Principal Research Scientist vs. Senior Research Scientist?

According to the MIT EECS pages, there are two tracks:

Academic Research Staff.  These are mostly shorter term (such as a Postdoctoral Fellow), and are funded externally (by grants and similar).
Sponsored Research Staff.  These are longer term appointments which are funded by the department.

Senior Research Scientist is an Academic Research Staff position, because while it is long-term, it is also a position for which the researcher is expected to procure their own funding.

From 5.3, the SRS's funding:

  Appointees to this rank generally are expected to raise funds to
  conduct research and cover their own salaries.

Principal Research Scientist is a Sponsored Research Staff position, and is funded by the department (though I'm sure they can get their own funding also, their salary is paid by the department).

From 5.2, the PRS's funding:

  Funding responsibility resides with the department, laboratory, or center that is the locus of the appointment.

From 5.1 on the difference:

  Two types of research appointments are described in the following
  sections: long-term appointments, which are classified as sponsored
  research staff appointments, with the exception of the Senior Research
  Scientist/Associate/ Engineer position; and short-term appointments,
  which are, in general, classified as academic research appointments.

  The purpose of the campus research appointment structure is to create
  professional sponsored research staff categories with employee
  benefits and privileges in order to encourage long-term research
  careers at MIT. The concept of long-term professional careers,
  independent of classroom teaching and supported entirely from research
  grants, is not a new one for the American research university. This
  mode of research, with professionals working in departments,
  laboratories, and centers, is an important mechanism for universities
  to maintain research viability, enter new fields, and bring
  researchers to the campus.

It seems evident that Senior RS is basically the same position as PRS, but not funded by the department.  In some cases, the PRS could earn more, because (for example) a NIH-funded SRS would be limited by NIH regulations, while a PRS who is funded by the department is only limited by whatever MIT chooses to pay them.


Faculty job on-campus interview: changing flights

If I skip the flight, will A know?

No.

  Do you have any suggestion for a more elegant solution?

If time permits, book a round-trip ticket out of pocket (i.e. paying for it yourself) to go from A to B and back to A, in time to make your long-haul flight.


How should I respond to full text requests from other researchers I don't know?

Journals have "author rights" policies on what you can do with your paper. (e.g.: https://www.elsevier.com/about/our-business/policies/copyright#Author-rights)
Most I have seen allow exactly this sort of sharing - at least of the pre-publication draft, if not the final formatted version.

You should look them up for the journal in question. Even if the policy doesn't allow it, send it anyway. Nuts to journals who try to prohibit one of the fundamental aspects of science.

(The reason to look it up is to never ever again submit to a journal who has this policy.)


Well, I believe you should not quit your research right now.
In my opinion what you said about your research situation was very good. You should know that the purpose of B.Sc. project and research is to get familiar with research world and to do something real in the Correct Way.

I think a helpful, devoting professor is like a gold in these situations. She can help you throw your bright future. It does not mean you should stick to this field for the rest of your life! Take it as a start for your future more professional research experiences.

Also, you can talk to her about different fields which you like. She may find you a combined nice problem to work on.


Due to my depression, the department wants to kick me out of the graduate program. How to stay in this environment?

I'm having some trouble with the way you're mixing the words trouble, troubled and troubling.

If a student shows some red flags for possible suicidal thoughts, it's a good thing when the people around him alert the department, in order for support to be offered.

On the other hand, targeting the troubled student and painting him as a troublemaker would not be good.

As you are currently not in as good shape, mental health-wise, as you would like, it's difficult for me to know how objectively you are able to be, currently, in your perceptions and interpretations.  That is, I'm not sure whether your colleagues are actually targeting you for possible removal from your academic program.

However, I will go ahead and do my best to answer.  I'm not sure what country you're in, or what the laws and regulations are where you are, so I'll write the answer I would give to someone facing the problems you described in the U.S.

People fear what they don't understand.  The key to acceptance of a mental health disability is education -- both of staff and peers.

In the U.S., I would ask NAMI, the National Alliance on Mental Illness, or a local disability rights group, or a county mental health association, to send a trained expert to give a mental health awareness presentation to the students, and a separate training session for staff.

Here is an example of a presentation that a college student gave about her neurological disability, Tourette Syndrome, to her classmates, with the help of a staff ally: https://youtu.be/zVY6B3ezY3k

I get the feeling from your post that you might not be in the right place at this time to give a presentation of this type yourself.  That's okay.  There are people who have experience giving presentations on behalf of a student.

Here is a nice website with suggestions for how to seek reasonable accommodations for a disability in the workplace (in the U.S.) -- I think this may give you some good ideas, and in general instill you with more of a belief that you are entitled to accommodations! -- Job Accommodation Network.

It would be great if you could participate in a peer to peer support group.  In the U.S., in order to find such a group, one can try to find such a group with the following techniques:

google
ask a mental health professional, since these providers often have an email discussion group through which they can query each other about such opportunities
ask a government information service (one reaches it by dialing 211)
ask a psychiatric ward at a local hospital
the campus counseling center may have organized some groups of this type
ask the county mental health association
ask NAMI
if necessary, take the initiative and form such a group


Number of academics in various EU countries

The data is roughly accurate for France. The French ministry's HR department releases data periodically, and one of the latest report (2017-2018) is available there: http://cache.media.enseignementsup-recherche.gouv.fr/file/statistiques/62/3/Note_NP_2017_2018_1146623.pdf

In summary, in 2018, there were 81,563 teachers in French public universities. This includes 62,491 permanent positions (full professors, lecturers, and full-time tenured teachers), and 19,072 non-permanent. Of these, 7110 are PhD students with teaching duties, and 4500 are "ATER" (a kind of "postdoc", it's complicated). Depending on how you want to count what, the 80k figure is probably overestimated if you exclude PhD students and postdocs, but it's in the ballpark.


What should one consider when pondering a career as a scientific editor?

I'm a former academic publisher, and assume you're looking to join an academic publisher full-time. Do note that absent a very few elite journals like Nature and Physical Review Letters, you are not likely to be handling only journals (or be directly involved in choosing the papers to publish). You will also be doing books.

  How many years' experience (after a PhD) is typical for an entry-level editor role?

For these entry-level positions, in principle, a Bachelor's degree suffices. In fact, many of my former colleagues had more or less completely forgotten everything they learned in university and they got along just fine. Especially ironic was the case of an English Literature graduate who couldn't read calculus symbols handling an engineering journal - and she did well enough to be promoted.

(In fact there are positions even more entry-level than these entry-level positions in which a high school degree suffices, but the job responsibilities are very mundane and tedious.)

But you have a PhD. This means you won't be working at entry-level. You'll have more advanced duties that people with Bachelor's degrees might not be comfortable doing. These could include:

Acquiring new projects (this is a big one). E.g. you might be expected to identify a niche in the market for a new book, write to people who can write that book, and commission them to do it.
Attending conferences. You might have to manage the publisher's booth, answer questions about your journals and review processes, network, and yes, acquire new papers/books.
Come up with a strategy to advance your journals. This isn't easy, but it has to be you, because most people with Bachelor's degrees will have no idea. It could involve, for example, finding a trendy topic and commissioning someone to edit a special issue on it; or perhaps to split the journal into two new journals each with different focus, etc.
Help the people with Bachelor's degrees out when they approach you with (academic) problems. In my experience this was actually quite rare because most of those people aren't confident enough to ask, but it can happen. Real-life example: a paper is accepted, then during copyediting the desk editor discovers that there are only four data points. The authors have drawn a line through two of the points, but since it's only four data points, they could equally have drawn one of several other lines that also go through two points (they would fit worse, but still look good enough to be viable). What do we do now?
Make a decision on whether to accept projects. The authors put together a publication proposal, the acquisition editor has gotten reviews for the proposal, and now you have to decide whether it's a good idea to take on the project. You'll need to appraise the reviews as well as how many copies of the book you can expect to sell, etc.

  What else should a recent PhD know when considering such a position?

You're going to experience a ton of rejections when acquiring projects. I think the ratio of the number of replies to the emails sent is at best ~20% (and that's only if you're good). The ratio of acquired projects to emails sent is obviously even lower. You have to be ready to deal with this.
You're going to meet people who're very critical of you because they view academic publishing as a scam, and you by working for an academic publisher are complicit in the scam. For example, you could be doing your best to get top management to approve a lower article processing charge (APC) for your journal, knowing that these lower APCs are going to lead to the journal making a (hopefully temporary) net loss, and then get the very authors you're trying to help openly wonder how it's acceptable for you to charge APCs at all in the first place. You have to be ready to deal with this. If you end up doing the job you linked in a comment, it's going to be especially bad, because lots of academics hate Elsevier.
Don't expect to be well-paid, at least at the beginning.


How can anyone assess their own Phd application prior to actually applying to determine its weaknesses and figure out what to do next?

Since students are admitted to such programs by people, and not by algorithms, you probably can't do it with any assurance. But note that the number of programs you target is very small and the number of potential applicants is very large. Thus, the competition is fierce. So, it doesn't depend on just you, but on the perceived quality of the others you compete with.

As Solar Mike suggests, the only way to know is to apply.

But one good way to get a fairly valid assessment without applying is to put together the materials needed for an application and ask one or two of your current professors to give you feedback on it. Do they see any missing parts? Can they suggest better ways to present yourself to a committee of their peers? ...

Some students with perfect GPAs get rejected from some programs because there just isn't room for everyone or they have other things in their record that makes them less of a "sure bet" for the committee.

On the other hand, there are plenty of other schools, not in your "top" category at which you can get a fine education and a firm foundation for a great academic career. Some schools have "niche" programs in certain sub fields that may be better suited to you and provide a better education that the top ten you suggest. You might also have a clearer path to completion at such schools.


What is the difference between a school and a department?

The term school and department are going to mean different things at different institutions. Generally speaking, the term school refers to a larger unit within a university than department and many schools will contain multiple departments. For example, Harvard University contains a School of Public Health (and other schools) which contains a Department of Epidemiology (and other departments).

That said, names are often not even used uniformly or consistently within universities. For example, at the same organizational level as the School of Public Health at Harvard is the Faculty of Arts and Sciences which runs both Harvard College and the Graduate School of Arts and Sciences. My current university uses the concept of an academic "unit". Many units are "schools" (e.g., the School of Public Health or the Information School) but others are not (e.g., the College of Arts of Sciences). There is also an organization within the university called the Graduate School which cuts across and oversees  work in different units and schools.

Sometimes, smaller "schools" will not contain separate departments. Sometimes, a large department in a large school might be larger than entire schools elsewhere in the university! Sometimes, the terms might be used interchangeably. In many other cases, they won't. In some cases, one or both terms might not even be used at all!


Supervising a research student with attention problems - what can I do to help the student be more independent?

OK. First of all, you are to be commended for having the awareness and sensitivity to take the initiative on this. LD/ADHD students tend to be treated rather badly in higher ed, so it's reassuring to see someone reach out for help.

I think the zeroth thing you should do is bring up your observations to the student for the following extremely important reason: If the student does have a disability, either the student already has a diagnosis and is worried about being judged negatively (or overestimates how well they're managing without accommodation), or the student has been struggling for years wondering what's wrong. It's impossible to address a problem correctly if you don't know what's causing it. With that in mind, I can only comment on ADHD, which is not difficulty paying attention, it's difficulty regulating attention.

Another preliminary observation is that if the student is ADHD, it's possible that they never developed good learning skills either as a direct result of the ADHD or as a result of the kind of spoon-feeding you are (correctly!) identifying as problematic. This kind of "accommodation" is often recommended for ADHD, but it's ultimately self-defeating. So you might be in a situation where the student is on the steep side of the learning curve for learning how to learn. It's tempting to just spoon-feed so that the student "makes progress," but this is bad advising, just as it would be bad parenting. So set the project scope and your expectations accordingly if this is the case. And the student might need an ADHD coach, academic tutor, or therapist to help with the logistics of just putting quality time in, which can be formidable for ADHDers.

In terms of  practical day-to-day suggestions:

Audio-recording meetings, or important parts of meetings, might be helpful. ADHDers often tune in and out without even being aware of it, so they don't know that they've missed something.
Work on the "big picture" first. This might seem counterintuitive, but the student might find it easier to recognize what to focus on once they have a clear idea of how the pieces fit together.
Ask the student to come up with their own suggestions about how to approach the project. Be open-minded about what the student comes back with.
Provide regular, structured, nonjudgmental feedback about your expectations and what is and isn't working.
Let the student know you're on their side and that you have confidence in their abilities. Anyone with a disability can tell you that the worst part isn't managing the disability, it's dealing with the low expectations and lack of inclusiveness from everyone else.

The main takeaway is that ADHD adults often do much better in more self-directed activities than they do when given close supervision. A common incorrect assumption is that because an ADHD student has trouble following instructions, then it must be the case that the student is incapable of working more independently. Which is not to say that the student should be left to their own devices, but rather that the support provided by the supervisor needs to be more student-centered to be effective (and efficient).


How much time Google Scholar take (generally) to index an arXiv document?

It usually takes a few days according to this answer, which is in-line with my experience (I don't really monitor it though). In some cases, I think it can take a couple of weeks for Crossref which may give an idea of how long it could take for Google Scholar.
If you want to, you can manually add the article to your Google Scholar profile. However, I'm not sure how quickly that affects indexing.


How can I mentally prepare for grad school?

PhD student here. I am especially prone to stress, and my PhD has been very stressful, and while I haven't been completely successful with coping, I know a thing or two about it.

First off, I assume that you have gone through some schooling prior to grad school, which is what got you here (BSc, Masters?). That was stressful too, no? I have heard from SOME PhD students that undergrad was actually worse in the long run, but that depends heavily on the person, the lab, and the supervisor.

What you can do to stave off stress depends on your program and your supervisor. The healthy recommendation is to limit your working time. Some people on this site will tell you that a 'normal' working week is fine. Others will tell you that 60 or 70 hour work weeks are standard. This thread may devolve into a debate between those two camps. Personally, what I do is I set my own hours according to when I work decently. If I don't need to be in the lab for an experimental reason, I'll allow myself to get enough sleep that I'm not falling over myself through the day. If that means I get in a little late, it also means I stay a little late, especially if I get into a groove when working.

Sometimes, if I don't have stuff going on in the lab, I stay at home and I work all day in my pajamas wrapped up in a blanket, analysing data or writing a report of what I've done. This is especially true if my previous week was spent in the lab (I work in cryogenics and when we use liquid helium we have to pack as many experiments into 100l of lelium as possible, which means being at work from 8am to 9pm sometimes). I let my supervisor know about this, and I answer emails, and I do actually work (usually). But that means I can take breaks when I want to, be in my comfort zone, and relax a bit more than usual. I'm an introvert and it helps me recharge. If you're an extrovert, maybe it's not a great idea. Again, you do you. That's the important thing.

I try to keep weekends for myself, but this won't always be possible. The point is to try to give yourself SOME fun time, even if you are bogged down with deadlines. The best way to avoid a stress-related breakdown is to have a life outside of work. That means friends, hobbies, and other things unrelated to what you do. Even if they are other PhD students, it's still better than nothing at all.

Sometimes at night, I have trouble sleeping because the problems of the day keep running through my head, or I'm worried about something going on tomorrow. I installed a program on my computer called f.lux which automatically limits the blue light coming from your screen after sunset. This reportedly stops the limitation of melatonin production if you are working into the night, and can help with sleep if you've been in front of a computer all day. It may actually work, or it may be placebo, but I've been sleeping better. Also, if you switch it off after you've gotten used to it, your screen looks like some kind of crazy holy entity. More generally, practice sleep hygiene. It really does help.

Another thing to watch out for is seasonal affective disorder, if you are anywhere remotely northerly. I live in a not-very-north place (France) and I managed to get a case of it pretty bad this year. Keeping a desk near a window helps, as does walking somewhere in the middle of the day (e.g. to a cafeteria for lunch). Going for a run mid-day (if you can) helps too. Don't be surprised if you get the winter blues, especially if you wake up before sunrise and leave for work during it, and if you go home well after sunset at night. It happens.

I'd recommend living alone so you can rest and recharge at the end of the day, but if you're extroverted, this may actually be worse for you.

Finally, maintain a healthy relationship with your supervisor. If you find yourself worrying about whether you are progressing properly, talk to them about it. Be sure to maintain your independence (that's the point of a PhD) but also go to them for guidance when you need it.

Be sure to keep good records of everything you do (lab book if experimental, and make PDFs of your results written up nicely) to avoid stress later when you have to write a thesis. I experienced it in my masters; not having good records, and forgetting what you did before. Write it all up. Not only is it weirdly relaxing to write up reports, but it will help you later.

If you're in the US, you will probably have courses and qualifying exams. We don't have that here so I can't really comment, but the usual advice applies; start work early, create a decent schedule for yourself, don't leave a deadline until the last minute. Work with your cohort; they are a great source of support as long as they are not overly competitive.

And finally, the first few months of your PhD, I have been told, no one really expects you to actually accomplish much (YMMV with institution, program, country, and so on). Learn your way around, learn how equipment works (make great notes for this part!), deal with administrative stuff. Don't pressure yourself into being a magical science genius who spits out papers like an academic wizard. I spent a week translating an instruction manual for a dilution fridge from French into English. I spent a month filling in forms. Go to meetings, go to journal clubs. Part of the point is networking and expanding the way you 'think', so don't think of journal club or seminars as being a waste of time. It's partially a way to unwind, and partially a way to get you to think like a scientist.

Go to conferences or meetings if you can. Meet people. Meet potential projects you can contribute to, and people you could collaborate with. And finally, talk to your supervisor and get ideas.

At the beginning of each week, make a list of everything you have to get done, personal and professional. Make separate lists for long term or short term tasks. When you finish one, take great pride in physically crossing it off the list. If you want, look into bullet journaling. Also, put EVERYTHING on a calendar which syncs with your email and across all your devices. I use Sunrise synced to my personal email, my iphone, my desktop and my work laptop.

I'll add more if I think of anything else. But try not to worry too much; you aren't even there yet! Right now, just get some rest, play some video games, go on a nice holiday. Celebrate your acceptance and look forward to the adventure you're about to have.


Submission changed to a different status, but with the same explanation as the previous status

Initial answer: (This answer assumes a regular type of full-length paper submission in the standard journal workflow.) This is probably an error in their explanation of the current status. The explanation is not in line with the typical journal workflow, especially the highlighted part:

  Article Status: Under Review

  Your paper is being reviewed by the journal’s editors and you will be contacted as soon as we have news.

In the typical journal workflow, the review is performed by the invited reviewers, rather than by the journal's editors.

You may contact the journal to task for clarification, but it probably won't matter in the end, as the process doesn't depend on this (incorrect) explanation.

Updated answer: (This update takes into account that the submission only has three pages, and that the journal uses a decision-making step based on consensus between the editorial board members.)  In this case, it's plausible that they're wont be additional reviewers involved. I speculate that the first status refers to the assigned editor handling the paper, and the second status refers to the editorial board making the decision. In this case, the status would not have any implication for the decision, other than removing the possibility of a desk-reject.


How to get the data to reproduce a published result?

Email the author nominated for communications, and ask them for a copy of their dataset and enough specifications to reproduce their numeric results. As a backstop, ask for the specific criteria they used to exclude cases. Consider offering co-authorship on any papers that will result from your analysis, as incentive. Give them enough context about you & your own work, so that they know your enquiry is serious, and that you're looking to constructively build on their work, (and not to stitch them up!)


I'm very frustrated about what "research collaboration" is

Collaboration is not something that can be forced. It is built on top of personal relationships, and requires some element of trust to have been established. The best collaborations emerge organically over time: really, the best strategy is just to spend as much time as you can working in the lab, talk to people, show interest in what they are doing, and allow relationships to develop.

Also, bear in mind that collaboration is a two-way street: both parties have to expect to benefit in the long run. You say that you are a masters student in a large university. From the perspective of a more senior researcher, this means you probably don't yet have enough experience or expertise to be particularly useful - or at least, you have not yet had the opportunity to demonstrate this. Again, the only real solution is to be visible, proactive, and give people an opportunity to see how you stand out from the crowd.


Difference between a letter/short article and a full length article?

In my experience, there is no real difference between "full" articles and "short" articles except for length.

Many journals, especially more recent online-only ones, do not bother with this distinction at all.  An article is simply as short or as long as the article turns out to be. Even with journals that do make the distinction, it often has little impact of the de facto length of the material once supplementary material is included---all that is affected is the fraction of the published "iceberg" that is "above water" in the main text. The peer review process is generally the same, and the perceived value the same, just simply some are shorter than others.

In terms of visibility and citations, short articles are typically just as visible (as you have noticed). I have never seen a citation attempt to distinguish between short and full articles, and most citation formats have no way that one could do so. For those who are affected by publication statistics (e.g., impact factor), that's not affected either: these are calculated by journal, not by article category within a journal.

In short: some things are just shorter than others, and that has little effect on their significance.  The editor thinks your article will work better in "short" than "long" format, so take their offer or risk rejection pointlessly.


Looking for conferences / journals with non blind peer review in computer science

You are looking for conferences or journals that have open reviews, that is, the submitted papers are visible to everyone, as well as the reviews. Possibly, the reviewers are even known to the public.

There are a few such conferences and journals. The Semantic Web Journal is a computer science journal where all submissions are visible to everyone and reviews are made public. By default, reviewers are known, unless they opt out and be anonymous (although their reviews become public). Authors of rejected papers can ask to have their submitted papers and accompanying reviews removed from the web site if they want. This journal is quite successful and has created a trend in the area of Semantic Web research to provide open reviews in related conferences. The European Semantic Web Conference 2018 had open reviews.

This is not the only example of open review process. I have seen another journal adhering to the open review process, although I don't remember which one right now.

Studies on the respective merrits of open vs. single blind vs. double blind reviews seem to be inexistent or very limited at the moment. Studies comparing reviewing policies seem to be focusing mostly (as far as I know) on comparing single blind vs. double blind, ignoring the open review scheme. So it is hard to say whether it is beneficial or not. There are people who are strongly against open reviews (citation needed, but I talked to some of them) and there are people strongly in favour of it (citation needed, but I talked to some as well).

I am myself a supporter of open reviews. I reviewed papers openly. You can see my open reviews for the Semantic Web Journal there: review on ActiveRaUL: Automatically Generated Web Interfaces for Creating RDF Data, review on Semantic Web Machine Reading with FRED (first submission), review on Semantic Web Machine Reading with FRED (revised version), review on Semantic Web Machine Reading with FRED (last version), review on loomp - mashup authoring and semantic annotation using linked data, review on Survey on complex ontology matching. I would disclose all of my reviews if I was allowed to do so.

I made other open reviews that have been removed because the authors requested it.


Why is online course enrollment limited to specific times when a course is offered?

Actually for both of them some courses are fully autonomous "anytime" courses, while others are restricted to being offered at particular times.  So far as I can tell, the time-restricted courses derive two benefits from being time-restricted:

It creates a "cohort" of students learning similar things and doing similar assignments at the same time, who can then help one another in the associated forums.
Resources needed to support the course (e.g., TA monitoring, course material updates) can track the progress of the students through the course, increasing the return on resources and minimizing disruption to students.


Do certificates from accredited online courses play any role in applying for a graduate program?

This is a personal view and I think that there would be a lot of variation in what people accept for a graduate program; especially for a doctoral program.
I would tend to discount almost all such courses for the simple reason that I have no real idea about what the student learned in the course, independent of whatever grade the received. I have no idea what they did and I have no idea how to evaluate a course that relies only on online quizzes and tests. To me, the value of a certificate is just that of a piece of paper. Probably virtual paper, actually.
I would think that such courses are fine for the person who simply wants to learn something and is willing to do a lot of work (exercises, projects,...) based on it, but not for any "accreditation" purposes.
The exception would be a reasonably scaled course with a professor and sufficient staff so that the student/staff ration is less than 30/1, preferably closer to 20/1. Most online courses don't have that characteristic (though Harvard's CS50 does, actually, as do courses run by Open University in UK).
A person learns through reinforcement and feedback. Massive online courses have no real way to judge whether such learning has happened. The reinforcement can't be enforced (so to speak) and the feedback to the student is minimal. An individual might be able to judge that they, themself, learned something, but an outsider would find it difficult to impossible.
I can't guarantee (or even guess) how many feel similarly, but the educational background of most of the people judging things now is very different from such massive "courses".
I don't think they are worthless, though it is impossible for me to make a judgement about their worth with enough confidence to predict the success of a student in a graduate program (especially, again) at the doctoral level. I would base my judgement on other factors, and especially those of recommenders.


Nobody will notice or care, unless you share a last name with your wife, in which case the strongest reaction is likely to be, "aw how cute, a husband and wife published a paper together."


Should I write that a student is a feminist in my recommendation letter?

First of all, your title doesn't quite match the rest of your question.  In your suggested quote you write "she is very interested in advancing women and other minorities in the STEM field," whereas according to the title you are asking whether you should write "She is a feminist."  Sadly, these things will not evoke equivalent responses in all parties -- the word "feminist" has unpleasant connotations in certain circles nowadays, more so than a generation ago.  (By the way, I am a feminist, and it makes me sick that the word is now taken in this way.  But it is by many, and so I think it is too loaded a word to use about someone else in such a context.)

The purpose of a recommendation letter is to successfully convey your impression of the recommended party.  In particular, if you feel strongly that the recommended party should get the position being applied for, then you want to write the letter that maximizes the chance of that happening (while staying appropriate, professional and truthful, of course).  With that in mind: how relevant "she is very interested in advancing women and other minorities in the STEM field" to the honors program the student is applying to?  Is this advancement one of the activities that students in the program will be participating in?  Or, beyond interest, does the candidate have a record of activities and/or accomplishments in advancing women and other minorities in the STEM field?  If the answer to either question is yes, I would suggest that you fill in further details accordingly: this is part of your argument that she is great fit for the program.  If not, then: are students selected for the honors program because of their progressive views -- or, much more cynically put, because of the alignment of their political and social views with those of the administrators of the program?  Probably not, right?  In particular, because "She is fantastic and I assume that she will get admitted," then I don't think you need to help her out in this particular way.  There is some risk that even a feminist could read "she is very interested in advancing women and other minorities in the STEM field" as a bit of a consolation prize.  Again, write the strongest letter you can.


Unfortunately, this will only apply to students and beginning faculty at larger institutions. Places with quite a few faculty members and, maybe with quite a few students as well.

But, at such a place, if you look around, you will probably find that there is a lot of collaboration already going on. You want to get connected to some of that in an area that interests you, at least a bit.

At some such places, senior faculty hold weekly seminars that aren't formal, but meet regularly. They will consist of the senior person, a few other faculty of various ranks, and a few students, usually advisees of some of those faculty. They are often organized around the main research interest of the senior person who organized and maintain it. People contribute ideas and discuss papers. Sometimes a member will be asked to make a presentation to the group (say half a dozen or ten) about some paper or some idea of interest. The key is people connected to ideas and to each other.

If you don't find such groups already formed, they may just be too small, with two or three faculty meeting in an office, or even at the coffee table, to discuss what they are working on and asking for advice.

If you don't find even that, it might be possible for you to form such a group, though in this case mostly students. Suppose you can find three or four other students with similar interests. Perhaps you've met them in class. Form a group yourself and go as a group to some faculty member and ask if s/he will "sponsor" you, by taking over the mentorship of your group. Perhaps they can give you some problem of interest for you to study together. Note that nothing formal needs to come from such a group, though it is great if it does. Think of it more as "expanding horizons" than as "goal directed". Before you start on anything serious, make sure you have worked out authorship issues. Don't neglect to be generous in that. In an ideal situation, these people can have a long term research relationship lasting beyond degrees.

If it is impossible to develop local relationships, then it is much harder. Being very social at conferences is a good way. Ask a lot of questions. Have coffee with a lot of people. Collect and distribute a lot of business cards, etc. The actual work of collaboration is a bit easier now with computer communication, but forming a compatible group is still quite difficult.


Polite way to ask professor's graduate research topics and if any matches an specific area

Researching a professor's recent publications is a great way to understand their focus, expertise and experience. How many publications have they produced, in the last 5-10 years? Additionally after performing this type of research it is possible to email them directly asking any additional questions you may have about their research focus.


Is it possible to ask the identity of a particular reviewer to oppose for future submission?

can I ask the handling editor that we don't want this particular reviewer?

No, because you don't know who they are, and you have no way to find out.

  can we ask the Editor of previous submission to disclose the identity of particular reviewer?

No, definitely not.  That would be an inappropriate request.  The editor would likely suspect that you wanted their name in order to retaliate against them in some way.  The editor would surely not comply, and might form doubts about your ethics, which could affect any future interactions you might have with the editor or the journal.

You could mention in your cover letter that you have had a problematic reviewer who said X,Y,Z, so that the editor would be forewarned.  However, I think this only helps if objections X,Y,Z are self-evidently absurd, which is probably not the case because three previous editors apparently took them seriously.  Also, it tends to draw attention to the fact that your paper has previously been rejected, which although it should not matter, may in practice bias the editor against it.

I would suggest instead:

Edit your paper to address the reviewer's objections as much as possible.  Even if their objections are completely wrong, you can clarify the paper to make it more clear that they are wrong.  "One might think that X is a problem here.  However, this is not the case, because of A."
Regarding the "related work", you need to update your paper to discuss this work.  Even if it didn't exist when you originally wrote the paper, it exists now, and when you sumbit to a new journal, it is your responsibility for your paper to properly address related work in the field as of the date of (the new) submission.  You can say something like "After our work was substantially finished, we became aware of X" in order to assert that you had priority.
Otherwise, be prepared for the possibility that you may get the same reviewer yet again.  If so, you can make the case to the editor that their objections are invalid, and ask for reconsideration.  But of course it will be up to the editor to judge.


Doesn't it depend on the context? I don't understand why you think it might be un-scientific. "However, at temperatures above 120C, the solution is liable to explode catastrophically". That might be worth saying in a scientific document.

Other literary phrases have a similar effect when the intent is to inform the reader. They also tend to mentally "flag" important phrases so that they are less likely to be overlooked. The word "however" especially gives the reader an immediate hint that the next phrase or sentence is somehow different from what has come before. A contrast is being presented. It "primes" the reader to consider the distinction. Other such words also have a traditional "flagging" use, though different from that of  "however".

The language is what it is. But each field has certain phrasing that is common there and the writing might seem awkward when it is abandoned. I'll guess, without evidence, that "however" is less common in math writing, than in, say, philosophy, where alternative arguments might need to be introduced. In mathematics, a paper will tend to drive inexorably toward a conclusion. However, in philosophy alternate views are often introduced so as to find a way to some truth. (You see what I did there?)


How to manage a colleague in your research group taking your idea?

Let’s start with one simple fact. On paper, your colleague didn’t do anything unethical. Perhaps they were thinking about something similar and you happened to as well, it’s not unheard of. So I don’t think that there’s much you can do apart from noting a colleague who’s not a very good collaborator.
If this is a pattern, then perhaps a discussion with a more senior person is warranted. I’d suggest you focus on getting more than one person to attest to this behavior and perhaps back it up with evidence e.g. email correspondence or the like.


Previous postdoc supervisor removed my name in the published article

It could be that your co-author attempted to reach out to you in order to get your permission to use your name but never got a response, i.e. old email/ not known address, ran out of time and had to publish without your name.
I would advise getting in touch with your colleague first in order to establish what happened before using the nuclear option.  It may be your colleague will assist in amending the published article.


Using an image under Creative Commons license in PhD thesis

License version

Note that the author licensed it under CC BY-SA 2.0 (that’s what it says on the Flickr page), while the blog post that made use of this image specifies CC BY-SA 4.0 instead. It’s allowed to license contributions to this image under a newer BY-SA license, but not the original work (only the author may choose to do this). So unless the blog post author got the permission from the image author, their attribution is not correct, and you should assume that the image is licensed under CC BY-SA 2.0.

Attribution

Your attribution isn’t sufficient.

For CC BY-SA 2.0, a correct attribution (for using the original image) contains (if available):

name (or pseudonym) of the author
title of the work
URI of the work

and you must specify

the URI of the license (or include a copy of the license)

So it could look like this:

  Chapter cover art: tricorderunbox4 (https://www.flickr.com/photos/bojo/4078685614) from Bobbie Johnson, licensed under CC BY-SA 2.0 (https://creativecommons.org/licenses/by-sa/2.0/)

or like this if hyperlinks are possible:

  Chapter cover art: tricorderunbox4 from Bobbie Johnson,  licensed under CC BY-SA 2.0

ShareAlike

The ShareAlike (SA) element of the license requires that derivative works have to be licensed under a compatible license, too.

Deciding whether or not a work becomes a derivative work isn’t always easy. And it’s not relevant if the image got modified:

A work could become a derivative even if the image is used unmodified.
If a work doesn’t become a derivative, you could still edit the image (it would only affect the license of that image, not your whole document).

In your case, I think that the thesis doesn’t become a derivative work, as the image doesn’t affect the rest of its content in any way. So it should be fine to not license your thesis, or to license it under a different license.


Are single author publications given more weight in math hiring?

All else being equal, solo papers can only be weighted more highly than joint papers in hiring decisions.  This is probably especially true at the very top: e.g. a joint Inventiones or Annals paper makes your application look fantastic.  A solo publication in either of these journals is a golden ticket for many academic jobs.

Things get much more complicated when one tries to determine how much more to weight solo papers than joint papers.  To the best of my knowledge few departments or universities have hard-and-fast rules or even written guidelines about this, so much of this evaluation goes on in the minds of the individual evaluators.  The truth is that in some situations jointly authored papers will count to exactly the same degree as solo authored papers, and in other situations the existence of coauthors will cause the work to be substantially discounted.

There is a dramatically increasing prevalence of joint papers in the mathematical profession.  Thirty years ago they were quite rare; and they are even more common now than at the beginning of my career, which was not much more than ten years ago.  There are now, for instance, certain conferences and workshops in which several people sign up in advance to work on a certain problem under the guidance of a senior mathematician.  And then everyone who came to the workshop gets their name put on the paper, even if everything they did was under the guidance of someone else.  This is a model much closer to that of the laboratory sciences than what used to be common in mathematics.  In my opinion, it is time for the profession as a whole and various groups within the profession to put down in writing some feelings about the merits of joint papers.  Of course this will be hard to do since the matter is so complicated: it matters whether your coauthors are "senior" or "junior" to you, it matters whether they have supervised you, it matters what percentage of your papers are joint and whether your papers are always joint with the same coauthors....

Sometimes I see certain publications listed on young people's CV's and think "I find it unlikely that they had a significant intellectual contribution to that work."  That's a problem both ways: i.e., people may be wrongly evaluating the merits of this type of work in either direction!


The basis for teaching university-level courses is publication, not so much the courses you may have taken. Therefore, in order to teach a PHY-xxx course, you should expect to be required to have published some research that is relevant for philosophy. That may be in the philosophy of logic, preferably in a philosophy journal.

How close your research has to be close to philosophy will be entirely dependent on the philosophy department and program as well as who their staff are. If they do not have a logic specialist they may be more open to consider you, but be assured that you have to give them reason to prefer you over one of their instructors (professor or lecturer). By allowing you to teach a PHI course the department clearly takes a risk (you are not "one of them"), a risk that is perceived to be higher than letting a philosophy professor teach a logic course, even if it is not that professor's main field.

Indeed, departments tend to take as granted that their professors are implicitly qualified to teach any of their courses (even though that may obviously not be the case), while being a priori suspicious of professors from other departments.

It may therefore be easier for you to give a course on a topic you hage to learn from scratch in mathematics than a course for which you think you are perfectly qualified in philosophy.

In any case, you should not go to the PHI department and argue that you have taken PHI courses which supposedly qualify you to compete with their professors who, after all, have a PhD in Philosophy. Write a couple of articles, a book, that is the way to do it. Or, offer to teach the course jointly with a PHI professor and see how it goes from there. Who knows, the other prof may take a sabbatical and hand you the course!


When someone says a paper is published "in Nature", does that mean it's published in *Nature*?

I've never heard a neuroscientist say they published in Nature, if it was in Nature Neuroscience.


Who to ask to write letter of recommendation: the professor who knows me better or the one that gave me a better grade?

The B instructor's letter is promising; it may be more insightful and more diligent. An impersonal letter that says "the student earned an A" may not sway any admissions committee. You could even inquire directly whether or not he's going to mention the B grade in the letter.


Can the decision to admit a PhD student be made by a single professor?

This varies greatly between departments.  In some cases (particularly European universities, I believe), Ph.D. students are admitted by individual professors.  There may be some basic requirements set by the department or university, but other than that it's up to the professor's judgment.

In other cases, decisions are 100% made by a committee.  For example, that's the case in my department.  Any professor can talk with the committee members and make a case for a particular candidate, but it would be unseemly to do this too often, and the committee can simply ignore these discussions if they choose to.  (In practice, they are willing to be convinced if someone makes a compelling case for why the student would be great, but they won't admit someone just because a potential advisor is in favor.)

  Many professors say on their websites not to email them because they cannot alone do not make the admission decisions, but rather it is the decision of a whole committee.

That's true in my case.  I can't evaluate most applications in isolation (unless someone is mediocre or obviously amazing, I won't know how they compare with the other applicants this year), and I'm not interested in lobbying the committee except in unusual cases where I have important information not available to them.  (If they know everything I do, then I don't want to offend them by suggesting that I don't think they are capable of doing a good job.)

  However, my undergraduate advisor said there is nothing stopping a single professor from admitting a student if they see fit. Is this true? And if so how often does it happen?

So the answer is that this is completely true in some departments, completely false in others, and may of course be in between in some cases.  How often it happens depends on the circumstances (what you are applying for and where).  If you are applying to U.S. math grad schools, for example, essentially all the decisions will be made by committees.  If you are applying for something else, then you'll have to look into that particular case.  But if you are seeing lots of statements on web pages saying that decisions are made by committee, that tells you something.


Requesting a copy of the PhD thesis from an author?

A PhD thesis is usually a published work, and is normally archived in a university's library. Almost all dissertations are available via reprints. So you could ask your own library how to order a copy of the thesis.

Alternatively, as you suggest, you can contact the author directly. As Anonymous Mathematician suggests in his comment, you can ask for a copy of the thesis, but you should definitely explain why you're interested in the thesis. However, it may be possible—and even more so for a humanities thesis—that the author is currently preparing it for publication, and may therefore be reluctant to share it via electronic means. However, it is just as likely that they're willing to share it.


When scheduling talks in a conference session, what is the etiquette, if any, regarding placement of multiple talks from the same research group?

You have to plan the symposium from the audience’s perspective, not the individual research group’s.

Presenting multiple talks from the same group back-to-back or even within the same session can become tedious, even if the work is nominally “distinct.” If I were planning multiple sessions, I would avoid putting abstracts from the same group in the same session, but instead spread the pairs out evenly among the three sessions (if possible).

If your sessions are thematic, I’d still try to separate the talks within the session, so that the talks are not back-to-back, but perhaps “bookending” the session or nearly so.


From the Harvard Dataset users guide:

  Download Citation

  You can find the citation for the dataset at the top of the dataset
  page in a blue box. Additionally, there is a Download Citation button
  that offers the option to download the citation as EndNote XML or RIS
  Format.

So if you go that route just upload your data and click that button.


Applying to schools in the US - Theoretical fundamental physics

Acceptance to a doctoral program in the US requires a broadly positive background and evidence that  you will succeed in the program you apply to. It is unlikely to hinge on any single thing. But letters of recommendation are very important, especially if they come from established researchers, preferably well known.

But the US has about 130 top research universities (R1). Some of them have larger programs and others are small. Relatively speaking Harvard and Princeton are small in any given discipline. State funded universities tend to be larger.

No one can predict what will happen based on such limited information. I suggest that you apply to several places, some at the top, as you have been advised and some others that are still excellent.

You can also do a bit of research on the places you might apply to. Figure out who is on the faculty and what their specialties are. Look at a paper or two from some of them to see if you are still interested. Note that a "top" university may not be "top" in every field. Look closely but cast a wide net.


What is a concise citation format for grant proposals given constraints on page counts?

Depending on whether the grant proposal is computer read only or not there is a possibility of hiding the References list from your MS Word (or some other word processing applications). Once clicked on, the References will pop up as a full list.

If the references have to be visible at all times, then the shortest way of referencing would be to use in-text numbered references. And in the end of the research proposal, you could change the font size/style to accommodate "more" space for your full references.

There are many different referencing styles (some more academic than others) but if the goal is to use up as little space as possible for the references then short form full references would work for you. A short googling session yielded this result for a short form citation style: http://anton.cromba.ch/2016/02/07/a-minimal-citation-stylefor-grant-proposals/

Another way of referencing to consider could be the under-line references on each page. That font style can be changed more before it begins to clash with the overall "style" of the document, making it possible to create very space efficient references. Although space efficient, some extra space is needed to accommodate the paragraph styles and readability.


What to do when professor is not responding to emails or calls and his action is required to commence a masters thesis?

You didn't really ask a clear question but I will answer the implied question: "How would you handle this situation?"

My experience with emails and professors is they are hit and miss. For some this is a very reliable method of communication, for others it is not. This isn't necessarily generational since quite often universities give young professors a new email address which becomes just one more thing they must monitor. In addition, as the semester progresses, most professors' inboxes become flooded with student email along with the usual administrative junk mail.

My suggestion would be find some way, phone call, in person visit or "ambush" outside of a regularly scheduled class. Once you find a way to make contact, explain your predicament with your boss and ask if there is a better method of communication. If the reply is "just use email" then explain this has proven unreliable and if you are to continue with the collaboration you need another method.

Bottom line is this is a collaboration.  If you are unable to collaborate, you will not finish your research and you will damage your reputation at your job.  If the professor is unable to communicate in a manner supporting the collaboration, you need to find a different professor of find a different thesis.


What advantages do libraries offer over the internet for doing a literature survey in Mathematics or CS

Almost none.

I recently wrote a research survey, while on sabbatical at an institution without a physical library, but with extensive electronic subscriptions.

I never missed having physical library access, even for papers dating back to the 1840s.  (In fact, the historical literature was more likely to be freely available than papers from the 1980s.)  Occasionally I had to use my home university's VPN to get access to a different subset of the electronic literature, and there were one or two books that I had to download via bittor—sorry, that I had to borrow from colleagues down the hall.  Yeah, that's it.


What is done in a workshop? How does it differ from an academic conference?

The reason why it is difficult to tell what workshops are about is because it is a catch-all category that many different types of academic meeting are labelled as. To illustrate, let me give examples of the nature of some of the events that I have attended in the last two years that all use the same word "workshop" to describe themselves:

A "baby conference" attached to a full-size conference, where the small meeting simply isn't large enough to meet on its own yet.
A project meeting for researchers who are all funded by the same large grant
A planning and discussion session aimed at helping determine the direction of a field
A joint industry/academia fact-finding meeting sponsored by an industry consortium
A specialty conference attended by around 100 people
A premier conference attended by several hundred people
A working meeting by a standards development group

The length of these meetings ranged from a single afternoon to a full week. Their programs ranged from nothing but loosely structured discussion to a full-on tightly packed conference schedule.  The level of peer review ranged from non-applicable to minimal to full-on single-blind review and revision.

In short: a workshop is whatever it wants to be, and different ones serve different purposes in the academic ecosystem.


Why are textbook authors often not the most famous/cited researchers?

You have already mentioned most of the things that are going on.

Someone who is good at doing research is not necessarily someone who is good at writing textbooks. These are different skills.
There are only 24 hours in a day, and an hour spent on writing textbook is an hour not spent on research. A person becomes a top-researcher by being strategic in the way (s)he manages her or his time. That often means not writing textbooks (see point below).
The "value" of a book differs a lot from (sub-(sub-))discipline to (sub-(sub-))discipline. Some value books (but even those not necessarily textbooks), and in some writing a book is basically a waste of time.


Repeating sections within the same paper

It likely depends on the field, and the norms at your particular institution. It is certainly common for dissertations to summarize portions of themselves (they are often 200-800+ pages, summaries are nice).

Based on your question, I wonder if you are concerned about self-plagiarism. I don't believe that this would rise to the level of self-plagiarism, as you are talking about a single document that is (usually) copyrighted by the author and will be published as a single document.

However, in my opinion, that is sloppy work. A good summary should be written to be concise and information dense, rather than an exact replication of other parts of the document. Instead of replicating, it may make sense for the student to reference the other chapters. For example "See Chapter III, Section [insert section] for a summary of [insert what is being summarized]".

Dissertations are already long enough, I don't believe that students need to draw them out through needless repetition.


Can a graduate student on a university stipend work a remote internship concurrently?

What are the legal, ethical, and practical implications of having another job while being on a research stipend?

Legally, this depends entirely on your university's policies and your contract.
Ethically, there will be a wide variety of opinions:

One line of thought will say that a research stipend is not a "normal" paycheck in exchange for your work, but rather an investment in your future by the donors or taxpayers. This investment is designed to cover your financial needs while you focus all your professional energies on launching your career. Such a view would be incompatible any paid work while receiving a research stipend.
Another line of thought will say that your research stipend is very much a normal paycheck, and whatever you do in your off hours is your own business. This view would allow students to do whatever they want on their own time.
But in your case, you say there is "significant overlap in my graduate research and the internship." This complicates the issue further, since even in the second point of view, you are not really doing the internship "on your own time." In this sense, your proposal could be considered equivalent to asking your advisor "could I work twice as much as your average student and get paid twice as much?" to which the answer is of course no.

Practically, of course it is difficult to sustain a very intense schedule, particularly for "creative" jobs. The fact that your internship and regular work are so similar exacerbates this, since you are using the same muscles for both efforts.

It it generally disallowed or discouraged?

I would say, generally discouraged and often disallowed. Though there are some exceptions, particularly in technological fields where students might be allowed or encouraged to do internships or even start their own companies on the side.

How do I negotiate such an arrangement with my advisor?

This will depend entirely on your university's policies, your performance, and the advisor's personality.


How to approach potential supervisors who have already expressed an interest in supervising me after submitting my grad application?

I don't think the rules require that you decline the other professor formally. I probably wouldn't do that. Reaching out to both could get tricky as you will need to choose at some point anyway.

For the introductory letter to the one you prefer, introduce yourself and say something about your own interests and background (very short). You don't need to praise the professor. Saying that you have read a bit of their work and if some particular part of it is interesting to you then say which.

I assume that you will get an invitation to meet since he/she has already expressed an interest. You don't need to praise yourself either. The prof will have an idea that you fit the requirements. It isn't a selling job, but an introduction and statement of interest.

It is too early to make decisions. Wait until you meet to jointly figure out how you would fit in. But that would come after acceptance.


How is the salary of professors and researchers in medicine?

For the US, I would have thought the data would be in the AAUP report, but I cannot find any data that breaks salaries down by field.

There is also CUPA-HR. The free data set has a break down by field with "HEALTH PROFESSIONS AND RELATED PROGRAMS" as a field. I would assume that this includes medical doctors, but also nurses. There is also some free data about non-tenure track salaries including "Medicine, Medical Clinical Sciences, Graduate Medical Studies".

In summary, I think defining the "medicine area" and equating job duties and responsibilities is tough. There appears to be a large variation in salaries.


Strategies to strengthen self-discipline as a PhD student

I recently finished High School and I'm about to start University. I had a similar problem when studying for my final exams. This really helped me so take it or leave it, here's what helped for me:

1) Don't commit to doing huge mountains of work, you will only find procrastinating easier. Only plan to do a small bit and if you don't get into the rhythm of things then that's all you have to do.

2) Go for a jog/run. I would go at a regular pace until I really wanted to stop, then I would go just a bit more, to the post ahead, then to the next post and so on, forcing myself to keep going. Then, with the same attitude in mind, I would study just doing one more paragraph, and the next, and so on. Little Victories.

3) Remember: Every time you fail or feel like stopping, somebody else just gave up and each time you keep on trying, you do better and better than the people who gave up when you didn't.

I hope this helps.


How to inform the editor that they sent me the wrong PDF attachment?

You may have to email an administrative contact in or outside the system. Keep trying. DO NOT include a revised version of your paper since that seems to have confused them. Let them know that you received a revision request for a different paper entitled "Whatever the other paper is called" by X and Y and Z, and that you'd like to see if you can get the required revisions request for your paper entitled "Whatever your paper is called" by A and B and C so that you can make the corrections. Even if you already have done them, try not to be confusing by resending the corrections to your paper.

I had an editor send me a PDF of required revisions once with the file named X.pdf. When I contacted him, he was very embarrassed because he had broken the blinding by admitting that X had submitted a paper that was under revision at the journal. Keep trying. Eventually they'll understand.


Why does the Clinical Journal of Sports Medicine think they will need quadrillions of DOIs?

This "answer" is really speculation - if you truly want to know their motivations, you have to ask them.

But I think the simplest and most likely explanation is that they don't consciously believe they will need that many DOIs; they just had to pick some format, and arbitrarily chose a number of digits that seemed more than adequate (as well as perhaps allowing for DOIs to be assigned in some other way than just serially; e.g. someday the DOI could identify volume, year, page number, etc).

They probably didn't even think about people needing to transcribe them by hand - and to be fair, in this age of electronic distribution and copy/paste, it's a pretty rare use case.


Can you do a masters in Canada with 3 years bachelor degree?

Most Canadian university will admit you to a master if you have an undergraduate degree. This could be a “license” in the European system or a bachelor degree. The reason why universities require a four year degree is because there is no College in the Canadian system ( with the exception of Quebec with its cégep system). Consequently, students enter universities at a young age ( around 17 or 18). If you have completed a bachelor equivalent I would try to apply. School registrar will judge your application based on which education system you are from.
Good luck in your application !


Short answer: No.

Long answer: If it is a good university, they will repeat the whole process, regardless of previous applications, even more if the application is different. It is possible that they consider the result of the previous judgment to see if anything changed, but I don't  think that is that likely..

The members of the committee itself may have changed as well. Unless you have the mother of all red-flags on your CV, that would make you unbelievably memorable, you are probably safe...


I am writing a briefing paper, and it only consists of facts and citations

Even if all that you are doing is summarizing pre-existing material, if you aren't writing in your own words, you are likely to produce terrible prose.

In summarization, you are necessarily making decisions about what to include and what to omit. You have reasons for making those decisions. That is your perspective on the material.

A good briefing can be quite exciting and compelling, even if it is filled to the brim with citations.  Too many quotations however, is likely to be a problem, because those quotations are taken from a different context and will not flow together to make a narrative.

If you are having trouble breaking away from these prior words, I might suggest the following radical technique: having first made you collection of material as you have described, open a fresh, blank, document, and starting writing without looking at any of the original material.  In this circumstance, your memory will be not good enough to continue using only the words of others, and you may be better able to start developing your own expression and perspective on the material.


Malfunctioning social media buttons on a conference website

I wouldn't say this is normal. That said, it need not raise a red flag or suggest that this would be a predatory conference or something you must stay away from. It doesn't inspire confidence, but it doesn't need to hurt confidence much either.

This sounds like a relatively minor issue and the kind of thing that is easy for the person setting up the conference website to miss in testing. Keep in mind that many prestigious conference have websites set up by academics volunteering to do so as part of service to their academic community, who are very busy, and for whom building robust websites is not their full time job.

There are predatory and sham conferences. If the conference is archival, check out Beall's List of potential, possible, or probable predatory scholarly open-access publishers and search around the web for information on the conference.

Email the organizers to tell them about the issue. You might even learn something about the credibility of the conference by who responds, and how.


Is it difficult to be fully funded for PhD in STEM field in US?

Yes it is appropriate to ask, both for the program and the individual professors. Hopefully you ask other important and research-related questions at the same time, but funding is not a taboo topic for a prospective student, and it should be one of the keys to your decision if you are accepted to multiple programs.

Many programs (in STEM in general, can't speak to civil engineering in particular) offer fully-funded programs (tuition+a stipend) for PhDs (less often for masters), but there may be limits (for example you may be guaranteed for only 5-6 years, and if it takes longer you might still get funding just not guaranteed), and you almost certainly won't be free to do whatever you want: you may be required to teach ("TA") whether you want to or not, you may be required to join a lab that has funding available ("RA"), even if that lab was not your first choice otherwise, or you might have to do other work for another lab/group that isn't directly related to your research (as an RA or PA). Fellowships or traineeships are directly funding YOU and are the best source of funding but are often competitive and may cover only a short period of time.

"Fully funded" could include ANY combination of the above, so you should ask questions about the types of funding and not just a guarantee. Current students are also a great resource.


How do I deal with diverse interests when applying for a PhD program?

(My experience with non-American PhD programs is limited, so some of what I say here may not be relevant or possible.)

First, I think you may have painted yourself into a corner.  More important than being specific, PhD applications should be honest.  Hopefully your applications described the breadth of your interests, perhaps with some extra emphasis and detail in one area, rather than implying falsely that you are only interested in one topic.  It's better to be rejected than to be accepted into a PhD program where you won't thrive.

I think you need to look for overlaps and connections between your various fields of interest.  Decision theory and machine learning are not that far apart.  Quantum computing and philosophy of computing are not that far apart.  Parallel computing and logic are not that far apart.  Decision theory and logic are not that far apart.  Machine learning and computer music are not that far apart.  Finding something at the intersection of five or six different areas is almost certainly impossible, but lots of interesting stuff happens at the interface between field X and field Y.

On the other hand, all the areas you describe are incredibly diverse within their own boundaries.  You may find enough different topics within (say) machine learning to keep your fickle heart satisfied.

One thing you should ask about (quickly!) is the possibility of having multiple (ie, two) advisors in different areas.  Some departments encourage inter-disciplinary co-advising; some don't.  Some advisors encourage collaboration with other faculty; others flatly forbid it.  (In many European PhD programs, students are attached to specific projects of specific faculty from day one, and moving between projects or fields is almost impossible.)

What worries me more than the diversity of your interests is this sentence: "Whenever I've tried to restrict myself to one topic of study - even for a month - that feeling is lost, and I am quickly bored".  You have to get over that.  Research requires long-term focused attention.  Early in your PhD program, you may be able to juggle a couple of different research projects at once, but eventually, you have to focus on a coherent thesis topic.  It can be an interdisciplinary topic, sure, but it has be coherent.  You will have to work on that one topic for years.  If that sounds awful to you, then maybe you don't want to be a PhD student after all.

My department head has changed fields several times in his career, so I think his advice on this topic is worth repeating.  Assuming good health and good luck, you have a 50-year research career ahead of you.  So if you're deeply interested in half a dozen different areas, you can afford to spend seven or eight years on each one.


I never finished my master's degree; how can I reflect the courses I took on my resume/CV?

You might consider something like this:

  Education

  Undergraduate Institution  B.S. in DEGREE FIELD, August 2005-December 2010

  Graduate Institution  Graduate-level coursework in Health
  Administration, August 2016-May 2017

If you want, after the graduate level coursework line, you could list relevant classes. For instance:

  Relevant courses: Hospital Administration, Global Health Policy, ...


How can a Master degree lead to 300 ECTS?

I'm guessing ECTS is the European Credit Transfer and Accumulation System. From that page, a bachelor's degree is worth 180-240 ECTS credits, and the master's is worth 60-120.

It sounds as though the institution you're interested in wants a master's degree and at least 300 ECTS credits. From the linked page, it's possible that you could have a master's but still only have 240 ECTS.


I do not think professors will take his personal life into consideration as long as he has great academic performance or social skills if needed for whatever he is trying to get reference letters for.


Withdrawing from PhD with or without a Master Degree

It's quite common for people to leave a Ph.D. program. In my experience, employers don't really see that as a negative; people leave for many reasons, and they'll likely rather focus on whether or not you learned anything while you were there that will help you do the job they're interviewing you for.

It sounds like you have a time-investment vs. reward tradeoff to consider here. A summer is not that long, but you may have to make some sacrifices in order to free up that time. A second MS in the same discipline is not going to help you very much at all, especially in industry jobs, unless there's something significant about it that makes it stand out (is it a thesis-based MS vs. a class-hours based MS, or perhaps it's slightly different but the difference in topic is something employers will respond to).

If you can delay a job search for the summer to get the second MS, and you'd like to cash out the "sweat equity" you've accumulated in your current program by getting a degree for it, then I don't think there's a big problem with doing that. If you didn't already have an MS, I'd say definitely get this one, but that's not your case. Just keep in mind that getting the additional MS is unlikely to open doors any wider for you, and not getting it is unlikely to close them.


Paths to mathematics/university/research while dealing with a few difficult situations

Universities typically demand qualifications, which you don't have. You could get some: You seem familiar with advanced areas of mathematics, perhaps you can study some revision guides, teach yourself whatever you need to know to get some qualifications. (I'm unsure which institutes you can enrol with in Australia. I presume such institutes must exist. They do elsewhere—not everyone follows the traditional route.) Alternatively, you could reach out to universities, explain your situation, negotiate why they should admit you without typically mandated qualifications. Perhaps you have someone who can help you, e.g., some staff member who happens to know an academic who is willing to help you navigate the system.


On writing a review (i.e. summary) for a problematic (published) paper

Your review should do three things (not necessarily in this order). It should tell the reader what the topic of the paper is, perhaps including the authors' main "theorem". (This presupposes that the paper is clear enough to have a topic; I've reviewed garbage that didn't have a discernible topic, but I gather from your question that this is not the case here.) It should make it clear that you think it's wrong. And it should give enough information about the error to allow people in the same area to understand why you think it's wrong. (Once you've explained the essential error, it's not necessary to list a lot of other errors, unless you think that doing so would help the reader or make it clearer that the paper is wrong.)

It is especially important to indicate accurately just how bad the paper is.  For example, is it nonsense, or is it just wrong, or does it give a possibly correct theorem but with inadequate or erroneous proof?  You can save potential readers of the paper a lot of trouble by making the situation clear.


How can I learn to establish good research questions?

Hmmm. Muddle. Try. Fail. Muddle. Repeat. Repeat. Try. Succeed (partially). Muddle. Refine. Muddle. Succeed (maybe).

To paraphrase a bit of wisdom from another field: Posing good questions comes from Experience. Experience comes from posing bad questions.

There isn't a plan in mathematical research (or in most other fields) that will guarantee success. You are moving into the unknown, which is, well, unknown.

But there are a few hints that work (sometimes...partially). First, you need to deeply understand the essence of what you are about. This requires insight and insight isn't always gained even by earning a doctorate. Insight is what knocks you off the donkey when you aren't expecting it. Insight is understanding something one moment that eluded  you the moment before. Insight sometimes comes from hard work, but it also sometimes comes from just riding on the donkey to get somewhere.

The hints:

Read a lot of papers.

Think about possible extensions of those papers.

Think about possible variations of those papers.

Think about applying the method of proof of those papers to some other, possibly unrelated sub-field.

Take a lot of notes and update them when you have any small insights. I find it useful to carry some of those notes around on index cards, just to refresh my memory (on the donkey).

Think hard about the essence. What is the derivative? What is the essence of the derivative? Why is the definition like it is? Are all of those parts essential? Can they be changed? What would I learn if I change something there? Derivatives work nicely on nice functions. What if the functions aren't nice.

Talk to a lot of people. Share ideas, don't hoard them. Work together. Ask "what if".

Take risks in your thinking. New sub-fields of math have often arisen from "risky thinking". Algebraic Geometry? What a wild idea.

And, finally:

No guarantees.

Try again. Make notes.


How to position myself to transition from doing wet lab research to doing computational work?

Some online bioinformatics resources that I can recommend:

Bioinformatics ALgorithms
Rosalind bioinformatics problems
The Biostar Handbook


Is it okay to reproduce the work as a teaching assistant?

I agree with user11388 that it would be good to "cite" the video you used, but otherwise I wouldn't worry much about this. Truth be told that most of us in academia, in the early part of our teaching career, "emulated" the teaching of our own teachers, especially the ones we most admired. Over time you learn to be more spontaneous, but at the start you try to follow a good model. It is partly what mentoring is about.
However, you will "add value" to the lecture just by being there to answer questions that might arise and to (hopefully) watch the student's reactions so that you can notice difficulties of comprehension.


Am I pursuing a “degree in” or “of computer science”?

In the context 'in' is right, even if the eventual degree is called "Master of Computer Science". I hold a degree in mathematics, but its formal title is 'Master of Mathematics'. My first degree, also in mathematics was, formally, Bachelor of Arts.

There is a distinction between the subject of a degree and its formal title.


I would understand "seminal" to indicate that  (a) the paper was the the first in some sense, and (b) that it led to a lot of subsequent research. For example, a paper proposes and tests a theoretical idea, and then lots of other people come along and test that idea building on the original study.

It doesn't matter that you are not established in a field. Anyone can use the word "seminal". It's just that using it correctly requires a good understanding of your field and the interconnections of research papers.

Having a lot of citations is necessary but not sufficient to show that a paper has led to subsequent research. Some citations don't mean much on its own.


Given a DOI, how can I programmatically obtain all the author affiliations?

First of all, the main sources of citation data are:

Proprietary data sources:

Google Scholar
Scopus
Web of Science (WoS)

Open access data:

Crossref
MEDLINE (focusing on medical papers)

Some papers compare the comprehensiveness between these different sources, e.g. see {1,2}.

To extract the author affiliations given a DOI, a few options (search for "affiliations" on the links below) :

https://support.datacite.org/docs/api-get-doi
https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html (MEDLINE database https://www.nlm.nih.gov/bsd/medline.html)
https://github.com/CrossRef/rest-api-doc  suggested by Anyon.

For option 3 (CrossRef API), one can use the https://github.com/CrossRef/rest-api-doc  API via the Python library https://gitlab.com/crossref/crossref_commons_py:
# If testing in Docker
docker run --interactive --tty ubuntu:18.04 bash
apt update; apt install -y git nano wget htop python3 python3-pip unzip

# Requirements
pip3 install crossref-commons

# Python code
import crossref_commons.retrieval
crossref_commons.retrieval.get_publication_as_json('10.5621/sciefictstud.40.2.0382')  # affiliations are empty
crossref_commons.retrieval.get_publication_as_json('10.1148/radiol.2018180887')       # affiliations are present

though it seems that quite often authors have no affiliations on CrossRef.
My guess is that MEDLINE (option 2) has more thorough metainformation (I based my guess given the information I see on the PubMed website, which relies on MEDLINE database, e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936069/ has author affiliations, but not crossref_commons.retrieval.get_publication_as_json('10.1186/s12920-019-0598-0'), even though 10.1186/s12920-019-0598-0 = PMC6936069. Anyon's comment also questions CrossRef's comprehensiveness for the author affiliations field). The MEDLINE database can either be downloaded or accessed via API (https://www.ncbi.nlm.nih.gov/home/develop/api/). See https://stackoverflow.com/a/62974197/395857 on how to access the MEDLINE database in Python.

If one cannot find the affiliation in the metainformation and if the PDF can be obtained from the DOI, one could use PDF-to-text extraction programs for scientific papers, such as:

https://github.com/kermitt2/grobid (has the ability to parse affiliation and address blocks)
https://github.com/allenai/science-parse
https://github.com/allenai/spv2

To test pybliometrics that BND refers to in their answer:
# If testing in Docker
docker run --interactive --tty ubuntu:18.04 bash
apt update; apt install -y git nano wget htop python3 python3-pip unzip

# Install and configure pybliometrics
pip3 install pybliometrics
from pybliometrics.scopus.utils import config
config['Authentication']['APIKey'] = '' # Enter Elsevier API key obtained on http//dev.elsevier.com/myapikey.html

# Retrieve author affiliations
from pybliometrics.scopus import AbstractRetrieval
ab = AbstractRetrieval("10.1016/j.softx.2019.100263")
from pybliometrics.scopus import AuthorRetrieval
au1 = AuthorRetrieval(ab.authors[0].auid)
print(au1.affiliation_current)

Unfortunately pybliometrics relies on Elsevier Scopus's API, which isn't free: some institutions have subscribed to it, but fewer and fewer are willing to feed the Elsevier sharks.

References:

{1} Harzing, Anne-Wil, and Satu Alakangas. "Google Scholar, Scopus and the Web of Science: a longitudinal and cross-disciplinary comparison." Scientometrics 106, no. 2 (2016): 787-804. https://web.archive.org/web/20170922223941/http://eprints.mdx.ac.uk/18511/1/gsscowos.pdf
{2} Van Eck, Nees Jan, Ludo Waltman, Vincent Larivière, and Cassidy Sugimoto. "Crossref as a new source of citation data: A comparison with Web of Science and Scopus." A blog post in the website of the Centre for Science and Technology Studies (CWTS), Leiden University, URL: https://www.cwts.nl/blog (2018). https://www.cwts.nl/blog?article=n-r2s234 (mirror)


Should a reviewer critique language and text copy-paste issues?

As Mikael said, copying and pasting from a textbook (or any other source), unless it's properly quoted and cited, is plagiarism. Now, it's possible that this varies a bit between fields and between cultures, but generally speaking, plagiarism is one of the most serious academic offenses, probably a step below outright fabrication of results. Well-respected tenured professors at major universities have lost their jobs and had their careers destroyed by a single instance of plagiarism. The point is, this is a very big no-no and you should treat it accordingly. You should definitely notify the editor, and see how they would like you to deal with it. I don't know exactly how that process works, whether the editor will just handle the paper themselves and let you know that your review will no longer be necessary, or whether they'll ask you to finish your review anyway and state your objections in it.

In the latter case, I would write an unequivocal recommendation against publishing the paper because of the plagiarism. Personally, I would be inclined not to even look at the scientific content of any such paper, although that may not work out in practice. But anyway, just pointing out the plagiarized parts and recommending against publication, in and of itself, is not mean. Just don't get carried away and start attacking the author. You could apply the same principle that is used at Stack Exchange, namely that it's about the behavior, not the person.

If you put aside the plagiarism, there is also the issue of sloppy English that you mentioned. In my experience, (nearly?) all reputable journals require papers to use proper spelling and grammar for standard English, or something reasonably close to it. Usually, the instructions for authors will advise non-native speakers of English to get a native speaker to check the paper for grammatical errors before submission. So it's reasonable for you to point out any such errors that you come across. Now, grammatical errors don't have to condemn a paper to oblivion the way plagiarism might, but if the grammar is bad enough, I would think it reasonable to recommend against publication in its current state. If the underlying ideas are sound, and otherwise qualified for publication, then you could recommend that the authors edit the paper to improve the grammar and resubmit it.


Why does NIH study section website robot.txt disallow search?

@Memming, this could be done for any number of reasons.  The two I can think of off the top of my head is 1) to prevent site slowdowns especially due to what is likely to be the duplication of information developed by indexing the NIH site and 2) to protect (to some extent) the privacy of the participants.

One suggestion, have you tried using Google to search the site?  Search is not the same as indexing.  So if you're looking for sections with "Joe Brown" you can try searching "Joe Brown site:csr.nih.gov".  I was able to get results with this approach using a name I picked at random from the study sessions.


The fact that you're not in academia is not proibitive for publication, but it sure makes things more difficult. If you think your paper is well written in the sense that it looks like an usual physics paper, you can simply find a proper journal and just submit your work.

But I'd recommend first making your work available online to get opinion from people in the field, as they can point you to the proper journal to submit, they can help you with your writting and, more importantly, they can check if what you claim makes sense or not. I'd recommend posting a question to Physics.SE about the issue you found with a link to your paper.


How to avoid the "you didn't consider this" review in a scientific publication?

I empathise with your difficulty and wish there was an easy fix. However, going by the question and comments, it does seem like you may need to rethink your approach a little. Consider the following:

(1) In an applied research field, the bar is not just solving a sub-problem; it is ensuring that the proposed solution will work with all other factors considered. To give a very trivial and crude (pardon me) example, if a car bonnet has to be light and strong, you cannot treat the two independently and use polythene (solving light) or concrete (solving strong).

The comment : "There is no way this is going to work when you consider E.c and E.d as well"." seems to suggest exactly that. I know my example is not perfectly analogous to your problem, but I hope the essential message is conveyed.

(2) There exists an industry standard S. Therefore, any proposal to change has merit only if it can replace S on all counts. If the method S scores 70%, 80%, 60% on some relevant metrics, your method E should not score 100%, 10%, 80% , even though 2/3 metrics are significantly improved (because one metric has fallen, and that could be unacceptable). Rather, an incremental 75%, 85%, 65% would be more acceptable.

There is a constant strain in such fields between novelty and applicability,  both need to be balanced out. Depending on what conference it is, one may carry more weight than the other, but the application bit can rarely be ignored.

What seems to me a better approach is:

(1) Tackle Eb/c/d in your study, even if briefly. Not just in the introduction, in the study and the results itself. Show that you are not simply highlighting problems (i.e. mentioning only in introduction), but doing something about them even if you don't solve them fully. Even analysing and rating the magnitude/importance of Eb/c/d is a meaningful contribution, supplementing your main work on Ea. So you don't need to solve them all, but you do need to consider them and look at inter-dependence.

(2) If possible, suggest ways in which E can be integrated with S. Then, the benefits of Ea can be used without the problems Eb, Ec. Again, you don't actually need to integrate the whole method. Look at ways to do it, what problems exist, how meaningful such an exercise is vs replacing an entire system.

These approaches should be good for such conferences which are indeed intended to share a developing idea. Even in those, your eye must be on the future- on how to develop it, what can be taken forward, what can be done to make it more complete.


I have an accepted conference paper with a major error in it, should I ask for it to be changed?

Yes!

Better to get it corrected than to be questioned/rejected later.


How much informal writing should there be in a research article?

...funny side of my personality pops up...which I have to delete...

Good. Keep it that way. There is absolutely no place for jokes in academic writing*. This includes funny puns or things like that. The purpose of a research paper is to communicate science. Unless you are researching humour, do not do it.

What good can come out of it? Do you envision someone thinking "oh, that's a funny guy! I should hire him!"? No. This does not happen.

Jokes and what is considered good humour changes with time. Things you find funny now were not funny 10 years ago, and vice versa. Once this gets in a paper, this is forever in the scientific record. No matter how funny or witty you think you are now, you will most probably look back regretting that you did. This is also a cultural thing: things that are funny in Europe may not be funny (or even offensive) in Asia. There is also a language barrier. Some people may not even realise it's a joke and try to understand it in the context of the paper. This can only lead to unnecessary confusion.

As a reader I want to understand the science, and only the science. If you want to be funny, open a Twitter account, write a blog, post it on Facebook, put it on a poster and hang it on your office door.

*Humour is acceptable if you're a distinguished professor that made abundant contributions to science and you're writing an opinion paper. You'd have to be over 70 years old for that. And even then, use it sparingly.

Also related:

Amusing remarks in papers
Should academic papers necessarily carry a sober tone?
How much of humor in a formal academic writing is considered as disrespect?