Should I mention that I worked as a professional online poker player on my university application?

I like @DanRomik's analysis, but the same analysis leads me to a different conclusion: yes, list it.

First, it gives a better picture of who you are and what you have been doing.

Second, while some people may be prejudiced against poker players, in most applications there are things (and lack of things) that may be viewed positively by some committee members and negatively by other committee members.  I don't think the concern should be too great that it will lead to too much veto-ing of your application, as might be the case for being incarcerated for a violent crime, say.  (Of course this is my personal opinion and not based on any hard data from surveys--I imagine it might be an issue at some schools, but probably not most.)  I personally would find lack of activity for 4 years more of a concern.

Third, the fact that you are no longer playing poker professionally (I infer this from your use of past tense) indicates that, even if you were addicted to gambling at some point, you overcame it.


Are there guidelines for amount and content of text in figure captions for theses?

I would imagine this may vary from field to field, but in the biological sciences the caption text in journal publications is often verbose to the point of absurdity. That being said, I would simply use common sense; If the description takes more than a paragraph, you should definitely "refer to text". Generally speaking, the caption is simply a textual guide as to how to read the plot, with (maybe) a sentence drawing the reader's attention to a particular feature of the plot. It should mostly describe the plot, and only sparingly discuss it.


Change affilation in printed publication

Is it possible to change affiliation after printing?

No, at this point it's almost certainly too late.  If the affiliation was correct at the time, then there's no problem at all; it's understood that affiliations change over time and old publications are not updated.  If there was a minor error or oversight, then there's still probably nothing you can do about it now.  You could ask the editor whether it's possible to issue an erratum, but it would have to be a remarkably serious error to justify that.  (For example, an erratum could be justified if there's an error in the affiliation that creates genuine ambiguity as to who the author is, say if the publisher accidentally confused you with someone else with a similar name and listed their affiliation instead of yours.)


Is it acceptable to ask a professor who is not your supervisor to provide comments on your thesis draft?

If you have an existing relationship with this professor, you could ask, but be prepared to hear "sorry, I don't have time".

If this professor is a stranger to you, this is probably an unreasonable request.


What are some good ways to lead a discussion session for a TA in a graduate-level STEM class?

Clear up common points of confusion you've encountered while grading.

If you are also grading homework for the class (or you know the grader...), you can identify common mistakes or points that students seem confused about. Even if you explain these on the individual homework papers on which students made those mistakes, (a) many students don't bother to follow up if they don't understand the grader's comments, and (b) it's possible that other students would have made those mistakes, and didn't only because they made a different mistake instead.

Discussion sessions are a great time to point out these potential pitfalls, warn students away from them, and discuss why they represent a wrong understanding.

Ask a question as a confused person.

I like to challenge a class (in the context of the discussion - not necessarily on an exam!) by asking a question that is ill-formed, confusing, or based on a mistaken premise. (Not to trick them - I warn them that this is what I'm doing.)

For example, I like to find questions asked by Real People on Stack Exchange sites (like Signal Processing Stack Exchange!) related to what I'm teaching, and challenge students to formulate a good answer. Then we discuss the answers as a group.

Answering a "real" question posed in this manner often requires much greater mastery of the material than solving the "nice" problems we usually give students.

Pose a design problem.

On a similar note, the "nice" problems we ask questions often have boring, "nice" solutions that require straightforward application of what they have learned, but not much original thought and critical thinking.

Raising a design problem - i.e. "How can we design a DSP pipeline to do X?" or "Here are two designs that solve a particular problem. What are the benefits and disadvantages of each?". These, too, can come from mailing lists and forums. Here's an example of the type of design problem I'm thinking of.

(Of course, these should be problems your students can solve, based on what they have learned.)

Have students nominate topics for discussion at the
beginning of a section.

At the beginning of the session, ask the students to suggest a few topics from the lecture or homework that they would like you to review in greater depth. Then have the class as a whole vote on the nominated topics to determine what to do with the session.

Source of this suggestion: TA handbook for UCSC

Ask the professor to provide you with past exam problems for use in the discussion sections.

Students seem to love working on past exam problems :)

Specifically, you may want to do it as follows:

  Hand out a printed copy of the questions (double-sided, stapled). For each question:

  Read the question aloud, or ask a student to read the question aloud.
  Ask if the question is clear.
  Have them discuss the answer in small
  groups.
  Ask for votes, or ask someone to explain their answer.
  If the
  class doesn't all agree on the correct answer, then you can have them
  discuss further, or you can try to clarify a difficult point.

Source of this suggestion: Jason Eisner

Give mini-lectures about things you think deserve to be retaught.

Especially if you have the time to also attend the professor's lectures, you can identify topics that he may have had to rush through.

Similarly, you may give a "refresher" on a prerequisite topic that students don't seem adequately prepared in.

Or, you can give a mini-lecture on a topic that, based on homework grades, students just aren't getting.

Source of this suggestion: Jason Eisner


How does a tenure track professor get money to recruit PhD students?

You name two of the ways that funds for this might be available. Including support for doctoral students in grants is common. If you want departmental or university funds, however, it is best to negotiate that as part of a "start up package" that some universities are able to provide.
But, most universities will normally make at least some minimal efforts to recruit graduate students and most will also provide funds for teaching and, perhaps, research assistants generally, so the funding may not be through the professor at all, but through the department. These funds generally require the student to perform some duties in return for the stipend.


Potential issues with uploading copyrighted material to TurnItIn?

This is a bit long for a comment, but I also acknowledge that only someone from TurnItIn could categorically answer this.

Since TurnItIn does not provide access to source material (other than small sections which actually match the submitted paper), I do not see how it could be a copyright issue. I get matches all the time from papers submitted to other schools, yet, TurnItIn does not allow me to see that paper.

Additionally, much of the content within TurnItIn is under copyright (blogs and others) and they do not purge it, further implying that they would not have a problem with your plan.

All that said, unless the content is quite new, or changed regularly, as soon as one student includes content, any other student including that same content will trigger a flag for you.

So, I do not believe your plan will have any problem but I am also not sure you need to worry about it unless you have a special set of texts you believe other students around the world will not have access to.


There is certainly no way that these mistakes alone will hurt your application.  If the admissions committee is concerned about your English fluency, there are other things they can look at: your GRE and/or TOEFL scores and your personal statement / statement of purpose.  If you are doing okay on those, then you have nothing to worry about.

Even if your verbal / writing / English skills do look somewhat shaky, that still should not get your application for a PhD in earth sciences automatically tossed out.  The committee would want to weigh your weaknesses there against your strengths in other areas.  What would be a problem is if your writing skills were so poor that they just couldn't understand you at all.  Based on the five line writing sample given by your question: this is absolutely not going to be the case.

In summary: don't worry, you should be fine.


How do you deal with the ridiculous catch 22 to get into grad school

I have been a CS professor at both large and small schools, so let me say a bit about getting into the program from both perspectives.

When I was working at a small school, we didn't have a large graduate population, so we accepted anyone who was qualified - regardless of research experience, etc. Anybody who was well-qualified (eg good grades and reasonable application package) also received a TAships covering the full cost of their degree. I still managed to get some fantastic students through this process. (Who didn't have research experience or were not from a traditional CS background.)

I am currently at a larger school, and we get something like 5x more applications than we are able to accept. So, most students get rejected, even highly qualified ones.

Based on this comparison, I'd suggest that you may need to look at a smaller school. Try to find an opening to work on a problem that might help you with a grad school application in the future.

In particular:

Find smaller schools with professors doing work in the area that you are interested in. Smaller schools can have very strong professors for many reasons. (Look particularly for recent publication activity.)
Read all of their recent papers.
E-mail ask research questions about their work. These questions should be genuine and should reflect a strong understanding of the work. You could even, for instance, ask if a project would be a suitable extension of the published work. (eg your method X works under conditions Y and Z. Would method W broaden the applicability of the approach? Or, would method V improve the performance when condition U also holds?)
Implement and try some of these ideas in practice. (You could even do this before doing #3.)
Use this to improve your graduate application. There are several ways to do this. First, if you have good communication with a professor, they may directly be able to help you get admitted to the program. But, this can also be part of your statement of purpose (SOP). I've read lots of awful SOPs. Your application will stand out if you can talk about a research problem you are interested in, why it interests you, and why it is a fit with the department/professors.

There are lots of variations on this approach, but I've had students use parts of the approach on me, and it worked.


I would classify a "junior" researcher as pretty much anyone who does not yet have a permanent position. (The question of whether a tenure-track faculty member is a "junior" researcher might be open, but anything "below" that is not, at least in my mind.)

So yes, someone who has had a research stay abroad and has recently received a PhD is still very much a "junior" researcher.


Is the usage of "vice versa" appropriate in academic writing?

I would make the position completely clear:

  Conversely, if the angle is …

technical writing is not a good place to leave people guessing or admitting the possibility of ambiguity: for a few extra words it is worth it IMHO...


Is it ethical to recieve stipend after publishing enough papers?

Whether this is appropriate ("ethical") or not depends on the applicable rules.

As per your comment, the funding agency's guidelines don't make the stipend conditional on any performance criteria beyond the two published papers. They also provide for a maximum duration of five years within which the stipend can be consumed.

Producing the papers during the first two or so years and consuming the stipend for the remaining time while advancing one's career in other ways (publishing more, writing grant proposals and applications...) doesn't contradict the applicables rules. It's perfectly appropriate, and perhaps even expected behavior.

If it were not, the agency could have attached further conditions to the continued payment of the stipend, it could have limited the payment to the time that is actually needed to publish the two papers and graduate, or it could have introduced regular performance reviews.

Aside: Most likely, if you graduate early, you will not consume the entire stipend but rather prepare for the job market and move on. Living on a stipend is not terribly attractive, and climbing to a more prestigious position, or one with better research opportunities, is a good career move. The agency will probably also have an interest in their alumni succeeding, "even" if this means paying out the full stipend they promised and budgeted for.


To fully answer a career path question will be very long. There are several questions need to be clarified first:

what do you value most in a job? Money, location, growth opportunity in the job, work-life balance, company/university culture...
why do you study biostatistics after a Ph.D.? If you want to get better pay, definitely go to industry, simply because academia is non-for-profit.
Do you have some specific research topics you want to explores? If not, it is likely you are not ready for an academic career.

I had a similar experience. I got my Ph.D. 3 years ago and did a career change due to funding and personal reasons. I quite enjoy my current job because I am doing research in a company and don't need to worry about the funding issues.


Repetitively citing studies in a literature review

You should definitely go with Structure 2. It is far more helpful to you (that is, it forces you to engage more deeply with the literature) and your readers (that is, it gives them a more useful review of the literature).

The article that is probably the most seminal in my field (information systems) on literature-review methodology is mostly famous because they clearly addressed precisely this distinction. Webster and Watson (2002) argued that author-centric literature reviews (your Structure 1) are not very useful. They are simply an extended bibliography. (When you think of it, all that does is little more than summarize the abstracts of each article, which are already summaries of the articles.) They argued instead for what they called a concept-centric approach to reviewing the literature.

The concept-centric approach is not quite the same as what you describe in Structure 2: what you describe, I would call a topic-centric approach. Webster and Watson’s concept-centric approach identifies the theoretical concepts in each article and then presents them as the structure of the review. Your Structure 2 identifies common topics in each article. While not as useful for developing theory as the concept-centric approach (and maybe developing theory is not your goal at all), it is far more useful than the author-centric (or more accurately, article-centric) approach of your Structure 1.

Reference

Webster, Jane, and Richard T. Watson. Analyzing the past to prepare for the future: Writing a literature review. MIS quarterly (2002): xiii-xxiii.


How to reuse/cite your paper in your thesis when both have same topic

Now I want to submit my thesis but I suppose it is self-plagiarism if I don't cite my paper.

Self-plagiarism isn't relevant here, your thesis isn't considered published.

  My question is, can use the same content in my thesis

Yes.

  then how do I mention that content is reused?

You can mention something along the lines of: This manuscript is based upon my PhD thesis [1].

  or should I rephrase my complete thesis now

There's no need.

  But if I rephrase then how about the experiment results and figures?

Again, there's no need.

  should I cite paper there as well?

Citing your thesis once suffices.


While doing PhD I did not consider the job prospects or requirements in my field. Will it be alright to ask my advisor for help with career path?

Most advisors don't know how to get jobs outside of academia, it's kind of humorous how delusional many of them are.


What happens after my paper is accepted?

After your paper is accepted, it is passed to the publisher's production department. They'll do things like copyedit it, typeset it, proofread it, organize the references, and so on.

Your involvement as an author isn't completely over. At some point in the production process, the publisher will show you proofs (which is what the paper looks like after all of the above has been done). You get to make final changes at that point, e.g., the editor might have decided to accept your article with some minor comments still outstanding from the reviewer - now is the time to make those changes. It's also possible the copyeditor will have questions about the text; this is also the best time to address them.

Your involvement usually ends when you approve the proofs (very uncommonly, problems might be found even later in the production process that requires author input). After you've approved the proofs, you can sit back and wait for the paper to appear.


Does anybody receive printed copies of new journal issues nowadays?

I do.

I have print subscriptions to three major journals in my field, all through optional add-ons to society memberships.

I do so for three reasons:

It forces me to read and interact with the literature. Online tables of contents, journal RSS feeds etc. can be ignored because another staff meeting is coming up, I really should submit an abstract, etc. The arrival of a printed journal gives me an excuse once a month/quarter/every two weeks etc. to sit down and engage with my field.
I read articles I would not otherwise read. General society journals have papers in areas that are not strictly my field. Sometimes, I read these, because I know the authors, liked a particular plot while I was flipping through, or because it pings my curiousity. I rarely read PDF papers outside my field.
Journals are more durable than print-and-staple publications. They live in my bag. I read them at lunch. I read them in the bathroom. I read them at the gym. I do things to them that I wouldn't dare do to either an iPad or other electronic reader or a few flimsy pieces of copier paper.


A manuscript I refereed gave me an idea for a paper, not sure how to proceed

I think there are two questions that need to be answered first.

Is it important to you (e.g. for career reasons) to publish solo, or would you consider publishing with the other author?  Keep in mind that publishing jointly may have extra benefits: the two of you together might come up with an even better solution, or it may lead to future collaborations on other projects.  Or do you perhaps not care about getting credit at all?
Is the manuscript public?  Has it been posted as a preprint on arXiv or a similar server, or on the author's website, etc?

Depending on the answers, there are a few cases:

You don't care about getting credit. Write your report on the paper: "The approach to agrobaric frobotzim via PDQ analysis is unworkable because of foo, bar and baz.  However, this could be fixed by using QPM analysis instead.  [Sketch your idea here.]  Pending this fix [and any other suggested revisions], I recommend the paper for publication."  Expect that when the paper is published, there will be an acknowledgement: "We thank the anonymous referee for suggesting the approach used in Section 5."
You want to publish jointly. Contact the editor: "The author's approach to agrobaric frobotzim via PDQ analysis is unworkable, and as such I cannot recommend the paper for publication as it stands.  However, I have some ideas about how to resolve the problem, and I would be interested in collaborating with the author to work them out.  Would you be willing to put me in touch with her?"

The editor says yes. Great!
The editor says no, and the manuscript is public. Submit your report pointing out the flaws and recommending rejection.  After a decent interval contact the author: "I saw your preprint, and had an idea to improve the results using QPM analysis.  Would you be interested in working together on this?"  Opinions vary on whether you should reveal that you were the referee; it is possible the author will guess anyway.
The editor says no, and the manuscript is not public, but you know who the author is. Submit your report pointing out the flaws and recommending rejection.  The next step is a bit controversial.  Some would say you should wait until it is public, so as not to break the anonymity of the reviewing process.  Others think it is fine to reveal yourself and contact the author directly to suggest collaboration.  I am not sure what to say here.
The editor says no, and the manuscript is not public, and you do not know who the author is (double-blind reviewing). You have no choice but to wait until the manuscript is made public (maybe until it is published somewhere else), since that's the only way to find the author and suggest collaboration.  If you think you should give up on finding the author and publish solo instead, see below.

You want to publish solo.  Write and submit your report.  Now, is the manuscript public?

The manuscript is public. You may write your paper, citing the other author's preprint and giving her due credit for noticing the problem.  This is ethical, but if you meet the author at a conference, don't expect her to buy you a beer: she was hoping to solve this problem but you beat her to it.
The manuscript is not public. You may not proceed.  As a reviewer, you received the manuscript in confidence, and to write a solo paper based on it would be to take unfair advantage of that access.  You must wait until the preprint appears publicly.  (This might be when it is published in another journal, or maybe never.)  It's possible that in the meantime, the author will discover your solution independently; those are the breaks.  This would be a great time to reconsider seeking joint authorship.

In case 2, if your field has a notion of "first authorship", that would be something you'd need to negotiate with the other author, based on your field's norms.  (Mine uses alphabetical ordering almost exclusively, so this issue wouldn't arise.)


Submitting an unsolved-problem paper to open access journals

If a person without good records and with bad records (many flawed papers on arxiv) submits a paper which claims a proof of the Riemann Hypothesis to a traditional journal, then will it be ignored certainly?

This person will have to make a very, very, very convincing case in order to be taken seriously. See I believe I have solved a famous open problem. How do I convince people in the field that I am not a crank?, especially the answer by Kaveh.

  If so, then will it make any good for him to submit it to an open-access journal which accepts articles in two weeks?

This will not lead to the paper being taken seriously by the research community. If that is your goal, don't waste your money.


Is dyslexia regarded as a severe disability for academic applications?

Dyslexia is widely recognized as a disability.
Deciding if dyslexia is "severe" is a matter of opinion.  Only one person has a well-informed opinion about the severity of your dyslexia: you.  If you think it is severe, no reasonable person will question it.
Your strategy of mentioning your disability in the context of how you were successful overcoming it is a good strategy.


Can I use the sentence "Most of the references in this paper" in my paper?

I would use the first option. If you know the papers which back your position, name them. Maybe not all of them, but three to five. Choose the papers with the most explicit wording and/or the authors with highest reputation in your field.

Note, some citation styles allow to write the list of cited papers more compact, e.g., [1,2,4-8,..15].


Contacting multiple potential supervisors at the same department?

TL;DR: You should contact all of the possible supervisors at the same time and ask for a meeting or a call. And you should be completely open about the fact that you contacted multiple advisors.

Why:

If you contact one after another this gives (possibly) a bad impression for everyone.
I understand that you would like to prevent the dilemma of multiple advisors being interested but this dilemma will show up anyways once you have chosen a advisor and started the work.
You do not want to be disrespectful but you are faced with a decision. Everyone should understand your dilemma and should appreciate your efforts to be as fair.
You should be honest to yourself. While I do support your way of thinking you are causing this dilemma yourself because you want to have the choice.

I would think that the etiquette will differ greatly across the world, so I don't know how well it is received that you would like to have a choice/control here. However, I think it is totally understandable and a good advisor will also understand your intent and process.


prospective English doctoral candidate: advice regarding weird relationship with potential advisor

I advise against sending an explanatory email. It will only make the waters murkier. An email can't correct what transpired. A better option is to meet with the professor in person to discuss your plans. This would give you a chance to demonstrate that you've changed and establish a new relationship with your professor. Don't spend time explaining your past failures. In your meeting, focus on what's positive in your record and your commitment to your new plans. Everyone screws up, you know. If this professor has the wisdom of his years and he sees a new spark in you, he will probably want to support you. Take a lesson from the past, forgive yourself for being human, and move on.


Should I include my (unofficial) class rank in my SOP?

In general, I think mentioning unofficial rank is fine. You could simply write:

  Note, though my university doesn't officially publish class ranks, I learned that my 3.6 GPA corresponds to the 94th percentile.

The only trouble is that they might not believe you; it would be better if you could get a professor to mention this fact in their letter.

Your case is a bit different, though. You don't know what your final class rank is (even unofficially); all you know is that two years ago, you were in the 94th percentile of a subset of the students after weighting for the number of credits completed. There is no concise, accurate way to describe this that doesn't appear desperate*, and you wouldn't want to be accused of trying to mislead them. So, I would skip mentioning this altogether.

*Actually, the one way I can think of is maybe you could present it as an award? "I was ranked in the top 6% of applicants and was therefore allowed to study abroad in Jamaica?" If study abroad is a competitive process that you "won", it may be fair to mention this.


English Bachelor of Computer Science - Germany

You can try out the Hochschulkompass (Higher Education Compass) of the Hochschulrektorenkonferenz (German Rectors' Conference).

Searching for international programs granted with a Bachelor degree in Informatik (computer science is mostly called that in Germany) ends with 13 results. Maybe you can find a fitting study program for you there.


admission in UK university for Masters/ PHD program

In many UK universities, a minimum requirement for admission to a doctoral programme is:

an upper-second-class or first-class undergraduate degree; or
a Master's degree.

And even if it is not a minimum requirement for admission, it is almost certainly a minimum requirement if you want a funded place.

Significant professional experience may mitigate poor prior academic attainment, but I am not convinced two years would be enough to compensate for a third-class undergraduate degree.

If you are happy to self-fund PhD studies, I suppose there is no harm in having a go at applying for a doctoral programme immediately (although I would recommend making at least one application for a Master's, in case nobody accepts you for a PhD at this juncture). But, if you want funding for PhD studies, you will almost certainly need stronger academic credentials than you have currently.


What is an "innovative statement" for faculty application?

What makes your research novel, exciting, ground-breaking or significant should be delineated in a innovative statement. How you are advancing your field by eventually accomplishing your aims.


How to list proposals I assisted in writing on CV

1) A great tip is to look at other successful people who have the same experience and see how or whether they listed that on their CV. If you know any postdocs in recent history with the same experience, look at their website or ask to see their CV as a template.

2) If your only contribution to the grant is that you developed your own Postdoc mentoring program, I'm not sure that I'd consider that grant writing experience. But, I don't really know- that's just my gut feeling.

3) Later in your career you would probably not list grant activity that you are not the PI or Co-PI for. For a postdoc or grad student you want to make it clear that you worked on grant writing but you're not an investigator.

You could have a section that looks something like:

Grant Activity - neither PI or Co-PI

Summary of contributions. (NSF Grant Number). Grant Title. $Award Amount. Date.

For example:

Grant Activity - neither PI or Co-PI

Editor, figure designer, and wrote mentoring plan. (NSF 123456789). Investigating Greatness by Posting on Stack Exchange. Awarded $300,000. 2017


In-text citations - First and subsequent citations - AMA

Yes, use again the same superscript as before.
Here is a random example from JAMA Network Open (this paper at p. 5). Note the repeated use of 1 or 24:


Listing rudimentary language proficiency in an application in that country despite English being working language

I think yes, you should list it with caveats at the end of CV, using something like

  Languages:

  English (fluent), Arabic (basic passive)

and it the country in question is in Europe, just use the EU proficiency levels: for example,

  English (C2), Portugese (A1)

Frankly, I don't think it would help. It can't hurt and it maybe gives you some points for being keen, but the time you waste thinking on this might be better spent studying something. Maybe even the language in question.


Applying for Masters Program at University I work at as a Developer

That depends on the university and its rules. General advice is probably worthless. It may be more lenient for an MS than a doctorate, perhaps. But the competition will still be there, and there may be specific rules about candidate selection.
I would expect that most places tuition reimbursement is a complete separate issue than placement into a program.
My advice, if you want an MS is to apply to more than one university. Include this one, of course, but don't cast a small net.


Why does Google Scholar provide a different number of references when sorting by relevance versus date?

(I'll repeat an earlier answer of mine, which is relevant here, although the question is not a duplicate. Nevertheless, the question itself is relevant. Why are you interested in how many Google Scholar results a particular search yields in the first place?)

The "approximate" ("about") number of hits Google reports is completely worthless - in all Google searches. To see why, look at this number on both the first and the tenth page of Google hits:

First results page

Tenth results page

When I just did this, I got "approximately 15,200,000 hits" reported on the first results page... but only "approximately 96 hits" on the tenth page.

Given the opacity of Google's search algorithms, which likely have a lot of sampling built in, it's not overly surprising to me that you get surprising results even if you only sort your results in a different way.

In addition, your results will probably vary depending on your search engine bubble (another reason why this number is useless).


Guide for Undergraduate Research (trying to find a PDF document)

After quizzing many colleagues, I was able to find the document again. Nevertheless, thank you for the help to anyone that took the time to consider the question.
If someone is interested:
https://cpb-us-e1.wpmucdn.com/sites.ucsc.edu/dist/4/216/files/2019/12/Thompson-On-being-a-successful-graduate-student-v9.pdf


Advice for interacting with students reported for cheating on their midterms

Just treat them the same as all the others during lectures.

If they want to meet you outside lectures to discuss the issue then you have two options : one: say that the issue is with the Head and the result / decision will be communicated to them, or have a discussion but I would not do this as it could affect the decision process.


Will not collaborating hurt the career of a math postdoc?

I am a math professor at a research-oriented university, and I have been on multiple hiring committees for tenure-track positions. If I were reading your file, your situation would raise two questions:

Are you doing research that is of broad interest?
Do you work well with others? Are you the kind of person that has ideas to share, that I would want to chat math with in the hallway, that would get graduate students interested in your subject?

Your application should offer evidence that the answer to both of these questions is yes. The first point will hopefully be addressed by your letter writers. It will also look good if your CV lists many invited conference or seminar talks.

The second point will again hopefully be addressed by your letter writers. If possible, I would suggest that at least one of them should be written by someone with whom you have talked math a great deal, and not just by your advisor and senior scientists who have read your papers. If you have engaged in any leadership activities (i.e., started a seminar, organized a conference, informally helped to mentor graduate students, etc.) I would make sure that your letter writers include someone who will attest to this.

And finally, like the other commenters, I would definitely recommend striking up some collaborations, although there is certainly nothing wrong with also doing work on your own.


Why do some PhD programs recruit only a handful of students and other recruit more than 100?

The reliability of a program depends on many things as does the number of slots available in a given year. I have no reason to doubt that the University of Lisboa is anything but reputable.
But, if they are willing to admit up to 110 students in a given year it doesn't necessarily mean that they will. They will apply some standards to every application and might fall short of the goal. The goal might change from year to year depending on graduation and drop-out rates. It might be half the next year, though unlikely.
But the reliability depends on the rate of graduation and where the graduates wind up and not on the absolute size of the program. In fact, there may be many specialties within such a faculty, so it may not seem so large to any particular student.
But a given faculty member can probably handle three or four (more?) doctoral students at a time if they are in different stages of their programs. Some can handle many more, depending on the organization.
Look to other factors.
I was in a large program, though not quite that big. Things have gotten bigger since that time, also. But the research seminar I was in had about three faculty members and half a dozen students. Graduate classes had about 30 students, and the entire graduate student population was spread over many courses. It can work and still have high quality. In fact there can be a certain synergy that comes with a large faculty.


How should LinkedIn summary look like for a person seeking PhD positions?

Look up some of the professors you are applying to. Unless they work in fields that have strong connections with industry, they will probably not have a profile at all; and if they don't have a profile, they won't even think of looking you up on it.

Even if they do, your application has a lot more information about you, and structured in a way that is more familiar to them (since everybody that applies has an application, but mostly do not have a linkedin account), so it is quicker to look up the information they may interested in.


Can I take the biochemistry GRE test if I am a biology graduate?

There are no requirements on who can take a GRE subject test. So long as you pay the test fee, they're happy to take your money, even if you've never taken a course in the subject in your life. You're a French major who wants to take the mathematics GRE? Bien sur !


What are some useful tips that allows PhD students to produce many publications of good quality throughout the duration of the PhD?

If you want to publish a lot of (scholarly) papers you need a lot of novel/new/interesting results. To get results you need (a) a lot of ideas and (b) a lot of hard work to develop those ideas.

If you are lucky then maybe a third of your initial ideas will end up in a result that is interesting enough to publish. Some of the ideas will be so easy to develop that they aren't worth publishing. Some of them will be so hard that you can make no progress in a reasonable amount of time.

To have a lot of ideas you need a firm foundation in your field, both what is known and what isn't yet known, but worth knowing if it could be arranged. Probably you won't be able to find those ideas yourself, or not very many of them, so you can work with other people who have ideas and with whom you can develop synergistic relationships to explore the unknown corners of your field.

To become a writer, you need to write a lot (as user henning suggests in a comment), but it takes more. You need to learn what is worth writing about first.

Since you are unlikely to know everything, or why some things are important or not, you need feedback on your work (and your writings). This is one of the reasons for having an advisor. He or she should be both a source of ideas and a sounding board for the ideas you have and how you develop them. So build a strong relationship with your advisor.

Another source of idea will be any state-of-the-art lectures that you can attend and any recent papers that explore ideas but leave some questions unanswered.

So, work with a lot of people. Listen to them and read what they write. Try a lot of things, expecting to leave much of it on the floor. Get a lot of feedback. Give out ideas as well as receive them. Make ideas your currency. Work hard. Take a lot of notes so that when something doesn't work out, but might later, you have a structured way to remember what you did earlier.

Always have something with you to read. Always have the means with you of writing down a quick note on an idea.

Papers, again, represent the successful exploration and development of ideas resulting in something known that was unknown before you started.


Is it okay to ask to "waive" the stipend when offered a fellowship for PhD program?

You can certainly ask for the stipend to be withdrawn. Most universities are happy to spend less money. They may not be happy if this also means that you are not doing the TA/RA work, depending on whether they have enough TAs/RAs.

You can also ask for the stipend to apply to tuition - no harm in asking. Less likely that this will be granted than just stipend withdrawal.

Volunteer work is usually accepted, so if you want to do the TA/RA work you may be able to, even without the stipend. The legal status of such work is the question, which you should ask a lawyer about.


Unless explicitly stated by your instructor, I believe you should be free to use any. Just for the context about what you might find in the relevant literature, the MLA is generally used in the field of arts and humanities, whereas APA is mostly used in psychology and other social science. However, they are used across the fields too.


What can I do if my paper doesn't fit any arXiv category?

The archive engrXiv is dedicated to engineering. Wikipedia has a list of preprint servers where you might find other possibilities, but the engrXiv is the only one dedicated to engineering, as far as I can see.

There are other solutions to publish preprints as well: your institutional repository or generic archives such as figshare or Zenodo. Both accept articles and will provide a DOI.


Research statement for a fellowship application: should I introduce my area?

You have to convince readers of two things:

The problem is important
You are qualified to tackle it

To that end, you should make the problem and likely outcome accessible to anyone, but your proposed approach can assume more skill.


PhD in CS after 4 year bachelors in ECE + 1 year CS masters

If you’re asking whether there exists a CS graduate program that’s likely to accept you, then probably yes. If you’re asking about top x% program in country Y, it starts to get complicated. I’d say that a lot depends on the quality of your masters work, in particular your publications (if any), your grades, your alma mater’s prestige, and last but not least - your reference letters.

Good luck!


Getting letters of recommendation for a master's degree if I don't get along with my current advisor

A few points regarding your questions:

Presenting a weak conference paper is only very slightly better than presenting no paper at all. It may even be worse, if someone evaluating your application saw the presentation and came away unimpressed.
There is no requirement that you get a letter from someone like your present advisor. Such a relationship is clearly not productive for either of you, and including a letter would definitely not help.
You do need to get letters from people who can comment on your work skills, so your old advisor would be acceptable. Other people with whom you have worked—so long as it's technical in origin, even if it's not explicitly research—could also write letters for you. If you can't get three such letters, then you should get them from people who know you beyond taking classes with them. Only if you exhaust all other possibilities should you rely on people who know you only from classwork.
Finally, find yourself a new advisor, if at all possible.


Minor degrees, are in fact, minor.  They should not be front-and-center like your major.  If the minor degree is totally taking the backseat, both degree-wise and research-wise, I'd maybe have a couple of words on my CV/resume, saying I minored in this and that would be it.  You could say that you intend to pursue a minor in this subject if you haven't officially declared it yet, although again, it's really only a few words on a subject; I personally wouldn't list a minor that I haven't declared yet because in my mind, it could be seen as lying on the CV.
Now if you plan on using your minor to form the basis of future research work, then it may be worth listing/talking about on your CV.  BUT ... if it's part of your research interests anyway, the majority of the talking about that should be done via your statement of purpose or recommendations, or maybe even any research you've done that may be related to that minor.
So in summary, you could say (intended) minor in this, removing the "intended" part afterwards when you actually declare it, but overall on a resume/CV it's only a couple of extra words and maybe only a big deal if you're applying for a relevant position; if not, you should have other things to talk about that are more related to what you're applying to anyway.
Hope this helps.


Collaboration tool for students and teachers

I understand you mean "school" as in "before university", so you are working with non professional researchers. In this case, I think the most important bit is to keep it simple, and use tools people know and are familiar with and just work. So,

Mailing list: for group-wide communication. There are tons of free alternatives.
File upload: shared Dropbox folder or ownCloud. With the extra benefit that everybody has a backup of everything, so nothing gets lost.
Everything else: any free wiki.

That should cover all your needs.


How can a would-be researcher overcome slow comprehension, obsession and poor communication skills?

As @ff524 mentioned in comments, it's hard to give advice to you after only these few lines, for no reason more than that what you describe as holding you back might equally well be a sign that you share certain characteristics very common among academic researchers.

As to 2), you essentially say that you like digging into a problem until you have a solution that pleases you, while forgetting the world (exam) around you. That ability, or obsession, must be one of the most important for a researcher, whatever the source (it could point to some excessive OCDness). It currently probably leads to you having crack answer to a few exam questions, while none or marginal ones to others, and so might prevent you from ever being a researcher. All it seems to take though is to keep reminding yourself to not obsess: write an answer outline to all questions, and then allow yourself to drill deeper. It's essentially an inability to multi-task, and there is lots of advice online how to address that.

The difficulty to orally communicate you mention in 3) is extremely common among professors. Your ability to speak can be improved in rhetoric classes, but being a poor speaker is often linked to issues such as anxiety too, and so is tricky. Communicating clearly in writing though can be easily improved in self-study. Get yourself a copy of Strunck&White, skip the 4th chapter, and ignore those telling you it's outdated. Zinsser's On Writing Well is even more helpful. It was a real life-changer for me.

Your issue 1) is unclear for someone not knowing you in person as well. You understand slowly. Says who? By comparison to who? Does the person explaining things to you suffer from your issue 3) as well? You might just be too hard on yourself. I had few teachers who truly helped me understand what I had to learn better, so few that all these years later they and what they said stick out in my memory. In terms of comprehending from reading, you seem to say that to truly learn, you need to re-read your books. That isn't too uncommon either. Additionally, from what you say in 2) which might allude to some OCDness or similar, you might be too harsh on yourself in judging when you have "learned" something. To this day, when I read a math book I have to fight feeling that I didn't read it carefully enough if there is any proof in it I couldn't provide on the spot. That's counter-productive.

I hope some of what i wrote actually fits your situation, or at least helps you maybe view it in a different light.


Is it considered cheating if I purchase an essay but then don't use it?

If your task is to write an essay and you let somebody do it for you, then you are cheating. If you copy somebody's work (even just a part of it) then you are cheating. If you try to let somebody's work pass as your own, then you are cheating.

You are saying that you are not using their work – I hope that means that you are not using their text (in total or parts of it), you have not just obfuscated the text and try to pass it as your own, or have not rewritten the essay in your own words (keeping the ideas and golden thread of the bought essay). If this is true, then (at least in my courses) you would not be a cheater. In all these cases you could replace the bought essay with the essay of a classmate and we would have a very similar question. The only difference is that you have paid money for it.


How to make your paper's materials available online? (personal webpages, Institutional server, etc?)

Try something like github which will provide not only a public place for storing your code, but also will give you version control.

Other similar sites exist such as GoogleDocs, FlipDrive, DropBox, ...


Am I allowed to do the work for a research assistant (RA) without having been awarded an assistantship?

It's a little unclear to me whether you're asking whether it's permitted to do work without getting paid for it, or if you're asking whether it's a good idea to do that. I'll address both questions.

Almost any faculty member will be happy to take you on without needing to fund you, provided you have a decent reputation and they have sufficient time to mentor a grad student. I've done this several times when neither I nor the faculty member had funding (or the readiness to commit) by enrolling in an independent study with that advisor. Depending on the institution, this is probably fairly common. You can say you've worked with this faculty member, but you won't be able to say you were an RA with that person because you weren't funded by them.

Let's move on to the question of whether this is a good idea. Barring any red flags on your financial situation that you haven't mentioned, YES. This is a phenomenal way to get job experience and familiarity with the group. It does make you look like a more dedicated grad student, which should impress your advisor when he/she considers funding you later. It would also give you a head start should you apply for a fellowship.

I would also urge you to discuss this with the person you're thinking of working with. They might consider funding you if they see that you're already willing to sacrifice (it's a long shot!). They will be better able to advise you than anyone online because they know their funding situation, their field of research, their institution, and the local cost of living. Plus, talking to them early gives you a chance to connect.


Should I become first author of a paper for which I did the statistical analysis?

In medicine, as in most biological fields that I know of, the first author is the person who did most of the hands-on work, while the last author is the one who had the idea and planned the project.  From what you've said, then, it would be appropriate for you to be first author and the doctor to be last.

That said, if you don't feel comfortable being first author (and especially in light of your comment that I do not agree fully with all the conclusions) it's also appropriate for you to request to not be first author -- some middle position (second author, or whatever) is also perfectly suitable for your contributions, from the sound of it.


What is the academic argument against Sci-Hub?

There are none.  The arguments against sci-hub are legal or economic.  Copyright is a legal right, not a moral or intellectual right.

You could argue that repositories like ArXiv or open access journals are better than sci-hub because they are more reliable.  But that is not an argument against sci-hub.


I am currently doing the exact same thing you are wanting to do: working full time as a data engineer and pursuing a Master's degree part-time in data analytics. It took me a very long time to find a program that was focused on BI or anything near that since it is still a relatively new field (new as in gaining traction in academia). Also, Business Intelligence is very wide, it encompasses a lot of different things. University College London (UCL) offers a part-time master's degree in Data Science which encompasses some BI stuff and more. If that's not exactly what you meant by "BI", then I would recommend searching for schools in London (or worldwide, in which case you'd be looking for online programs - which is also very possible) that offer a BI program, and then seeing if it can be part-time or not.


What college education could help an experienced executive climb the ladder?

If you have 14 years experience, academic achievements are almost irrelevant.

Instead, look at professional certifications, experience managing teams or projects, business achievements etc. as these are what others will look at.

You could go for an MBA - that could be appropriate at the level you are at, but it may not be worth the time and money to go through it. I looked at an MBA 15 years ago and it didn't have anything then that I couldn't get from other avenues. I have revisited the decision now I am looking at some more Director roles, and while it is a bit more tempting, it doesn't give me much for the time and money, whereas my professional certifications and board roles are much higher value to me.


Not publishing an author photo on Elsevier journals

ASK THE EDITOR prior to submission.

In practice, some Elsevier editors do accept the absense of a photo.

(That's all, folks; there is not much more to be said about it.)


My former post-doc host failed to credit my work in a paper - what to do?

First, please remember that human memory is fallible. People have honestly forgotten work done by their students or their postdocs or even themselves. So I'd be inclined to assume, unless there's evidence to the contrary, that your supervisor has forgotten your work on the broader concept Y that subsumes the "new" concept X, and that he hasn't had time to study the arXiv preprint that you sent him.
Second, what should you do about it? I think that, under the assumption that no malice was intended, you could write your former supervisor an email along the lines of "It seems to me that the concept X in your paper "[title]" is an instance of the general concept Y studied in my paper "[title]" [arXiv link] which I sent you a preprint of a while ago. I hope that my work on Y will be useful to you if you contiue to explore X." It seems to me that something like this should alert him to pay attention to Y and cite you in further work on X.  (Of course, you can put personal things like "I hope you are well" before and/or after the main message.)
I think you're unlikely to get a citation in the already published paper (unless it has an on-line version that gets updated), but if your supervisor produces more papers about X, you might get some citations in them.


What is the right way to patent an idea under PhD studies?

You should ask yourself why do you want a patent. You should only do if your goal is to commercialize the idea. Because patent is very expensive to file, and also expensive to maintain.

If money is not a problem, filing a patent is extremely simple. Here are some absurd patents. You only need a vague idea, no need implementation, evaluation etc. You don't need to be better than the state-of-the-art, you only need to be "different".

I'm a mediocre researcher who had never published more than 3 papers a year. More than 6 months in my current company, I already submitted 4 patents. Believe me, this is not what I want.

I said it is extremely simple because at my company, there is a team of lawyers that prepare the documents, and they also hire lawyers from another company. All I need to do is to present some slides. However, if I have to prepare these documents myself, I would not be able to do it.


How do you organise scientific articles with and without annotations?

Mendeley

This should cover nearly all your requirements -- with or without annotation.

Although my personal choice would be BibDesk (which I use nearly every day), Mendeley hits it for a cross-platform mobile-friendly experience.


Are Researchers at Private Companies Allowed to Publish Papers?

Speaking as a researcher at a private for-profit company, who also publishes frequently, it all depends on the nature of the business model and the position.

Most people at companies do not publish, either because the company has no interest in publishing or because their particular job doesn't involve much of scientific interest. For companies that are involved in cutting edge work, however, scientific publishing can gain credibility and visibility for the organization just like it does for people at universities. This is the case for the company I work for, particularly given that many of our projects are federally funded research where the government is paying us in part to disseminate knowledge.

Nor is there any necessary conflict between protecting intellectual property and publishing. The three main strategies for protecting IP are copyright, patent, and trade secret. Of those, only trade secret is incompatible with publishing, and it is generally the most fragile and least used in any case.

The biggest obstacle to publishing in private industry is simply priority and time. Writing a manuscript is a lot of work, and if management doesn't see much benefit, they will likely want you to use those hours for things more directly connected to the bottom line. You might be able to publish out of hours, but that can be a more complex negotiation.

Bottom line: it really depends on the particular circumstances. The best way to know if you will be able to publish is to look at whether others in the group you are joining publish. If so, you probably can. If not, there are likely major obstacles, whether formal or merely pragmatic.


What courses should be included as "Course Highlight" in Resume for Master's application?

I am in physics, not computer science, and things may vary by field. But in my experience, it's very unusual to see "course[work] highlights" in an undergraduate resume, unless you have taken courses that are (a) relevant to your application, and (b) not the typical required courses that every applicant has taken. In particular, this section is not about grades. If your grades are excellent, you should list your GPA (or "GPA in major") in the same section where you list your school, degree type, etc.


How to express an ongoing PhD degree in suffix

No, you cannot use a title or degree that you haven't earned yet.


Can I become a professor if I were expelled from the uni?

Yes, you can become a professor. Your expulsion (for unsatisfactory marks) seems equivalent to failing your degree. Failing a degree doesn't preclude becoming professor. But you'll (likely) need a degree to become one. (The definition of professor varies between countries.)
From comments:

[is] failing a degree...dishonourable...something [to] be ashamed of?

Failure isn't shameful nor disgraceful: A professor who hasn't failed, hasn't challenged themselves enough.

Do you think, as a professor, you have the right to keep it to yourself or be transparent?

In the immediate future, universities and employers will want to know why you dropped out, failed, were excluded, however you want to phrase it. Just be honest. Explain your situation. You were burning out, deteriorating mentally and physically, these aren't shameful/disgraceful events.
A professor (depending on definition) probably need never mention distant failures: In the future, historic details (even failing a degree) become irrelevant.


What do we know about working times of great living scientists?

This popular book http://www.amazon.com/Daily-Rituals-How-Artists-Work/dp/0307273601 contains precisely descriptions of working routines of various creative people, including several scientists and mathematicians.


Sending manuscript to a journal that rejected an earlier paper

This is perfectly legit. You are not forbidden to submit ever again to a journal that has rejected one of your earlier manuscripts. Indeed, rejections happen for everyone. It is best not to take them too badly.

Now, it would be a different story if you resubmitted the same paper that was previously rejected, or a version with only minor updates. Sending an entirely new manuscript, or a much more mature version, is unproblematic.

  Or is there going to be some bias because of earlier rejections ?

Important journals get many submissions, the majority of which they have to reject. I think it is very unlikely that the responsible editor even remembers that you already had a paper rejected a few years back. And even if (s)he does, it is unlikely that (s)he holds it against you. As I said, rejection is something that happens to every researcher, at least now and then.


I disagree with @Formite's answer. My perspective is mostly related to NSF grants and faculty applications, not NIH proposals, but it's very common and not at all bad for new faculty to have nothing to list for external support. Many people list their university start-up funds -- this is a good thing to do, since it shows university commitment. I think it would be seen as misleading to write down grants for which you weren't a PI, for example things that funded you as a graduate student or postdoc.


Gift for mentor after his thesis defense?

A short (1-2 paragraph) hand written note on a card or postcard would be an appropriate gift.

I have mentored about a dozen undergraduates and I still have the thank you notes they sent to me on my pin board in my office. The notes are nice reminders about the impact I had on the students.


Asking previous advisor for a better letter of reference

You can certainly ask, and might be successful, or not. It is impossible to say. But a better approach might be for the scholarship people to ask the professor for a better letter on your behalf, explaining the reasoning and perhaps the fact that his is an outlier.

Having an advocate may be more effective in a situation like this. Another professor might also prevail upon your advisor, but it would be impossible to hide the fact that you'd seen the letter.


How to write my name and my job description in a publication?

Write your affiliation similar to how you'll do it with a university.

  First Last [Designation,] Dept., Institution

If your hospital does not split members into departments, then Dept. part can be omitted.

Examples:

Aaron Stone
Neurosurgeon, XYZ Clinic

Cathy Miller
Researcher, Cancer Research Lab, BCD Hospital

Greg Thompson
Cryogenics, GHI Health Institute

Note that it is not always necessary to include your designation (job description), unless the publisher asks for it.


If it is truly an ordered list of funders and grant numbers, then there is no original idea that you are plagiarising. It is like reusing a list of affiliations in the author list. If you are describing how each person/funder/agency contributed, then there might be some originality in the statements and the exact contribution potentially changed between studies.


How do academics make money from applying their research?

I mean if I was a very smart researcher, and discovered something that no-one has known before, then first thing for me would be to create a company and sell it.

Come on, do you even think it is so easy for someone to start a company and start making money? The skills needed to make a product (corporate world) are different from those necessary to create an idea (academia). A simple well-thought out, well-exposited algorithm may bring plaudits in academia, but in the industry you need to implement the algorithm as a small part of a large system, subject it to rigorous testing, find people to market the product and suitable customers to buy, etc. And then there is the whole HR team which has to do its thing...

Patents are the way to go if you have to make money from a smart idea in the academia. (EDIT: Generally, both the University and the inventor share equitably the royalties and other income arising out of inventions developed under University auspices.)

Professors do engage themselves in collaborative work with the industry; at times, they are funded by the university for setting up small companies (see this question.). The lifestyles of people in the academia and the industry are vastly different; for one, professors have much more freedom with respect to timings than in the industry and afford greater time for their family - not a bad thing in exchange for money, after all.

Successful researchers in academia are unlikely to quibble about low income compared to people in the industry. Happiness versus money is a concave function - beyond a point, more money is unlikely to make one happier.


It is hard, if not impossible, to pre-empt accusations of plagiarism. The key is to be prepared to defend yourself. People rediscover stuff all the time. I would make sure that you keep all of your notes, drafts and any literature searches you may have done. I think keeping them privately would be fine, but if you really wanted to, you could make them publicly available in an archival manner to demonstrate that it is really your work.


How to acknowledge my professor who isn't helping much with my master's thesis?

You could get around it by thanking him for the opportunity to work in his lab and the chance to explore this particular avenue of research.

All at the same time, you can thank the PhD student for all the insightful chats and helping hands throughout the project which should be clear to the reader who was primarily advising you.


How often is transfer of Copyright to University required to submit PhD Thesis?

Without the copyright agreement in question, it's hard to be specific to your situation. Nevertheless, this sounds quite odd - while it could be the case, I think you've either misinterpreted it or left out a vital piece of information. In particular, the following, if correct, is extremely disconcerting:

  The copyright agreement, as written, seems to prevent them from publishing the work elsewhere after the work is submitted

This could potentially limit your ability to publish your thesis as academic journal articles after you've assigned the copyright (On the other hand, since these are rarely word-for-word from the thesis, you may still be OK. Ask a copyright lawyer.)

Typically, there is some transfer of rights from the student to the university, for a few reasons:

So that the university can keep a copy in the library, allow people to consult it, provide to other institutions via interlibrary lending systems
So that the university can provide a copy online, via their institutional digital repository
So that the university can provide the thesis, or details thereof, to external indexing systems and repositories (e.g. EThOS)

Typically, the student/supervisor can request temporary or permanent embargo of these rights if there's an appropriate justification. Some (non-exhaustive) examples:

To allow time for the preparation of journal articles/monographs from the work contained in the thesis
Releasing the thesis would violate third party copyright on material that is integral to the thesis
Releasing the thesis would create some risk to the supervisor, student, institution or a third party
Releasing the thesis violates confidentiality/non-disclosure agreements with a third party (e.g. an industrial research sponsor or interview subjects)

Finally, there may be specific restrictions on an individual's project (this is sort of covered by the last point above). Most commonly, these would be industrial/third party sponsors who own the IP generated in the project and don't want it republished for all the world to see.

I am wondering if you are confusing some other, specific, restriction for a general policy? For instance, if you have an industrial sponsor, you may have assigned the IP arising from your project to them. Although such an agreement would usually exclude the copyright on the thesis per se, it would include a confidentiality clause for the thesis because the other IP in the thesis (potential trade secrets or patentable IP) would belong to them.

Typically, you would expect to assign your university non-exclusive royalty-free rights to your thesis.


Is it a good practice to put the initial work and improved version (both published) in PhD thesis?

If you can connect the two methods as part of a broader narrative, then you can do so and maybe should. If the second approach entirely subsumes the first, and it doesn't benefit or motivate the discussion to show the original approach, then you can skip it. Sometimes the story is about telling a story, and sometimes it's just about the solution.


How should I consider a possibly rude reply from a potential PhD advisor?

He/she is probably very busy, and has repeated the same message probably N times.  Also, we all assume students will find the required information by themselves.  Nowadays, I find that students simply don't spend the time to look for information.  Their first instinct is to simply to message me, and hope that I will solve their problems for them; this is very similar to a kid asking their parents, can you please clean up after me? It is ok if you are 2 year old, but not OK after a certain age.
As for whether the professor should be a supervisor, you should look at whether he/she is successful in supervising students.  Yes, he/she may not entertain trivial questions and tell you off, but that may mean you need to work independently and at a high level.


Scimago (Scopus) or Journal Citations Report? Which one is more important?

JCR is easily the gold standard. It's the one that is used to calculate the impact factor, after all.
A heuristic is, the fewer journals are indexed, the more exclusive the index, and therefore the more prestigious.


Referee says the proof is wrong, but it is not, what to do?

While you might be able to appeal to the editor, once you've been rejected, you're probably not going to get a change in decision.  I would instead recommend focusing on a new submission to another journal.

Before you do so, however, I would strongly advise performing a major revision on your presentation of the proofs.  Assuming that your proofs are in fact correct, you clearly did not convey them in such a way that their correctness and significance were obvious to the reviewer.  The reviewer may have been a sloppy or shallow reader, but so in fact will be many of your other readers after publication.

In short, take the feedback as an indicator of how your paper needs to be improved before you submit it to another journal.


Do graduate programs concentrated on complex analysis exist?

Actually, check out CUNY Grad Center.  iirc, lots of faculty at CUNY list complex analysis as one of their research areas.


Main author might want to exclude me from the list of authors

If he's stopped responding to your emails and you don't know him personally, it could be very difficult for you to figure out where and when he may submit this paper, and without that information, you can't contact the publisher to explain your position. It may be wise to maintain records (ideally timestamped) of your email correspondence with him, and of your version of the paper.

If you have these artifacts saved, and you later see the paper without your name attached in a journal somewhere, then you can contact the publisher to explain the situation, and provide your timestamped records as evidence that the paper contains your intellectual property.

I would recommend continuing to try and contact the professor. If you're very concerned about them publishing without your name, you could email him and ask that if he publishes the paper, not to use the version you wrote, and not to attach your name to it (save any and all of this correspondence). In this case, you would lose the opportunity to be published, but you would also retain your intellectual property and refrain from having your name put on a paper published without your knowledge.


I believe the help page describes the current endorsement policy.  You may also have fallen into the category described by "We may give some people automatic endorsements based on topic, previous submissions, and academic affiliation."

As I understand it, most people are in that category and never see the endorsement system in action.  In practice, it seems to get applied to cranks and to people who look like they might possibly be cranks (e.g., people with no academic affiliation, or who are writing on controversial topics).


Do most customers choose predatory publishers knowingly?

There is some circumstantial evidence against the claim that most people who publish with predatory publishers are aware that they are not publishing with a regular scientific publisher.

Many authors of papers published in predatory journals are inexperienced with academic publication. From [1]:

  The majority of authors who publish in predatory journals have no other publications, whereas the second largest group consists of authors with fewer than five journal publications elsewhere; very few authors have published more than 10 articles. In contrast, the histogram reveals that group 2 authors, those who publish in OA journals that have a robust review process and subsequently rejected Bohannon's false submission, generally have a stronger publication record. With the exception of a few new authors, most group 2 authors have published journal articles previously; in fact, some authors have published more than 30 articles.

(Group-1 journals are open-access journals with low-quality or no peer review; group-2 journals are open-access journals that have more rigorous peer-review process than the journals in group 1. All are biomedical-science journals.)
Many prospective authors are unfamiliar with predatory journals and unaware of predatory practices in the academic publishing industry.

In a survey of 145 medical and veterinary science participants in a scientific writing workshop [2]:

  Thirty-four of 142 (23.9%) respondents were aware of the DOAJ; 7/143 (4.8%) were aware of Beall’s list, 33/143 (23.0%) were aware of the term “predatory journal”, and 24/142 (16.9%) were aware of the Science article about predatory journals.

In another (very small) survey of U.S.-based authors who published in criminal-justice journals on Beall’s list [3]:

  Just under half (44%; 4 respondents) of the respondents had heard of the “Scholarly Open Access List” and one-third of the respondents had heard of the term “Predatory Journal.” Furthermore, all but one of the respondents was not aware that they had published an article in a journal associated with the predatory journal list. One respondent questioned the accuracy of their association with a predatory journal, and stated

    … should not be on the list. They had more referees than any other journal I’ve pursued and I’m [the] author of 20 peer reviewed papers (sic).

References:

[1]: Xia J, Harmon JL, Connolly KG, Donnelly RM, Anderson MR, Howard HA. Who publishes in “predatory” journals?. Journal of the Association for Information Science and Technology. 2015 Jul 1;66(7):1406-17. DOI: 10.1002/asi.23265

[2]: Christopher MM, Young KM. Awareness of “Predatory” open-access journals among prospective veterinary and medical authors attending scientific writing workshops. Frontiers in Veterinary Science. 2015;2. DOI: 10.3389/fvets.2015.00022

[3]: Noga-Styron KE, Olivero JM, Britto S. Predatory Journals in the Criminal Justices Sciences: Getting our Cite on the Target. Journal of Criminal Justice Education. 2016 Jul 8:1-8. DOI: 10.1080/10511253.2016.1195421


How should I refer to my master's thesis in its text? A paper?

It's not a paper because this term usually denotes journal articles.

You can use the term thesis or the more generic work, instead.


Will there be consequences for not participating in ShutDownSTEM?

Will our disobedience lead to trouble later?

Anything is possible, and some things are a lot more possible these days than they were just a couple of months ago. It’s quite reasonable for you to be worried.
But let’s be clear. You didn’t “think it was a joke”. That is a poor way to explain your outlook and increases the chance that you will be criticized, perhaps harshly, by people who don’t have patience for nuance, facts, and the intricacies of human nature in these turbulent times. It’s probably more accurate and more productive to say that the whole thing was so unexpected and took you so much by surprise that you did not immediately appreciate how important the shutdownstem event was as a way of expressing your support for an important social movement. Thrown off, unsure what to do, and being a creature of habit and passionate about your work and its importance to science and to society, you ended up sticking with your usual routine. ... Right?
Similarly, I think it’s a mistake to use the word “disobedience” to frame your behavior. Researchers in US academia do not take orders from anyone about when or with whom to hold meetings. If you carefully read the emails you received I am sure you will discover that none of the stuff about canceling meetings and participating in the shutdown day is phrased as a directive. It was almost certainly a “suggestion” or “strong recommendation”, or you were “encouraged to participate”, “invited to reflect on systemic racism”, etc. And indeed I am confident that you reflected on many important issues that day (and most other days in the last couple of months), as pretty much everyone has been doing. Do not play into the hands of overzealous activists who presume to see into your heart and know what you care about and what you don’t care about by professing to a willful disobedience you are not guilty of. Instead, anyone criticizing you for not participating should be forced to acknowledge that the invitation to participate was precisely that - an invitation, making it entirely reasonable and acceptable to decline.
I could go on with a few similar things in your post that suggest a somewhat cavalier attitude that opens you up to a heightened level of scrutiny and criticism. Please try not to give anyone asking about the shutdown the impression that you find the recent nationwide events uninteresting, unimportant, or not worthy of being thought about or taken seriously. When you write things like “I purposely isolated myself from real-world news”, “reflect on ... something”, and “send them on their way” you sound dismissive and create a serious risk of being misunderstood. Since you support the cause of the activists, it would be foolish of them to come after you, but if by your words you give them the wrong impression, it’s quite possible that some of them will not be as thoughtful or charitable to you as they should be.
Bottom line: think defensively about this. Your actions were reasonable, but much could depend on the precise way in which you explain what happened if questioned. Also, find allies who know you and would be willing to come to your defense if push comes to shove. I hope it doesn’t come to that though, and it very well might not. Good luck!

Edit: note that I am posting here using my real identity. In such times when discussing potentially controversial topics I’m always cognizant of the possibility that in the process of offering advice to some anonymous person I never met I may be inadvertently opening myself up for potential attack or criticism by anyone who disagrees with what I wrote or interprets what I wrote in a different way than how I intended.
Oh well, it is what it is I guess. But just to clarify in case anyone gets the wrong idea about what I’m saying: in this answer I’m addressing OP’s concern about possible criticism and/or career damage given their actions during the recent STEM shutdown day of protest, and only that. I’m not commenting on any political movements or points of view and their significance, worthiness, virtue etc, so please do not interpret any of what I wrote as commentary of that type.


Should I reach out to my future advisor before accepting PhD admission?

Yes. If you're certain about the advisor you'll be working with, feel free to get in contact with them. Even if you change advisors before beginning the program - or even if you don't join that program - it will not hurt to introduce yourself and to start planning.


How important is it to tailor personal statements to different departments, in mathematics?

@RoboKaren's advice is good for many fields, and the basic point that you should know something about the departments you're applying to certainly applies in mathematics — you don't want to, for example, say it's your dream to study number theory in an application to a department which has no number theorists.  However, mathematics is extremely specialized, and incoming PhD students (in the US, at least) are not expected to have a very specific idea of what they will work on.  Most likely, you wouldn't even understand the abstract of your PhD thesis if you were to read it now.  This is true even for the exceptional few students who have done truly substantial undergraduate research; typically their PhD research is only very loosely related to it.

The implication of this for which schools you should apply to is that you should generally aim for departments which are strong in a broad spectrum of fields.  Fortunately, there are lots of them.

It's good to say something about your research interests in general terms, but the admission committee understands that by the time you start on your thesis they may have changed radically (say, from group theory to mathematical biology). If you yourself clearly don't understand that, it can create the impression that you don't know some basic things about how the field works.  (And of course you don't; you haven't even been to graduate school yet!  But nevertheless, you don't want to draw attention to that ignorance unnecessarily.)  Bringing up research interests is more important for demonstrating that you've been exposed to some substantial mathematics than for indicating why you're interested in a particular department.

So, to finally come to your actual question:

  I'm applying to math graduate programs at the moment. How important is it to tailor the personal statement to the different departments to which I'm applying?

Unless you've already discussed possible thesis topics with someone in the department — which is extremely rare in mathematics and not at all expected — I would say, not much.  Mentioning broad categories like "geometric analysis" is sufficient — again, as long as there actually are geometric analysts on the faculty!

All of this is intended as general advice for "typical" prospective PhD students in mathematics in the US (where "typical" includes even most successful applicants to top programs).  The exceptional few who have substantial research as undergraduates and want to continue in the same direction presumably have research mentors who can give them advice tailored to their personal situations.


How can I contact potential PhD advisors without jeopardizing my position in my current PhD program?

I don’t have an answer to the first part, but the only possible answer to the second part is to say something along the lines of:

  Due to unreconcilable personal issues, I’m unable to complete my PhD at the University of Stack Exchange. I have the highest regard for the faculty there and Professor Advisor was an excellent supervisor, but I could not continue to pursue my studies there. These issues would not interfere with my ability to pursue a PhD at the University of Overflow.

You shouldn’t lie and pretend there was some kind of problem with the university. I think that making it clear that you have no issue with the university and your professor is probably the best thing you can do to avoid accidentally starting any rumors or make it seem like you’re besmirching the old university. I think it’s important to simultaneously stress the the issues are personal and that they won’t follow you to your new location.

I do think that being forthright and honest, but vague, is your best approach. I would seriously recommend putting this in your statement of purpose as well. At the end of the day it’s never not going to occur to the people reading your application to ask, and you’re usually better off heading off and explaining obvious worries than letting them sit there in their mind.

I know someone who was sexually assaulted by a community member at his university and found himself in a similar position. This is along the lines of what he did.


Should I focus on my grades or on finishing my degree on time?

Usually there is a scheduled time and an expected number of credits for a degree. A BSc normally takes 4 years, with a given number of classes. This is because the ability to absorb the material in the allotted time is part of the evaluation of the student.

Ordinarily that is. But you mention health issues.

If you had some major life altering illness then it is something you should discuss with the university. I mean something like as serious as pneumonia. I had pneumonia a couple years ago. If it had happened in university it would certainly have cost me a term, maybe a full year.

Under such circumstances, and presuming you now have some kind of control of the situation, you should consider repeating either a term or a year, depending.

First talk to your favorite prof or your department chair. Ask if there is the possibility of repeating the year. Or possibly repeating only some of the classes. In most cases, they will want to help you. It looks good for them for you to perform well in the university. They will nearly always want to help you finish the degree.

Be open to their suggestions. They may have suggestions of alternatives.


How to tell professors I am not interested in working with them right now, but might want to, later?

You probably know your professors better than anyone on here, as you have interacted with them. Different people respond to rejection in different ways, and this can be a delicate matter.

However, you did note that the professors that you don't want to work with were all responsive to you, which may indicate that they are invested in students. In my experience, faculty who are invested in students want them to do well, and understand that students' research interests will not always perfectly mirror their research interests. Getting a Ph.D. is a long, difficult process, and your professors have gone through it themselves! Thus, they likely know the importance of selecting a research area/advisor that will work best for the student.

My personal advice: Be honest with the professors that you don't want to work with. Tell them that, while you are interested in their research topics/methods, you found a faculty member whose research interests are highly congruent with your personal interests and long-term career goals. You can also tell them that you feel scared that the other faculty member won't take you on, which could open the door for you to directly ask them if they are agreeable to you coming back to work with them, should your relationship with your first choice advisor not work out. Express your appreciation for their responsiveness and for them giving you a chance to work with them.

Some faculty may respond negatively to you, and they may view you as being unreliable or untrustworthy, since you are leaving the projects. I would hope that your faculty will be understanding, if you are able to be open about the situation.

Best of luck!


Frankly, I would suggest you just ask them. There is usually a contact at universities and similar whose role is student services or enrolment support or similar. They should be able to advise you on exactly what is required. Often there is even a dedicated officer for international students.

Taking an educated guess, it may be they require something like a letter of reference, written by a teacher of yours who can attest to your English proficiency, or perhaps academic results from some sort of English class, or an example of your skills, such as a document you have written.

Keep in mind that this is a general question written with the expectation that many applicants will not speak English as their first language. You don't need to prove you're the next Ernest Hemingway, just that you understand English to a sufficient degree that you will not struggle to understand your teachers.


I think the quality of your research depends a lot on the quality of your environment. If you publish a few good papers, you have a higher chance to find a postdoc in a strong group and publish even more good papers, which will improve the chance to find a faculty position. No one will ask how long your PhD took. If you get lucky with your first postdoc, in the sense that you keep publishing high quality work with them, you may not have to do a second, or you would get a very strong second position and then obtain a faculty position.

On the other hand, if your intention is to eventually find a job in industry, or you already have some great opportunity, finishing early is a good idea. The extra-year would only give you more time to do a proper job search in this case.


Software for personal remote monitoring of exams

I intend to use no such software, because it does not work (there are many ways to work around it, depending on its complexity), and it is incredibly invasive of student privacy (and the harder to circumvent it is, the more invasive it is).
When you ask students to take exams using software like this, you are asking them to:

invite a camera into their home
install invasive software that can take substantial control of their computer
subject themselves to continuous monitoring, either by a person (looking into their home!) or an AI system
if the monitoring is by an AI system, subject themselves to all of its errors and biases, running a nontrivial risk of being falsely flagged as cheating, especially if they are a racial minority, poor (so they have less space for the kind of 'clean' environment the software expects), in any way act in a way the system does not expect (e.g. does a student stare off into the corner when they are thinking? what will the system due with that change in eye contact?)
expose their computer to potential security vulnerabilities, because invasive software, that may be employing clever workarounds for operating system features designed to protect the user from software trying to exercise the level of control it demands, probably has some security vulnerabilities of its own

And all of this as a prerequisite for obtaining their education, and the students who want to cheat will find a way to do so anyway. All it accomplishes, in practice, is invading the privacy of honest students.
I believe it is better to structure assessments to disincentivize cheating and/or be robust to it, rather than to subject students to substantial privacy invasion and circumvention of their computers' security in order to try to prevent it.


How to write a decent report introduction on work you have created?

First and foremost, despite the conventional wisdom to the contrary, it's actually often entirely acceptable to write technical documents in the first person.  Unless you are specifically required to avoid it, it's OK.  Furthermore, even if you can't keep it, you can always start by writing in first person, and then transform to passive voice later.

From there, a good general skeleton of an introduction is sort of a "cone" funneling a reader towards more specific information:

What is the context for the work that you have done?
What was the goal for the work?
What exactly did you accomplish, and how can it be quantified and verified?
What are the implications of this work?

Finally, if a piece of work is genuinely simple, it's OK if the introduction is quite short.  I have written some reports whose introduction went on for many pages, and others that were a single paragraph, depending on what needed to be explained and in what detail.


Is it common to not send rejection letters?

Based on rumor, it is quite common not to send rejection letters at American universities.  I would expect that this happens at a substantially higher rate for undergraduate summer research programs because they have an exceptionally high ratio of applications to funding.  At many universities, the summer research programs are more competitive than the PhD programs but have zero administrative staff.  PhD programs, postdoctoral positions, and faculty positions also may not send rejections.  For some jobs, one will also find that nobody was hired at all.

Some Australian universities have an official no rejection letter policy.

I definitely recommend sending rejection letters, particularly if applicants paid an application fee.


How to proceed when reviewers reject your manuscript but you believe there is no scientific basis for their objections?

You can complain to the editor, but you should not expect too much from it. Remember that reviewers work for free, so unless there are a lot of complaints about one reviewer, the editor will not take action because the reviewer would just stop reviewing for this journal. Moreover the editor, who quite often is  also working for free, may not take your complaints seriously, or judge that your case is not important enough for him to invest some hours of work - remember that he has to read your article to judge your case.

So the easiest thing to do is to submit your paper somewhere else, there are plenty of possibilities. However, if it is rejected again, and you didn't aim at the best journals, you should think really hard about trying again. There are many articles that should not have been written.


How to apply Sigconf proceedings template to MS Word paper

The idea of that word file is that it already contains the correct layout for an article. You only need to change the text and overwrite what is in the word file, except for the formatting. Whenever you add new section headings and the like, make sure to copy the style from the previous section headings. The layout file already contains examples for many elements of a manuscript, such as figures, equations, and the like. Again, if you want to use equations, figures, and so on, you just copy them from the layout example file to your file and just change the content, without changing the style.
When you are done with your article, you perform the final steps mentioned in the "abstract" of the template, which appears to contain concrete instructions for this step.
Note that in many of the better conferences, rejection of papers positively correlates with the paper being written in Word. So many authors would use LaTeX right from the start to not give the first impression that the paper is a rejection candidate (in addition to other reasons for using LaTeX). Of course, reviewers should not care about this, but there may be a subconscious bias against your contribution because of the correlation.


Buying out of teaching duties vs. all duties using grant money

A university doesn't "obtain" funds through buyout -- rather, it frees up salary money that it would otherwise have to spend if the research funds were not in place.

What a university is allowed to do with such funds likely has to do with where the money came from.  In many cases, such funds will be unencumbered, and they can do whatever they want with them.

There are certain kinds of funds that might need to be used to support research, like (in theory) indirect funds from a granting agency.  "Support research" can have broad meaning, such as pay library staff, or keep the rooms where research goes on heated.

I'm not sure I understand the whole situation, the way you've expressed it, but it seems like it gives the university more freedom to creatively release people from responsibilities, and it doesn't set up any alarms for me.


Is simplified writing/accessible tone frowned upon in publications?

It depends on the intended audience.

There is no one rule for writing, academic paper or otherwise. You should always "mold" your content to the level of the average reader of the venue.

Think Nature versus Scientific American, for instance. While I often read SciAm as an undergrad, I didn't really understand most of the Nature articles I had to read recently, because they are dense and full of acronyms that don't mean anything for me. Am I stupid? Maybe, but surely I'm not part of the intended audience of these specific papers. Clearly, both venues are different, one is more technical, the other is focused on scientific dissemination in a broader level. Submitting a very technical paper to a dissemination venue would be a bad idea, and vice versa.

From personal experience, even between technical venues, there is a significant difference. For my research, I alternate between heavily mathematical theory and applications. When I send articles to the IEEE VIS (or TVCG), the reviewers mostly skip the mathematical parts and expect a very "digested", non-mathematical analysis of the results.

I recently sent an article to a more mathematical conference (ISMM), following somewhat the same format I usually use for VIS, with a more detailed mathematical section, but with the same "digested" analysis afterwards. While the mathematical part was accepted mostly as is, the analysis part was heavily criticized, for being "vague" and mathematically inaccurate. It was my fault, I didn't fully mold the content to the venue.

EDIT: Let me more clearly phrase my point: Sometimes reviewers will complain that the paper was too accessible. My example was exactly that, by aiming at a larger audience, writing in "digested" English, instead of harder to understand mathematical definitions, my text was "too vague"/"cryptic".


Should I list conference session chairmanship in CV?

The short answer is yes. Anything that can be considered meriting can (or should) be added to a CV in my opinion. I have a heading "Other meriting academic miissions" in my CV where I list things that I consider meriting but do not fit under other headings where the list is longer. this includes, invited talks, tenure evaluations, etc.

My strategy with my CV is to add everything into a "master CV" and then remove parts depending on the purpose of the CV. Therefore, add the meriting tasks you are asked to do. It is easy to remove them if they are irrelevant for the specific purpose.