Should a graduate student set up a research program flexible to a change in adviser? If so, how?

It is really your advisor's responsibility to make provisions for you. That's not to say that you bear no responsibility, or that they couldn't leave you in the lurch. But in general, it is reasonable for students to expect that their faculty will stay in place for the duration of their PhD, unless told otherwise. If the advisor does leave, they should work something out with you -- collaborating remotely, traveling with them, switching to another professor, etc.

Still, it can't hurt to ask about it. In your case, you are not willing/able to follow your advisor to a new university, and there may not be other local professors that could adopt you. So, it's reasonable to express your concern about getting stuck if they were to switch universities. Based on this conversation, you can decide if you want to change your research direction.

My guess is that he is planning to be around for at least the next 2-3 years (or he wouldn't have hired you); if he moves 4 years from now, you should be far enough along that you can finish up independently and check in via e-mail.


Co-author contributed almost nothing and is blocking publication

As with the another answer, I couldn't help but notice the almost literary way in which the Bob character is depicted:

  Clearly, his decisions are driven by spite and malevolence only

Unless the OP is Bob (what a twist!), she is really not in a position to make that claim.  In my experience, in 99% of all human behavior, after sufficient scrutiny, one finds that "driven by spite and malevolence only" is not the right explanation.  Moreover, I'm not sure I've ever seen an academic make a professional decision to spite someone else even though it hurt their own career as well. Regarding this the OP wrote:

  Bob is already tenured and has no pressure to publish.

Now I really think the OP cannot be Bob, because tenured people still have pressure to publish.  The stakes may be different from that of their long term academic survival, but they are not necessarily lesser or viewed as lesser by the tenured faculty.

Anyway, here's the heart of the matter in my mind:

  The contribution (data collection, analysis, writing) was 100% Alice and 0% Bob, except that the original idea was initiated during a conversation between Alice and Bob. Bob acknowledged several times in private that he did not contribute to the project, but he claimed co-authorship for the idea and Alice did not object to that.

I accept the premise of the story that Bob has done nothing on the paper past one initial conversation and is now (for some reason or reasons) acting against its timely publication in an appropriate venue.  Which is terrible behavior on his part, of course.  However, I must point out that Alice has also made a terrible mistake at some point in the process.  Bob "claimed" coauthorship for a project that someone else worked on for a year and that he had one conversation about.  That's egregiously improper behavior.  You shouldn't "claim coauthorship" under any circumstances; you should propose coauthorship and that proposal should be accompanied by specific proposed contributions.  If Alice went away after one conversation and worked for an entire year without telling Bob what she was doing, that's a mistake (and by the way, it could much more plausibly be part of what made Bob upset).  If she did tell Bob what she was working on, she should have clarified that if he wanted to be involved in the project he needed to do....something.  And no matter how they get to the endpoint, where Alice has a paper and Bob asks her to put his name on the paper, she needed to object to this.  In fact (although this is not the point), Alice's lack of objection could be construed as academic dishonesty: it misleads the reader as to the level of Bob's contribution.

This act of misleading seems to have come back to bite Alice in the behind.  It is much more awkward for her to take back sole control of her work after having submitted the jointly authored paper.  However, it may still be the right thing to do if the publication of the paper is important enough to her.  I do not see an ethical problem with Alice deciding to pull away with her work, given that it actually is solely her work.  That she may not be able to prove that to the satisfaction of all interested parties makes the action more risky, not less ethical.  If Alice and Bob really cannot agree on where to submit the paper, Alice has the right to say "I'm sorry it didn't work out.  I am taking my work with me...which as you know is everything except the original idea, which I will credit you for so that you can write a paper on your alternate development/implementation of the idea if you choose."  She should not allow the hypothetical threat of Bob's academic dishonesty (i.e., the possibility that he might tell other people that he did the work) to hold sway.

In fact, if Alice convinces Bob that she is serious about pulling away, then with any luck he will see that he has nothing to gain by pressing a fraudulent claim that the work was his that he wouldn't gain better and more easily just by allowing a joint submission to the journal Alice wants.


How to cite a database from R or another source

What about this?

@article{tong1990non,
title={Non-linear time series},
author={Tong, Howell},
journal={A Dynamical System Approach},
year={1990},
publisher={Oxford Univ. Press}
}

I used google scholar to find the right citation. Took less than a minute :)


Promising things in the rebuttal phase of a review

Rebuttal phases offer authors an opportunity to swing the opinion of reviewers. To swing the opinion of a reviewer, authors must present convincing evidence. If a reviewer wants more experiments, then it is (IMO) reasonable for authors to promise them. However, that won't swing the reviewer's opinion. To swing their opinion, authors need to convince reviewers that the additional experiments can be added before the camera-ready deadline. That is, authors must show that these experiments can be conducted quickly.


For many years on-line (a/k/a, "distance learning") degrees have been offered by regionally accredited universities In the USA. Until a decade or so ago, most of the degrees were earned by schools that specialized in distance learning. Even graduates of schools that had physical campuses and regional accreditation who studied full-time on campus were perceived as having earned their degrees through distance learning. Over the course of many decades with little or no government regulations, legitimate distance learning programs were viewed as "mail order" degrees and thus, looked down upon by brick and mortar schools as well as the business world. Schools often refused to accept transfer credits or admit holders of such degrees into their graduate programs. Employers, at least of top firms tended to reject such job applicants.

In more recent years however, many top tier universities have been offering on-line degrees adding legitimacy. American institutions of higher learning are slow to adapt new methodologies but are beginning to recognize we have already passed through the "Information Age."

So Daveel, I would say that if you earn your degree from a top tier university and your diploma does not make note that the degree is from the school's on-line division, your degree will increase its likelihood of being accepted in both the academic and business worlds. This is especially true of earned degrees in areas that are a natural match for on-line study, namely anything that has to do with computers.

Daveel, I suggest that you do an internet search on the history of distance learning. You will better understand the negative views that were held in the not so distant past. I would also highly suggest that you discuss the validity of such a degree with people in position to make such judgments. This specifically means academics people who hire professors in universities and human resource managers who are responsible for hiring in your intended field. If your degree is intended to be used for licensing purposes, contact the government agency that sets the licensing requirements. They will be the ones who can best answer your question.

Best wishes to you Daveel.


Does personal use include using the data for publication purpose

Yes, you contact them and get permission.

Section 1 that you quote states:

  You may access, view and make copies of the Data in the Site for your
  personal, non-commercial use and will not publish or otherwise
  distribute the Data for any other purpose

Which means you cannot publish that data in any form, which is what you say you wish to do.

So, contact them, you might find they give you qualified permission.

Edit: Buffy's comment is important, so I have borrowed it:

you have to assume that a non response means you cannot use it. Permission is required


Is it acceptable to copy verbatim the description of a software package?

As long as a proper reference and quotation indications are provided, there is nothing wrong with it - as with any other type of verbatim text copy. However; it is debatable whether this is a desirable approach, and this may vary with the traditions in individual fields.

If no reference is given it is (a mild form of) plagiarism.


Can a (stapler) PhD thesis comprise multiple unrelated papers?

This is dependent on your supervisor, the comittee and the referees (in the systems I know, almost exclusively the supervisor). Moreover, I would expect from any sane supervisor that they know the projects you are working on and at least warn you if you work too much on topics which can not be put into your thesis.

Most of the time (if your supervisor agrees) and you write an introduction outlining connections between the topics, you are fine. I have seen theses where the introduction was "We present some.papers in the area X, here is an introduction to X" and everything was great. It's just a formality.


As a teaching assistant, how to make tutorials more stimulating

You could take a jigsaw approach to teaching this.

Put students in groups.
Each group solves their problem
You work with each group to be sure it's correct.
Remix the groups so that each new group has at least one member from the original question group.
In the new group each person teaches the other members how to solve their question that they completed in the original group.

Everyone is engaged and you provide support as necessary. Each group should probably be no bigger than 4-5 members otherwise people start to get bored


Fellow student seems to be chasing rainbows. Should I step in?

Which kind of interaction, if any, is ethical and reasonable for me to engage in?

Discuss your concerns with your peer.

  How are similar problems usually handled in academia?

Through discussion.

  Are people like my fellow student...left alone to their own
  judgement,

Largely, yes, but...

  or do co-academics talk them out of seemingly bad ideas?

...in an ideal world colleagues (who they've discussed their work with) will try to bring them back on track.

  Do people criticize each others' research a lot?

Yes! Constructive criticism is central to the research process (unconstructive criticism is unfortunately common).


How to download references to database that a paper includes and all articles that cite the paper?

Yes, use Web of Science (Thomson Reuter's) database called Cited Reference Searching.  You can download a list of citations, which can be exported as *.csv.  Here is a link showing some of the basic functionalities.


What are some examples of "service activities" for the inexperienced/up-and-coming academic?

As for the question in the title, some common examples would be organising a seminar, helping to organise a conference or workshop, or serving on a committee.

I don't think that the activities you mention are generally considered 'service'.  They are definitely activities worth mentioning in other contexts, though.

If you really don't have any experience in 'service activities', then perhaps a good way to respond to questions about service would be to admit that you don't have such experience so far, but express interest in gaining such experience (with specific details of the kinds of service you are especially interested in).  I have no idea whether this is good advice, though, as I'm only a postdoc myself and have never been on a search committee.


Applying for second masters/Which GPA matters most?

A masters admissions committee will be interested in your grades in the highest level coursework that prepared you for the master's program you are applying for.  You did not say what discipline you are seeking a degree in.  Your teaching experience should count for more than your past course work, if you are teaching in a related area.


Is it normal for an Associate Editor to keep the paper for over a month after the reviews are done?

Unfortunately, turnaround for journals in most areas of computer science can be extremely slow. While I am not familiar with your area or this particular journal, the whole process can take anywhere from months to a couple of years. The typical reasons for the delay include:

Computer scientists care more about conferences than journals, so they focus their efforts on that, whereas journals have no hard deadlines;
Difficulty of finding reviewers (would-be reviewers say they don't have time); and
Reviewers who take months or years to submit their review (it sits on their backlog until the editor pesters them enough to complete it).

In your particular case, note that "awaiting AE decision" does require some work on the editor's part, or maybe even further discussion from the reviewers. So you can't assume that just because the status has changed, the paper is finished reviewing and ready to give back to you.

I would not worry about this. Consider putting your paper up on the arXiv. I have had journal papers take around a year for the whole process, and I have heard of some taking 2-3 years.


Plagiarism or self-plagiarism, when there are multiple non-coinciding authors

If A, B, and C write paper X together, then they are all taking responsibility as co-authors for its content, which effectively belongs to all of them jointly.

Now, let's say that A reuses text in an inappropriate way in paper Y, authored by A, D, and E.  Even if A wasn't the one who originally wrote the reused text, A was certainly part of the editing and revision process and has actively affirmed that this text is a good expression of A's understanding of the material in paper X.

I would thus count such reuse as self-plagiarism: the material from paper X is part of A's prior work, and the issue is that this text has been reused in an uncredited manner.

In fact, I would even count it as self-plagiarism if is was D or E that copied the material (this situation could actually happen fairly easily, if D or E copies the material as "placeholder material" into a first draft, expecting it to later be revised).  Again, the supposition is that A, as an author of paper X, will know their own work and has a responsibility to ensure that it is properly credited or properly paraphrased in its new context in paper Y.


Is investigating a new technology a justification in itself?

Usually, in life there are multiple options and methods to do things. Some are more common, others are rather uncommon.
Why are the uncommon ones uncommon? Sometimes they are just more inconvenient than the common ones for most people, so the uncommon option is not "catered for" and just falls behind, although it is perfectly fine. Other times, they have been tried and discarded a long time ago. In very rare cases, nobody really thought about it, although it is great.

It is similar in science.

A new technique can be groundbreaking. Or lost time and effort. The problem with this is, if there are enough well-established ways to do the same thing then you at least need to point out some flaws of these technologies that yours might not have (to make it similarly convenient). Otherwise, you are re-inventing the wheel, maybe even a very complicated to use wheel (that might have been discarded previously, as failures are unfortunately still rarely published you wouldn't necessarily know). You need at least one valid answer to "But why would we need this instead of all of the other methods?"


What is the "right" rate at which my papers should get accepted (to computer science conferences)?

To a first approximation, promotion depends on top-tier publications and nothing else. If career concerns are important (and they always are) keep submitting to top-tier venues (as long as you believe the work is good), even if it takes several iterations to get in.

There's so much variability in what gets accepted that it's best not to take the outcome of any single set of reviews too seriously.  If you start to see a consensus among reviewers as to why they recommend rejection, then of course you will need to address that.  But otherwise, don't lose hope and keep submitting.

Context: I'm a social scientist.


How shall I reply to the editor after a major revision of my paper?

Generally, you want to make the editor's and reviewers' job as easy as possible. As a reviewer I appreciate if the authors simply copy the reviewer comments and answer each and every of them while also helpfully pointing out related changes to the manuscript. Personally, I'd even address referee comments that point out typos (e.g., by answering them with "corrected"). At least, that demonstrates due diligence. It also doesn't require defining a threshold for a comment requiring an answer.

Of course, you should also write a short introduction and summary to that list of answers and changes.

So, yes, list all changes, but integrate that list into your answers to reviewer comments.


Advice on rejecting job offer from recommender

Say that you really wish you could accept her offer but, unfortunately, lack of money is becoming an issue for you. You need to start earning money (in order to live). With regret you will have to find a funded position even if it is not so desirable.


Hypothesis for an engineering project that can't be tested due to time constraints

For your specific case:

You could create a basic version of the system in a short time and conduct a study with a small number of clinicians. Have one group of them use it, and one group not use it. Define metrics that capture user variables (ease of use, tangible benefits) and system variables (how much different features are used, how much it adds to any existing discussion on products etc.). Make small changes in the system to change these variables, and map the outputs. By doing this, you already have an alpha-test, which will help you pitch the system when it is actually developed.

For the general case:

Often it is not possible to test the actual system/design/product in a limited time-frame. A good solution is to identify different parts of the system/design/product, compare these with existing systems and isolate parts that are unique and/or critical improvements. Develop just these parts, and test them either physically or through some kind of simulation. If it is a simulation, do some validation testing to increase confidence. Document everything, and generate sensible statistics during testing. Honestly report all the positive outcomes, the flaws and methods to tackle the flaws.


What is the process for getting sponsored by big companies for PhD research?

In order to do research with a big company's research arm you need to make contact with them. A blind request is probably not going to go anywhere. You need to use some intermediary who is trusted by them. Much of their research is proprietary and so they are required to be secretive about it.

Your advisor or another professor at your university who already has contact with the company might be a good way to get a proposal heard. Another way, oddly enough, is another graduate student who is employed by that company in an important position.

Such companies also have occasional public events, even at your own university, where their researchers look for talent and ideas. Sometimes their researchers will be presenters at conferences (as happens frequently in CS) and you can meet people there.

However, these days, many big companies that did basic research in the past have focused quite closely on product oriented applied research. There is less of an opportunity now for them to spend time and effort on your ideas unless they already align with their own.


Affiliation and address when writing under a pseudonym

The Encyclopedia of Types of Algebras 2010 was published in the Nankai Series in Pure, Applied Mathematics and Theoretical Physics under the name "G. W. Zinbiel", a fictitious mathematician – the name was formed by taking the name "Gottfried Wilhelm Leibniz" and reversing the order of the letters in the last name (really it was Jean-Louis Loday). As you can see, the affiliation is the famous "Zinbiel Institute of Mathematics, France"... an inexistent math institute (I heard it was located in Loday's apartment in Strasbourg).

From this example (published in 2012, so it certainly reflects modern practices), my guess is that as long as the editors accept it, you can pretty much put anything you like in the "affiliation".


I start with you related questions:

  Can I still be a good researcher if I constantly doubt the quality of my work?

You got it the wrong way. The real question is: Can I be a good researcher without constant doubt of the quality of my work? And the answer to this question is no. You should always question your work and and strive to make it better. Doubt is an integral part of research. But beware, that you should come out of this with "yes, my work matters/is of good quality/is relevant…" often enough either by your own conclusion of by feedback of others.

  Is there something that I can do to mitigate this part of the process?

Not sure, but you do not really need to. Please read this thread to see how to deal with insecurity and doubt as a researcher. You'll also find that the answer to

  Are self-doubt and desperation a normal part of scientific writing?

is most likely to be yes for most people regarding doubt and partly regarding desperation (assuming that "scientific writing" and "doing research" are quite similar in this respect). As Nate Eldredge notes, you should critically ask yourself if your self-doubt is close to be "pathological". I am not qualified in any way to give advice on how to diagnose yourself but you may want to read about the impostor syndrome.


Do conference attendees care about conference bags?

Having gone to quite a number of scientific conferences, my observation is that the degree to which attendees care about conference swag (both bags and otherwise) is inversely correlated to the number of conferences that they have attended.

Bags and other conference swag is wonderful, magical, and exciting when you haven't gone to many conferences.  It's a visible sign of scientific merit that you can even plop onto  the counter at the grocery store!  Forget bags, I've known people who have even saved their name badges as keepsakes.  For graduate students or occasional attendees, for those who go to only one or two conferences per year, these things can be very personally significant markers of acceptance and belonging.

As the saying goes, however, familiarity breeds contempt.  At this point in my career, I have a cupboard full of canvas bags.  When I go to a conference, I mostly just ignore the swag, and most of my close colleagues do as well.  But their graduate students, bright-eyed and so excited to be giving their first poster presentation ever, are likely to feel quite differently.

So, would people be OK receiving nothing but their badges? In many cases, it's just fine to give people nothing but their badges, and for more specialized meetings, that's just what they do.  But if people are paying a hefty fee to be there and there's a lot of graduate students or occasional attendees, why not give the little bit of extra to let the people who want to feel special are able to feel special?  A decent custom tote bag can cost as little as $1, so it's a remarkably small cost for the conference (far less than the leaden afternoon brownies mandated by the contract with the conference venue).  It will make some of the attendees very happy, and the people who really don't care can simply shove it in the back of their bag closet like I do.


Best way to apply for position as a teaching assistant

I would omit all the materials in your initial email, and just ask the lecturer a simple concise question:

I would be interested in working as a teaching assistant for your course.  Are there any openings, and if so, what is the procedure to apply?
If not, do you know who I would contact about working as a teaching assistant for another course?

There is no point in attaching your materials until you know that they are wanted and that you are sending them to the right person.


What can I do if one of my referees falsifies information in a Letter of Recommendation?

This is a most unusual situation. It's extremely rare for there to be such a large discrepancy between what a student thinks a professor thinks about them and what the professor actually thinks about them. Considering also that in this case the professor's opinion is wrong (as I will assume for the purposes of the answer, though I know nothing of the details of course), this scenario falls right through the cracks of the whole system of letters of recommendation, which was simply not designed with such situations in mind.

With that said, I think that somewhat ironically, the very strangeness of the situation offers a glimmer of hope, since it means that you can consider unusual steps that would not be acceptable in a more normal situation. Specifically, two such steps that I can think of are:

You could write a letter to the schools to which you applied (specifically, email it to the admissions committee, and make sure to cc a staff member and ask for an acknowledgement) in which you explain the situation. If your letter is well-written and the explanation that you offer is credible, this may counter the effect of the hypothetical damaging letter from the professor. You may want to line up another letter writer in advance of sending your letter to substitute for the bad one.
You could complain about the professor's behavior to the department chair or another professor you trust at your university, explain the details of the story, and ask them to write to the schools you applied to. This would not be a normal letter of recommendation. It should be an email sent directly to the admissions committee (rather than uploaded via some kind of automated system for LORs), again explaining the situation. Having the explanation come from the chair or another faculty member, if they agree to do it, will be more credible and increase the chances of success. In fact, the chair may very well know of similar stories of odd behavior involving your professor that you were not aware of, which he could mention or hint at in his/her letter, further strengthening the credibility of your claims.

Note that in both of these suggestions you will have to disclose all the information about what took place between you and your professor to make the explanation credible and have a realistic hope that the professor's false accusations will be ignored. If some of what took place is embarrassing or damaging to you due to real rather than imagined reasons, I'm afraid that's just a risk you'll have to take. Good luck!


For early researchers, how does the ranking of a university relate to future career in high ranked universities?

Let me tell you what I told a friend who was struggling with a decision between a great department without people in his area and a good department with people in his area (including collaborators):

Go to the better school.  They're not in the same league, and you may have a chance in the future to get more people in your area.  You can still travel to the other school to collaborate, but you'll get much better students and postdocs at the better place.  You'll be in a better environment exchanging ideas with top people.

This answer of JeffE to a related question discusses the "better environment" aspect more.

He did in fact go to the better school, and afterwards was happy with his decision.  One thing he remarked was just because of the what university it is, they had top people coming in all the time and he got to interact with so many of them in a year, which wouldn't have been possible at the other school.

While I won't say this is universally what you should do (there may be other factors that matter to you here), I don't see much advantage of B, unless the people at B are truly top people in the area (in which case they might leave soon) that you want to work closly with, and wouldn't be likely to if you went to A.  Since you say University B is not research intensive, you may not have as much time as you would for research at University A (e.g., the teaching expectations might be much more per class, or more administrative duties).  Note there can also be tension in a department when part of the faculty is research active and part is effectively not.


Potential consequences of the UK Research Excellence Framework (REF) for US job prospects

The REF credits departments for grant capture and not the individual. This means that large grants with multiple PIs tend to be prioritized over smaller grants to individuals. In terms of the US job market, being able to demonstrate grant capture at the individual level is important in many fields. For example, generally in the US being the only PI on a $200,000 grant is viewed better than being one of ten PIs on a $5,000,000 grant.

The REF "requires" academics to "produce" 4 high "quality" publications over a 4 year period. Only the 4 "best" publications matter. This results in a push for splashy, as opposed to solid, research. The goal for the REF is to make your work look important to people peripherally related to your field and not the people who specialize in your subarea. Authorship across the 4 publications can also be shared so teaming up with a more senior colleague and being a secondary author is very desirable for the REF. For the REF, someone who is a co-author on 4 Nature papers with colleagues at different universities, and nothing else, could easily get a position as an associate professor, if not a full professor. In the US, search committees want to see a body of solid work that is clearly done by the applicant.

Being able to demonstrate impact is also important for the REF. This requires wider engagement with people outside your field. Having research that can be link to a "change in process" is key for the REF. For example, a clinical trial that shows X is better than Y would be considered "high impact" while the development of X would have less impact. Blue skies basic research has essentially no impact and is discuraged. US job searches do not really care about impact.


Finding a place in interdisciplinary sciences as someone who develops computational methods and algorithms for other fields?

There is a concept of a research programmer, but it's pretty rare. My primary degrees are in maths and social sciences. While my PhD is in computer science, I use programming as a tool to do social science and am not really a great programmer. However, there is a lot of programming in the research projects that I tend to be involved in. For some projects, we would include a research programmer - someone with excellent programming skills who is doing methods development research. That is, the person would be developing new algorithms to solve some social science problem and implementing it. It sounds like this is what you are trying to find.

If so, such jobs do exist. However, they do not lead to a stable academic job since there's not a clear set of subjects that such a person can teach. Furthermore, the jobs are fairly rare.

Nevertheless, if you want this sort of job, you really need to work out what you ARE interested in. That is, economics or physics or whatever else. After that, you can think about what sort of problems are amenable to computational methods for their solutions. For example, look at computational social sciences (I do network science and agent-based modelling) and computational economics.


When the co-author of a potential paper is not responsible

The answer to your question is the same as for 50% of the other questions on this website: Talk to your adviser. Find out what the hold-up is, how you can help, what other roles you could take on in the lab to free him from work that holds up his side of the collaboration. Communicate about what your issues are.


In my field (chemistry), the practice is: for those journals that make a clear distinction between minor and major revision requests, “major revision” means that the paper will have to undergo further review after revision, usually by the same referees, while “minor revision” means that while changes should be made, no further reviewing is needed.

Not all journals make this distinction, however: for some, the need for further reviewing will be decided by the editor upon reading your response to the reviewers’ comments.

For example, here are screenshots of the web interface facing the reviewer of ACS and RSC journals when he has to fill in his review. You can see that the categories are different for different journals.

Example 1:

Example 2:


How to politely follow up after contacting potential postdoc advisor?

I've encountered this situation recently. My personal strategy has worked well on multiple occasion.

Send back the first e-mail with a beginning similar to this (I suggest you adapt it):
Dear Dr Smith,

I'm afraid my precedent e-mail arrived in your junk mail. Just in case, here it is again.
Thank you very much for your attention.

Edit: I don't resend an e-mail after only a week. I usually wait 2-3 weeks...even more !


Writing multiple areas of interest in SOP

The Statement of Purpose should reflect your interest in your mathematics and give an impression of both you as a scholar and why the department you are applying to should think that you will be successful. As such, you have great freedom in explaining what you find exciting and interesting, and if that includes your desire to look into multiple areas, then that seems like a fine approach to writing a SoP.

In other words, I would not overthink this: Write why you want to go to grad school and why anyone should think that you will succeed there!

(As a comment on the side: I would suggest you spend more time proof reading what you write. There is a typo in the title of your question, and multiple language and grammar mistakes in the question itself. I don't know whether English is your first language, but at the very least typos are completely avoidable; not proofreading what you write just makes you look sloppy and unprofessional.)


Unhappy with my PHD CS research topic. What should I do?

In general, a proof or demonstration that something does not work for a particular application can be as valuable as proving that something does work. This is especially true if a priori, the thing should seem to work.

You might explore with your advisor whether this is a viable direction for your work to take. I can't predict what he/she would say, but it is worth spending some time in the exploration before you bail out. You probably have some deep insights into the problem that you can bring to bear.

Again, research is about knowledge, not about doing some inappropriate thing just to "force" it to kind of work. Extract the knowledge from the project.

But your advisor is likely the final judge here.


Why aren't B.Th., B.Ed., Mus.B., B.Chir. or M.B. degree holders members of Cambridge's Senate?

To some extent, the answer is "because the statutes and ordinances say so". However: these are not 'standard' Cambridge undergraduate degrees. If you go to Cambridge and study a 3-year undergraduate programme in theology, education, music or medicine, you will graduate with a BA degree. The listed degrees are/were awarded for specific, somewhat vocational, courses - for example, the BTh is a special two-year programme for people training for ordination.


When is it appropriate to use a university seal as a graduate student, post-doc or research scientist?

It is my personal understanding as a professor and former chair of a program that you can use the letterhead for job searches as long as you retain a position of some kind at the university: postdoc, doctoral candidate, visiting professor, lecturer, research scientist, etc.

As an appropriate proxy, use the letterhead as long as you have a university e-mail address (that isn't an alumni one).

Once you're no longer affiliated with the university because you graduated or separated, then you should not use the letterhead.

[Note that use of letterhead for job searches is a special case. Do not use the letterhead for other personal purposes - such as writing a letter to your congressperson - if you're in a liminal position as the possible blowback can be hazardous to your career].


What are the steps to establish an academic journal?

This question is indeed rather broad. The specific questions you ask are at once basic and easily researched (you can get basic information about ISSN, ISBN and DOI on Wikipedia, for example) and quite complex (indices have their own rules). This leads me to think that you don't know what you don't know.

I suggest that you contact

A managing editor or production manager of a journal in your field
The publication liaison of your learned society
The acquisitions or new projects person at one of the big journal publishers like Elsevier or Wiley

Good luck.


How can I carefully find out if a professor's work is well-respected within the department?

First of all, every academic has their own opinion of others' work. Just because a student (or your advisor) thought that someone else's work was not significant does not necessarily mean that it is the truth. Although your advisor cites "others" in relaying his opinions, maybe your advisor and the professor in question hate each other, maybe the department places little importance on the professor's work, etc. On the other hand, note that if the professor is publishing in the top journals, then there are some people who think that your professor's work is great also! The point here is that most of the time, opinions are subjective.

There are a couple of ways that you can judge someone's work, being junior.

The first is to see how their students do after graduation. Look at their recent students and postdocs, and see how many remain in academia. Did they manage to secure good positions? Are they productive with research? These are good indications of whether your professor's work is derivative or original.

Secondly, talk to the older grad students or postdocs. They have been around the field long enough to understand what work is important, but not long enough that they are straightforward with you. Talk to a lot of them, and see if there is a consensus, although it would be difficult to get a fair sample!

But most of all, do what interests you! It is good to have an influential advisor, but unless you really believe in your work, I don't think it matters too much whether your research is important or not.


What do you think is the decision on my paper? Reject or accept?

Decision pending. Likely, this means that the review phase of the paper is finished, and is currently awaiting a final verdict by the associate editor or editor-in-chief.


Phd Supervisor is asking me to work remotely with him for next 3-4 years? What should I do?

You don't mention where you live; my answer is based on experience in the US.  You also don't say whether your advisor is moving to a different department, moving to a different university, leaving academia for industry, or simply retiring; my answer assumes they're moving to a different university.

You and your supervisor should have been talking about this from the moment they decided to leave (if not sooner).  If you haven't been, START NOW!  By agreeing to advise you, they accepted an ethical responsibility to guide you to the completion of your degree to the best of their ability.  That obligation survives their departure and extends to their new employer.  Similarly, by admitting you into the PhD program, your current department accepted an obligation to help you complete your degree, despite your advisor's departure.  Everyone involved is supposed to have your back.

When faculty move from one university to another, they rarely move only the books in their office; they more typically move a large fraction of the system that supports their research.  That can include funding, equipment, postdocs, and yes, PhD students.  It's quite common for students to keep their advisors even after they move.  I've seen this happen a few different ways:

The student enrolls in the PhD program in advisor's new department and moves to the new department.  This can happen "off-cycle", bypassing the normal admissions calendar if the advisor negotiates for that.  If the new PhD program has course requirements, the student may be able to transfer some or all of the courses taken at their original department, especially if the advisor negotiates for that.
The student moves to the advisor's department, but remains formally enrolled in their original PhD program.  This may require the advisor to negotiate with both departments, to retain advising rights and grants in the old department, and to get access to office space and equipment for a non-student in the new department.  This may also require the advisor and student to physically travel to the old department for formalities like the defense.
The student formally enrolls in the advisor's new department, but remains physically at the old department.  (Some students have family or other geographic constraints.)
The student stays in the original department, both physically and formally, and is advised remotely by their advisor via email, phone calls, video chats, and sporadic physical visits.  This is really advisable only for students late in the PhD program, who can work more independently.  If the advisor retains advising rights in the old department, they can remain the advisor or record; otherwise, the student needs to find a local co-advisor to sign the paperwork.  The advisor would likely need to retain some funding at the old institution.
The student transitions to a new (co-)advisor at the old department, with the old advisor's help.  This may require your current advisor to delay their departure for a semester or two while the transition is underway.

There are similar options for faculty who are retiring, and possibly (depending on their new job) even faculty moving to industry.

All of these options require your current advisor to negotiate on your behalf.  This is why it is absolutely vital to discuss your options with your advisor as soon as possible.


How do you ask someone what he or she would prefer to be called?

I think that it is best to err on the side of being too formal. I tend to ask after I refer to their name for the first time: "It's so nice to talk with you, Dr. Smith- Do you prefer Dr. Smith or do you go by another name or title?..." Then continue with your conversation.


Is there any term that describes the main example that goes through the entire research paper?

When I use a running example (as I frequently do), I just call it a running example.  I don't know any reason why that wouldn't be a good enough term.


but what I wonder is if I can transfer these money to my stipend if I don't use it totally?

No, usually you can't.

In Italy, typically, funds cannot be transferred directly to non-employees (a PhD student is not an employee of a university), and only certain funds, like those coming from research contracts, can be transferred to employees. In the latter case, the payment should be approved by the department.

Moreover, as a PhD student, you are probably not even directly responsible of those research funds, which are probably under the responsibility of your advisor.


Should you tell grad students to apply for grants you know they won't get?

If what you say about your students' writing skills and their chances of getting a major grant is accurate, I would say that it's a complete waste of everyone's time - theirs, yours, and the reviewers - to have them write such major grant proposals. Forget about using such proposal writing as a vehicle to improve their writing skills. The experience won't benefit them if their current writing skills are really as bad as you say they are. Instead, have them focus on the smaller-ticket grants. If any of them show evidence of more promise and growth after such experiences, then you can direct these more promising students towards targets that are higher up on the grant ladder.


How to avoid self-plagiarism when adapting dissertation into a paper?

The dissertation is not a published work in the same sense as a journal or conference paper.  It is normal for a recent graduate to take large chunks of their thesis, with minimal or no modification, and use the excerpts in more formal publications.  You do not need to worry about self plagiarism in this context.

The copying often goes the other way as well.  If you already have published papers when it's time to write your dissertation, you may take large chunks of the published papers and reuse them in the dissertation.  In some fields (mathematics or theoretical physics, for example), this is quite commonplace.  People talk about "stapling your papers together" to make a thesis.  In reality, there is more to it than that.  Introductory and concluding material are needed, but many theses have chapters that are based on published manuscripts, with relatively little editing.


Expounding implementation details of a paper and provide a full computational analysis

This is a problem with a lot of research these days: reproducibility. From my experience publishing an implementation approach to a paper, when no approach was given is a valid academic contribution, as there could be various approaches each with its own advantages and disadvantages. If you can expand your work to include multiple reasonable potential approaches and their outcomes, as well as potential pitfalls that could arise (you probably already went through both of these with your work), it would be a significant worthwhile contribution.

The next question is whether the journal you submit to sees it this way, and that can be a hit or miss. The only way to know is to try. Try to frame your work as "Approaches to X (where X is the sub-problem you tackled), instead of linking it too heavily with the original work (where X is e.g. the name of the original paper). If everything else fails, you can always try a conference or open publication although the "social credit" for these will be much less.

I also support the idea of publishing your code on github. The more we share the better off we all will be. This open sharing approach has aided in the significant machine learning publishing boom, and fast pace of improvements we are seeing.


Is it unethical to submit for review multiple articles which overlap in some respect?

You should avoid self-plagiarism. Having an identical section in both papers would be ethically questionable. They could have the same overall meaning, but I would try to rephrase them differently as you might already have done.
Also have your papers cite each other as being submitted, and possibly update the final manuscript with full citations.
It may be a good idea to let the journal editor know that this is happening. They may be able to provide you with specific guidelines.


Does posting a preprint to the arXiv reduce the chances to acceptance?

I'd say the answer will depend on the field. In maths it is hard to find new papers that were not posted to arxiv first. Disregarding or even disallowing such papers would spell death for a journal. Thus, regarding acceptance there are no pros and cons, it will simply not matter. Regarding all the other aspects, such as visibility, etc., publishing a preprint is an obvious choice, but that topic has been discussed extensively in previous questions.
I guess the same will hold true for physics and CS. It might be different in other fields where arxiv and similar sites are used less often, but it seems to me that there is a slow convergence towards extensive use of preprint repositories in all branches of science.


Different CV for applying to university and applying to fellowship?

Unlike a resume, the contents of your CV should typically be comprehensive and complete, including both research experience and service.  You might want to reshuffle the positions of sections within the CV for a target where you want to emphasize one aspect vs. another, but the content should be no different.


Is sending a CV with recommendation letter a good idea?

It's a little unusual. Typically you insert relevant material into the letter. Something like

  Dear So and So,
      I'm awesome in these 10 different ways

  Now let me tell you about Candidate.


Presenting a survey/review paper at a conference

There are several reasons for this point of view:

when looking for a survey/review paper in a journal or talk at a conference, the first thing I do – is looking at the name of the researcher, how good (and how many) are his works in this field (and subfield of the overview talk).
to give a good survey talk, you both have to have a "big-picture" vision, as well as exposure to various details in many methods. It is hard to achieve both at the early stages of your career. And, most importantly, your potential audience has a tendency to think that it is unlikely.
giving review talk is, in my opinion, harder than a novel research one. The structure is different, and you cannot focus on the novel idea that is your baby and you are presenting. I would say, you need better presentation and slides' organization skills to prepare a similar quality survey talk.
presenting survey talks and publishing review papers is not perceived as good for your academic career. While it counts as a publication (and is no doubt useful for the research community), it is no equal in terms of the impact on your CV. Surveys can rarely define somebody's career and they play less of a role during application for a tenure-track position.

Is it fair? No. Can a young researcher give an excellent, inspiring, and even novel overview talk? Sure. Can that boost your research reputation? Sure. Still, unlikely in general.

I can totally see why the preparation of the survey paper itself is very useful:

by preparing a review paper you learn the subject matter, past and recent progress in the best possible way
you create a quality publication for others to enjoy
you learn the skill of writing a survey paper itself (which is different from a regular paper in a journal)

However, in my opinion, the benefits of actually presenting such a paper at a conference are limited for an early-career researcher.


Can a theoretical physicist win a Nobel Prize anymore?

We've now seen three Nobel prizes in physics awarded since the posting of this question (February 2016), and I think it's fair to say that the answer has proven to be an unequivocal 'yes'. So far, four out of nine physics Nobel laureates have been theorists.

The 2016 prize was awarded to three condensed matter theorists (Thouless, Haldane, and Kosterlitz) "for theoretical discoveries of topological phase transitions and topological phases of matter". The 2017 prize was awarded to Weiss, Barish, and Thorne "for decisive contributions to the LIGO detector and the observation of gravitational waves." Of these, Kip Thorne is very much a theorist, known for his work in relativity and astrophysics, and for being one of the authors of that one thick book with an apple on the cover.


How can I find journals in my field that do not charge author fees?

You can use websites like DOAJ.org to search for relevant open access journals that do not charge publication fees.

This example query for 'algorithms' reveals 40 such cost-free open access journals, some of which may be relevant to you, depending on what exact type of algorithm you're publishing.

Using this I found The Electronic Journal of Combinatorics & Image Processing Online (IPOL Journal) which both look like reputable, high-quality, publication-fee-free, algorithm-relevant journals to me.

Some of the information is a little out of date though, for instance the journal Algorithms (MDPI) I think now charges 300 CHF (Swiss Francs) although initially it was free, in the past.


Can I write a book based on my own published papers?

If your book is simply reprinting your papers it certainly isn't plagiarism. However, if you are re-writing and re-phrasing them, to bring them together as a whole, you should do it just as if you were writing a book based on the work of others.

In other words, when you quote or paraphrase your old papers, give a citation, just as if it were someone else's paper. This makes your intent clear to the reader. More importantly, however, is that it lets the reader go back to your originals for any context that they feel they might want.

Moreover, if your book contains new material as well as the old, the citations should make it clear what is new and what was previously written.

But just restating what you said before without citation is, today, considered self plagiarism. In some circles it is considered very serious, but mostly as it prevents the reader from finding that original context along with your references and such.

Even a statement at the beginning of your book that says that you will be copying and/or paraphrasing without citation would not be appreciated by your readers.

Treat your own work like you would that of any other scholar. This is true in general, not just for the example of a book.


A journal is interested in my column proposal, but so is another journal that initially rejected it. What are my obligations?

If you don't care which journal your column appears in, then you probably, at the very least, owe Journal A a note that says something along the lines of

  Since receiving your original rejection on Date X, 2015, I subsequently proposed the column to another journal. They have since also asked me for a draft to review. At this time, please consider my original column proposal withdrawn.

If you strongly prefer publishing with Journal A, then you have more of a quandary on your hands and should probably get in touch with the editor at Journal B handling your proposal to have a frank and open discussion about the situation. If the difference between Journal A and B is substantial in your field, then the editor at B might be understanding and cut you some ethical/personal slack and suggest that you pull your column proposal from Journal B and go back to A.

I think there's a case to be made that Journal B now has priority (dibs) over Journal A in competition for the column. Journal A originally passed on the proposal, and some sort of release from B is warranted before giving A another shot at it. In my opinion, the editor at B is in no way required to give up their priority position. You might be able to talk them into it, but since A had the initial shot at your column and passed, they don't have much room to complain that they should be the first to publish the column.


Credit with helping to write a PhD thesis

In some fields, almost all work is done as a collaboration. In these fields, it is not at all unusual for this collaborative work to end up in a student's thesis. However, the thesis text should clearly state "This chapter describes joint work with X" (e.g. in a footnote).

However, to really get credit for this joint research, you should prepare a manuscript and try to get it published, or at least release a preprint you can put online (if there isn't time to get it published before you apply to grad school).

For the editing assistance, the most you can get is a thanks in the acknowledgements, and help with editing is not likely to impress an admissions committee.


I think the few different statuses you would typically indicate are:

Submitted: after submission but before you’ve received any indication that it’s being reviewed
Under review: during the entire back and forth of reviews, revisions, rebuttals, etc.
Forthcoming (also called “In press”): once it’s been accepted but hasn’t yet been published.

As for formatting, it probably doesn't matter much as long as all the relevant info is there, but a few options to consider are:

  [1] A. Author et al., Brilliant Title That Draws Attention, J. Phys. B, submitted August, 2019. Under review. [arXiv:1908.12345]

or

  [1] A. Author et al., Brilliant Title That Draws Attention, under review at J. Phys. B, submitted August, 2019. [arXiv:1908.12345]

I'm sure you can find other examples elsewhere (such as this post).


Which date should I include in personal statement?

If this is for an application for university, then you do not need to date your personal statement. That is because your application as a whole is dated and signed by you at the very end.

Otherwise, you can initialize and date it at the end of the document, e.g.:

KN
2014.06.30


What is the strategy to identify natural experiment as a PhD student?

Don't sit in your cubicle!

Go to the library (a physical one assuming you have one still). Read the newspapers (physical ones are easier to browse but you can do this on line).  Look at the controversies, the scandals, that are emerging daily on the news: political lies, child abuse, discriminative policies, public funding, privatization, quantitative easing, bank bail outs. Look at states with different parties in control. Get hold of the latest and previous census data. Get hold of the Enron emails. Get access to the data that companies are building up through loyalty cards and credit cards.  Talk to you med school or a disability charity about mining their data.  Have a look at the data mining literature - talk to the people at your university who do this and what contacts they have...


How much should a supervisor expect from students who have graduated?

She might be panicking. Normally, it's good practice (though not strictly required) to hand-over such lab information in a well-documented process. It is a good idea to make a hand-over closing date (even with friendly people) to make clear that/when the process is finished (of course, you could help for isolated questions, but this should be the conclusion of the main process).

My suggestion is: create an overview of what you need to document and with which your task can be considered essentially complete. She cannot expect you to document everything - unfortunately, that transition would have had to happen earlier, with a newer research student. When a research student leaves, it is normal that know-how leaves with them, sadly.

The fact that you write papers together lets this boundary blur, so you may have to pay a higher "tribute" cost to her if you want to maintain relations. However, I think, with friendly pointers to the precise locations where it's written and trying to promoting a habit of actually looking it up there, you may get somewhere. Some people have a hard time to follow rules of search for other people's work, and your task is to try to break that habit gently.


What is feasibility analysis in thesis proposal?

Feasibility is about whether the research can, in fact, be successfully completed with the time and other resources available. In an undergraduate course, a study requiring three years is infeasible.
If the research suggests building something, feasibility also involves whether it is possible to build such a thing given costs, and even, potentially, the laws of physics.
Another way to look at it for such a course is to ask, is this project actually do-able in the timeframe required. And if the answer comes up no, then you need to rescale or otherwise modify the proposal.


Do you list a long-term visit as an affiliation (in a paper, presentation, etc.)?

I don't think that this question has a general answer as there might be guidelines applying to specific institutions.
I know of some institutions that explicitly require long-term visitors to state their affiliation. You should probably inquire about this with your institution. The institutions that I know that have rules about this usually require you to state your affiliation, and I have never seen a rule where you would be disallowed from doing that. So in any case, if a lot of the work has been carried out at the other institution and thus been taking advantage of their resources, an acknowledgement of that should probably be given in some way, whether it is in the form of a full affiliation, an affiliation with a footnote, or mentioning them in the acknowledgement section of the publication.


When you first refer to it say something like "the Algorithm proposed by (Xia, et al. 2008) which we refer to as XAB" where you replace XAB with the first letters of the authors' last names in the order that they appear in the bibliography. So if the authors are Xia, Alpha, Beta, you would use XAB. If the authors are Xia, Yen, Ping, you would use XYP. I wouldn't use more than about the first 3 or 4 author's last names, however.

This way if you are referring to multiple algorithms, you can give a clear reference to each. If it turns out that multiple algorithms you are referencing would have the same name given this scheme, you can also throw in the last two digits of the year. So you would have XAB08 and XAB09.


Can a blind person do a post-doc in the humanities?

In the United States there's what is known as the Americans with Disabilities Act (ADA)

which prohibits discrimination based on disabilities and mandates reasonable accomodations. Full or partial blindness will definitely fall under that category, and so they are legally prohibited from discriminating against you and if hired will work with you to help out. Many other locations have similar laws. In Canada the laws vary from province to province, but most of Canada has similar laws. Many (although not all) European countries have similar laws or regulations as well.


One of the things that is too much overlooked is that an abstract is read by a more diverse crowd of people than the rest of your paper. So, you have three different goals:

Give a take-home message to people who aren't interested enough to read the full paper.
Convince the undecided to read it.
Make it easier for experts to find it.

Nowadays, #3 is not so much of a constraint: Google and other search engines allow for full-text searching. So, focus on #1 and #2: be concise, crystal-clear, attractive.

Enough with the generalities. I love to critique, so I'll give it a try: I'm not in your field, which I think makes me a good test reader for your abstract, but also makes it harder for me to actually suggest actual changes to it. Anyway…

I think it's decent: no catastrophe, but far from enthusiastic. My main comment would be that it lacks a clear statement of the broader issue you are trying to address. You could start with it, something like:

  The past few years have seen large advances in the statistical modeling of DNA sequences, mostly based on genetic algorithms. In this work, we explore the efficiency of an alternative and simpler route, and show how to efficiently choose within a class of distribution models.

I have filled in with semi-random keywords/buzzwords, just to give you a sense of how to achieve it. The idea is to put your findings in perspective:

Roughly, what subfield are you working in?
What is the main trend in this field?
How do you position your work with respect to this recent research?

Then trim down the rest of the text:

  We showcase a method to select a Bayesian model for a collection of DNA sequences, generated from a specifically chosen distribution model capture long range correlation structure. We choose the model based its prior predictive distribution. Applying this method to model human and mouse Recombination Signal Sequences (RSS), we predict which of a larger group of sequences are RSS in the context of a cross-validation setup.

(I hope I did not lose or betray some of the meaning, it's hard when you don't get the finer points of the text… but you get the idea anyway!)


Difference between Phd degree while remaining a student, and after quitting a Japanese university?

Disclaimer: my Japanese is quite good, but I'm not a native speaker, so please keep that in mind.

Based on the degree statutes of your university (広島大学学位規則), you need not be enrolled in the graduate program to submit a thesis and apply for a defense (Article 2 Section 3). However, non-matriculated students must pay a fee of 57,000 JPY for the defense. This fee can be waived if the applicant is not currently enrolled, but has completed the program and left the university without defending within the past year (Article 4 Section 3). If you wait longer than one year you can technically still submit and apply to defend, but you would have to pay the fee.

I spent 10 years at a Japanese university, although not the same as yours. I can recall one person who got their degree in the non-traditional way, so it is possible but uncommon.

I assume you don't have Japanese citizenship, so have you considered what will happen to your residency status? I can't recall the procedures, but you could run into trouble unless you have a job lined up and can change your status easily. I would discuss this with your adviser, but I can almost guarantee things will go more smoothly if you just wait for the paper to be accepted.  You may need to revise the paper based on reviewer comments as well. In the meantime, maybe you can apply for positions or spend time making your CV and dissertation look amazing.


Journals have deadlines for publication. Everything that will go into issue X needs to be ready by date Y. If you meet their deadlines you increase your chances for early publication, otherwise you may be put off.

However another problem is that while the reviewing is "normal" the editorial process of choosing papers for issue X also comes in to play. The other language of the publisher's reply might imply conditional acceptance if returned by the date given. After that, unless you already have acceptance, it might become more tenuous.

Basically, what they are saying is "We have constraints here. Please help us meet them." It would be good, if not essential, to honor that.


How are mathematics conference presentations usually done and what to expect from the question and answer component?

I'm not sure I really understand what you want to know.  Have you never seen a conference talk? (If you haven't, you can watch some here.)  Perhaps you're going to different conferences from me.  The question and answer part is usually 2 minutes at the end of the talk; occasionally no one has a question, but often to be polite people will ask for a clarification of some point or ask about a connection to something they free-associated about during your talk.  You should do your best to answer, but people will understand if you say "Gee, I hadn't thought about it that way" or "Let's discuss that during the break."  Generally people are eager to get to lunch/coffee break and won't draw it out too long.


What affiliation do I choose if my scientific work is unrelated to my job?

There are two main paths here:

You can list yourself as an independent researcher, which is appropriate if you are not doing this "on the clock" at your current position and use no company resources.
You can list yourself under your current employer, which is appropriate if you are doing this using work time and/or company resources, even if the work is not related to your position's responsibilities.

If you are working at a company that participates in research (even if in another field), they probably have policies that apply (possibly including pre-submission review), and you should have a discussion with your supervisor and/or other folks who are engaged in research there. A clause in your employment agreement might even mean that you cannot be an independent researcher.

If, on the other hand, you are working for a completely non-research organization (e.g., a paper company), then you probably should be doing this as an independent researcher and keeping everything off the clock.

Finally, there is a somewhat more complex third possibility to also consider: if these collaborations are part of a long-term relationship with a university, your collaborators might be able to get you some sort of "visiting researcher" or "associated researcher" affiliation. These "positions" have no money associated with them and are really just there to simplify the logistics of collaboration, so they are often pretty simple to arrange, and could actually be the most appropriate description of your position with regards to your research.


How to cite several papers at once with first same authors?

The APA reference guide from Purdue denotes how the articles should be listed and referred to inline. So my understanding of the two links above would be something like (using the examples they have):

  [the claim you want to use the reference] (Wegener et al. 2000; Wegener et al. 1994).

would be inline reference and in the references list it would be

  Wegener, D. T., Kerr, N. L., Fleming, M. A., & Petty, R. E. (2000). Flexible corrections of juror judgments: Implications for jury instructions. Psychology, Public Policy, and Law, 6, 629-654.

  Wegener, D. T., Petty, R. E., & Klein, D. J. (1994). Effects of mood on high elaboration attitude change: The mediating role of likelihood judgments. European Journal of Social Psychology, 24, 25-43.

On a separate note: Are you using a reference manager like papers3, mendeley or zotero? If so just insert the citekey for the articles and choose the style, let the software do the work for you. Saves you the headache..


How many courses should I discuss in an academic video interview?

Think about your audience. They are asking this question because they want to know how you'll contribute to the teaching of the department. Only listing the title of the course would provide a little information (what you'll teach), but probably not all of what they're listening for (how you'll teach or how your teaching interests will fit in their department).

So, for each course you would answer for, be ready to give at least two sentences that focus on any of the following:

Key learning objectives - what would you focus on?
Motivation - why does designing this course interest you?
Fit - how do you see this course fitting in? Is it for majors? Is it a core requirement? Is it a special topics course?
Key curricular approach - how would you teach it?

Which elements you choose depends on you, your field, and the program you're applying to. For me, if it was an established course that's part of their own major curriculum, I'd talk about motivation or curricular approaches, since it's not like I anticipate changing the learning objectives radically at the start. If I'm proposing something not in their major plan, I'd want to address fit, because it may not be obvious how I see the course contributing to their department. If it's a fairly broad course like a survey, I'd speak more to learning objectives or (again) curricular approaches, since people can approach surveys in a variety of ways. In other words, I explain what I think would be either most interesting or least obvious to my audience.

Also, consider the balance of speaking to what you'd like to do and what the department needs in the next year or two. They do want to hear the former, but it may also help if they know you'd be interested in teaching a workhorse course that's always in demand. If you can communicate that you'd teach that workhorse course in an interesting way, even better.

The number of courses to describe is dependent on field. In English, I had a freshman composition course, a sophomore-level survey, and an upper-division course ready to go, and I'd talk about 1-2 of them in any given first interview, and then add examples of other courses to teach at the end of a question. I'd take about 2 minutes total with that question, and select the courses based on research.


How to tell an over-confident student they still have a lot to learn?

I would suggest against [a deleted answer telling to put a lot of weight on simplest textbook examples] (I consider "ha! you missed the example from chapter 2" to be highly unpedagogical, as it is "appeal to authority" and "you should read and remember rather than think").

I think two things may help:

give him problems and require written solutions (it is harder to boast, or mask omissions, when one writes), solved "down to the last $\epsilon$", as you "want to see the proof, not just be convinced that he can prove it",
give more advanced problems (still, which are within his reach), for which answer cannot be hand-waved (e.g. "what is sum of", "give an example of set, such that...") OR don't tell the answer in advance (so instead of "prove X given Y" ask "decide whether X holds for all Y").

In both cases, I would tell him (in person) that he is very smart, and you give him more advanced problems because of that. (And that he still needs to learn to be precise enough for mathematics.)

Maybe he does want to show you that he is smart, and as you do not acknowledge it he, well, tries again.

In any case, I would not undermine his skills. In mathematics & theoretical physics I know a lot of people who underestimate their skills, but not many who overestimate for a longer time (such subject makes one humble, sooner or later).


Is it alright to contact lab members of a lab you interviewed at for an update on your PhD application?

Contact the person who interviewed you, not a student. I doubt a PhD student will know anything about who is going to be made an offer.
It's perfectly fine (especially after four months) to send a short, polite email to your interviewer asking when you can expect to hear from them.


The "why it matters" of a research proposal

This has a lot of possible answers. One wants to say, as many answers as there are research proposals.

In mathematics, some things matter just for the pure beauty of it. The same may be true in other fields. Probably true in the arts as well.

In CS one can often search for improvements on current best practice - faster, more secure, smaller, simpler.

Some problems matter because the search for answers has been long and unfruitful. Some things in physics are like that.

Some things matter because they provide synergy between existing ideas thought to be distinct. Drug research, pedagogical research.

Some things are useful. And, as you say, one can hope that other things become useful in the future. Very fresh pure math may have few current uses. But potentially future uses.

Think about why you want to do the research. Think about how it will complete something from the past. Think about how it might foreshadow the future.

I'm sure you can come up with something. And it need not matter to everyone. Sometimes it will only "matter" to a small group of specialists. Math can be like that too.

And they aren't mutually exclusive. Quite a few of these were manifest in my own doctoral research.


Generally speaking "management" in a university takes a different role and faculty are generally expected to know what to do and to do it to a high standard. In a certain sense, every faculty member is an independent entity and they only need to coordinate on a few things. Those things, such as curriculum and grading policy, are normally handled by committees of faculty, not handed down from above.
Typically a department will have monthly faculty meetings in which things are communicated and new opportunities and directions are discussed. Solutions are normally by consensus. The meetings may be mandatory or not, but the mandate can be pretty loose.
There are few situations in which a tenured professor is told what to do by "management". And some of the layers of management, such as department heads and even deans may actually be chosen by vote of the faculty.
So, in a forty year career, I seldom "reported" to anyone in the traditional sense and no one "managed" me and my work. True, I submitted an annual report of my activities and said there how I worked toward the three traditional goals of the university: teaching, research, and service. The department head or dean would respond to that report, perhaps making suggestions, usually minor, on things I might do in the coming year.
Even it times of conflict, such as when a student complains, the complaint often is handled by faculty rather than by "management."
Faculty normally self organize into seminars and such, and normally worry about their funding. There may be some pressure about that in top universities.
In the traditional (Medieval) university, the faculty IS the university and it would hire "managers" to do those tasks that they found unsatisfying. It is still somewhat similar in many places, but less so in large R1 and State Universities.
There is a story about Rockefeller Columbia University (if I remember correctly) that when ex-president Dwight Eisenhower became the university president, he held a meeting and told the faculty all the "wonderful things the university would do for the faculty." The head of the faculty (an elected position) stood up and said something to the effect that the university couldn't do anything FOR the faculty. The university WAS the faculty.
There are, however, many support offices in a university that are managed in a traditional sense. There is often a funding support office, an enrollment office, a counseling office, etc. It can be very extensive. But they don't manage faculty. Instead, they provide support services to faculty and others, though internally they may be traditionally managed. A "student recruiter" would probably answer to a "boss".


New to USA - Masters vs. Staying with my mentor

Depends on what you expect to get from a master's degree.

From the sounds of it, your career path certainly isn't going to be dependent on the credentials, but could perhaps be aided by a degree.

Personally, I could see you getting benefit out of a good Masters on a couple of counts:

An introduction to where the state of the art lies. Since it sounds like you have an entrepreneurial bent, finding this state of the art could help point you in the direction of problems which have been solved, but not productized... could be a great start for a company.
Another mentor. Having multiple people to bounce ideas off of is a valuable thing, especially when they have substantially different backgrounds.
A chance to exercise your grit, away from the perhaps comfortable situation you're in now. A masters will force you outside your comfort zone.
The benefits you list are going to be there for sure; an immersion into American culture and life.

Of course, getting all of this doesn't require a Masters degree. You're already living in the USA, and you can try to stretch your research legs on your own.


Should one introduce past work in PhD statement of interest?

I don't think Ben's answer says this strongly enough:

Your statement must include a description of your past work, if you have any.

The primary feature that PhD admissions committees looking for in applicants is evidence of potential for high-quality independent research.  The strongest possible evidence of your potential to do high-quality independent research is the fact that you have actually published high-quality independent research.

It doesn't matter whether your past research is on the same topics that you want to pursue in the future.  It's easy to communicate a change in interests in your statement with a single sentence: "More recently, however, my interests have shifted to quantum tropical M-theory."  (Obviously this sentence should be followed by a description of your specific interests in quantum tropical M-theory, written with enough maturity to convince experts in quantum tropical M-theory that you have the necessary knowledge and skills to be successful in quantum tropical M-theory, but that's what you were going to write anyway.)

Crucially, if your previous papers have coauthors, your statement (and your recommendation letters!) should focus on your specific technical contributions to those papers.  Remember that you are not trying to sell the work as good mathematics; you are trying to sell yourself as a good mathematician.

In particular, you are not trying to sell your past work to experts in your subsubfield of (past) interest, so you should not merely quote the abstracts.  You are trying to sell yourself to a general audience of trained mathematicians, some of whom are experts in your subsubfield of (past) interest.  So your description needs to be understandable to that broader audience, but still interesting enough to experts that they will want to read your papers for the actual technical details.

Obviously you should provide direct links to arXiv versions of your papers, in both your CV and your statement, so that interested committee members can read them without having to search.

[I'm an American theoretical computer scientist, which means I'm like a mathematician, except that I write less code.]


Alma mater and alumnus status when dropping out

A person who drops out is technically an alumnus however the term normally is used for someone who actually graduated. It can refer to anyone who is a former student or even employee of an institution.


Publishing datasets as a journal articles

If I search on Web of Science for TOPIC: (natural language processing) AND DOCUMENT TYPES: (Data Paper), then I find various results from Scientific Data (which you mentioned already), one from BMC Bioinformatics, one from Bioinformatics, and one from the International Journal of Robotics Research.

BMC Bioinformatics asks for APCs of $2490.00, but offers waivers on a case-by-case basis.

Bioinformatics: I did not find any information about APCs (though, according to their Instructions, they charge for OA licenses, for colour figures, and for excess pages).

International Journal of Robotics Research: I did not find any information about APCs - but to be sure, have a careful look at their submission guidelines.

By the way, Data in Brief also offers reduced APCs or even total waivers under special circumstances (see here).


I assume you would cite your earlier paper somewhere in the introduction of the new paper.  You could write something like this:

Recently, we (Author1, Author2, & Author3, 2016) presented a series of experimental and modelling results for a pure system.  With the current paper, we would like to extend ...

Alternatively, a footnote may be appropiate to indicate that the first authors are the same.

Also, see this publication on the topic of name changes in academia: The Ripple Effect of Women's Name Changes


What are potential downsides of (universal) author IDs pushed for by publishers etc.?

Your question is long and somewhat argumentative. I'll answer here to a small part of it. You say:

  “Are you sure that you will still be proud of your last paper in 20 years time? In some cases you might prefer to not include a certain article in your next grant/job application.”

To me, the sounds very contradictory with the principles and aims of scientific publishing, regardless of how identification is performed. Once something is published under your name, it is part of the academic record and should not disappear, even if you don't like it anymore.

It is actually a very good thing that the integrity of the academic record, including published literature, is maintained throughout history. It is even part of scholarly publishers' duties to do so. That it is associated with your name and affiliation(s), or with a unique identifier, doesn't change naught. To given an example, if an academic were to produce a full list of publications (as part of a long CV or grant application) and willingly omit a publication from this list, I would consider it unethical (though I don't think it is something that often happens).


Will my age affect my chances of finding a funded PhD position?

The short answer is: no. Quite the contrary, many universities value the experience (preferably from industry) so it is beneficial. Also, your conference papers will be the most important factors in getting the PhD position and/or funding. I'd also emphasize that you should highlight the fact that you have a journal article (preferably A or A*) in progress.

I have not seen any such requirement which is restricting PhD or any academic degree to a specific age. In fact, doing so is illegal in most (read: all) European countries as it comes under age discrimination.

To narrow it down further, different funding bodies could impose their own restrictions per project, for instance DAAD's grant that you mentioned is "to promote and fund young artists" according to them, that is why it is restricted to a certain age group. A similar example could be feminist studies where it could be restricted to a single gender. Again, this has nothing to do with general conditions of admission.


How to find graduate programs in chemistry based on my research interests

One approach would be to look up interesting papers in spectroscopy or whatever you want to study and then identify what research groups they are coming out of. That is, figure out who is the senior author on the paper (often the last author) and then look at their website and see what else they are working on. Get a list of at least three maybe more like five different people doing research that you think sounds cool and who are at universities where you wouldn't mind working and check to make sure they are the kind of people who actually take graduate student.

Send each one of those professors an email outlining who you are, your research interests, and why you think you would be a good fit for their lab. Attach a copy of your CV.

Some of them will probably be interested in having you apply to their university's graduate program with the idea of taking you into their research group once you are admitted.


Created a figure for a colleague's thesis, want to use that myself as well

With all due respect to your TikZ prowess (which indeed is more impressive than my own non-existent TikZ skills), these figures are... not exactly the Mona Lisa. Anyway, they are your work and you should feel free to use them and not say anything at all about the circumstances of their creation. If we had to give credit for every microscopic idea that inspired a turn of phrase or visual idea in the papers we write, they would all be three times as long and virtually unreadable. The situation you are describing is simply too trivial and unimportant to warrant mentioning in my opinion.

As for the future, if in the future you contribute a more substantial intellectual product to a project that then publishes it without an acknowledgement to you, then later want to use the same product in your own publication, then because of the concerns you mention here it may be sensible to accompany the figure or whatever it is with a footnote along the lines of "This figure is the author's original work, and was used with permission in [insert reference to earlier work that used your figure]."


How can I avoid the embarrassment associated with needing a sabbatical for alcoholism and mental health treatment?

This is a tough question, and you have my sympathies.

A sabbatical is time off from on-campus responsibilities given to enhance your long term scholarly life.  It varies in its implementation from place to place (and in fact they do not exist at my institution), but most commonly you propose travel and research plans.

Alcoholism and mental health issues are two kinds of recognized medical problems.  It is my understanding that you do not take a sabbatical because of medical problems; rather you go on medical leave of one kind or another.  Trying to hide medical problems under cover of a sabbatical sounds, at the least, to be very risky, and you seem to recognize that this is not practical in your case.  So I would recommend that you look into going on medical leave instead of sabbatical.

Treatment of either of your medical issues will probably involve a psychiatric / counseling component.  I am not a psychiatrist or a counselor (rather, I am a mathematician: really not close!), but I would humbly and tentatively suggest that even before you go on medical leave you seek some counseling.  In particular you mention the embarrassment of being sick in the way that you are.  I think it is completely normal and understandable for you to feel embarrassed / ashamed about these problems, but those kinds of feelings could lead you down very unproductive paths, so I suggest that you concentrate some of your earliest counseling sessions on dealing with that.  In particular, a counselor probably has very helpful things to tell you about disclosing your problems to others: whether, when, how much, and to whom.  As far as I know, it should be possible for you to get the same medical leave and considerations as someone with less socially stigmatized medical problems without having to disclose the details of your medical issues to anyone in your department, unless you want to.

I wish you all the best.  I hope you do take medical leave and get knowledgeable, helpful care.


Yes you made the right decision of submitting a comment to the paper. Publicly commenting papers happens much too rarely, for reasons that may be at least partly technical. (Compare publishing your comment to writing here at StackExchange in terms of time and effort.)

As for future consequences, nobody knows. But if your comment is good, journals editors could get the idea of soliciting you for reviewing papers.


Should papers presented at local conferences be put in list of publications?

These conference proceedings were not published in any journal.

Were they published at all?  If there were no proceedings, then they don't count as publications, because nothing was actually published.  (You could still list them as talks rather than publications.)  If there were official proceedings in which other people can read and cite the paper (not just an abstract) even after the conference is over, then it's a form of publication, regardless of whether the proceedings appeared in a journal or as a stand-alone volume.

There may be other considerations you should take into account when including this material in your CV.  For example, were the papers peer reviewed?  Does your field consider them to be archival publications?  However, these are more of an issue of how meaningful the publications are, rather than whether they count as publications in the first place.


Paper accepted subject to minor changes – should I comply if I do not consider them minor?

Whether you should comply or not should be ruled by asking yourself if doing so will improve your work. If you come to the conclusion that it would improve the paper, you really should follow the advice. Most other considerations such as if it is a lot of work should be very low (if at all) on your list.

As a self-confident researcher the quality of your work should be in your focus. It is therefore never mandatory to follow reviewer advice, but it is mandatory to explain the reasons if you decide against it. If there are good reasons not to do as requested, you can explain it accordingly to the editor. In any case, the editor is the one to convince, so you could discuss your question with her/him.


How to include research done for masters thesis on CV?

Normally, it goes under Education. You can list a separate bullet point under your MS (expected on ...) with some details on your thesis.

A separate group for Research seems fine too, as long as you can furnish it and your CV stays at 1 page (assuming you are looking for industry internships, academic CVs can run longer).


This is based on my experience in mathematics in the United States (other cases may differ):

In principle, a postdoctoral position could start at any time if grant funding is available.  In practice, it is generally tied to the academic calendar the same way other positions are, and any deviations from that schedule would be unusual.  If you are doing an advertised search for a candidate, then there are enormous advantages to timing it with the usual job market cycle (at other times of year very few applicants will be available), so off-season hiring typically takes place only when a perfect match is made through personal connections.  The other issue is that most Ph.D. students get their degrees at the end of the spring semester, and most faculty positions start in the fall semester, so academic-year-based postdocs are convenient for most applicants.


I'm Applying for mech eng MS as an undergrad in pet eng, will it matter if i take another mech eng course my last sem or not?

IMO, it won't matter.  Given that you're in the process of applying (which is a time commitment as well) I would recommend option #2.

A reassuring piece of advice a PI gave me as I began the application process was:
the admissions committee and PIs you apply to work with do not look to see that you are already an expert in the area you apply to, they are looking for evidence that you have the aptitude to succeed in their graduate program.

NB: I'm in neuroscience--not engineering.

Good luck!


COVID-19 - Should I start applying for other jobs having accepted a post-doc verbal offer months ago?

You should only accept formal written offers.  If you follow that practice, you will never be in this situation.

Since it is too late for that, you should request a formal written offer immediately.  Yes, you should look for alternate employment.  There are several possibilities:

You never get the formal offer.  In this case, get a job elsewhere.
You get the offer and can start the job.  Then start the job.
You get the offer and cannot start the job because you cannot get a visa.  Since you do not have a visa, even if you accept the offer the agreement is invalid.  Find a job elsewhere.
You do not get the offer, but do get a job elsewhere.  In this case, inform the university that, if you do not get the offer in a reasonable period of time, you will no longer be available.
You get a job elsewhere, and after a long time you get the written offer and visa.  Now you have the opportunity to experience both jobs!


Email from editorial assistant from different journal?

Journals published by the same publisher generally have a shared editorial system.  They may actually share some or all of their editorial staff.  So the second journal's editorial staff may be aware of what has been submitted to the first journal.

Moreover, different journals have different levels of prestige.  A top-tier journal is not going to be able to publish every correct paper they receive, only the most interesting/important ones.  If the same publisher has lower-tier journals in the same area, it often makes the most sense to resubmit papers that are rejected by the top journal to its less prestigious sibling.  The peer review process can be streamlined, since the publisher typically already has access to at least one round of referee reports.  This head start on the review process can speed things up, which is generally advantageous for all concerned.

So if a paper is rejected by a top journal, not because it has serious problems with the content, but because it is deemed to be not important enough, a less-prestigious sibling journal may contact the authors and suggest submitting it to the second journal instead.  Sometimes, depending on the what the referees have already had to say, the lower-tier journal may offer to publish the paper without any further rounds of reviewing.  (I had this happen to me once; and, in fact, I got the offer to publish the paper without change in the lower journal a few hours before I even got the rejection from the better journal.)

In this case, the editorial staff may have jumped the gun by assuming that you are automatically planning to resubmit your paper to the next journal down on the prestige ladder.  However, their is otherwise nothing untoward going on.  Clearly, the lower-level journal is interested in your paper, and there's a good chance that submitting it there will the best course of action to take.


Ways to tell interviewers you want some time to think about your decision (Employment in Academia)

Usually, no one expects you to respond to an offer on the spot.

An important distinction to make is that the PI may offer you a verbal offer on the spot but generally it takes some time to get the formal offer. Accepting the verbal offer does not necessarily mean you have the job.

If the PI gives you a verbal offer, then just respond with a compliment (e.g., "Thank you, I am very impressed with your lab") and then ask when to expect the formal offer and when you should respond by.


Prospective PhD-How to keep in touch with potential PhD supervisor

I fear that "close contact" is probably too much to hope for. Academics are very busy and it is rarely possible to devote a lot of time to prospective students. Close contact (hopefully) comes once you are their student, but usually not before. The best thing to do would be to see if conversation grows organically. Thank them for their email and recommendations now and let them know you are applying. Meanwhile, get in contact with them if you have something kind to say, interesting to report or important to ask: that you are coming for a visit and would like to meet, that you have finished all the suggested readings and wonder if they might have more recommendations on another subject, to congratulate them on a new publication, etc.

Don't be offended, however, if you do not get much response to these. Like I said, we don't have much spare time for such correspondence before you are a student.


After having published a paper, am I still free to use & distribute it as I wish?

In most cases, journals ask for transfer of your copyright to the publisher. In these cases, you cannot technically distribute copies of the article any more without the publisher's consent.

The details of what you can and cannot do, however, differ between publishers. You will get a form upon acceptance of your paper that lists the legal details and that the publisher requires you to sign before they publish the article.