper 1
** Paper 2
   DEADLINE: <2012-05-04 Fri>

You can set deadlines for any task by pressing C-c C-d, which will
generate the the DEADLINE: line you see above.  Setting a deadline for
a task will make the task show up in the agenda view (accessed through
C-c a a), which is my main project planning tool for day to day
work inside of Org-mode.

You can also track the time you spend on tasks with C-c C-x C-i,
which will clock you in to a task and C-c C-x C-o, which clocks you
out.  The tracked time will show up in the agenda view and can be
useful for project planning or reporting.  You can also generate
separate standalone tables inside your .org files if you prefer a bit
more customization.

All of this can be done with a vanilla Org-mode install and no
customization.  I have my tasks set as multi-state TODO lists that I
can cycle from TODO->STARTED->WAITING->DONE->CANCELED.  I have my
keywords set in my .emacs configuration file with the following:

(setq org-todo-keywords
       '((sequence "TODO" "STARTED" "WAITING" "|" "DONE" "CANCELED")))

The "|" separates in process keywords from finished state keywords.
If you are looking for more elaborate reports, such as Gantt charts,
my answer to this question briefly discusses some of the options
available.

Outlining

For outlining and writing long documents, you can just create a new
.org file and outline using the * heading approach.  Org-mode makes it
easy to move headings around if you want to restructure your document
at any stage.  For example, if you had this outline:

* Intro
* Part 2
** Part 2a
** Part 2b
* Part 1
** Part 1a
** Part 1b

You realize that Part 1 should really come before Part 2 so you move
the cursor to the Part 2 heading and press C-<down arrow>, and Part
2 and all of its subheadings will move to the proper position.

* Intro
* Part 1
** Part 1a
** Part 1b
* Part 2
** Part 2a
** Part 2b

Depending on your needs, writing a paper based on the outline can be
done in much the same way.  Org-mode has support for LaTeX, both for
inline fragments and for environments.  Since you mention LyX, I would
imagine the transition to stand-alone LaTeX should not be too onerous.  The Org-mode LaTeX export does a fairly good job but if you have a document with a significant amount of LaTeX syntax, it may be better to just write the draft in LaTeX using AUCTeX, but this is beyond the scope of the question.

Reference Management

I use a combination of Org-mode and RefTeX (available with AUCTeX) to
manage my references and to make notes.  As mentioned in John
Moeller's answer this takes some non-trivial configuration.  I used
this setup almost verbatim to start my reference management, and I
have found that it works well.  This link was inspired by the same setup and may be useful for both reference management and writing drafts in Org-mode that contain extensive references.

I start with a master .bib file, that contains the bibliographic
material for each reference.  After adding updating the .bib file, I
use C-c ) to insert a new heading into my notes.org file.  The
customization will generate a heading with the title of the paper and
a link to the PDF of the paper.  For any notes I take on the paper, I
can use the rest of Org-mode's abilities to either have multi-heading
outline style notes as subheadings, or just write paragraphs separated
by a blank line.  The end result is an .org file with headings for
papers, textbooks, etc. and subheadings for each paper with links to PDFs and all my notes in a single file.

Tips for Starting Out

There are a few ways to help smooth the way to working with Emacs,
Org-mode, and AUCTeX.

Install Emacs 24 pretest instead of Emacs 23.  Emacs 24 has package
management included in the vanilla install which makes it much
easier to add packages without a lot of programming experience.  It
also has Org-mode included in the default install.  This link gives
instructions for a variety of operating systems.  I have been using it for awhile now and I have found it to be very stable.
Go through the Emacs tutorial, accessed via C-h t.  This will give
you the basics of navigating using the Emacs keys. It will likely
take some getting used to, especially how Emacs handles selection,
cutting, and pasting.  This will likely be the biggest hurdle if
you are used to the cutting/pasting/navigation in word processors.
Keep this reference card handy.  It has nearly all of the commands
that you will use on a daily basis.
For Org-mode specifically, look through the manual, but more
importantly look at the tutorials.  Specifically the general
introductions and the power users describe their setup sections
(the first two sections linked above).  These tutorials will
highlight the customizations made to the initialization file
(.emacs) for these users.  Even without elisp experience, you
should be able to find something close to your desired workflow and
be able to modify it with some trial and error.

When I started with Emacs and Org-mode I had very little experience
with Emacs.  A vanilla Org-mode install with no customization is still a powerful tool.  As you get more comfortable with working in Org-mode you can start to work on customization. Even with very little interest in programming there is a significant enough user base that someone may have already done something close to what you are looking for.

After I got comfortable with Org-mode, I started using Bernt Hansen's set-up with no
changes.  It is a bit intimidating on the whole as he has some extensive customizations, but he documents them well and explains almost everything he does.
Then after using it for awhile, I was able to modify
the initialization to something that better suited my workflow.  It
took some trial and error and a bit of extra time on the learning
side, but I believe that it has payed off in the long run.

Once you are comfortable with Emacs, I would also recommend the Emacs
wiki.  It has some descriptions of useful packages, some discussion,
and even some configuration suggestions to help build up your
initialization file.  If you ever get to the point in your setup where you think, "I wish I could do XXX", the odds are someone else has written a package that covers what you need.


How do I get editing help for technical (mathematic/statistic) paper publishing?

I suggest these four steps:

Identify your research community. The problems you are working on should have some connections with previous works. If not, it will be hard to publish your work anywhere, because it is harder to draw the attention of other researchers on your topic. You can use search engines such as Google Scholar for this purpose.
It is likely that the authors of these papers use the same notations, publish in the same journals and use a similar article structure to describe their work. Become familiar with the format by reading related articles.
Write down a draft, following the usual format of your field. If your English is weak, you can ask someone to fix your mistakes (he/she should not need to be familiar with your work, but it is easier if he/she has some scientific background).
Contact a researcher working on close topics, asking him/her for feedback on your draft. If the feedback is positive, a collaboration might be possible.

I have followed these steps and this has lead me to my first research paper (co-authored with my "mentor"). It takes a lot of time but it is worth the effort.


What should I say about a publication that I have not contributed to?

Cut shortly, use it to your advantage, but be honest. If you're in the project, that means you should know the aims, tasks and problems of it. Even if you did not contribute to the article directly, experimental or literature research is still relevant and could be used by your colleagues. Try to figure out to see it clearly and be able to explain.
And of course if you include this publication to your CV, you should know as much as possible about the topic. That could be educational for you as an undergraduate.
Good luck!


What does the "final published version" refer to in copyright?

The usual workflow with Springer is:

You prepare your paper, and submit it as a PDF file to the conference.
The conference reviews the paper, and you get the acceptance notification + conference reviews back.
You revise your paper, and submit the source code to Springer.
Springer does copyediting, and you get the page proofs back.
You check the page proofs and submit your corrections to Springer.
Springer prepares the final PDF and posts it on their web page.

(Note that steps 1–3 involve work from you + research community. Steps 4–6 involve some added value from the publisher.)

The "author-created version" refers to your output after step 1 or 3. This is what you can self-archive.

The "final published version" refers to Springer's output after step 6. This is a version you cannot self-archive.

(IANAL, etc.)


How to effectively get a post-doc position

I would recommend both applying for the postdoc positions advertised, and also writing to professors with research groups that you are interested to join.

Applying for a postdoc is similar to any other job application. You are responsible for sending out the applications or reaching out the future employers. A pro-active approach will invariably be beneficial to the applicant.

As an applicant, I would not recommend worrying about the fairness of the jobs advertised. Just apply.


Using leaked proprietary information in scientific paper

Sounds like you have found an interesting source and are considering the moral implications of using it. What I will say is based purely on personal opinion and probably what I would do unless instructed otherwise.

Leaks are a fact of life. With the proliferation of digital material they are commonplace. Look at Wikileaks, the Snowden revelations etc. Once material has become public there is - fortunately or unfortunately - no going back, regardless of how that information became public. It is the responsibility of the owner/creator of the material to ensure it says secure.

Dissemination of such material could be highly fruitful - but think of it this way - will your publishing research based on the material be ultimately constructive or destructive? Will it benefit just you or the wider world? Who is it really advantageous for? If the answer is just you, I would probably withhold your research based on it. If it has wider ramifications of great import, go with it. Also consider the reasons why it is confidential. Who does it serve - who does it protect? Was the confidentially because of financial reasons, incomplete research, company policy, or 'national security'?

There is a heavy moral tinge to this question, and you may have to do some soul-searching. But ultimately, if it serves the wider discipline in a positive way, and such servitude grossly outweighs the few individuals who it would ire, I would use it, as long as there are no legal implications for yourself [unlikely since a third party leaked it, but you can never be too careful].