Why do journals have limits on the number of references?

Journals aim to publish an organized set of articles of some approximate length in an attractive format.

Journals set limits on the number of references to shape the form, format, and quality of the submitted articles.

This organization is a good thing, in terms of disseminating scientific information. Given the limited space of one article, there is definitely some appropriate range for the number of essential and useful references that relate to the presented work.

This is less restrictive that it might sound, as these rules set by the journal are seldom hard limits. If you have good reason to include a couple of extra references, you can usually work with the editor to get them included.

Another reason to include limits is to try to encourage authors to examine references more closely, and to be more selective in their choices of what to include. Just as many journals have rules against gratuitous figures and tables (e.g. all figs must be referenced in the text), these limits are meant to discourage gratuitous inclusion of references that are not directly related to the discussion in the manuscript.

In response to the expanded question: "What happened in the 80's?" ...

The Science Citation Index was launched in 1964. With its growth and success, and the addition of other field-specific indices, it became possible to compute statistical journal and author comparisons (e.g. Impact Factor). This concerted effort to index citations made being cited in the work of others more important, and the use of numerous citations became much more common. The benefits of these author and journal metrics were much lauded during the 70's and 80's, but people were also increasingly aware that this arrangement was vulnerable to abuse, i.e. gaming the system by inflating citations. SCI grew to become Web of Knowledge, then Web of Science and along the way (1992) it was acquired by a large media company and today it's run by Thomson-Reuters.

The question posed invites speculation; we can't know exactly what the owners and editors of the various scientific journals were thinking when they started implementing citation limits. However, I would hazard a guess that they realized gratuitous citations might be an issue, probably had a few bad apples, and decided that limits were a good idea to keep the quality of the submissions high.


What are good strategies for not losing sight of the novelty and nontriviality of one's work?

You are not the only researcher who experiences this. Certainly I personally also do.

It sounds to me like your question is whether these feelings of overexposure to your own work are:

pathological--the result of some psychological process which makes you feel disenchanted with your old papers, regardless of their actual merit--or:
simply accurate--that is, as time passes, you come to have a more accurate appraisal of your own papers.

You already have suspicions about which of these two possibilities is actually correct. Personally, I try not to second-guess my own negative feelings about myself, so here is a strategy which I have found totally avoids the need to decide between possibilities #1 and #2: by working on a massive, multi-year, very ambitious project which requires many, many papers to develop, explain, and "make good on", I find that my feelings of overexposure about my own old papers, my own looking-at-my-old-papers-and-immediately-seeing-everything-I-could-have-done-better, those feelings are overcome by my excitement for the future of this broader long-term project and the small piece of that project that each of those imperfect papers puts into place. Being able to say to myself "I wish I would have written that old paper more elegantly, or proven this stronger result," or whatever, these feelings are washed away by the feeling of "That paper, no matter how wretched and ugly, still allows me to carry out the next step in the broader project," and then I can live with having written it. Maybe this approach can work for you too.


As a recent PhD entering jobhunt, should I agree to host a weekly seminar?

It's in your interest to focus on research, then job search, then teaching, then service. This is service, so lowest priority. See if you can get a student assistant (grad or undergrad) to do a lot of the grunt work, while you handle the higher level logistical stuff. If you can't get some help, doesn't sound like it's worth your time.


Authorship of code published in Zenodo for non-contributing authors of main paper

It is an interesting situation. Clearly the 'authors of the code' have the copyright (and the repository shows who actually contributed). But the purpose of the code was to address a question broadly, as demonstrated by the broader group on the paper. For the purposes of a DOI (which does not indicate IP ownership on the code) I think having the same author list as the paper is acceptable, but not necessary.
As something else to think about, would the code have been developed outside the context of the project leading to the paper? Did the non-code-writing collaborators have no intellectual input to the code?
As an aside, if the repository URL disappears, then  the DOI link will die as well.


Obtaining academic positions after doing research in logic

The perception, at least within logic, is that finding research positions in logic is even harder than in most specialities in mathematics - most research hiring is restricted to a specialty, and there are rarely new positions created in mathematical logic.

I'm not sure how true that perception is.  As far as I can tell, every field perceives hiring as very tight.  There are more qualified people than available jobs in all fields of math; there are fewer positions in logic than, say, algebra, but there are also fewer new PhD's in logic, and I don't know of any data on how the actual ratios compare.  But it's certainly hard to get an academic position in logic, and every year very good researchers decide to give up pursuing academic positions.

My impression is that logicians do slightly better than the average mathematician at getting positions at schools that are less research oriented - schools that are hiring based mostly on teaching ability, but want their professors to also be doing some research.  (Partially, I think, because those schools often want people who can teach a variety of undergrad classes, and many logicians these days are trained to be able to do that.)  But that obviously depends on being a very good teacher.

Regarding applied logic, it's very rare these days for someone with a math PhD to get hired to an interdisciplinary position, at least in the US.  Someone who's already established can sometimes can an honorary position in another department, but they still have to be hired (and eventually tenured) by their home department.  I think that's different in Europe, where there's a lot more mathematical logic going on in CS departments.


Giving a talk on a different topic than what we discussed

If you haven't come to an agreement on what you would discuss, then I think you are pretty free. But as a courtesy, if nothing else, send him a note about your topic. If he disagrees you might want to re-think it.

However, a talk about partially unformed ideas, if presented that way can be very valuable. It can give ideas about research the listeners might explore. If you do it right, it can give ideas about how to come up with such ideas and how to begin to tackle them. What insight do you have into the problems?

In the best case it can lead to collaborations on that topic and others that might emerge from the exploration.

In fact, a talk on "things worth exploring" is probably more interesting to a mathematician than one on "things done and finished."


What can I do with like-new, recent-edition textbooks that I'm not allowed to sell?

Ask your employer.

You should be able to work out a solution both parties are happy with pretty easily. The obvious one is to sell the books and then give your employer the profits. If they don't care, you can also pocket the profits yourself, perhaps recycle the books or donate them to your university's library.


On grid lines

It depends on the points you would like to make with the graph. If you're just going to show an upward or downward trend, then the grid lines are probably redundant. If you'd need refer back to a certain point of a curve, and knowing the vertical position of that point would be crucial, then grid lines can help. It's not about the graphs (or I may go so far to say even within publication culture,) it's about the points you are trying to get across. If the grid lines will get people there with less puzzling or work, then yes to grid lines. In all other occasions, then no.

  I'm being told that displaying horizontal grid lines implies a greater
  accuracy in modelling data and therefore should be absent in the case
  of this carbon sequestration modelling since it's not the results of
  measurements

This is perhaps the oddest graphical rule I have heard in the last 12 months. For most grid lines are just an extension of the tick mark on the axes. As long as you provide the tick marks on the y-axis, anyone can draw horizontal grid lines.

It is, however, not advisable to provide tick marks or grid lines finer than what your instrument or model can discern. For example, if your measurement or prediction is in the unit of meter. Then, at most I'd just put grid lines at 0.5 m increment. I wouldn't go so far to put 0.01 or even 0.1 m increments. That would imply some precision that I never had. I believe your partner author's concern may be more related to this problem. In that case, you two need to talk and make sure at least the tick marks make sense.

On caption vs. title

  I'm told that titles are a no go, captions only. (I've found a Uni
  spec online for science papers saying titles are mandatory). I'm told
  titles are rare in journals.

Yes, they are rare in my field (biomedical.) We use captions (located below the graph) most of the time. The caption usually starts with something like this:

Figure 1. The [would have been title]
[texts explaining the graph.]

If you have a title in the illustration, it only serves to duplicate information, making it redundant ink.

Though, depending on fields and journals, the rule may differ. Check with the journal's guideline and other published work in that journal for clues.


Assuming the department has been using rotations for a bit, I can't imagine this is such an unusual situation for the professor. Simply based on my own experience, I imagine that that most students don't reach out to the professor they're paired with prior to assignment. (I very well may be wrong here, but that's definitely my experience.)

Within that framework, I would read up on the professor's research and simply send an introductory email with an offer to meet at his or her convenience. They'll probably be able to walk you through expectations and requirements when you first meet.

If you're really nervous about violating social norms specific to this department, I would consult with the head of the graduate program and ask for their advice. They can guide you better than we would be able to in any event.


For a professor in the US, How important is one's relationship with the dean?

The question, although reasonable, seems hard to answer in general terms.  Programmatic change is generally not done by individual faculty members in a department, but by groups and/or committees of them, in confluence with the department Chair/Head.

Many programmatic changes do not "go through" the Dean -- in particular "day to day" business usually does not -- but those involving nontrivial financial changes usually do.  For all but the smallest colleges it is rare for individual faculty members other than the Head to have substantive conversations with the Dean about such things: again, it would be better if they went through the department as a whole and/or the Head.  When it comes to financial outlays that must be approved by the Dean: I've seen plenty of instances where the Dean approves but "just doesn't have the money," so I would have to think that even mild disapproval of the initiative would sink it pretty thoroughly.

Perhaps the most useful thing I can say is: look at where the program is now and look at where it was in the recent past.  If you are really unhappy with the current position or the perceived trajectory of the department, then you should not count on being happy with it in the future (no matter who the Dean is).  Conversely, if those look reasonably good to you, talk with the faculty and see how they feel about the future.  If there's some important change coming around the bend, I hope they will let you know.  But it is more likely that being in the department for the next ten years or so will be roughly like having been in the department for the last ten years or so.  The Dean does not reside in the department, so unless s/he is actively at war with the members and interests of the department, some disagreement in the overall vision need not affect the actual working life of a professor in the department unduly.

By the way, the bit about the Dean "may leave in the next 5 years" sounds way too vague to take seriously.  Maybe s/he will and maybe s/he won't.  If s/he does, maybe the next Dean will be better or maybe worse.  It is very hard to plan for the future with regard to this kind of thing: honestly, I probably wouldn't even try.


My masters project is very unclear, is it realistic to expect me to complete it successfully?

Welcome to the wonderful world of research! You're describing what research is like: nobody really knows the answers, so nobody can really give you concrete guidance; nobody really knows what will work, so the only thing to say is "try it and see what happens". It might sound optimistic, and in some sense it's a good optimism, because no matter what happens you've discovered something new.

So relax and do your best. If you try something and it doesn't work, explain why it doesn't work to your supervisor. If you get stuck, also let your supervisor know. Your supervisor cannot really spell out what to do for you every time; it's quite possible he'll say "okay, we're stuck. What do you think we should do next?" and you can try thinking of something (don't worry if you fail; after some time he'll probably think of something himself).

Finally don't worry about what happens if the project turns out to be unfeasible or not work as expected. Nobody can guarantee beforehand if the project is going to work as expected. You're likely to be graded over your work, not your results. If your supervisor had given you a project that turned out to be more complicated than expected, he'll undoubtedly factor that into the grade, as well.


How to politely turn down others' request for collaboration?

Thank you so much for keeping me in mind for this. Even though the idea sounds exciting, I'm currently swamped with work, and cannot join a new collaboration at this point. I'm very sorry!

Depending on whether you see the chance to collaborate in the future, or you just want to get rid of them: You can also add that they can contact you again at some later point, or even that you will contact them.


A group run by my advisor's former student keeps scooping my work. Is my advisor sabotaging me?

Something is clearly wrong here. If your supervisor is not alarmed, talk to another senior person and make pretty damn sure your supervisor is correct not to be alarmed. There are many people you can ask: your thesis committee, your head of department, a trusted faculty member, someone from the School of Graduate Studies, and so on.
Ask to speak in confidence - something is clearly wrong, and that something could be your supervisor.


speed of problem solving in grad school in mathematics

Success in well-designed qualifying exams in mathematics will depend very little on "problem-solving" speed or talent, but, rather, will depend on whether you've already done problems nearly identical to the problems which appear.

That is, as you observe, it would be prohibitively slow to "solve" many of those problems "in real time". Thus, that is not the expectation. Rather, the "test" is whether examinees have studied sufficiently broadly so as to have seen examples resembling the instances occurring in the given exam.

And, no, it's not about "memorization", either, which tends to be insufficiently flexible to allow easy adaptation to slightly changed situations.

So, really, it's not about "speeding up in problem-solving", but to be able to merely "remember" instead of "solving".


Should I contact the EIC for additional information regarding his decision on my paper?

I have never been an EIC but I have spoke to some, I have been a reviewer of many papers, and I have had the similar experiences as you described.

It is probably useless to further inquire about your paper. The EIC decision could have been based on the private communication channels of the review process. The reviewer might have been lukewarm about your paper - maybe it was not a case of a substantial error but that the result was uninteresting. It could also be the case that the new EIC did not have the time for a careful consideration of your paper, of balancing the different reviews and based her decision on the less positive one. EIC are usually very overloaded and some of them explicitly use the rule of deciding based on the most negative review. If it is any of these two cases, you will not receive any further information from the EIC regarding your paper.

My personal experience is that I was only able to change a EIC decision once, when the negative review was reasonably detailed and I could show that some of the  main points made by the reviewer were 100% opposite of what was already written in the paper. The other occasions where I asked for more info or criticized what I thought was a wrong interpretation of the paper, I would receive a polite answer that the decision was made.

Now, I wait a week until the frustration and the anger of how "dumb is this reviewer" subsides, make the the changes I think are reasonable and send to the another journal.


Is it OK to use the content of my own paper which is not yet submitted, in my other paper?

Most journals require that the submitted manuscript has not been submitted total or partially to any other journal. Of course different policies apply to open access journals. If I were you I would check the journal's policy regarding this issue and contact the editors if necessary to get their opinion (probably they will require details on what will be duplicated). To the very least discuss this with your supervisor. You can find yourself in a very unpleasant position if you are not careful (not to mention having your papers rejected), as indicated by @Enthusiastic Student


Improve my relationship with this professor?

What exactly "avoid" means in your situation? Is there any specific event or occasion?

To me, building a relationship with someone is hard especially when It comes to professional life (e.g. academia). It takes lots of effort and time. Did you spend time with him like asking questions in his class, talk to him, or even disagree (debate) with him on a certain topic? I don't talk about the relationship outside of the classroom.

I think this is just your bias about what that professor think or feel about you and you care too much about that. Most of the time people don't care much about other people unless there is common voice or opposition about something between them.

So, if you want to have a better relationship with that professor, my suggestions could be something like (based on my experience):

Actively discuss when you're in his class.
Email him asking about some of your ideas.
Buy him a cup of coffee :)

I'm not sure if this helps but hope you feel better.


Publication database backend for academic web sites

This sounds like a job for an institutional repository (though you don't have to publicise its existence as such...)

The two most commonly used open-source packages for repositories are ePrints and D-Space, though there's a few others. Anecdotally, D-Space is somewhat more complex to set up than ePrints, though I've only got experience of the latter.

Both have comparable levels of functionality, including metadata feeds/export, and it should be easy enough to export material into a Wordpress site - I've certainly seen it done, for example in this rough proof-of-concept. I'll see if I can find a more polished example.


Difference between inclusion and exclusion criteria

In some ways the second is clearer since no one will interpret it as the inclusion criteria overriding the exclusion. Your criteria is and for all items. Between 18 - 60 AND ... AND doesn't have disease y.

But in general, if it is clear what you mean it should be fine. Clarity trumps form.


How to weigh these pros and cons of applying to PhD programs?

My advice is do a serious job search now of salaries and do a rough "expected value" calculation of how much more money you would make with a PhD compared to without one. Perhaps even ask any contacts you have about this. Then you can see if that amount is worth it to spend four years doing a PhD and the possible better job you might get with one, if it would indeed be better. Money is actually pretty important, so it's a good idea you have an actual figure in mind, even if it is a rough estimate.

My next recommendation is to expand your school applications if you do go for a PhD. If it's enjoyment of research that you're after, the top schools won't necessarily get you a better experience. You'll do better at a less stressful school based on your mental makeup. I did not personally find a PhD very stressful and I think applying might actually be the most difficult part.

I'd also like to say that it's not really necessary to be extremely competitive to get a great career. Most people who will compete with you at all levels of education and career will just go on to do something so different from you that they won't even matter one year down the road.


In your introduction you can explain the context of your study, and the research questions you want to treat. Then, in the last sentence of the introduction you can write something like:

To answer the research question, we treat a case study dealing with a
particular company. For privacy reasons we cannot give the exact name
of the company, so we will simply refer to it as "the company" throughout this paper.

Then in the paper you can use sentences like:

Productivity in the company was boosted by increasing the light
intensity at the workstations
The company that is the focus of our study is a tech company of 500 employees which has grown very much in the last 5 years.

In this way everyone is aware of the fact that a fake name was used.
ps I haven't written any papers that involved this kind of dilemma, but this is what I would do.


Equivalent of french CAPES or agrégation exam without having to teach

Note that if you pass the "agrégation" (i.e. successfully pass the exams) but don't teach after, then you cannot call yourself "agrégé de mathématiques" (as it's reserved for people who then teach) but you are allowed to say on your CV that you successfully passed the exams (I think it's "reçu au concours de l'agrégation", but not 100% certain). I shall not comment on the morality of potentially taking up a place in a competitive exam with limited number of places (the Mathematics one always has more places that admissible candidates, but still...). However it sounds like a lot of effort just to get a diploma.
The more traditional route is to get a "Licence" in another subject by taking online classes -- so there aren't any mandatory classes -- for the year of L3 at a nearby University (provided you can get an equivalency for the first two years of L1-L2), and taking the exam. It's not uncommon for students in Physics, Mathematics, or Computer Science for instance to get one or more degrees in related topics this way. If the secondary discipline is less closely related to Mathematics (say Philosophy or Ancient Languages), then it may be trickier to get the equivalency, although it's always easier to go from Mathematics to anything else than the reverse.


My 2 cents. I would say that getting hired in the theory area in CS departments, even in good times like now, is difficult and depends on many factors. Counting on getting hired even with a productive postdoc is not a good idea. You should try but keep the expectations reasonable and be prepared to be hired in math and enjoy doing the work you like at the interface. If things work out really nicely you can try moving later in your career as well.


Should I send a follow up email to a prospective PhD advisor?

There is nothing wrong to write an email to inquire about your application status, but I will suggest first contact the admission office. Remember it varies from school to school that how much a supervisor can play a role in admission process.


If I am building on results of my earlier works, do I have to include them in my bibliography?

Are these works available in any published form or any other permanent online form, such as a technical report? If so then cite. If not, then there's nothing to cite. In my opinion, it would look strange to cite a project done in some previous course.

What you can do is put an acknowledgment in the back of your thesis/paper to your previous "co-authors".


I have nothing to show for the last five years but graduate school and I can't finish/want to leave this field

The skills acquired as a graduate student are often very employable outside academia. I was doing a PhD in Linguistics with a focus on corpus linguistics. As part of my education, I learned statistics, Python scripting, Mandarin Chinese and technical writing. Those skills ended up getting me a job offer from a major computer software company, which I accepted and left grad school to take.

You probably have more employable skills than you think. Spend some time thinking about what skills you possess and what professions need those skills. a PhD to your name is not the first thing employers look for - they look for whether you have the skills that they need.

Stop thinking about your degree and start thinking about your skillset.


How can I help to participate in data collection or research work as a field researcher?

The first step before starting a PhD would be to find a potential supervisor who has some expertise in the research domain (not necessarily the specific topic). First there will be some discussion with this supervisor about the exact research topic and the motivations for the research: a PhD student's expertise in a particular topic is not enough to justify research on this topic, there must be some scientific reasons why this topic is a relevant research area.

Then you will see with your supervisor about the best method(s) to achieve these research goals. Imho it's unlikely that a supervisor would agree with a method which involves you as a subject, but I'm not at all in this kind of domain. In any case your expertise would certainly be useful in contacting subjects and targeting the right research questions.


Falsified student signatures in class attendance list

The system you're describing sounds like a bureaucratic nightmare to me (both for the students and for you; these things generally go hand in hand). I would therefore sympathize with (and turn a blind eye to) students tricking their way through it to the extent that is necessary to let them focus on the actual work. It's sad that they are getting free lessons in forgery when they ought to be learning something more wholesome, but as long as they are doing the coursework without academic dishonesty (as in, homework plagiarism), this should not count against them. A class is not a test of conscentiousness.

If you want to push your students to attend the class, there are other methods that don't involve automatic failure, such as giving mild homework hints in your lectures.

[Extended from my comment.]


I understand your confusion to opt an interest or to go with skills which will yield you a corporate job. I had been in the same pass; I thought to leave my PhD in Electronics Engineering and join PhD programme in Biophotonics. I got full tuition waiver with a handsome scholarship from a top UK university but I considered the following points to reach a conclusion.

Firstly, there are many more industry jobs for electronics people when compared to a Biophotonics PhD. Secondly, I can always try for teaching positions with a PhD in electronics engineering i.e. I have two career paths to choose from. However, if I talk about Biophotonics PhD, chances to find a job in industry would be pretty less (given my undergrads in electronics engineering). Ultimately, I'll be forced to find a birth place in some university or college. Salaries in universities/college when compared to corporate world needs no introduction.

I would suggest you to carry on your PhD in Software Engineering and you can always work on Mathematics after your PhD (obviously not in the form of a PhD). Mathematical research doesn't needs lab as such so you can carry on your research after your office hours and do publish them.

Another important point, you will spend ages to gain a ninja level of mathematics knowledge which is essential to finish your PhD in Mathematics (if you enroll). That being said, where is the progression in the life? Personally, I am a strong follower of "Money is the ultimate motivation" and don't overlook your family anytime while taking a decision. (I continued my PhD in electronics engineering and after graduating I have a nicely paying job in industry.)


Does it look bad if none of my recommendation letters for grad school are from past professors?

Letters from "lower-status" people but who've really seen you doing the thing (rather than taking classes in "the thing") are infinitely better than (routine) letters from routine-coursework instructors, regardless of their status.


It means exactly what it says:

"Accepted for publication pending revisions".

It's accepted...pending the requested revisions. Essentially, they are going to ask for some changes (usually pretty minor and straightforward) and once those are done to the editor's satisfaction, the paper is accepted.


Acknowledging funding originally intended for another purpose

This depends very strongly on your position and the nature of the grants.  The main deciding factors are:

Is your time clearly accounted to particular grants?  Postdocs are sometimes asked to fill out time-sheets that bill specific hours of work to specific grants, and sometimes simply "supported" by their grants.  If your hours are being specifically billed, then you must acknowledge funding on any publication that has had work billed to it (whether you should have done that is a different question).
How specific is the funding vehicle's mission and expectations?  For example, in the US, most NSF funding vehicles just want to see strong publications in an area plausibly related to the subject of the grant.  A DARPA contract, however, might be much more tightly focused and it could draw ire from the program manager if you appear to have been "wasting their money" on projects unrelated to the contract "mission."

The second point is very subjective and often depends strongly on not just the agency but the particular program manager and contract.  The PI of the grants should know the situation here, and be able to advise you on the preferred course of action.


Can I submit a review paper to a journal without being invited?

Yes, it is absolutely possible to write a review paper without being invited to do so.

How do I know this?

I've done it, several times, in the biological sciences.

The key is to recognize that the review needs to be invited at some point, but that point need not be "before you've written anything down*. If you have a target journal, and you think it is a decent fit for the review paper, I would suggest that you find the email for the appropriate section editor (or the Editor-in-Chief if there is none) and write them a polite email inquiring as to whether or not they would be interested in inviting a review on X topic, a draft of which is attached. Articulate why you think this is useful and interesting to their readership, and hope for the best.

And before we get on the "A PhD isn't enough clout to write a review", my first review was published with an undergraduate as the primary author.


Will taking a temporary staff position between post-docs end my academic (tenure track aspirations) career

I would think it's not advisable to take this position unless you already have a research position lined up for a local university in the near future (under a year at least). At least in my field, getting tenure anywhere at all is hard. Unless you are particularly in demand (which seems unlikely from your described position so far), if you want tenure you have to put that above location (even to some extent country, not just city), and then apply at every opportunity to move to something where you want, in the hope that one day you will get it. It's not a good situation, but there are too many people for the number of jobs available.


How do professors learn how to write letters of recommendation?

As with most professorial duties, it's a sink-or-swim process.  There is no formal or official training they receive for this task.  They're just thrown into the situation with no experience and are expected to perform well at it immediately.  If they've seen other recommendations during their other duties (that they likely also weren't trained for) they can use that, otherwise they can try asking colleagues or do google searches.  So for the most part it's a bunch of untrained people relying on other untrained people and crossing their fingers that the other guys were able to figure out a good approach.


How do you avoid favoritism and personal relationships from affecting grading?

I would suggest to design a rubric to assess the work of students. The design of a rubric is difficult and may require a lot of work for the teacher, but it will isolate the grading process from other factors. Here you can find a book about rubrics.

One of the advantages of using a rubric is that students can easily observe how their work is going to be evaluated. Another advantage is that teachers can easily apply the same criteria across all the work to be graded.


Question about ethics and possible misappropriation of research funds

I cannot really tell what you question is about, but let me try and clarify a few things.

First, being the PI on an institutional review board application does not make you the PI for the funded project. It is not clear what you mean by "your" project funds, but from your description it does not sound like it is your funding, but rather funding that your supervisor was awarded and is providing you access to for you to accomplish your thesis.

Second, applications for funding generally have around 3 aims. The linkage between these aims can be pretty loose. It is not uncommon for students working on different aims of the same grant to think their projects are completely independent. Often a grant might not provide funding for all the staff required to complete the aims. In fact a selling point to potential funders is the ability to leverage their funding with "outside" funds like a departmental studentship.

The real issue I think in your question is if it is ethical for your supervisor to use her funding to pay PhD students different amount. The answer to this is that it is most likely ethical. It is possible your supervisor has circumvented the policies of both the funder and the department, but this seems unlikely. It is quite likely that your department has a fixed, relatively low, stipend for internally funded PhD students, but allows for PhD students funded from outside grants to be paid more. In my mind there is nothing unethical about that.

So then the question is why is your lab mate being funded by the grant while you are being funded by the school. No one but your supervisor can answer this. Maybe she flipped a coin. Maybe she thought your the project of your lab mate was closer aligned to the aims of the grant. Maybe, as you say, she likes your lab mate better and cannot be trusted. Before going down that road, you need to remember that it is quite possible that the decision of who to fund from where may have been made prior to either of you applying to grad school.


Is a letter of recommendation from undergraduate professor different from the major I am applying to OK?

Sometimes when getting a letter of recommendation you have to do what you have to do.  Letters of recommendation are generally supposed to be speaking of you in the best light possible.  Ideally you would want one for the major your are applying to, and, even more ideally, from somebody who has supervised you in a research setting.  BUT, sometimes you would be better off getting a letter from somebody with a lower title if they can speak the world about you in a positive light.  Remember, that the purpose of recommendations is to describe competencies, skills, and other personality traits that will enable you to succeed in graduate school, something that grades can't show.  As such, you will want recommendations to be from the people who know you best, not just people in a specific department.  Personally, even though I had done a small amount of research at my undergraduate institution, I asked for two professors whom I had TA'd under to provide me with recommendations for an REU I participated in that subsequent summer.
You haven't provided too much about your situation, though, so it is kind of unclear what the exact situation is for you, such as why you are going from engineering to international studies or why you don't have any international studies faculty at your current institution to ask for recommendations or why you think the engineering faculty may be better for providing recommendations.


How long does it typically take for Chinese universities to accept or reject applicants?

It depends on the programme of studies, the director that will see your application, plus whether there are additional requirements for your discipline, for example a portfolio. You might get lucky if you can email admissions again to ask which state your application is in, and how many stages you have before they conclude the process. Normally in a Chinese uni though they will ignore you until it is time to inform you.


What time of day should I schedule my thesis defense?

First, I have never heard of any research backing up the idea that defenses will be more less successful based on the time of day the defense is held.

Second, the best time to defend is whenever your committee can actually make it. When I defended, my goal was to get get at least three of our four committee members in same physical room (one non-chair member could attend via video). Within a six-week window, I felt lucky to find any two hour-window to schedule the defense.

Finally, you are overthinking things. Pour your energy and concern into the content and remember that if your committee is encouraging you to defend, it's because they think you are ready. Surprises are unlikely.

Of course if you are in the enviable position of having to choose a time of day, I personally like defenses at the end of the work day so that you can head out with others — e.g., students, family members, maybe even committee members — for a celebratory post-defense drink or meal.


Is there an efficient way to give a large class of students feedback about their assignments?

If the class has 700 students there should be a lot of students who are making the same mistakes. Therefore, I do not see much benefit in personalized feedback due to the impracticality of the context.

I would consider it wiser to determine what are the common mistakes that the majority of the students made and provide the same feedback to all students on how to address these common mistakes. This will help the majority of the students without having to commit to the time-intensive effort of personalization.

If there is someone who wants additional explanation they can speak with the TAs.


How to write/format a digression in conference/thesis papers

Maybe you can format it as a remark. These are essentially paragraphs typeset with a special header, a bit like theorems. Example from a paper in my field:

Note that the text of the paragraph is typeset in a roman typeface, not in italic like a theorem. If you are using Latex, with amsmath, there is a command \theoremstyle{remark} that can be used to get theorem-like environments with that formatting.


How can I prove that I did a review for a journal?

Ask the editorial office. You write that you've already asked them, but send them a reminder. Tell explicitly what you're looking for. In my experience for example, a letter saying you performed a review, on official Elsevier letterhead paper & with the desk editor's signature, suffices. This really should be something the journal office can do quickly. If they haven't responded my guess is that they're waiting for the editor-in-chief to respond, which is unnecessary.


Please ensure that you refer to Figure 3 in your text as, if accepted, production will need this reference to link the reader to the figure

Did you mention the other figures and tables in your text? Usually, you should have a sentence like "as shown in fig. 3" or "in table 9, we see..." for each and every table and figure.

Maybe the editor just gave examples - you should do it for all of them.

Edit to incorporate the comment into the answer:

It might be a misunderstanding. Since you should address all reviewer's / editor's comments, you should write something like "fig. 3 and table 9 are mentioned on p.x line y. If this is not sufficient, I did not understand your remark, please elaborate on this issue"


Can publisher alter or invent writing and attribute that to the author without consultation?

A publisher will typically require authors to sign a contract. That contract dictates what the publisher can do.

Contracts typically stipulate that the publisher can make editorial, formatting, stylistic, ... changes. Thus, a publisher can alter or invent writing. Whether the publisher can do so without consulting the author depends on the contract.

A contract might permit the publisher to derive promotional materials bearing the author's name, without further consultation with the author (i.e., contracts might grant such rights), hence, it might be legal to publish a document under an author's name without consultation.

Since the publisher is typically granted permission to make changes, it is possible that those changes lead to publication of a manuscript that is radically altered to the extent of say the opposite of the original.

Although I have reasoned that it is possible, it really depends upon the contract that was signed.


Structure of a paper: Development of a simulation approach

It depends on your target audience, but my inclination would be to say that unless you're specifically targeting an audience that would be interested in the detailed implementation (say, computer science), the means by which you implemented the theoretical model may not be sufficiently interesting to include in the main text.  With that in mind, I'd recommend the following structure:

Introduction
Methods

Theoretical Model

Reference to the appendix for implementation details

Use Cases

Results of use cases

Confirmation of model validity with use cases
Novel findings produced by the model

Conclusions
Appendix (or supplemental material, depending on the journal's requirements)

Details of implementation
Public location where source code will be available following publication

This structure comes with the caveat that I work in a field where models are valued for their ability to generate new findings, and are of lesser interest when they don't advance the state of knowledge within the field.  If your field is more interested in the implementation details you may want to go with your original layout and place the implementation description within the main text.

As for the other questions, I would describe the model in detail in the methods section, and compare the modelling approaches broadly in the introduction (with the bare minimum amount of detail to justify your new approach), and specifically in the methods, with an emphasis on why your approach addresses a weakness of the previous approach.


Can I patent part of my work presented that in my own research paper?

There are caveats to the grace period but the U.S. you have a one year grace period to file.
35 U.S.C. 102 Conditions for patentability; novelty.

(a) NOVELTY; PRIOR ART.—A person shall be entitled to a patent unless—
    (1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention; or
    (2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
(b) EXCEPTIONS.—
    (1) DISCLOSURES MADE 1 YEAR OR LESS BEFORE THE EFFECTIVE FILING DATE OF THE CLAIMED INVENTION.—A disclosure made 1 year or less before the effective filing date of a claimed invention shall not be prior art to the claimed invention under subsection (a)(1) if—
        (A) the disclosure was made by the inventor or joint inventor or by another who obtained the subject matter disclosed directly or indirectly from the inventor or a joint inventor; or

For most all of the rest of the world, the day something is published it is no longer patentable, at least to the extent of what was disclosed. Nor is anything patentable that is obvious from what was published.


Repeated demand for citing a certain paper in the referee report

Apart from the editors, should there be a way to control this excessive use of the refereeing power?

Straight-forward answer: no. This is what an editor should check for. If (s)he does not care or does not agree with you, your only option is to go for a different journal, with consequently a different editor.

I should also add that, in my experience, few reviewers request their papers to be added willy-nilly. If this reviewer thinks her or his work is missing, you should at least do a thorough check of why (s)he would think so, and then accurately report in your response letter. It seems unsurprising to me that your paper was rejected if your response to "important related work from XYZ is missing" was "we did some high-level searching and it seemed kinda unrelated, so we skipped it". I as an editor would also consider this at least a substantial nudge into "reject" territory.


Dvorak keyboard accepted for testing purpose?

When it comes to the big standardized admission tests for (mostly) US graduate programs, such as the GRE and TOEFL tests, typically only Qwerty is allowed. See below for their policies. That said, they do make some accommodations for disabilities. Being a Dvorak typist does not count by itself, but if you have carpal tunnel it can't hurt to ask for special accommodations ahead of time. By the way, that link leads to a Dvorak community on Reddit. You might get better answers there.

For admissions and placement tests administered by individual universities, you would have to ask them. No universal rules there. For computer based exams and similar once admitted to a program, I think your chances are quite good. Few people would care about what keyboard layout you use, and even if they would, student disability offices tend to be quite flexible.

GRE

  The GRE General Test uses a standard English-language (QWERTY) computer keyboard. It takes its name from the first 6 letters in the third row of the keyboard. If you haven't used this kind of keyboard before, practice on one before test day to become familiar with it.

The GRE Bulletin Supplement for Test Takers with Disabilities or Health-related Needs does mention some keyboard-related accommodations (e.g. ergonomic keyboard), but I don't see anything about layout. Unfortunately, I don't know how likely they are to make other accommodations.

TOEFL

  The TOEFL iBT test uses a standard English-language (QWERTY) computer keyboard. It takes its name from the first 6 letters in the third row of the keyboard. If you haven't used this kind of keyboard before, practice on one before test day to become familiar with it. In some countries, the common keyboard used is configured to QWERTY and a template is provided to each test taker to help with locating the few keys that are in a different location.


What do you call a “practice” class that accompanies a lecture?

Try "tutorial".

Example writeup on what tutorials are from the University of New South Wales.


Should I say congratulations to my professor? What is the best way for this?

Professors are people too, hence any acknowledgement of achievements and, as in this case, their part in an achievement is always a nice thing to do.

It would probably not be a good idea to make too much of a big deal of it - but an email or a chat of congratulations to your professor is a polite acknowledgement and appreciation of a significant achievement.

Most of all, know that you are working with an academic that has, in some way, facilitated a student earning a great award.  Just keep that in mind in all your future interactions with the Professor.


Do you list journals you have reviewed for on your CV?

On the one hand, it shows that you are engaged in this necessary part
  of scientific research that is peer-review.

That's one of the major reasons why people list it. If your CV is being viewed as part of a performance review or hiring decision, or even for awards, this constitutes "service to the community" and indicates that you're a good citizen.

It's a noisy signal for the reasons you indicate, and so it doesn't carry a whole lot of weight compared to things like technical committee memberships and leadership roles, but it's part of the larger picture. Moreover, for more junior researchers who haven't yet had the chance to take on leadership roles, this is a good signal of service.


How to proceed when graduate advisor treats me terribly, possibly because of age?

Don't walk. Run.

Your advisor's behavior is unfair, disrespectful, abusive, and deeply unprofessional.  Their behavior reflects horribly on the department, and since it's unlikely that you are the only victim, may undermine the value of your degree.

The moment the professor blew up at you for using another textbook, it would have been appropriate for you to walk out of his office/classroom without another word, drop the class, report his behavior  (both in writing and in person) to the department head, and find (and/or demand) a new thesis advisor.  Even now, I would recommend all of those responses.

If the department has your back, break all contact with your old advisor, finish the degree, and get out.  Block his phone number (but save his voice mails).  Reroute his emails to a separate folder (but don't delete them).  If he shows up at your office, ask him to leave; if he refuses, leave yourself; if he follows you, walk to the department chair's office.  In any case, document everything.

If the the department is unwilling or unable to help you separate from your abusive advisor and finish your degree, then the department is being abusive and unprofessional.  Again, since you are unlikely to be the only victim of this abuse, it will get out, and it will undermine the value of your degree.  Then your best choice is to leave the degree program, apply elsewhere, and try to transfer as much credit and research progress as possible.

I recommend contacting the associate professor who left to act as a potential reference, and for more general advice about how to proceed.  She knows the local political landscape far better than any random stranger on the internet.

Your age and educational background is not relevant here.  Your advisor's behavior is completely unacceptable, and you should not have to put up with it for even a second longer.  Get. Out. Now.


What do I have to do in preparation for applying for a PhD?

Get good grades.
Make sure (some of) your lecturers know who you are, so that you can ask for a recommendation letter.
Get involved in some kind of research, either a thesis or something extracurricular.
Work out what topic you want to study; at least have a first idea.
Select relevant coursework based on the previous point.
Don't be afraid of going abroad. Prepare yourself mentally for this now, so when the time comes to actually decide, you'll be ready. Check details such as visa requirements, as these can take 3-4 months to obtain.
Research good universities who do what you want to do. Find out about their application procedure is and their deadline.


Its not illegal, but not in good taste either. Not talking specifically about algorithms, but even equations, constants, methods - these are usually named by others, post-publication.
Having said that, I know of atleast one instance where the authors named something after themselves, but I don't see subsequent work using that name. Can be an embarassment if that happens.


Switching postdoc position (station) in China

Did you go through the process of registering on chinapostdoctor.org? If so, then you are probably right that you are in a system somewhere. However, this should not affect anything because you never actually started your original position.
Nevertheless, I would proactively explain your situation to your current prospective supervisor so they (or their students) will be prepared to help you in case of any snags.
No matter what, it will not be an issue that derails your appointment. If there is an issue, it will be a clerical one that can be sorted out by the school with a phone call or two.


How to cite an interactive dataviz (Shiny app)?

You could cite it the way you would cite R packages, example: https://www.r-bloggers.com/how-to-cite-packages/

Or you can check out how it is cited following different citation benchmarks using Google scholar. See here on Yihui Xie's page

Or you can indeed cite it as a website, as @ff524 added.


Should I order references on surname or paper title when using Harvard style?

From Harvard website:

  The entries in the list should be in alphabetical order by the
  author's last name [sic].

As pointed out by aeismail in the comment, the second criterion is the date:

  Works by the same author should be ordered chronologically, from oldest to most recent

Of course, you might have many articles with the same author and same year, in that case, they say that:

  If your reference list includes multiple works by the same author in
  the same year, identify them in your parenthetical citations and in
  your reference list by a lowercase letter after the year, assigning
  each letter in alphabetical order by the title of the work


Different behaviour with wildcards on PubMed using quotation marks or not

Ah PubMed made to much automatism of it. This isn't the exact search string PubMed will proceed. Try it and see the Search Details on the right to find out what PubMed made out of it.

The solution is to put the words in quotation marks. Only in that case PubMed take them as they are without doing something out of your control.

"telerobot*"[tiab] NOT "*robot*"[tiab]


When writing a synopsis "review", may I contact the authors with questions?

I contacted the zbMATH editors with this question, and received the following reply from staff member David Biesenack:

  It is totally okay, if
  you contact the author for clarification.


Paper on mathematical analysis using tools from other (almost unrelated) field: how to introduce them?

An appendix, maybe
In many other fields it is typical to first choose a journal and only then start writing. In mathematics this is often not done. But here it might be relevant to consider your target audience and thereby target journal.
If the problem is from analysis and you want to publish it in a journal devoted to analysis (or in any non-stochastics journal), an appendix with the stochastics might be appropriate. In any case, formatting the paper so that it can be read without the material in the appendix is a worthwhile task. It also makes it simple to react to referee comments concerning the usefulness of the appendix, if you get such: you can keep it, integrate it back into the main text or remove it with only a little trouble.
If you think the paper is of (more) interest to people into Malliavin calculus, or would be easier to publish in a journal close to stochastics, then maybe leaving out the basics is desirable. But remember to motivate the problem sufficiently.


Is it permitted to not take Ph.D. students who have girlfriends/are married/don't come in weekends...?

A disclaimer:  I'm not an attorney.  My opinion is my own but I'll give you my sources.

Here in the US only, universities are probably not prohibited from considering otherwise protected status in admissions, c.f., Fisher v. University of Texas at Austin, which upheld racial preferences in admissions.

But under Title VII of the Civil Rights Act of 1964, as amended, once the question becomes one of employment (e.g., they work for you and get paid a stipend) you cannot discriminate based on any of the factors you cite.  You should also carefully avoid asking questions that suggest you're even thinking about it, c.f., "Federal Laws Prohibiting Job Discrimination Questions And Answers" and "Pre-Employment Inquiries and Marital Status or Number of Children" on the EEOC site.

Added: I agree with Anonymous. Even if you think you can get away with it, perhaps because it's not illegal in your country, I also think it would still be wrong.

Added:  If you are the victim of unlawful discrimination in the workplace, HR is not your friend. A priori, their objective is to make sure discrimination complaints don't happen. But after the fact, their objective is to circle the wagons and make sure a complaint dies without the institution having to pay a settlement or admit that any wrongdoing has ever happened.  A great outcome for HR is that you just quit and the problem goes away.  From your latest performance reviews and interviews with your co-workers, it's clear you were unhappy and have been for months and it's been showing up in your work.  So you quit.  Poof!  Problem solved.  Separately, they'll figure out what to do with the others involved.  If you think you may be a victim of unlawful discrimination, you should go first to your own attorney for competent legal advice, not HR.


What is the etiquette for resubmitting math papers?

How do I credit an unknown referee?

Thank anonymous referees in the acknowledgements.

  If I am resubmitting a paper to a different publication what is proper to mention about the earlier submission?

You should follow the venue's rules, they may require you to mention, they may not.


Should I simultaneously apply for multiple jobs in different ranks at the same university?

My experience is in mathematics in the US. My personal experience is that people will not read anything especially deep into applying for both jobs.  Everybody understands that the market is tough, and basically expects everybody to apply to every opening.  I've seen instances where a person was considered both for a postdoc and TT position at the same university, and this was not seen as an issue at all (there was much more strategizing around the question of whether they would come for a postdoc).

In the vast majority of cases (without, say, a severe geographical constraint), I think if you consider TT and postdoc at the same place as both reasonable options for you and plausible possibilities, you're probably kidding yourself on one score or another. Generally if you'd even be seriously looked at for a TT job at University X, then when the postdoc committee looks at your file, they'll say "We could hire this person for a TT job.  There's no way that a postdoc at University X is the best job they'll get." and they probably won't offer you the position.    But unless you feel confident about which way it is, I don't see any problem with applying to both.

EDIT: One thing I'll add, which is mathematics specific: if you're applying MathJobs, the visual difference between applications for the different jobs is negligible.  There is a column where you can see what positions the applicant applied for, but it's not very noticeable.  So, it's quite possible the committee for one job won't even notice you applied for the other (I have seen this happen).


Being a Dishonest Cheat. How do I live with this?

It seems that you already know what to do. You said it yourself, you've struggled with engineering since you started and you had to cheat on an exam that is a pre-req for your future courses. Classes aren't going to get easier and you would be wasting your time and money pursuing this degree. Is there a reason why you're still in engineering? Is there anything personal keeping you in this curriculum? Re-evaluate where you want your life to head.


Which differences are there between Math PhD programs in the US and in the UK regarding admission, funding, and reputation?

I am a first-year PhD student at Oxford, having done some graduate work (and my undergrad) in the US. My answer might be a bit institution specific as Ruadhai Dervan suggested above, but it appears there are some trends across the UK that are quite different from in the US.

"Are there any fundamental differences in the way UK PhD programs admit and train their students?" - Most students seem to enter a PhD program in the UK with a fairly specific field of study in mind. For my applications to Manchester, Warwick, and Oxford I had to write a research proposal for a fairly specific topic for each application, as well as have an idea of who might supervise this research. Many students deviate substantially from these ideas, but almost all students here work in a very similar area to what they applied for. In contrast, I know many US students who started out doing pure mathematics preliminary exams and found themselves finishing a thesis in a very different area, such as Numerical Analysis or Mathematical Biology. These things happen much more infrequently in the UK, in part because the programs are much shorter. The Oxford PhD is designed as a 3 year course, though many students take 4 or more years in practice. Some institutions are starting Doctoral Training Centres where a first year of training and project mentoring occurs. This is similar in flavour to US institutions having preliminary or qualifying exams, but these are often much more directed than in the US. I have not heard of any UK program where anything like preliminary or qualifying exams takes place, so that appears to be a US component of graduate school not present here. I would suggest looking at specific institution overviews of their PhD courses to get an idea of how they compare to US PhD programs.

Another important difference is the emphasis here on research as opposed to teaching. Most students in my program do some teaching, but it is frequently less than three hours a week. In comparison, my MS program in the States had me teaching 10+ hours a week, often with 10 or so hours of prep and grading. I also began doing research the week I arrived, whereas a US student may spend some years deciding on a specific topic to study. PhD students here also spend less time attending classes, and coursework requirements seem to be incredibly minimal compared to most programs in the US.

"As an international student would I also be able to obtain funding for my education the same way I would be able to in the United States?" - Probably not in general. Most US students in my experience are funded as Teaching Assistants, and they spend a lot of time teaching. Students are paid for their teaching services here, but the quantity is so much less that the funding from teaching is nowhere near enough to cover tuition and living expenses for most students. Exceptions probably exist, but most students here seem to be funded from grants their supervisors have, grants or scholarships they have gotten (e.g. Fullbright, Marshall scholarships), or similar things. You can apply for loans subsidized by the US government as well, just as you would for a domestic program. Many students are now funded through the Doctoral Training Centres, but at Oxford the funding for these is almost entirely for UK/EU students.

Your third question is a bit difficult for me to answer without any experience, so I will refrain from conjecturing. Most people have suggested to me that other factors, such as quantity and quality of publications, conferences and connections made, etc, are more important than where you obtained your PhD.

I would suggest finding a copy of Steven Krantz' book4, and read through it as soon as you can. It is directed almost entirely at students applying for or entering US programs, and is useful just to get an idea of what the whole enterprise of a PhD is about.


How do we explain a timing diagram in a technical talk?

If your audience cannot be expected to be fully familiar with timing diagrams, begin by explaining what they are - a lot of software people are unfamiliar with them.

I suggest alternating between showing the complete diagram for context and showing an expanded view of a portion of it. The expanded portion will be easier to read, and will call attention to the points you are currently making. You can add annotations that would not fit on the full diagram. When you show the full diagram, put a box around the piece you are going to explain next, so that the audience can see how it fits in the full diagram.

In the expanded views, I would keep all the signals in their normal order, but possibly bold the ones that are relevant to the current discussion.


Unhelpful and Overoptimistic PhD Supervisor

Is your supervisor overly optimistic? At least not obviously so. Getting a major revision and two rejections is a 1/3 success rate. That is actually pretty good for a round of first submissions, especially to top venues. But in the end it's of course your choice where you submit your work, and if you don't plan on staying in academia, you may wish to be more pragmatic.
Is your supervisor unhelpful? At least not less helpful than other supervisors of advanced PhD students. It's not uncommon for PhD students to eventually surpass their supervisors with respect to their research topic. At some point, you become the foremost expert on your specialization. All your supervisor can then do is offer hands-off guidance and mentoring, which they seem to be doing by evaluating your papers on an abstract level and suggesting suitable venues.
How can you get better substantive feedback? I understand you also need substantive feedback that goes beyond soft guidance. Here are some sources:

Submit early and often to respected journals to get feedback by reviewers. Reviewers are selected based on their specialization, so the feedback will be more specific than what you seem to get from your supervisor. (You're already tapping this source, good.)
Attend specialist workshops and conferences (especially if, like me, you're in a "journal field" where conferences are largely for work-in-progress).
Approach selected specialists and ask them for feedback on one of your drafts. The worst that can happen is that they ignore you, but many people are surprisingly generous, and specialists are often interested in what people in their subfield are working on. As incentive, you could also offer to reciprocate. (Even if you feel you're not senior enough to offer them advice, there's often something you can do - be a discussant in a panel, read a draft for overall consistency etc.) And who knows - this might even lead to a cooperation.
Share drafts with other students on your own level. Even if they don't have the specific expertise you are looking for, their feedback can improve your paper, and their misunderstandings can improve the clarity of your exposition (and thinking).
Finally, you might also consider looking for a more specialist co-supervisor. I know of some graduate programs that even require a second supervisor that can be selected at a later time.


My professor told us a previous version of our textbook would be okay, but has now decided that it isn't?

I've been both in situations where I told my students "I've looked at the 1st edition of the text and it's OK to use it" and "I've looked at the 1st edition of the text and it's not OK to use it". It sounds (unless I misunderstand your story) that your professor never looked at the prior edition and just assumed that it would be OK. I hope that "never assume" will be one of the lessons learned in this class by everyone, including your professor.
The professor tried to mitigate their mistake. (Other possible solutions might be to limit the topics of the guided inquiry to the material in the old edition, but that would not be fair to the students who do have the new edition.) Clearly, this creates a huge inconvenience for you (and the other people with the old edition), but also, more importantly, you're missing out on the material that's in the latest edition and is missing in the one you have.
My advice to you is twofold:

You're missing out on gaining the knowledge which is the goal of your being in this class and in school. You're not learning as much as the other students who have access to the current edition. Get hold of the current edition of the text book (buy it new, buy it used, rent it, download it for free from pirate sites, borrow from somebody). It may cost you, but the alternative is that you won't learn in this class whatever you've set out to learn.

Do not say anything to the professor. Nothing good is likely come out of it. The professor already knows that students who have the old text are inconvenienced. You have nothing new to say. The professor sounds very unlikely to change anything again, but also sounds like the type who might retaliate and dng your grade for complaining. If your school conducts course evaluations at the end of the semester, explain there clearly what went wrong.


What field should I choose if I want to do quantum information in future but there isn't a group in my university?

I am going to give you the same (very good) advice that I received when I asked a similar question a few months ago: don't ask us, ask them.

Find the names of some quantum information theorists.
Send a brief and polite email expressing interest in their research.
Ask them what kind of things you should specialise in, or what type
of courses you should take to help you reach your goal.
Don't be surprised if you don't get too many responses; academics are busy people.
Keep trying. If that's the area of research you really want to pursue, go for it. Read some journal articles. Find a good textbook and get stuck in.

Finally (and this is an important one), as Martin said in his answer to my question:

  "Quite a lot of people in senior levels in cosmology are interested in
  cosmology and are glad to find interest in cosmology in other people."

and this applies to quantum information too.


How should I respond to a reviewer comment that I didn't make changes when I did?

Treat it as a mistake.

It sounds like the reviewer may be looking at the old version of the manuscript, either due to their own mistake or someone else's.  Alternatively, the reviewer might not have noticed the changes (which sound somewhat minor).

You should assume the reviewer is simply mistaken and respond with that in mind.  Something like:

  Sorry, there seems to be a misunderstanding.  I did indeed update the paper with changes in response to the reviewer's request...

Did you also include a point-by-point response to the reviewer?

From the situation you describe, it sounds like you may not have.  Even if you agree and make the changes, you should still say so, and state what you have done.  For example:

  The references list needs to be updated. There are old references
  (1980s – 1990s) that can be replaced with more recent ones. Please see
  below a number of suggested recent papers that can replace old
  references. If the authors are not willing to omit old references at
  least can use them together with more recent ones.

  We have added several more recent references.  Thanks for the suggested papers.

This should remove the possibility of such a misunderstanding occurring.

If you did not do so initially, include it now when you respond to the reviewer's objection (and I would apologize for not making the changes clear in the first place).


You can base it on the data collected by other people already. There are many facts about user behaviors available in various research papers. This list has a seemingly good compilation of conferences.

So you base your design on facts and observations and user preferences that someone has published. Then your contribution can be using those principles to create a user interface for a domain, device, or a situation that no one else has explored yet.

I am not a usability person, but since the question was on research method, I thought I would provide my opinion.


Applied Math or Computer Science for graduate school

Thinking about "the industry" you want to end up in should play some role in your decision. For some careers applied math would be better than more cs, for some the opposite.

I suggest you find a program in an area you find particularly interesting. Enjoy your graduate studies, then think about jobs.

Your undergraduate studies suggest you'll be OK in grad school.


Accepting a scholarship for masters just to get the money and fund a future masters

First, my advice is to never think of a graduate school stipend as a way to earn a living (or to save for future goals). Stipends are design to barely cover minimum costs of living, and often fall short of that goal.

Second, I'm not sure whether a Master's degree in theoretical physics will help or hurt an application to a maths Ph.D. It seems that it could be related, depending on the subfield of maths that interests you.

Third, in many fields you can apply to Ph.D. programs directly without a completed M.S. degree first. Maybe that is also possible in your case.


What can be done if a former supervisor is giving a bad review?

Most job applications ask you to provide references or recommendation letters. Usually, you can choose which names you put on that list (and exclude former supervisors if you don't trust their reference).


Use plural or singular first person in abstract of a talk on collaborative work?

Use "we", because although only one person will be giving the talk, you are representing the work of multiple people.


Double major vs single major and multiple minors

I get this question a lot in undergraduate CS advising here at Michigan.  The context is usually that the student feels they can do more than just the minimum to earn their degree and they're wondering if it's worthwhile to put the extra effort into a minor or a dual degree.

If they're expecting or hoping it will make them more attractive to employers, the answer is no.  In fact, it can make them less attractive.  A resume that lists, e.g., dual majors in CS and ME, or CS and math (to pick real examples I'm familiar with) instantly raises a question in a hiring manager's mind:  What job are you looking for?  Do you want to be a computer scientist or a mechanical engineer?  A software engineer or a mathematician?  They only have particular job to fill and they're looking for someone who really wants that job, not someone who's not sure what they want.  To get a job, students with dual degrees or minors usually have to carefully craft their resumes to make very clear what they want, downplaying, almost to the point of burying the minor or dual degree.  (Again, I'm giving you real examples of what really happened.)

For those hoping to make themselves more attractive to employers, the far better choice is to put the extra effort into graduate school.  In CS, a master's is definitely the degree to get for those headed for industry.  In my experience (in 40+ years in industry) most hiring managers on high-performing teams have a master's (often earned part-time while working) and they like candidates with master's degrees.  It'll typically get you bumped to the top of the pile of resumes and, if they make an offer, it'll typically come with a small bump in salary, title and assignment.  If you work for 45 years and change jobs every 3 to 5 years, that's 9 to 15 times you'll get that bump.

The one great (but sole!) reason to go for a minor or a dual degree is that you simply love the subject and you recognize (correctly) that you have one chance to be an undergraduate and one chance to follow your dreams.  Certainly, if you go take a job as a software engineer, they'll pay for a master's but they're not going to pay for you to take philosophy courses.


Inform the search committee of another university about your current campus interview

I suspect that what you suggest is risky. It might bump them in either direction. If they are interested in you they will let you know, but probably on their own schedule. If you try to force the issue, it may be easier for them to say good-bye unless they really really want you.

Some places have fairly strict rules about things and may not be able to say more than they have. That would result in a general answer, of course.

I'd suggest you don't press too hard. Go to the other interview, evaluate what you hear there. If it sounds good, you can always ask for a delayed acceptance to see what happens at your preferred place. It might be acceptable or not, in which case you need to make a decision.

I would also guess that they aren't so naive as to think that you aren't exploring other options. It is certainly assumed that you are.


What could it signify if I find most forms of abstract math (e.g. Calculus) much easier than Physics, Chemistry, and so on?

I have felt more or less the same about certain topics within mathematics and to an extent about physics, biology etc, so I thought I would share my experience and thoughts. My level is different from yours but the feelings are certainly similar.
In early years of high school, I did both math and physics competitions to the National Olympiad level but I picked math because I excelled at it much more than I did at physics. Continuing with the math, I competed at IMO's; however, the topics like combinatorics came much harder to me than the other areas. I have known a number of students who are way better than I was at combinatorics but overall did not remotely reach my level because of the other areas math. Nevertheless, I always felt that those students, if tried as hard and was interested in geometry, algebra, and number theory as much as I did, would have blown me out of the water.
Now I am about to finish my PhD and still feel the same way about topics like Algebra, Topology etc. They just don't come naturally to me as do Analysis or Probability. Venturing into non-math subjects, I failed art history and botany 101, the latter of which is often considered as a free-A class. On the other hand, I have heard similar stories from my peers who are doing excellent research in Algebra - they would struggle quite a bit in an introductory analysis course, for instance.
What I am trying to get at in my ramblings is that certain things are just easier for some people and not for others. This, compounded with the lack of interest you have in certain subjects, most likely lead to the feeling of "inadequacy" that you are perhaps describing.


Potential referee for a journal submission

You shouldn't propose referees that have conflicts of interest. Any employee of your institute is conflicted. NSF adopt a similar stance for panelists: a panelist employed by the same institute as an applicant is conflicted. (Source: https://www.nsf.gov/attachments/108234/public/coi_1230P.doc.)

Conflicts may be real or perceived. For instance, an employee of your institute might be perceived as having a conflict, yet there might be no real conflict. Nonetheless, all conflicts should be avoided, because no one wants to be accused of malice.

That said, you are ultimately bound by the journal's definition of conflict and you should follow their guidance. Unfortunately, many journals are rather vague about conflicts, so you might need to establish your own position.


What should be the path to go from an R3 to R2 or R1 school?

I'd suggest two things. First is that you don't risk not getting tenure. So, keep doing the things that your current institution values and do them well.
But to move on into a more research oriented situation, you can get yourself connected to others who do serious research and work with them as a collaborator and eventually a co-author. This can build a reputation for yourself that might be attractive to an R1 or R2 institution.
I suspect, from your "handle" here that you are in mathematics. Fortunately that field is easier than many others for collaboration at a distance. You can attend seminars at some nearby R1, perhaps, and introduce yourself. Conferences are another possibility. Your school library may not be adequate, but interlibrary loan will get you anything you need.
The plan may take a while to reach fruition, but it can be done.


How should I respond when an audience points out an issue in my research in my talk?

Whatever you say, don't get defensive or passive-aggressive. Just discuss the remark as it is. He may be right, he may be wrong, and he may just have an interesting point, which, while not invalidating your approach, may show you some ways not to go. I've seen various possibilities and derailed at least one talk myself. Such situation is not very common but it happens now and then and what it really calls for is pursuing the issue to the end (not necessarily during the talk; you'll have to think when discussing such stuff, and being at the blackboard with 20 people looking at you slows your brain down quite a bit).

If it is not immediately clear that the observation just kills the presentation completely (in which case the only decent exit is to step down) the obvious immediate response would be something along the lines "Thanks for the observation. I haven't noticed that. Let's discuss it right after the talk". In most cases people will be happy to do it and you'll learn something new in the process. It is normally understood that the discussion of a controversial point during the talk itself is not a great idea.

As to how serious it is, it won't hurt your reputation much, if that was the question, but it may be serious enough to force you to completely abandon your current approach and that is something you'll need to find out. Don't expect the objection disappear once that professor is out of the room. If it was a valid point, it will arise again and again, so you'd better address the issue right away.


When is it most appropriate to post a preprint?

It makes the most sense to put it on arXiv when the preprint is complete (i.e. when xou submit it to a journal). (Some people even post to arXiv, wait a few days to maybe get interesting comments from other people (comments which improve the paper), and then submit it to a journal.) So the community can use your results before formal publication.

However, if for some reason or another, your supervisor does not want to do this, then their opinion trumps this argument.


What are the pros and cons of doing PhD study at a big vs. small department?

The main disadvantage of being a student in a big department is that the professor can not actually provide in-depth mentorship to that many people: your "real" advisor will most likely be some post-doc instead. The quality of post-doc advice is more variable since they haven't had as long as a professor to prove and improve themselves. (This one bit me personally, and I switched from a largeish department to a small one where I like it much better.)

On the plus side, a big team will likely have several different funding sources, so if your main grant runs out but you don't have enough work to graduate yet, it'll be easier to find you another contract to tide you over.


Using postdoc as a bridge to switch fields and transition from academia to industry

A PhD is a very high level qualification but going from psychology to biomedical engineering is quite a big change. So anybody who wants to hire somebody to do biomedical engineering would need some pretty strong arguments why they should hire you as a psychology phd. This applies to the professor looking for a postdoc the same way as in industry.

In comments you said you already have a postdoc offer. This seems to change things a lot because after the postdoc you can apply to biomedical engineering jobs and show you are qualified for them with the postdoc. Currently it seems very hard to judge your qualifications in that field.


Asking potential advisor about their post-interview opinion on my profile for PhD application

Typically application deadlines for fall admission are around December 1st; this timing gives the admissions committee time to review applications and have students interview at the university in Jan-Feb, with admission decisions coming in Mar-Apr.

I think the graduate coordinator saying spring admission is unusual might be a polite way of saying they don't really admit for spring; if you are applying to a program that is at all competitive, it isn't about not having red flags on your application, it's about being a stronger candidate than all but a handful of applicants.

If the professor you contacted isn't making a truly special effort to get you in for the spring, I don't think you should hold out hope for that. So far, everything you said - you had a nice interview, she contacted your references - sounds typical, not like she has taken an unusual interest in you that would allow you to bypass the typical admission procedures.

(note: you said you had your interview already; I'm assuming this was an informal interview with the professor you mentioned, and not an official interview conducted after you officially applied to the program)


The introduction of a paper has many important tasks. It introduces the topic you will discuss, it gives an overview over the field, etc. One important point, that is sometimes forgotten when strictly following the formal rules, is that a good introduction should answer the readers question "Why should I care about this?". For this, you need to know your reader, you need to know who is your target audience. If you are writing for a broad audience, then it is good to first introduce the general setting, as proposed by your advisor. If, on the other hand, you are writing for a very specific audience of experts, they might get bored if you spend two pages telling them what they already know. Thus, step one should be to figure out who you are writing for. Once you have this figured out, ask yourself how you can motivate them to read your work, to be interested in your results. Do your results have some sort of impact on their life, on their work? If yes, this should be made clear in the introduction.

In short, a good introduction covers all needed points (overview of the field, content of the paper, etc.) and furthermore motivates the reader to keep reading. Note that this motivation is also influenced by your writing style, your language skills, etc.

edit: Regarding the question who is right, your instructor or the other authors: I googled STS and found the term "Society for Science & the Public", so it looks like it might be for a public audience. However, I'd advice you to look into it a little more before deciding, maybe also ask your advisor about it.


How to write a Cover Letter for applying to a PhD programme

There's plenty of examples on the Web of the basic format a cover letter should take. There's a good template here on page 23 from Harvard. (Make sure to do it in TeX if applying for a math or comp. sci. PhD.)

Otherwise, my own personal advice ...

What not to do

The most common mistake I have found in cover letters is that they are too generic. Either they could have been written by anyone ("I have a keen interest in science. I was always curious as a ...") or could have been written for any programme ("I want to do a PhD as I believe I would be well-suited to a career in academia ..."). Keep such generic sentences to a minimum: the more of these a cover letter has, the more impersonal and unremarkable it is, and the more it leaves the suspicion that the same cover letter has been recycled for multiple applications and/or by multiple students.

Also, avoid hyperbole ("I am the best candidate for this position because ..."). You cannot know that you are the best candidate. This is an academic application, not an industrial one.

What to do

Make your cover letter personal, remarkable (i.e., stands out from other cover letters), specific to you and specific to the position at hand. Be enthusiastic. Be specific. Show that you've put thought into the position and why you are applying.

Relate your specific skill sets and previous experience to the programme you are applying for. Relate the content of specific aspects of your CV to the programme:

"During my masters, I enjoyed working on the topic of A, which relates to your programme [in this way]"

"I worked three summers at company B, where I gained experience in topic C ..."

"I visited your university in March last year and was impressed by ..."

"I read paper entitled 'D' published by your group at 'E' and was interested in ..."

"I recently published a paper 'F', which I believe compliments work by 'G' in your department on 'H' ..."

... and so forth.


What kind of opportunities exist in the industry for someone with a Ph.D in theoretical CS?

AT&T, Google, IBM, and Microsoft all have thriving basic research labs that regularly hire PhDs in theoretical computer science, and whose members regularly publish in theoretical computer science conferences and journals.  Yes, research at those labs is colored by the needs of their parent companies, but not as much as you might think.  All four companies (and several others) have thriving internship programs.

As with any other research job, your best bet in finding opportunities is to talk personally with people at the labs.  Go to FOCS/STOC/SODA, sit at the same lunch table as David Johnson or Muthu or Ken Clarkson or Yuval Peres, and just talk to them.  (It obviously helps if you have some research results that they care about.)  Ask your advisor to introduce you if you don't feel comfortable just introducing yourself.

(I'm about to get some angry emails from David, Muthu, Ken, and Yuval, aren't I?)


Applying to PhD programmes in multiple universities

Yes.

In the United States, it is expected that applicants are applying to many schools at the same time.

I applied to around 10 simultaneously, for example.


Appropriate response to misattributed title?

The standard answer to such issues is to ignore. By and large, these situations arise because the editor etc. did not care to look up the recipient's real title. There is no malicious intent, actually there is likely no intent at all other than trying to use a catch-all title that the editor assumes will not offend anybody (typically Dr. or Prof.). No harm is done by not rectifying this error, and indeed spending more than a short chuckle on this is too much effort.

(also, being addressed by the wrong title is, at least for me, so common that I mostly stopped noticing it)


Is it important to list the merits of a research paper?

Somehow it is common to start an introduction with a general blah-blah, basically saying that a field is important and repeating some popular facts.

However, in my opinion, the most important thing of the introduction is to say

what is there,
what is the actual contribution

and said in a precise way, so reader will know if the content is useful for her. And in such a way as "we prove X1 and X2, under the assumption of Y, and conjecture Z" instead of "we investigate X1, X2 and Z".

Of course, giving the general context is extremely important, but not more that saying what's there.

Personally, I wasted a lot of time reading papers whose abstract or introduction left me believing that they solve a general problem, when in fact it was only n=2,3,4 case, or just something tangentially related to my research interests.

There is an incentive to write introduction in a big talk / general blah-blah style (because it sounds serious, because it may bait uninterested readers, etc), but (IMHO) it is very counterproductive, sometimes verging on the edge of scientific dishonesty (i.e. an implicit overclaim).


How important is a online reputation for academics?

Generally speaking, online presence is not so important with respect to your career advancement in academia. Your professional stature is based on your publications, presentations, connections, and ability to obtain grant funding. When you look for positions, you'll be judged primarily on these criteria; blogs and media appearances are a very minor factor, if considered at all.

That being said, it may be beneficial in other respects. A strong online presence can significantly boost your visibility to those outside the academic environment. This can lead to consultation opportunities, collaboration opportunities with those outside of academia (think business ventures), and possibly job leads in industry. To the extent you're interested in those, you may want to invest in creating a strong online presence to help you advertise yourself.


Alternative ( and programmable) referencing tools for word on mac

Jabref: A cross platform, nice tool with a ton of useful features. Does not have big dependencies, and does no rely on obscure formats. Has good import/export and manages links to pdfs.


Referencing forum comments and translating citations using the Harvard citation style

This University of Birmingham document has a comprehensive guide as to cite references from different sources, specifically pages 5-6 have how to cite a forum post.

With regards to your second question, I would translate the quote to the language you are writing in and in the intext reference state "(translated from author, year)".


Sharing an old (never used) Phd Proposal with another student

If you are applying with that proposal, then you should not share it. How would you feel if they present it better than you and get a post while you don't? It is your work, present it and use it yourself.

Why not offer to read and help them edit their proposal? But let them write their own.


Sorry to say this, but if this is an adjunct position, I'd advise you to run like hell from it if you have indeed set your sights on a future TT position in a research university.

No matter what they say publicly, there are many who view a history of adjuncting on an applicant's c.v. as the mark of Cain when it comes to hiring for a TT position, at least in science and engineering.

I suspect people might be a bit more reasonable in the liberal arts and at teaching focused institutions.


How to get a PC member's attention to comment on or review my submission?

The PC member may be a professor, but I promise, they are human just like you and me. In your place, I'd find out the email address of professor and write a polite email making your case that

you are both researchers in the same field
you noticed the professor is actively participating in that special PhD consortium
your submission to that consortium was accepted
you have been following/citing that professor's work, but be very brief and direct about it! you're a researcher, but neither fan nor worshipper!
you care for a meeting at the conference to which that consortium is associated
you appreciate that professor's opinion

Or, if you really just care for feedback on that submission, you can flat out ask for an opinion on your submission.

These worked quite well for me. Also, direct approaches during coffee breaks are opportunities as well, but (T)PC members often have closed meetings during those so you would have to take your chances ...

But seriously, experts in their research areas care for the work of other researchers ... or you needn't care for their opinion.


How to handle an interview out of my league

Be happy for the opportunity to meet with the PI who's invited you for an interview, and go to the interview with an open mind and attitude. Answer questions you receive honestly and without artifice. Show rather than tell your enthusiasm for what's going on.

What's important is what you can do in the lab, and how you go about doing it. You might have a unique capability or perspective to bring that you don't know about it. Maybe your references are better than you think they are (and by extension you're undervaluing your skills!).

And try to avoid the impostor syndrome trap.


Should a translated thesis get a new DOI?

A translation of a book gets another ISBN than the original one:

  Each different language edition of a book will need its own ISBN.

Source

The same holds true for electronic books.

Regarding your thesis, you should follow this rule for the assignment of DOIs as well. A translation is always a new publication, especially if you publish the translation seperately/delayed on a pre-print server.

Think about it this way: Another translator might also produce a translation of your work. That one would differ from yours because translations depend on the translators. Each translation should have its own DOI to differenciate between them.

You should refer on the title page of the translation or on an extra page the original thesis (DOI) and mention that this ist a translation where you are the translator.

Additionally, Crossref, a DOI registration agency, explicitely states how to relate the DOI of the translation to the DOI of the original work in the metadata deposited along with the DOI:

  isTranslationOf

Source