What are some criteria to get an Australian PhD scholarship?

For Australia, both the supervisor and the university might reject a PhD student.  Universities may often reject PhD students for inadequate language ability even if the supervisor wants the student.  These decisions are based on a threshold, not based on who else applies.
Some supervisors have funding they can use to pay PhD students at their discretion, but most PhD students are funded through a university program.  The fact that a position has been advertised does not mean the supervisor necessarily has funding for that position.  For funding by a university, research experience is essential.  Marks (not called GPA in Australia) are also considered.  There is a fixed amount of funding available, so decisions depend on who else applies.


Is it reasonable to submit a paper to a journal that I have uploaded to the Arxiv 4 years ago?

In math, it commonly happens that, for whatever reason, an unpublished work gets cited several times.  (This is rather annoying when it is something useful but not easily accessible, though this is not quite your case.)

I think that whether you can easily publish it depends on how similar the work is now to published work.  A collaborator and I were in a somewhat similar situation (though not the same), but our focus was different and we discussed some different things so it was publishable.  (He didn't think it was interesting enough to publish originally many years ago, but then we did some additional things that made it more interesting, even after someone else had published the main result with the same method independently.)

If you want to publish it, here are two suggestions:  1) try to publish as is in conference proceedings, or 2) incorporate your old paper into a new paper which does some other things (it could be expository, or with additional new research).

As for whether publishing it will help your career, my guess it won't make a huge difference, unless you only have 1 or 2 publications, though it may help some.  (It's not likely to get into a top journal unless you do something else.)  It sounds like people know about your work, so letter writers can talk about it if they think it's important (in which case maybe you should've published it! but one doesn't always know in advance what will be interesting), and on your CV you can always list it as a preprint.


My university requires unrestricted access to my personal laptop. What should I do?

My university requires unrestricted access to my personal computer for an afternoon to install a certain software.

Your university has messed up. Are you really sure that it's the university requiring this? Maybe it's the isolated action of your professor, in agreement with their department IT (not the university one).

  He has explicitly stated that there are no alternatives to the standard process of giving in my computer to the tech department for one afternoon.

I've never, ever seen an academic software licence requiring such a procedure.

  On one side am reluctant to give unrestricted access to my computer for security reasons

You're rightly reluctant.

  How can I avoid giving unrestricted access to my personal machine while still obtaining this software?

First, contact your course mates to start a collective action. I suggest you to write an email, signed by all students, to the dean supervising the courses of your field, the head of the department to which your professor belongs to, and, if there is one, the head of the IT university service. Copy the email to the rector too. Express clearly your concerns and state that is totally unacceptable to require students to give access to their personal computers. If your university insists on this position, ask them a copy of the licence agreement.


Publishing with APS open access with a CC-BY license on a preprint server

I got a reply from APS on this issue. My question was:

  We accidentally chose the CC-BY 4.0 license https://creativecommons.org/licenses/by/4.0/ for our arXiv preprint of a manuscript submitted for publication in Physical Review Letters instead of the standard arXiv license.

  Does this license conflict with the standard Transfer of Copyright
  agreement? If so, is it possible to instead choose the option "Retain
  copyright and complete the Creative Commons publication agreement"?

  As far as I understand, the second option should work, since APS would
  publish under the same CC-BY 4.0 license as we used for the arXiv
  submission. Is this correct?

APS answered:

  Choosing a CC-BY-4.0 license for your arXiv submission does
  not conflict with choosing the standard Transfer of Copyright
  Agreement for submission to an APS Journal.

So in short, you can use a CC-BY-4.0 license for your arXiv preprint and still publish the manuscript in PRL under the usual conditions (i.e., not open-access).


What is the typical time period after which an incoming grad student is expected to start publishing?

This wil vary significantly according to advisor, but I'd say a typical plan is:

Years 1-2: coursework, begin research
Summer of year 2: Small research publications (in my field, 2-4 page conference proceedings, small steps)
Year 3: Get some real research done, more small papers
Year 4+: ~1/2 paper a year, ish

However, the variance may be too great for this to be meaningful. I have a friend who published 17 papers during his 6 year graduate student tenure, and I have a number of friends who published zero peer-reviewed papers during my grad school tenure. Take the numbers with a grain of salt.


What did Universities use in lectures before they starting using PowerPoint?

I can go back to 1989, when I enrolled at the university (engineering). The first two years were mostly devoted to mathematics, physics, chemistry and circuit theory. No overheads were employed in those courses, just plain old blackboard. There was just a course on Fortran and Pascal where the professor probably employed overheads, but I skipped all the lectures so, well, I'm not sure about that.

Overheads really started to appear from the third year on, mainly for engineering courses about algorithms, digital circuits or solid state physics (alas, these were abysmal). Lecturers would deposit a printed copy of the handouts at a local photocopy shop, so that everyone could buy a copy. Certain courses had packs of around 1000 handouts, and frequently the handouts were not available till the end of the course. Luckily, most of the courses about analogue circuits, advanced electromagnetics and quantum physics were still delivered through the blackboard.

It is worth recalling that at the time "overhead transitions" were implemented by means of patches and adhesive tapes. When printed, these "effects" would leave black marks of various shapes on the handouts.

Overheads were typically in full colours when handwritten, but the handouts were of course black and white, and writings in lighter colours were barely readable. Program listings were instead printed with black and white printers: no syntax colouring at the time.

Edit: I've just found under a pile of papers one of those packs of handouts. Here is how one of the pages looked like (two overheads per page; the pack is dated 1987):

The first overhead, on the left, is the text of an exercise ("Design a circuit with three inputs x,y,z [...]"), the overhead on the right is part of the solution. You might notice that on the upper right corner of the left overhead there are two page numbers: probably the overheads had been renumbered along the years.


What information to put in Bibliography for a Online Course

It should be appropriate to acknowledge the "head-start" you got from that course in the acknowledgements section of the thesis. It would be unusual to list a course in the bibliography unless there really was no more authoritative source available for some information or a method that you directly used.

The purpose of a bibliography is to cite the primary source of any information directly used in your work. If you use something from the online course worth citing, then you should cite it. However, it's unlikely the information in the course is new, so you should try to track down and cite the original source in a peer-reviewed article or textbook.


Is it acceptable to transform an accepted paper (tier-1 conf.) as a patent?

Any information which you disclosed in your publication will count as prior art, and cannot be patented by you or by anyone else. If you wish to write publications about an invention which you also wish to patent, you must file for patents first. Hence, a paper cannot be "transformed" into a patent. If you have an invention which builds upon the information disclosed in the paper, this may be patentable.

Patents cost money to file, and expensive to maintain. There is also considerable skill in writing patents. There is no point in filing for a patent unless you intend to exploit it. As such, the academic/career benefits do not justify filing for a patent per se, and without a good plan to commercialise the invention, it will simply be a waste of money.


Will my methods chapter be less solid, if it is based on one book or the work of one scholar?

Literature on virtual ethnography or netnography is not restricted only to these authors. A cursory Google Scholar search reveals many other authors.

Having said this, ~50% of my methodological approach in my work is through grounded theory by using semi-structured interviews. The gold standard for grounded theory is:

Glaser, Barney G & Strauss, Anselm L., 1967. The Discovery of Grounded Theory: Strategies for Qualitative Research, Chicago, Aldine Publishing Company

... and I would wager that ~95% of papers using grounded theory cite only them in the methods sections of their papers.

This does not necessarily make your methods poorer or stronger. You should make sure that you understand the methodological process perfectly and then implement it.

Make sure that you do talk about credibility, transferability, dependability and confirmability as well !


What are the challenges in changing a PhD supervisor after 2/3 of PhD is done

I have seen a lot of people switching advisers during my PhD. There are a few challenges I think you will face:

Your adviser, knowing his personality, won't let you go easily. He might tell other faculty there will be consequences if they take you as a student. It depends on his relationship to his colleagues and position within the department if he can make good of his threats. You should choose your future adviser from the faculty he cannot influence. If that is not possible, be prepared to transfer to a different graduate school. You may need to take a qualifier exam there again. They could also be happy to admit you if you have taken it already at your current school.
If you need to switch to a very different field, you should expect another 2-3 years as a beginner. You would graduate later.
You seem to be already burnt out. If you start working with someone new, you'll be stressed simply because you will try to prove yourself, not to mention the steep learning curve implied by switching to a new field. It would be a good idea to take a vacation before.
Some departments have rules that limit the availability of funding from teaching assistantships once you have been long enough in the program. Make sure your new adviser can support you.
If you have family, you have to make sure they understand that you were forced to switch advisers and you might finish the PhD later.

Given what you wrote, I believe switching advisers would be a good move. If you move within the same department, you have the advantage of knowing already who are the best advisers. If you don't, talk to their students and postdocs before switching.


Masters programs that require publication (with extra requirements)

In my part of Europe this list is the minimum suggested for a PhD. By suggested I mean that it is common, in the sense that is customary, but not strictly required, i.e. there are ways to graduate without it, your advisor just needs to work extra hard to get the committee to approve you thesis.

Master students are encouraged to publish, but that is in no way a requirement. Many of them publish as first authors a short paper on a local conference, or a poster at an lower tiered international one. Papers with more impact are not unheard of, but are usually limited to co-authorship.

The "list of good" venues is a problematic point for many computer science departments. For example, while it is widely held that for computer science, conferences are the primary publication venues, my institution still insists on at least one journal publication for PhD students as it is a recommendation that holds for all departments at the university.


I didn't hear back after a postdoc interview. Can I set a deadline for a response?

You should let them know that you have other opportunities at other universities that you need to respond to, and what those deadlines are.
If they can, they will try to avoid the situation where they can not hire you because you have been forced to agree to another job. That does not mean they can.
Generally speaking, people being informed is good.  Setting deadlines that look arbitrary is not.


To what extent is being a quick problem solver (e.g. doing well in brain teasers) predictive of research success?

I hope to begin a PhD
understanding technical papers

You should not expect to understand technical papers even as an advanced undergraduate. These are often written to impress and placate referees more than to make readers' life easy. Sure, some papers will be fun to read, but most of the time reading a paper is a painful exercise in balancing between patience and criticism. I have read 0 non-expository papers in my 5 years of undergrad.

how important is raw speed of technical problem solving?

As a cause: probably fairly unimportant. Your output won't suffer much because you are a slow thinker. Researchers don't usually spend much of their time solving problems; it's closer to 10% problem solving and 90% bookkeeping, teaching, and other chores. If the former 10% take up 20% of your research time instead, well, you'll have a little bit less spare time then, or do worse at teaching, or compensate otherwise.
As a symptom or correlate: possibly, if the theories about thinking speed being (highly correlated to) a central component of intelligence (read the unending flamewars around Spearman's g if you think modern science has gotten boring) are true. But if several of your mentors have vouched for your motivation, willpower and creativity, you're likely not in much trouble either way. Very few scientists have "maxed out" all these attributes together.
Sorry, this was somewhat of a reddit-style answer, but then again it is a reddit-style question. Quantitative results are scarce. I don't recall seeing any studies correlating academic success with thinking speed; most studies use measures like SAT, which themselves are mediated by thinking speed. Feel free to respond with citations :)


Colleague stole my work and is publishing it as his own; my PhD supervisor supports him; I got the paper to review. How to proceed?

You shouldn't even think about it, do not review that paper, it's a clear conflict of interest, even more because the author is your direct colleague. And the only solution is to sit all together and explain to them that your contribution to said article is significant and you would like to be a co-author. If they have problems with you being a co-author and you have done substantial work then I would seriously consider if you want to be in this research group.


A trivial correction to my currently-under-review paper - What to do?

As you indicated, usually a paper is accepted with some suggestions - that is, the referee has a list of suggestions/errors. The author then addresses those suggestions/errors, and sends the edited manuscript back to the journal with a list of changes. This version is the one that officially gets accepted (I guess it's possible to go through multiple rounds of this, but I've never heard of this occurring in practice).

Since the errors/omissions you found are minor, I would just wait to hear back from the referee, since they don't truly affect your paper in any significant way, and in fact the referee might find most of them. (If your paper is on the arxiv, you might consider updating it there).

For what it's worth, you'll get the opportunity to correct typos even after the refereeing process; there is usually some editing for typos from the journal's side, and you'll also get a chance to make small changes to proofs before publication.


Can someone change PhD supervisor without changing research direction?

The few times I've seen this happen, usually the new advisor in your home department is willing to let one continue on with the same research project. Beware that you'll have less support from your advisor than you might have had otherwise, but if you have strong people in the field outside your university,  as it sounds like you do, then you should be ok. Another thing to beware is that your advisor's letter of recommendation is going to be crucial if you apply for postdocs or other academic positions down the line. Having your advisor not really know your field, or understand your work in depth is likely going to lead to a much shallower, less effective letter simply because your new advisor won't be able to speak with the same degree of knowledge about what exactly your contribution is.

So, you're going to have to weight these two potential cons against the cost in time and effort of simply starting over from scratch with a new advisor.


Possibility of doing Masters in astronomy with only bachelors in CS

I can't speak for all the institutions, but in general, you're out of luck. It's true a lot of modern astronomy is programming, but there's also a lot that isn't. You need to be familiar with things like the Fourier transform, vector calculus, and classical mechanics / general relativity.

Here's an example of the entry requirements for astronomy at Lund University in Sweden.

  Bachelor’s degree of at least 180 credits in physics or the equivalent. The degree must include at least 90 credits in physics. Proficiency in English equivalent to English 6/B from Swedish upper-secondary school.

You'll have to get the physics training if you want to pursue this, unfortunately.


How to improve myself as a recitation (discussion,lab,tutorial) teacher?

I've taught Biology discussion sections, and trained graduate students to teach. I'm a biology education researcher, so I am familiar with studies that measure student learning in different environments. I'd summarize good teaching as follows:

Find the student misconceptions.
If you are good at your subject, you likely have not struggled to learn it. Your biggest mystery is what do students not understand. Unfortunately, students don't have the meta-awareness to tell you, so you'll need to figure the misconceptions out together, at least for the first run-through of the course.
Show students their misconceptions.
Because students don't know what they don't know, they often feel like they understand material that they actually do not. When you show them they don't understand, they are more eager to fix the problem.
Give students an opportunity to learn.
Your class activities will indeed include a lot of group work, because discussing a problem, asking questions and answering them keeps everyone improving right at the sticky points. The big secret to group work so that everyone stays busy? Groups must be only 2 or 3 students. And you'll be walking around and asking the quiet students what they have figured out, so there is no slacking.

Here is an example of how to make this work. It's copied from an earlier answer of mine.

Look over the problem set the night before, and determine the easy ones from the hard ones.
When students arrive, tell them to start work on a difficult problem. Plan on giving them 5-10 minutes -- whatever they need until many of them slow down. Walk around as they work and just see how they choose to work.
After several are stuck, have them get into groups of three and compare their techniques and what they found difficult.

(note: students hate group work because it is more painful than just listening. Most classes will try not getting into groups, or not really talking, just to see if they can get out of it. A cheerful forcefulness works well on American students)

Walk around again and ask questions like, "Tell me how far you are. Can you show me a part that is difficult? Can you get out your lecture notes and find the section relevant to this problem?"
Usually at this point you will see a sticky point that more than one student is wrestling with. Now is a great time to pull everyone's attention back to the front of the room and you can work through that problem (or one similar) and answer questions for 5-10 minutes.
Have students return to the problem and complete it. Then they can do a similar problem on their own to reinforce.
Move on to the next topic and assign a new, difficult problem.

As you can see, this process shows both you and the students what they don't understand, and provides space and motivation to fix the problem. Because you're visiting the groups, they must produce.

Things I wouldn't recommend for a recitation:

Making course notes or a study guide. Students should be making their own.
More lecturing
Questionnaires are fine, but again, students don't know what they don't know

We've actually posted an example of discussion work for biology here: http://vimeo.com/33801546


How do undergraduate theses affect master's application?

It has, typically, no harmful effect.

In most cases, you will declare the title of the thesis within your CV, or upon request of either potential supervisor or admission committee. Furthermore, as your current advisor would, supposedly, be among your referenvces, she might talk about it within addressing your applied effort onto the thesis progression, probablely.

As you notice, required pointers to the thesis will be taken into account, even without its completion, within your application.

Good luck


Updating an application for a faculty position

I assume you're talking about making updates to your application materials after they have been submitted.  If you applied using a website that has a built-in facility for updates, then sure, go ahead.  It might not help (someone who already read an earlier version may never notice the update, or they might not bother to read updates received after the application deadline), but a few reasonable updates won't hurt your chances.

On the other hand, you should be wary of making updates if they aren't handled automatically, for example if you have to send an e-mail.  If a staff member has to update your file, you should be respectful of their time and avoid submitting any unnecessary updates.  A nontrivial change to your CV (such as a prize, or a grant/paper acceptance if you don't have many so far) could be worth an update, but you should not ask a staff member to run about making minor tweaks to your file.


What to include in Abstract and Conclusion (and what not to include) of article

What exactly goes into the abstract depends on your field / research problem. It is helpful to remember when the abstract/conclusion is read and what purpose it should fulfill.

The abstract is normally read before the actual paper and the reader needs to decide whether or not the paper is interesting to them and if it worth to invest the time reading it. Therefore, it should include

the problem that was tackled (maybe with a motivation for that problem)
the methods used
what makes the paper stand out from similar work
what kind of results you got

The conclusion is read in the end and should sum up what you want the reader to remember about your work. A motivation is probably not necessary because they took the time to read (most of) your work so it is unlikely they were not interested. The content is similar to the abstract but more focused on the results.

the problem that was solved
the methods used
what makes the paper stand out from similar work
a more in-depth description of the results
limitations
future work


Should I mention the target audience in the abstract of a paper?

What you are describing is called Review Article (sometimes: survey article) and a common type of publication. This keyword should suffice to find some similar papers from your field. There is also a review-articles tag on this site.

Some journals go one step further and distinguish between regular reviews for readers who want to update their knowledge on a given field and introductory reviews for readers who wish to learn about a field from scratch. The latter can have all sorts of names.

Having your review labeled review article (or similar) should suffice to clarify the nature of the article for most readers. Additionally your abstract will not contain key phrases such as we study or we find, but rather we review or we give an overview. If your paper is aimed at a specific group of newcomers (e.g., semantic segmentation from a physicist’s point of view), then it may be indeed worth mentioning them in the abstract.

Note that some journals do not accept unsolicited review articles for peer review, but ask you to discuss your plans before you start writing. If you have a special target audience, you should discuss this with the journal at this point.


Applying for PhD with a 3.2 GPA - Do I even stand a chance?

It depends. Different schools, programs, and faculty have different ways of looking at applicants. Based on my limited experience, a 3.30 GPA from an R1 will likely count for more than a 3.30 from a less reputable institution. However, if you are applying to top-tier programs, you may be competing with students who have higher GPAs, also from R1s.

The reddit link that you posted is from one single professor at one institution. Without knowing the specific institution, program, and/or faculty member you are applying to, it is impossible to say what will be weighed, as there are not standardized admission formulas.

Some faculty are looking for students who match their research agenda and have research experience (i.e., they are proficient enough at research so they won't suck the faculty member's time). Others may prioritize GPA, and some might place more emphasis on quantitative GRE scores.

The link that you posted and the link from @henning both have good advice for tailoring applications to fit the department, institution, or faculty member.

If you are uncertain about applying, it might not hurt to contact a faculty member you are interested in working with to ask if they would consider your application. Even better, you could find a common contact/reference (maybe your undergrad advisor/professor/? knows someone in the Ph.D. department you want to apply to?) who can introduce you.

You might also want to check out college/graduate school/institution GPA policies to see what the minimum GPA for doctoral study is at your prospective institutions. If you have to maintain a 3.0 as a doc student, some faculty may question your ability to succeed at a more rigorous level.

To summarize: Ask the faculty member you are interested in working with what they consider when selecting doctoral applicants.


How to cite the same source multiple times in a row IEEE

According to this guidance document (See page 7) on the IEEE website it appears that you do should the following when citing the same source multiple times in a row.

  References Within a Reference:

  Check the reference list for ibid. or op. cit.
  These refer to a previous reference and should be eliminated from the reference section. In text, repeat the earlier reference number and renumber the  reference section accordingly. If the ibid. gives a new page number, or other information, use the following forms:

  [3, Th. 1]; [3, Lemma 2]; [3, pp. 5-10]; [3, eq. (2)]; [3, Fig. 1]; [3, Appendix I]; [3, Sec. 4.5]; [3, Ch. 2, pp. 5-10]; [3, Algorithm 5].

  NOTE: Editing of references may entail careful renumbering of references, as well as the citations in text.

On the same page (7) of the document in the section referring to references it states that;

  ... they appear on the line, in square brackets inside the punctuation

It would appear from this guidance note that the example that gave is correct unless you are referring to different pages of the same document then you need to reference as per form above.

Also the IEEE document says that you may refer to The Chicago Manual of Style, published by the University of Chicago Press, for anything not covered in their own guide.


How can I express "I can't find any papers written about this"?

(disclaimer - I come from computer science, and the little I know about conventions in philosophy is from hearsay)

  I'd like to be able to say "I looked around on Google scholar, etc, and I couldn't find anything about this topic"

The usual expression for this kind of thing in my field is "to the best of our knowledge, this topic/idea has so far not been considered in literature". It tells the reader that you think that nobody has published this idea yet, but clearly the absence of existing literature is something very difficult to be sure about. Hence the rather defensive formulation.

  In general, is there a technique to demonstrate the absence of literature about a certain topic?

Nope. How would you do that? It's a bit like proving a hypothesis - you can only find counterexamples (papers that do cover the topic), but you cannot prove that in some weird journal nobody reads somebody has expressed your thoughts already.

  What kind of evidence is appropriate in this situation? Would providing something like the number of results of a search on Google scholar be worthwhile?

The accepted convention in my field is to explain the methodology of how you searched for literature (you had a defined methodology, right?), and then explain / list / discuss what you found. Be specific - which keywords did you use and why? Why Google Scholar and not something else? Can you be sure that all papers that you would expect to be relevant are indexed by Scholar (some of those should be pretty old, long before the Internet was a thing)? Did you also check your library for dead-tree literature?  Number of results and or similar metrics seem pretty much useless to me and would likely not improve your paper in any way.


What to do if reviewers reject a paper without understanding the content?

F'x has ably covered one possible reason: that it's not you, it's them.

I'm going to cover the other side of things. That is, starting from the assumption that the editor has made a good decision.

The authors should consider rewriting the abstract and introduction. If two peer reviewers didn't understand the paper, the paper may just need a savage reworking.

The authors may also wish to try working with a freelance development editor.

Finally, the authors might want to bring on board a co-author who's been frequently published: I expect that many decent-sized, decent-quality departments have at least one person whose quality of writing leads to get manuscripts getting accepted first time, pretty much every time.

And then submit to a different journal. I don't know the field, but I'm willing to speculate that there are a few reputable journals where the article could be published.


What is the most appropriate time frame to apply to a Postdoc?

Charles answer here (https://academia.stackexchange.com/a/5303/4231) applies to your case. Some positions will start right away and some positions will have a fixed start date set in the future. I suggest you start looking around 6 months into your 1 year postdoc, at first focus on positions starting later: that info should be in the job advertisment. Then, if you have not found something suitable, focus on positions starting right away when you approach the end of your postdoc.

Do not wait until your postdoc is finished to look for a new position.


Co-author conflict after paper got accepted

It is unlikely that a journal will publish a paper if one of its authors states that it should not be published at this point (for various reasons). However, it would also be more than questionable for you to demote the other author to only be included in the acknowledgements section (at least if you did not do everything that you could to resolve the situation).

So that leaves you with trying to resolve the situation. One way of dealing with such problems is to elevate the issue. Possible points of contacts could be the dean of your former department or your dean of studies. In some places, where you have a secondary advisor whose role is to help you in case of precisely such problems, then she/he should be your point of contact.

To prepare any of these meetings, make sure that you have a statement of what happened that it is as accusation-free as possible, while trying to stick to the facts. While such issues are better discussed face-to-face, preparing the statements helps with getting your point across in an organized way.


How to follow up with a professor who had received my transcripts but did not reply?

Keep waiting.  4 days is not very long.  If you have not heard anything in 3-4 weeks, send another email asking politely if he has had a chance to think about your request.


As a Master Thesis supervisor, how should I assist students with poor fundamental skills (e.g., problem solving)?

There are a range of possibilities, not all good. At one end of the scale you can just provide answers, maybe working out the answer for the student. This is the worst option considered here. Along the scale is your solution which is to solve it with them. Much better, especially if you let them lead. At the other (far) end of the scale is to simply provide them with some resource that is tailored to letting them do it on their own without further help. Even something like a section or even a page in a book. Or a search online that gives them help. This may be too little help for most students.
My own solution would be closer to the latter end, and exactly there with some students. Students need to gain insight and to do that they need to work through the crux of the problems they face. But sometimes they don't notice something that is blocking them. If you work with them a bit, asking for what they have done so far and why, perhaps you will get an idea about the nature of the block. If you can redirect them a bit, with a minimal hint, they will come out ahead in the end.
Students and some inexperienced instructors seem to think that the point of exercises is the answers, when in fact it is the learning that leads to being able to provide the answers. Keep that distinction in mind and also make sure your students understand that. Done well, it can also lessen the amount of cheating/copying that goes on.


In APA, do we italicize the names of wars and treaties?

The APA guidance doesn't say exactly.  Gives a list of what to italicize and examples of what not to.  I would definitely opt for not doing it though.  The implication of the directions are much more to only italicize what you need to, not italicize everything not forbidden.

https://academicguides.waldenu.edu/writingcenter/apa/other/italics

Note also, that I'm really unaware of ANY style (just checked Harcourt Brace and Merriam Webster, as well as personal experience) that recommends italics for wars or treaties (or legislation).  I have only seen treaties in italics when the entire treaty (not just a word within it) is cited in a foreign language (often French, Latin or German), but then you are treating it as foreign text, not because it's a treaty.  Oh...and don't italicize a single foreign word within a war or treaty.  Keep entire thing normal text (but capitalized first letters, like a book).  I have never seen wars italicized--perhaps you are wondering because ships are?

Note though that court cases are often italicized.


Switching group due to a lack of interest; How to break the news to an advisor who has been very supportive

Wow! a really tough situation. On one hand you have the opportunity to continue to be supported by someone whom cares and believes in you. On the other you want to be free to make decisions about your own life without anyone taking it personal. In life people take things personal! Yes, it's not professional but when someone puts time and resources into you they want you to remain committed despite your reservations.

Yes you could leave your group and go for something you're more passionate about, but would you get the same type of  deal? People talk to each other even if they seem like they don't. Would your new group look at you as a "trader" if they found out you had support and turned your back on your previous team because it got a little rough? Drama, folks love it, thrive off of it and will at your expense. I would say have a heart to heart with your current team let them know of your intentions while remaining politically correct and discuss with the new professor about your reservations to leave your old team but you can be more committed to this new challenge.

Do what's in you, try and be prepared if things don't work out the way you want. Live with whatever you may regret.


Is it permissible to request a new reviewing editor?

As chief editor of a journal, I can say that I would see such a request as reasonable under certain circumstances (and it has happened). However, in the case you describe I do not see what it is that the editor has really done. The reviewers comments form the basis for your revisions and the editor should judge if any comments are more important than others and summarize what the editor sees as important revisions you should make. It is then up to you to do these as you see fit and if you disagree argue against those that need such action.

Change of editor requests come when an author feel a paper has been unfairly judged (usually rejected) and I know of one case where an editor rejected a paper after using a set of reviewers that were marked as "non-preferred" due to a conflict of interest. I also know of cases where a zealous copy-editor has modified the language to a degree that the science was almost completely lost. In your case, it is not clear what has happened to the manuscript, has it been rejected? have you written a rebuttal and argued against changes imposed?

I would suggest that you make the revisions you think are reasonable and provide a rebuttal on the suggested changes to your paper. If you encounter more unreasonable resistance from the editor, I think it is only fair to write to the Editor-in-Chief and state that you think you have been unfairly treated and wish to get a second opinion on the handling.


How to confront possible theft of ideas?

I found myself in a similar situation once, also with a blog post, though in my case the poster fully admitted posting my ideas and appeared to see nothing wrong with it.  Fortunately, I later determined the specific idea wasn't as fruitful a line of inquiry as I initially imagined and happily moved on.

So, my suggestions to you:

It is fishy, and one clear lesson to learn is to not trust this person with your work in the future.
Hold on to records of your communication, in particular any emails where you discuss this idea and/or send him drafts.  As was pointed out in the comments, blog posts aren't publications, but it's still possible someone notices in the future and asks you about it.  Having the email where you sent your work to the poster for review from before they posted it is a solid defense.
Mention it to your advisor, but I would personally only do it as an aside, as something that annoyed you.  You can handle it!  If they, knowing you and the situation and the work itself, have other suggestions, they'll offer it at this point.
Don't bother bringing it up with that individual.  If they did steal the idea from you, they can just deny it and all you have is circumstantial evidence.  On the other hand, if they had indeed done similar work on their own already, then it seems they posted this in order to get their name on it before you (they can always claim their anonymous blog later), in which case you're competing to get this published.  Therefore,
Take it as motivation to push through and finish your work both well and promptly.

Good luck!


Do proofs count as post-prints for sharing purposes?

I am pretty sure that Proofs of a paper are considered publisher's version. They are definitely not covered by the word "postprint", which excludes any action by the production team of the publisher (as opposed to the editorial team, including referees). Similar terms such as "Accepted Manuscript" (AM, used by e.g. CUP) have the same property: the AM is the paper as it as been accepted by the editors, thus before entering production (and thus proofs are not an AM).

So, unless specifically allowed beyond any ambiguity, you should expect green-OA compatible journals not to allow you to share the proofs on your web page or on repositories.


Should Self-Assessments be Scored? (not Graded)

The purpose for student self-assessment is formative in nature and is typically to encourage reflection and monitoring of learning.  There are several papers that highlight effective practises in formative assessment in higher education, the foremost being Sadler[1] and Nicol[2].

Central to both of these is students knowing what constitutes good performance.  Depending upon the nature of your questions, an overall met/not met summary of expectations presented to the student can provide them with a measure of performance. It is simply an indicator that they still have to practise and work on some aspects to achieve a desired performance level.

Sadler, D. R. (1989). "Formative assessment and the design of instructional systems." Instructional Science 18: 119-144.

Nicol, D. and D. Macfarlane-Dick (2006). "Formative Assessment and self-regulated
learning: a model and seven principles of good feedback practice." Studies in Higher Education 31(No.2): 199-218.


How to explain a missing grade card in unofficial transcript for online graduate application?

If you don't apply, you don't get in. Simple. If you do, then there may be some difficulties, but many of them can probably be overcome in the eyes of most institutions. Given the current pandemic, people are going to have to be flexible.

I'd suggest that you have someone, maybe the department head, provide an unofficial listing of your courses and grades for that semester. Perhaps they are allowed access to grades, but they can also contact your professors to verify the grades if necessary. Explaining the grading process at your university would also be useful in such a note.

A note from you explaining the situation might be helpful, since the reason was medical and the delay is well explained.

I can't guarantee that anyone would necessarily accept this, but suspect that most will, especially since they only need official transcripts later.

But, again, you have little (almost nothing) to lose by making a good faith attempt and putting together the best record you can for admission. People will be looking for evidence that you will succeed. Provide that.


How can a master thesis in STEM approach the level of a doctoral thesis?

Requirements vary widely from program to program and from institution to institution.

Some programs require a doctoral candidate to publish in a peer-reviewed journal (probably most programs would take issue if you didn't publish or present anything). Most programs (or committees) wouldn't let you graduate with a PhD unless you published at least once, and would expect at least twice.

My general hunch is that a doctoral dissertation (rarely called a "doctoral thesis") is generally several times longer. While a masters thesis might be 20-50 pages, dissertations are routinely 80-150 pages...and sometimes way more (this varies widely by discipline, by the academic culture of your institution, and by your committee). Some programs allow the doctoral candidate to use three publications, combined into a single manuscript, as his or her dissertation.

Lastly, the doctoral degree is intended to show that the recipient can perform original research. Masters degrees have a wide variety of understandings or intents, from "the recipient passed our comprehensive exams", to "the recipient performed an original research project and published it".

Whatever you've done for your masters thesis, focus on research for your PhD. Learn what interesting questions are in your field and choose one to focus on. Read the background literature to learn how others have approached the problem. Work with your advisor and committee to figure out how you can contribute something new and useful to the field, and then do it. Publish your findings in a journal; present your results and network with peers at conferences. Finally, write it all up in your dissertation, defend it, and graduate. That sums up getting a PhD. The rest are details.

You may find this page useful.


Same presentation topic for different conferences

It's entirely reasonable to give the same (or nearly the same) presentation for different audiences.  This frequently happens with invited talks, which are often expected to present a survey rather than a particular new result.  Thus, there is no expectation of novelty and thus no issue with plagiarism.

If you are presenting on a paper, on the other hand, the talk should be novel simply because it is about a paper that is novel.


For schools that require "at least 3" letters of recommendation for a grad school application, is it smart to send 4?

Personally, having one extra (a 4th) is probably not a bad idea.  However, there are risks involved.  First, just the logistics for interacting with 3 people for getting 3 recommendations is challenging enough.  If you add a 4th person to ask for a recommendation then your work may go up by a good amount.  Second, having a 4th raises the risk of having a negative statement from a recommendor that could hurt your chances.


Acceptability of 'not possible' for master thesis research

You have to discuss this with your supervisor / advisor.

Then you can agree the direction.


Can I keep using my old academic affiliation for publishing?

When you are really not affiliated to the institution anymore, you should not put it on your publications. Certainly not, when the work you are publishing has not been initiated during your stay at the institution.

Many institutions have the possibility to offer you a 'zero hours' contract. In this scheme you remain affiliated to the institution, and can use their facilities (e.g., email address, etc), but do not receive any monetary compensation.

If you agree to such an arrangement with your previous institution, you obviously can still use the affiliation on your publications.


My supervisors take long time to respond to me

There isn't a lot you can do on your own. The supervisors have their habits. The best advice I can give is to try to find someone to speak to them on your behalf to get them to help you meet the deadlines. You want an advocate that will be respected by the supervisors. Deans are good for this sort of thing, actually.

But if you can meet face to face with people, either the supervisors or an advocate to help impress on them the urgency it would be better than trying to do things by email, which is asynchronous by design.


Qualitative approach to evaluation of academic production

I'm from Brazil and I understand you very well about our research/funding system.

Let's branch the problem in topics:

CAPES classify the papers by "research impact", it's basically how hard is the congress/conference... to accept your paper: (A1,A2,B1,B2,B3,B4,B5,C).
CAPES is responsible for funding research presentations and they have a very limited money.
Only A1, A2 and sometimes B1 are really relevant for the society. Nevertheless both are commonly international congress. (let's consider international travels are expensive in Brazil, plus the conference taxes)
Let's also consider, poor relevance conferences (B2,B3,B4,B5,C) are commonly in Brazil, sometimes on places where there are a lot of universities, e.g São Paulo, Rio, Rio Grande do Sul, etc. Furthermore, all of them are in Portuguese.

Well, at this time I guess you already see the problem... Summarizing, the Brazilian research is very correlated with local congress and that makes everything easy even for CAPES (due to funding), even for researchers (due to easy paper acceptance), then you create a perfect productivity system... With a lot of useless research.

In my opinion, poor impact research are irrelevant. Then, I guess the solution would be change the impact rank  and  funding to only classify (A1, A2 and B1). This probably would make everyone work hard and then you probably would change the status quo in a long-term.

Note that is theoretical scenario. As I said before, this kind of system is perfect for lazy researchers and their financiers.


Should my bachelor's degree match the graduate program that I am trying to get into?

Rather than providing you with my opinion (I think you're aspirations are realistic), I think you should contact the admissions and academic advisers of your chosen post-graduate institution and ask them.

Ask them about your proposed course of graduate studies.

Ask them about how much course work you may need in order to "catch up" to other students planning to enter that major field of study.

I believe most institutions will allow you to start your post-graduate studies while you're still taking any undergraduate classes you may need.  The only way to know for sure is talk to someone at the University.


What does it take to get a worthwhile recommendation letter

I mean, is it OK to ask a professor write a recommendation letter for you only based on your behavior in his/her class?

This is fine for one letter, especially if you did really well in their class, went to office hours, got to know them, etc. As you say, your main letters should come from research advisors or people who know you better than just one class.


Well, I had quite a few postdoc interviews and I can tell you that it is NORMAL for a PI not answer you back. Of course it is a shitty situation, even more when you thought the interview was good, but that's how life is when you are searching for postdoc positions.
1 email as a follow up or an update is ok. But don't insist on it. The truth is: you know as soon as you finish the interview if you would hire the applicant or not, so if you don't hear from them after a week consider it a no.


What is the point in publishing a paper in a journal rather than arXiv?

Papers published in (reputable) journals are reviewed by other scientists (peer review), which usually makes it considerably more difficult to publish a paper there. By contrast papers on the ArXiv only receive a brief inspection to keep out utter crap. Thus, most academic evaluations consider only peer-reviewed publications or value them considerably higher.

Moreover, often only peer-reviewed papers are considered citable, in particular for purposes of backing up your claims. This may extend to papers that are considered certain to be eventually peer-reviewed¹, but this is unlikely to apply to your paper. As being cited (by peer-reviewed papers) is another important academic evaluation metric, this is another advantageous aspect of journal publications.

As a sidenote: There are a lot of physics journals where you can publish without a fee.

¹ in particular in fast-moving fields or fields with long peer review such as parts of mathematics


Is it plagiarism/OK if I use big parts of someones literature review for the introduction section of my paper?

If you copy the review text from the web into your own thesis it is a clear case of plagiarism.

When you write academic text where there is a need to provide the sources for your information (as references) you need to have read the sources. It is not ok to quote sources without having even looked at them. In very rare cases, may it be acceptable to quote a source quoted by someone else in a publication. These cases may include very hard to find literature or literature in a different language. But, such secondary references should not be used unless deemed absolutely unavoidable.

If you need to cite the on-line review, you will need to look at how web-sources are cited at your school (if they are allowed). you can also look at the recommendations at American Psychological Association (APA; very appropriate for you) and their style site. You may find many other bits and pieces that are of interest to you.


Search for authors on Google Scholar by their field of study and country

You can search multiple keywords with something like this:

label:robotics + label:machine_learning

in the author search. Narrowing by country can be trickier. You can potentially narrow by the email address. For example, if their profile is verified with a UK email address it will end in .ac.uk. Thus you can search:

label:robotics + label:machine_learning + .ac.uk

and only get UK researchers. You'll probably get some false positives and negatives with this technique so it's not perfect but will help narrow the scope.

Here's a related question pertaining to narrowing country on Google Scholar:

Google Scholar: how to exclude some countries from the search?


How to overcome feeling that published articles lack public interest?

What should I do to start looking to my research and my made publications with a different attitude?

I'm gonna go out on a limb here and say that your problem isn't that you are working in applied sciences vs. theory. Further, I am not sure if your problems are of medical nature (but this can of course not be ruled out from what you wrote). Let me recap some things you wrote and provide some interpretation. I am not sure to what extend this will answer your question, but I hope my ramblings will provide input and perspective anyways. Maybe somebody else will provide a more direct answer to the question.

You are a master student who published 6 papers during his masters at a university of applied sciences. All of the papers have been in IEEE/Scopus venues. Yet you still can't get a PhD position.

First of, IEEE conferences or indexed in Scopus isn't the quality label you maybe hope it is. There are terrible venues for which both of these things are true. The fact that you say you have very little time for research, and still wrote 6 of those things indicates that the quality of your papers may be not all that super. If this is the case, the problem that prevents your papers from having impact isn't that they are applied, it is that they may simply not be very good.

This may also be the issue with your PhD applications. For me, and many others, papers below a certain (subjective) quality standard count for next to nothing. Really bad papers may actively work against you. Again, "IEEE conferences or indexed in Scopus" does not rule out either of these cases, so try to evaluate your publications independently of these labels. For instance, pick a few PhD student papers from the group that you are applying to. Try to neutrally evaluate whether your papers play in the same league as those. If all papers of PhD students of the prof. or lab you are applying to are much better, and/or have appeared in much better venues than your papers, I am uncertain how much your publications will help your case.

You worry that your papers do not have a strong impact.

I think this point warrants some additional explanation. One of the sad realities of research is that most papers in all but the very top venues of your field (think ICSE or CHI for applied computer science) have very little to zero impact on the research community - and even the papers in the top venues often have close to zero impact on anybody outside your research community. Papers that really get the attention of your fellow researchers are few and far between. I have written papers that I personally consider good to great, which remain pretty much uncited (and, presumably, almost unread) to this day.

You want to progress as a researcher, but you work almost exclusively as a lecturer.

Try to see your situation as it is. Similarly to above, your problem isn't so much that you are working in a university of applied sciences - your problem is that your current position is incompatible with your career goals. You want to do research, but your job is teaching. Your situation would be none the better if you worked as a pure lecturer in a research institution (maybe this would in fact be even more frustrating for you). What you need to do is either (a) find a job or stipend that allows you to do what you want to do, or (b) accept that you are currently not on a research track.


Uncertainty about following academic career

Sitting on two chairs in never a good idea. (If try nevertheless, you should damn well know what you are doing.) Satisfying the industy and satisfying academic curiosity is not a task for everybody. From the experience of many of my prior colleagues, if you try to do both, you are likely to fail in publishing.

Said that, going to the industry is often a one-way ticket. More often that you would like to hear.

Sorry for discouraging.

On the other hand, if you ran out of ideas in academia, you have to go to the industry.


Answering the "why do you want to do a PhD?" question

Let's consider why "you are telling [professors that] they shouldn't admit you!":

I felt I'm in a dead-end job...

That doesn't show motivation for doing a PhD.

I wanted to swap careers...

You don't need a PhD to swap careers.

I choose this field because...

...it provides transferable skills to the careers I want to move to...

This requires more detail to be relevant.

...because I'm sufficiently interested in it to want to keep up to date with its most recent developments...

You can do that without a PhD

...(even though I probably won't stay in it as a researcher, per the
fact that the odds of finding an academic job are very low).

This doesn't show motivation for doing a PhD.

I did well in my Masters (which was in the same field)...

Many "do well" in their Masters, PhD students do better.

...including the research component, so I believe I can also do well in a PhD.

This requires more detail to be relevant.

I can afford it.

This doesn't distinguish you.


How to reply to a potential PhD supervisor who asks if I have my own funding?

Just answer the question honestly.
If you have your own funding, say so.
If you do not have your own funding, say so.

If you do have your own funding, there is really no problem.
If you don't have your own funding, it may be possible to arrange some for you.


You should have a serious sit-down conversation with your advisor about your goals and interests, and talk about what the obstacles are that will need to be overcome. If you will not be able to work on something due to lack of funding, that is exactly something you need to be clear on if you aren't already.

If they don't have funding for the Project X you want, and only instead have funding for work on Project Y, you can A) ask what options they are aware of to get involved in work with something like Project X, B) ask for other potential alternatives beyond Project Y, and/or C) decide to try Project Y and maybe decide it works for your long-term goals (or not), even if it isn't what you had in mind originally.

As to the question, "should you just be thinking about graduating" - no, you should be thinking about what you are doing to do after you graduate, and how to use these years to contribute towards what you want to do beyond the immediate program. I don't know what you want long-term, and I don't know how Project X or Project Y fits in to that - but that's exactly what you need to find out for yourself.

Things don't always go as we plan, so you'll have to remain focused on the big picture and be willing to be creative to find way to make what is available work for you. This could conceivably mean a different program, but it seems awfully early in the process to conclude that because 1-2 people don't have funding for one project you were interested in that you now have to change institutions. There could be other people, other projects, other labs - but the time to do that is before it's too late, such as when they are announcing you passed your defense and it's time for you to get out and take your diploma with you.


How many assistant professor or postdoc jobs do people usually apply for in mathematics?

1) Unless you have something close to an Annals level paper, I would say you should be applying for close to 100.  This probably isn't actually possible; to hit this number reasonably, you have to apply for temporary positions and for non-research oriented positions.  Think of it this way.  Positions taking applications on Mathjobs are getting something like 500 applicants.  You're probably more qualified than most applicants, but if you're in the top 100, and a position hires uniformly at random from the top 100, then you need to apply to 100 to have expected value of one job.

2) Most recommenders are willing - they're blaming the university for not taking Mathjobs applications, not you.  If you want to save your recommenders trouble at the expense of your money, you can use Interfolio, which is a company that sends out applications - including confidential letters - for you.


Accidentally finding the solution to an exercise

Literature research is a legitimate process in science, they can't blame you for that. Clearly, however, you did not "rediscover" the result. One option would be to tell the tutor that you found a solution in the literature and if s/he could give you an alternative assignment instead.


MLA convention for words and phrases used as words?

There doesn't appear to be a direct rule regarding these "words and phrases used as words". The closest I can find to an opinion on the matter is under an MLA resource for plagiarism, which implies that quotation marks are only appropriate when the words or phrases are directly borrowed from the original author or authors. Those would of course require a citation.

The article, to me, suggests that quotation marks shouldn't be used without a corresponding citation. It definitely leaves room for interpretation, however.

On a purely stylistic note, it is incredibly easy to start weighing a paper down with excessive quotation marks when you're new to a field because every other concept seems profound. The first draft of my thesis probably had these in nearly every paragraph - making it hard to read and just a little bit pretentious. So I would say it's probably better to err on the side of caution and limit your use of quotation marks for these types of words and phrases. You're going to explain the concept regardless!


How to work authorship of software developed with another University

I don't see the problem here as one of co-authorship, but one of potential plagiarism. That is easy to avoid with proper citation. But it depends, also, on what you intend to do in the papers.

In a similar case, suppose you found the software and the original papers online or elsewhere and you do some derived work. The originals were done by people who are strangers to you. You cite the original and acknowledge the people who form the foundation. But you don't have to invite the strangers to be co-authors. I don't necessarily see a difference here.

If they don't participate in the new work they aren't co-authors of it.

But, it might be worth some effort to try to convince them to participate fully and, thus, become co-authors.

It would be a different case if you were re-writing the original papers.

As for the software, you have to be sure that you have an appropriate license to extend it. If you haven't ceded ownership to someone else, then you have joint ownership among the three(?) of you. Get their written permission to extend it, and list everyone as co-authors (co-creators) of the software. But the software and its use are separate things. If you find novel uses of the software without the help of the others, they aren't co-authors of the resulting papers.


How should you address academic colleagues in the United States? Is the "Prof" title necessary?

In the US, you generally address colleagues of a similar status by their first names—so your fellow faculty members would definitely be addressed informally. This would of course extend to collaborators and acquaintances in other departments.

I think the only exception to this would be in the case of formal communications—an official memorandum or letter from a faculty member to someone in the university administration, for instance. But otherwise, in any oral or informal written correspondence, I'd stick to first names.

(In other countries, follow the appropriate local traditions, as they may be very different from US standards.)


Are undergrads applying to top math Phd programs expected to have taken core graduate clases?

No, possibly except for Princeton.
Berkeley in particular has a long tradition of accepting domestic graduate students who have less background but strong potential.  (I had not learned Galois theory or anything about manifolds when I started graduate school there, and I still have never learned the Lebesgue integral.)
Graduate admissions committees in the US trust what recommendation letters say (with evidence) about the potential of students, and take that into account a great deal, in many cases attaching more importance to this than any actual achievements of students.  Their statistics based on how students have done in their programs and after finishing is that how much math you know coming in actually doesn't make much of a difference; much more important is your demonstrated capacity to learn math and solve problems.
Keep in mind that it is quite possible to do quite impressive undergraduate theses despite not knowing much mathematics if one has a good advisor (who can explain how the problem can be reduced to an elementary(*) one), works hard, and is clever.  (It's quite common for PhD advisors to complain that their weaker students don't actually understand their own dissertations.)  Keep in mind that undergraduate admissions at Harvard or Stanford is extremely selective - generally more so than graduate admissions in fact - and every student at Harvard or Stanford is very clever.
(*) elementary meaning not requiring knowing lots of mathematics, not meaning easy.


How to not lose focus after each disruption in flow

A very simple solution, that might work, and is worth a try. When you reach such a block, jot a note to yourself that captures the problem or the crux. Then get up from your desk and take a ten minute or so walk. Get your blood moving a bit and break the flow explicitly. Take the note and a pencil/pen, so that you can write ideas that might occur.

You may find that the solution will come to you, but at least, the break may help to clear your mind of the reason you may be pursuing the wrong solution.

This won't work for everyone, of course, but it is a painless way to experiment.

Oh, and don't be checking your phone on the walk or texting, or ... It might even be best to leave it behind since you will only be away for a few minutes.


Reviewer questioned credibility of paper and results after first revision, which led to us finding a major error. Should we revise or withdraw?

I suggest that you should withdraw your submission until you can figure out what's going on. Good science should be reproducible, and this is not. You did not appropriately critique your own results, and put forth a result that seemed to "look good". You've now changed some part of your modeling methodology, and gotten another set of results that "look good", even though you cannot articulate any theoretical or practical reason why this set of results is any more sound than the last. The first result did not pass the "smell test" of reasonable performance, and you kind of shot yourself in the foot by failing to investigate. Now you have a result that does pass the "smell test", but the reviewer is aware that your diligence in self-criticism is somewhat lacking.
You're essentially telling the reviewer that "the last result was an error, but this one is not, although we are unable to explain any difference between the two." It's a really big ask for the reviewer to have confidence in your updated methodology, if you yourself cannot explain why it is any more correct than what you did the first time around.


Can I use my master's degree thesis as a Research Project Proposal for a phd application?

If you are asking whether you can repeat your MS work to get a doctorate, then the answer is no. If you are asking whether you can work to resolve still-open research questions that you already worked on earlier then the answer is a qualified yes.

But it depends on where you are and also on your advisor. In the US, for example, you don't normally need to make such a proposal to apply for doctoral study. Other places you do, and in those places the advisor will need to ok the proposal.

It's acceptance also depends on whether the advisor would consider the proposal to have sufficient depth to be suitable as a doctoral research project. So, again, if you are looking for an easy way through the doctorate, the answer would be a likely no.

But in the right place, with the right advisor, and the right problem, it can all come together for a yes, and your prior work might be considered a plus.


If these names are trademarked in the US, it's my understanding that it is legal in the US to use these marks to refer to companies that they describe in any publication. Look at how financial sections of newspapers or websites daily refer to the companies that they report on and the products they sell. However, it's possible but unlikely that you could be sued anyway. If there's any confusion in your writing that Coca-cola or Pepsi in endorsing your article, watch out. You and your publisher may be in their sights. This is unlikely if you're simply doing a taste test or comparing marketing strategies, but you should be careful with the use of other's property without their explicit permission. Just like the Fair Use defense in the copyright context, a nominative use is a defense in court if you get sued, not a get-out-of-jail free card. These kinds of suits are so rare against academics that I can't name or find any.


How to write papers fast and efficiently?

I'm not sure if it helps, but here are two ideas that work for me (sometimes).

Don't try to write the paper in its order. Instead, start from the technical parts. This is simple - it is just writing your algorithm. Now, once you try to write the algorithm (and abstract it from code into pseudo-code), you will get stuck because something is missing (notations? a neat observation? a cool idea that makes things clearer?); note these down. Then, expand on the things you wrote down. Another way to begin is with the "cold" facts: the numbers, the experiments - just write the details down in the most dry way...  (After the technical parts are written, move to writing the introduction and conclusion; by that time, you will have already broken your "writer's block", and the writing will flow much easier).

tl;dr start with the most simple (and technical) parts just to make the writing start.
Writing a paper is telling a story. You can't write it down? Try this - tell "the story of you paper" to someone else, say, a colleague or a family member. Do this twice or thrice, until you have a complete "story" in your head, and you gained some practice in telling it. Now, writing it down (just following the conversation you had with real people) may be way more simple.

Addendum: This is not a competition. Writing a paper well, takes about a month. Writing a good draft takes at least 2 weeks (of intense work!). Of course, some people can pull an all-nighter and come up with a paper. Don't pay attention to those, they are at the tail of the distribution.


It is perfectly appropriate since most university dress codes for students is to make sure nothing offensive or too revealing is worn (local definitions for both of those are widely variable). It sounds like you are having trouble working out if it is simply that you are unusual or if it is actually a problem. The simple solution is to ask some of the folks in your lab what they think.

If it turns out you are worrying on their behalf when they don't care, then keep wearing nice clothes.

If it turns out they care then you actually need to address that, whether by asserting your right to wear what you choose to within the official dress code or by making adjustments. Since clothes are social markers it might be what they perceive to be your statement that is the problem and not the clothes themselves.

It is always possible they are glaring at you for completely unrelated reasons. Again feeling that out is worth your time.

A personal story, I wear Hawaiian print shirts every day while teaching. One day I wore a plain button down shirt and my students asked what was wrong. It was laundry day. So don't discount the possibility that the only thing going on is that you stand out from the norm and nothing beyond that.


Where to publish research if I do not want a peer review process?

"…a quick- one, two, you're published!"

That's not how it works.

What works is:

Make it a publicly available preprint (online repositories like
arXiv, a preprint series of some institute, university, maybe via your personal website or blog…).
Submit to some peer reviewed journal that complies with papers that are available as preprints (and there are journals that do not cost you anything; you will not get "open access" for free, but in many cases the preprint can stay freely available).
Put the paper in your CV and add "submitted for publication".

Then the paper will be visible and checkable and it also shows that you know how scientific publishing works.


How can I tell if I am short-listed for postdoc position?

I think the answer you've got was pretty clear:

If you are short listed (for interview), you will be informed.
The process (including interviews and decisions) will be completed by end of July.

Typically, the shortlist is made within a week of the application deadline and interviews are conducted within another few weeks. The decision (of whom if any to make an offer to) is typically made immediately after the last interview and then it takes some more time before an offer is accepted.

In your case, this all fits nicely within the time frame of 5 weeks (24 June until end of July). So, if above typical scenario applies, then the fact that you haven't heard from them, implies that you were not shortlisted. But there may be other reasons, such as a delay in the process.

IMHO not informing those not shortlisted at the stage when the shortlist has been made (as is the case here) is a rather poor practice.

Don't be disheartened by a failed attempt to get shortlisted at a postdoc application. There are many applicants and you must expect to make several applications before getting there. You may ask them for feedback to improve your application (but most importantly: add publications to your CV).


What would be the difference between the public and private graduate schools in US?

For graduate school, there are generally few differences. A couple potential factors:

Funding and other resources may be easier to obtain at private schools. On the other hand, there are rich public schools and less well-off private schools. The other factor is that public schools are often larger, so they sometimes have better shared resources (e.g. computing clusters).
Probably the biggest difference is the undergraduate make-up, which only affects you indirectly. At larger public schools you are more likely to TA as a graduate student, which is both good (easy to get TA funding) and bad (may be harder to avoid TAing).
Some public schools have unionized graduate students/teaching assistants. Almost no private schools have these unions. Whether this is good or bad is an open question.
In very rare circumstances, public school funding can be affected by political winds. There was one recent high-profile case where a large public university's budget was severely cut over a couple of years, but I can't think of any other recent cases. This is extremely unlikely, but possibly a factor if future cuts are being discussed.

The type (public/private) of the graduate program you go to is unlikely to make a major difference in your experience. What matters much more is the quality and characteristics of the program, which is largely independent of public vs. private. Each department is unique, and it's worth closely researching both the research being done and the culture that exists there when choosing where to apply to and where to go.


Reviewer noticed a significant overlap of my submitted draft with an earlier paper of mine

There are two issues here; self plagiarism and possible copyright infringement. If your previous work has been published then you may not hold copyright to it any more and your rights to reuse the text may be limited. You should check that. If you do still hold copyright or a sufficient license from the publisher then you are clear on that.

But self plagiarism is a separate issue. When a scholar reads a paper they also want the context in which the ideas were developed. So, if we use another work, we cite it so that the scholar can follow links, including the citations made in the earlier text, etc. If you just copy part of your own old work without citing it, you (probably) break that chain of context. You make the current work seem new and deny the scholar the chance of easily examining the context.

If you have copyright to your work, you can probably safely reuse longer parts of the old work than if it were by another, but you still need to cite it. In such a case, quoting long passages is probably acceptable provided that you can find a suitable typographic convention to show what is old and what is new. But citation is still needed.

The fact that a reviewer has raised the issue suggests that you have some work to do. First, you need to be clear about your copyright or your license. Second, you have to provide proper citations of things you use (i.e. quote) from the old work. Failing that, you are subject to having the work rejected.

Rephrasing the old work is not the issue. That can be viewed as an attempt to disguise your intent, just as if you rephrased the work of someone else without citation.

The fact that self plagiarism is viewed differently by different people is irrelevant here. This publication has raised the issue, so it is important to you. It is also, in general, safer to be conservative in such things just to protect your own reputation. If you use it, cite it. Easy rule.


How to acknowledge someone beloved in a publication for his/her support in writing the manuscript?

The authors would like to thank Jane Doe for her assistance in the preparation of this article.

or some variation of the sentence above.


Should I email a potential supervisor who agreed to support me?

Yes, in general it's entirely appropriate to remind faculty members about letters/recommendations/paperwork they've previously agreed to.

In fact many faculty members I've known (and I cannot, alas, wholeheartedly exclude myself) rely on such reminders to a greater or lesser extent.  Faculty nowadays are faced with so much paperwork / routine correspondence (and are not necessarily trained or culturally aligned to regard such things as being important) that we start to believe also in the converse: what we have heard about once and never been reminded of must not be very important.

Just now I got a second email from a secretary in my department about an annual inventory issue.  She sent the first email just a few days before and included a hard deadline in both emails. In other words, she knows all the tricks to get faculty to do things without causing resentment.  The keys: be polite but persistent, and make the convergence to the deadline clear by ramping up the email reminders accordingly.  It really works: pardon me while I run down to her office so she can tag my laptop!


How to prevent work from exacerbating situational depression?

You are mistakenly conflating hours spent in the lab with productivity. There is certainly a point of "diminished returns," where extra hours don't actually improve your productivity, and actively harms it in the longer run.

A few ways to change up your routine:

Work on your most important task first thing in the morning.
Focus exclusively on your work for 20-30 minutes at a time. This means no checking email, no chatting with lab mates, or other distractions. After you're done with your block of time, take a few minutes to recharge before restarting (or moving to a new task).
Avoid obsessively checking your email. Pick a few times per day to answer your email and engage in social media, and stick to it. (And don't spend multiple hours during such sessions; figure out what's important and what isn't, so that you can be finished in 15-20 minutes or so.)

You'll find you probably get more done in less time following such an approach than just spending tons of hours in the laboratory. This will also give you time for your personal life, which brings me to my other point:

  "Block out" time in your schedule for "recharging" activities.

The nature of the "recharging" activity will depend on what works best for you: some people exercise, others engage in artistic or creative activities, and still others meditate. It doesn't really matter what you do to clear your mind and "recharge your batteries"; however, you should make time for it, and make sure that you stick to it. It doesn't need to be an extensive commitment: even an hour or two per week can suffice.


Phd at same uni as MSc, possible offer but would like to change topic/group if possible

Two partial answers:

It's not a problem for you to ask Prof. B about the chances of you doing a PhD for him. Even if it is in "secret". You are looking for employment, and you're not obligated to tell prospective employers about the other positions you are looking at. Any professor will assume that their MSc students apply for several (PhD or industry or both) positions, especially if the professor has given them just a "maybe" for continuing with a PhD.
If you get a positive answer from Prof B., I can't imagine there would be a problem saying to Prof. A: "I've been thinking, and I would prefer to do my PhD with Prof. B because I am more interested in researching Topic X, which his/her group is doing". If Prof. A's reaction to that is getting angry, you don't want him/her as your PhD supervisor or collaborator anyway.


One of the biggest reasons for moving around is so that you learn, over time, a variety of techniques and viewpoints. If you stay in a place too long as a student, you may already know whatever it is that they are able to teach you.

But that isn't your situation. You are moving to a new situation within the university, broadening your horizons with these other people. My guess is that it would be good to take advantage of the situation. You also, as you say, seen a variety of different faculties already, so it is less important to move on than if your education had all been in one place.

Don't stay forever, of course, but learn what you can from the people able to give it.


To what extent may someone use the content of a published paper in an expository piece on that paper?

From an ethical point of view, you must cite your original source appropriately. Clearly indicate

when you are using ideas, words, or figures from another work by citing the source
when you use something verbatim (typically by putting it in quotation marks or blockquotes)

As long as you attribute your sources properly, there isn't really an ethical problem with excessive use of a source.

From a legal perspective, it can be trickier. In summary,

Copying large amounts of text verbatim: may violate copyright
Copying small amounts of text verbatim, for academic purposes: typically allowed under fair use, though like everything legal, this varies by jurisdiction
Paraphrasing text: does not violate copyright. The intellectual content of a paper is not subject to copyright (as opposed to the words used to present it, which are).
Reusing figures: may violate copyright. Check the policy of the source's publisher.

From a "best practices" standpoint, work that involves an excessive amount of paraphrasing is often lacking original intellectual content. Even if your work is expository, you're supposed to be adding some value for the reader, not just stating the content of the original source in other words. So be careful of this, too :)


You could consider contacting the editor of the journal that published your paper. Presumably you transferred the copyright to the journal. They have a vested interest in protecting their copyright. They may be able to request the other journal make a correction on your behalf


How should I write thank you letters to members on my thesis comittee?

Instead of a letter, thank them in the 'Acknowledgements' section of your thesis

You can thank your supervisors for guiding you in the course of writing the thesis.

You can thank your examiners for giving helpful feedback that led to improvements in your work (you can do this even if the examiners are anonymous -- it is not unusual for published academic work to thank anonymous peer reviewers for helpful suggestions).

If a specific comment/lead/idea was particularly useful, you can mention it. If one or more supervisors or examiners helped you on the road to publication, mention it.

An example might read like this (feel free to adapt nomenclature to local context and customise with more detail):

  I would like to thank my supervisors, Dr Josephine Bloggs and Dr A.N. Other, both of the Department of Futile Studies, for their support and guidance over several years. I am particularly grateful for their detailed advice and encouragement on how to adapt Chapter 4 of this thesis for publication in The Journal of the Royal Society for the Furtherance of Futile Studies. I would like to thank my examiners, Prof. Isaac Newton and Prof. Immanuel Kant for engaging with my thesis diligently and enthusiastically, providing valuable suggestions: in particular, they helped me clarify my theory on 'The Noumenality of Lincolnshire apples during the plague'. Finally, I would like to thank the lay convenor for my thesis committee, Mr Charles Dickens, senior secretary of the Department of Circumlocution, for his exemplary efficiency in conducting the examination of the thesis.


To my knowledge, there isn't any universal set of rules for this sort of thing. Certainly citation styles differ between fields. You could obtain any widely used style guide (e.g. the Chicago Manual of Style) and follow that.

If this is an assignment for a class, you could ask your professor what she prefers; if it's a journal submission, see if they have any style guidelines; etc.

You might want to find some published material, in a similar genre to whatever you are writing, and imitate their formatting choices. For example, if you are an undergraduate mathematics student, you could look through back issues of the American Mathematical Monthly. If practices differ, then pick something which you think looks good.

Keep in mind that "different pages" is ambiguous. As you work on the essay, footnotes that appeared on the same page might later appear on different pages, or vice versa. Also, if you submit your work for publication, then the published version would be likely to have different pagination, and the copyeditors might edit things like "Ibid." to be in their own style anyway. So I'd recommend you choose something that doesn't cause yourself a lot of tedium.


Should listed citations in a historical overview be ordered numerically or chronologically?

If you adopt an official citation style, then this will dictate the rules for ordering in-text citations and end of document references.

In-text citation ordering rules

When  multiple authors appear in one citation block, then there are various rules depending on the citation style: (a) alphabetically by first author surname, (b) arbitrary when using a numbered reference style, except are typically consecutive (e.g., 1-3, or 1,3,4), although based on @Jessica's answer ordering may not be required by all style guides.

End of document reference ordering rules

Two common rules are (a) alphabetically by surname and then by year for papers by the same author (e.g., APA style), (b) in order of appearance in the manuscript (i.e., when using superscript numbers).

General points about showing historical development of ideas

If you want to show the development of ideas include something in the text that indicates this development.  For example ,

  Jones (2000) was the first to propose the idea. Several researchers further developed the idea including Smith (2005),  Brown (2007), and then Cooper (2009).

or euivalently:

  Jones (1) was the first to propose the idea. Several researchers further developed the idea including Smith (2),  Brown (3), and then Cooper (4).


Is it appropriate to "cite" random conversations as the inspiration for a research direction?

You can cite it as a "private communication" but it's more common (at least in my field, which is physics) to mention the person in the acknowledgements, for example, "We thank A. Smith and B. Jones for useful discussions". You can make the phrasing more specific if you want, for example, "We thank C. Davies for an insighful discussion about deep learning that inspired our approach to this work".


Do interviews require taking vacation days?

You should ask your advisor, but it is reasonable for an advisor to allow you time (potentially several weeks or months) to essentially be away from the lab and your research in order to interview for jobs. In my opinion, this is a concession that is reasonable to give as a reward for hard work during previous phases of an advisee's research. If not, the advisor likely does not have the advisee's interests in mind. That could come back to bite him/her later when attempting to find new advisees.

On the other hand, if you're spending a lot of extra leisure time on the trips that is not part of the interview, then it should probably be considered vacation time.


Is it good to emphasize that one obtained a PhD from a prestigious university

It could be taken to mean that your PhD from CalTech was a high point of your career and you want to make sure people know that. Depending on the context, that may be a bad or good thing. At a CalTech alumni meeting, it could be very good.


Are technical news websites acceptable as references in the introduction or motivation section?

As a general rule, a reference should be reliable/authoritative for what it says. So whether or not a reference is acceptable depends on what claim you are using it to support, and whether the source has the authority/evidence to make that claim.

A news website would not be an authoritative reference for technical information. For example, this would not be OK:

"With 5G wireless technology, a web page will load in a millisecond [1]." The writer of the article is not an expert in 5G technology, and there is no evidence in the article to support this claim. Instead, to make this claim, you should cite a reliable technical reference that offers evidence.

However, a news website might be a useful reference for other things where it is an authoritative reference. For example:

"Media portrayals of 5G have not necessarily been realistic - for example, Adweek has claimed that with 5G technology, web pages will load in a millisecond [1], but the IMT 2020 technical requirements for 5G [2] specify at least 1 millisecond of latency for just a small subset of the network path." Note that Adweek is not a good source for the claim that web pages will load in a millisecond - the writer of the article is not an expert on 5G! - but it is an acceptable source for how 5G technology has been portrayed in the media.
"Bob Metcalfe, who is called the 'father of Ethernet', said that the developers of the Ethernet standard believed voice and video over Ethernet would be impossible [3]." Here, Bob Metcalfe is a reliable source as to what the developers of the Ethernet standard thought at the time, and an interview with him is authoritative for this.


When is it wrong for students to ask about previous exams known to change?

The ethical answer for students is easy in this case: if it's not clear, and remotely borderline, ask the professor.  Ideally, ask the professor publicly, so that everyone hears the answer.

That said, the real problem is that in this situation, the professor should be dealing with this publicly in one of two ways: either clearly instructing the first class not to discuss the exam until the second class has taken it, or making the exam available directly to the second class (so as not to benefit students who have friends in the first class over those who don't).


Letting grant funder know that funds no longer needed?

I would ask the representative. Procedures differ wildly from funding agency to funding agency.

However, I would not be worried: everybody acted in good faith, and you are asking for less money. So in all likelihood the response will just be a short email thanking you for letting them know, and telling you that they look forward to receiving new applications from you in the future.


How do I transition from a Ph.D. in engineering to a career in medicine?

Medical doctors with a previous experience in engineering are indeed in an excellent position to do clinical research involving technology or modelling. From your question it seems like you are more interested in the practice of medicine than research, and that is fine because in some fields of medicine (e.g. radiology) an engineering background is a definite advantage to practice medicine efficiently.

I know 3 people who started (a 6 years) medical school after another degree. Two after a degree in Physics and one after a PhD in biomedical engineering. All 3 are happy with their choice but their situation is not yours. Can you afford to go to school for many more years?

If you do, in North America a previous degree (and engineering is a frequent one) is usually required prior to entering medical school. Med school usually lasts 4 years. Admission criteria vary between schools but the previous degree should typically include the following, according to the Association of American Medical Colleges:

  At a minimum, students will likely complete the following types of courses:

  One year of biology
  One year of physics
  One year of English
  Two years of chemistry (through organic chemistry)

To browse through institutions, you might find this site useful.

At the institution I know, the requirements include:

1 year of biology
2 years of chemistry
1 year of physics
some laboratory experience
1 year of maths (calculus and stats)
1 year of a course requiring writing.
"[being] comfortable with upper-level mathematics (through differential equations and linear algebra), biochemistry, and molecular biology

An additional requirement is that you completed at least one year of university in the USA or Canada.

In Europe it varies a lot. For Germany, Switzerland and Austria, there are no requirements for a previous undergrad degree and it's usually hard to skip years if you have one. Most universities require that you have a high school diploma from a country they recognize. The programs are usually over a 6 years period. They typically involve a lot less mathematics than in North America. You need to be reasonably fluent in the local language.


How to cope with the change from easy undergrad. to difficult masters?

Feelings of inadequacy are quite common when starting a new graduate program—you are surrounded by talented people (if they weren't, presumably they wouldn't be graduate students!), and there is often a big leap in expectations between the requirements of a bachelor's program and the corresponding graduate program, particularly if you're at a top program in your field.

As one of the commenters mentioned, talking to your professors or teaching assistants may be one good way to get help, or to get at least some reassurance about how you're doing. Depending on what your university or department provides, they may be able to provide you with resources to help you study or prepare for your exams. This might be as much as arranging a tutor for you, or as simple as providing you with sample exams from previous course offerings. If your department has a "graduate student council" or "society" or something like that designed to help out the students, then a lot of these may have already been collected by students from previous years for use by students in later years.

In general, though, don't get too discouraged. It is recognized by most instructors that graduate school is harder than an undergraduate, and the grading tends to match that view. There are very few graduate school courses that are not graded "on a curve"; otherwise everybody would have bad grades! (When the top score on an exam is 60/100, most schools won't let you fail everybody!)