Should I mention my interest in teaching in SOP and recommendation letter?

For a SOP, you may mention something about your desire to teach. However, I think at most higher-ranking economics departments, this would not be viewed as positively as having a strong research interest and agenda. You may gain a small benefit if the reader of the SOP gets the sense that you are a "team player" who will do a good job TAing and not make a fuss about it.

(I will note here that my advisor has told me that some faculty are extra  suspicious about investing effort when they hear too much discussion of teaching from a woman - they already think of women as being less serious about research because of biases and discussion of teaching by a woman can support their stereotypes. So note this if you are a woman.)

I would say that it is not inappropriate to talk to your recommenders about your desire to teach economics. However, I would tend to frame it as and interest IN ADDITION TO research. You can say, I really see myself ending up at an institution that combines teaching with research - what would you recommend I do at this point to make myself the most competitive for those types of places?


Maximum allowed time for PhD (Doktor) in Germany

The typical times for a PhD in Germany vary mostly between three and six years, depending on the specific field you're in.

Legally, the university is allowed to give you fixed-term contracts for a total maximum of six years while you're working towards your PhD. However, there are extensions of this limit for childcare, so you would be well below this limit.

For a postdoc position, I don't think the time taken for your PhD would be a major factor in evaluating your application.


Do some universities employ full-time TA in North America?

I'm aware of at least one R1 University in the US that allows some graduate students to be full time (100% equivalent appointment as a TA) during the summer, if they have no classes or other position, and if teaching needs require it. But in any case this was considered quite rare. My understanding was that the typical case was when the student was to be an instructor of record for a course, particularly one they designed or won a grant to develop, and usually they were also part of a teaching-preparation/certificate program. Even then the person would generally only hold such an appointment for one summer only.

At least in the US, part of the reason why this isn't more common is employment rules - a full-time teaching assistant would be a de facto employee of the University, and entitled to full rights and compensation for that time period, unlike the odd "not exactly just a student, not exactly an employee" category that graduate students possess in the US.

As GEdgar noted in comments, there are full-time people who are not full faculty in the US, but they are not called a TA (which is a title reserved for graduate students doing work part-time while also being a student); these people hold titles such as Instructor, Adjunct, etc.


Does a student need official permission to publish an independent research article with university affiliation?

First, check if your university has rules/policies/guidelines in place. If so, follow them.
Otherwise, use your university name as affiliation. No need to ask them. (Trust me, they are much more worried about people forgetting to use the affiliation, than the other way around!)


Do I have a chance to get into a great cs grad school?

Top PhD programs in Computer Science are very selective. Just having good or even excellent grades is not enough. At least, you need to have very strong recommendation letters and preferably some undergraduate research experience. I would suggest applying not only to top schools but also to second tier schools.


What value does self-learning a course (or several) have in graduate admissions?

Does it carry any importance? (to admissions)

Little to none.  Anyone can claim to have studied something independently.  If you want to increase your chances of admissions, you need to provide evidence that the admissions committee can easily check.  Your repository does not count.
You should, however, do sufficient self study that you are able to succeed in graduate school.  You may be required to complete graduate courses and to take qualifying exams; do start preparing for those things if they are applicable.
Successful research experience is more important; the purpose of a PhD is to do research.  If you have already done it, that is very convincing to an admissions committee.


Help me understand plagiarism concerning computer programming

As mentioned in my comment, this does not seem like plagiarism (as described here) - as no written material has been copied between the students.

Specifically:

  student "A" decides to help is class-mate and the other student "understands" the solution and implement the same

Student A tutored the other student. At the very most, student A could have been acknowledged, but really is not necessary.

  he discusses these steps with a "person who is good at coding". the person tells him the libraries to use and discussions(no coding) . He does all that and takes his help for "debug" "when he got stuck" and WRITES IN HIS OWN WORDS

This is also really tutoring.

Both are rather nice examples of sharing knowledge and skills.

It is probably a case that the students helping out did so because they are just simply happy to help.

One major thing to consider, these examples show classmates collaborating - drawing on each other's strengths. Each person in those interactions already benefit.  This is also touches on a transferable skill - collaborative work.

But whether or not the level of collaboration is within the rules there is another matter (but really should be checked).

Not everything needs to result in a person's name in lights. These are not really examples of plagiarism, but to be absolutely certain, it would not hurt to read up on the institution's plagiarism policies.


I forgot to add preprint submission (BioRxiv) before the actual journal submission, what can I do now?

You are being very careful, though inexperience, and this speaks to your good will. It is no big deal. Just submit the preprint and notify the journal, stating that preprint submission was done after journal submission. Most journals have a "contact" link in the "action menu" for your submission that will contact directly the person managing your submission. If you cannot find such a link, look for a "managing editor" rather than "editor in chief," and make sure to include your submission number in the communication.

I would also let your PI know. There should be no reason for them getting angry at you, and it will make you look good that you own your mistake and try to rectify promptly.


Would/could PIs hire a consulting company to do partial work that's not in his/her field

Do you exclusively mean non-academics? Sometimes a collaborator is included in another department or another academic institution to bring in such expertise. This can have it's downsides depending on which agency you are including since there may be costs to subcontracting or collaborating with another entity. It's possible that a Computer Scientist or Engineer down the hall or across campus has the student that can do the work without having to write in a professional contractor, though it is certainly possible to use a contractor. My wife works for a web firm and is currently responding to an RFP from a university to do user experience work for a web-based NSF project.


How to choose a topic for a PhD in organisational behaviour?

Find a supervisor

A supervisor will typically help you refine your PhD topic.
So the first step is to identify researchers in organisational behaviour in universities you are able to attend. It of course helps if you have an understanding of the area that you want to work in so that the supervisor can see the alignment with their research interests.

In general, organisational behaviour researchers go by a range of names and appear in a range of different departments.
Look beyond organisational behaviour to also examine areas like human resource management, management, and industrial/organisational psychology. You may find such people in management departments, business schools, I/O psychology programs, as well as a range other areas.

Get to know the literature

Read journal articles in the field to get a feel for what is current. Some of the highest impact journals related to organizational behaviour include:

Journal of Applied Psychology
Personnel Psychology
Academy of Management Journal
Academy of Management Review
Organizational Behavior and Human Decision Processes
Administrative Science Quarterly
Journal of Management
Journal of Organizational Behavior
Organizational Research Methods
Journal of Vocational Behavior

Attend major conferences to network and get to know what are the current issues.
Some of the biggest conferences are SIOP and Academy of Management in the United States.
However, there are many other conferences depending on your specific interests and where you are in the world. For example, Australia has an I/O psychology conference every two years.

Learn about practical problems

Organisational behaviour is an applied field. It aims to improve the performance and well-being of workers and organisations. So, it helps to learn about the practical problems that people in organisations are experiencing.

You can gain this experience in a range of ways. But in general its helpful to actually work or consult related to your area of interest. Talk to practitioners such as consultants, managers, and so on.


Printing a poster near a conference location at a cheap price

First off, avoid the print shop at any conference location, which is quite likely to be both overbooked and expensive.

Second, make sure to send your poster far enough ahead of time to avoid a potential last-minute rush (particularly at large conferences).

Finally, you can use Internet map sites (Google Maps, Apple Maps, etc.) to search for copy shops near the conference location, and call to find out their rates.


What are "fake", "shady", and/or "predatory" journals?

A "fake" or "shady" journal is a low-quality journal that does little or no quality control.

They are often called "predatory" because they prey on people who are under a lot of pressure to publish, charging high author fees for promises of quick publication. (Since they do little, if any, peer review, the time from submission of a paper to publication is often very quick in these journals).

They often engage in deceptive practices to make themselves appear legitimate, such as:

Pretending to be affiliated with a reputable professional society
Claiming an "impact factor" when they do not have one, or when they have an "impact factor" from some entity other than Thomson Reuters ISI
Listing important academics on their editorial board, when these people never agreed to serve in this capacity.

Publishing in one of these journals can be very damaging to your academic career. At best, it shows that you don't know what journals are considered reputable in your field; at worst, it makes you look like you are trying to "get" publications without doing the work required to publish in a reputable, high-quality journal.

An academic librarian named Jeffrey Beall kept a list of open-access journals and publishers that he considered to be "predatory." (The links are to archived versions of the pages).  His lists were quite well-known - you may hear people refer to "Beall's List" when talking about predatory journals.

Between the growth of open-access and the Internet making it possible for literally anyone to start a "journal," these "journals" have been popping up at an alarming rate. The NY Times even ran a story about it recently.


What is the significance of the overview slide in a presentation?

I often skip the overview slide in short talks. Instead, after giving motivation I simply say what the talk it is about: This talk will introduce you to Nutella, analyze its deliciousness, and compare it to peanut butter. Finally, we will talk about Nutella extensions - chunky Nutella, with chopped hazelnut.

In general, the overview slide allows the listeners to pace themselves, and understand where in the presentation you are.


Is there a standard way of referencing line numbers in a draft?

Use whatever protocol you like, but explain your protocol to the editor and authors.  For example, you could include something like the following (quoting from someone else's review of one of my own papers):

  Throughout this review, "p.5(17)" refers to line 17 on page 5.


Misrepresentation of credentials on LinkedIn

If you are sure he is a master student, you could report him on LinkedIn and give him a chance of repenting and stop misrepresenting being a masters student.

Because, if you report it on LinkedIn (there is a anonymous form for it ,kind of hidden, in their help menu - you have to login but the person you report never knows it was you), after you contest their credential, LinkedIn will ask them for a proof (most of the times), if they don't provide proof they are allowed to just remove and forget the content (yes, they can get caught and go free), but if they do prove it they can keep the information.

Or else, you could email the ombudsman of the department or university and take more formal (and probably harsher) attitude, because it probably goes against the university code of conduct/ethics.


Is there a difference in academic writing styles between engineering and women's studies?

CS and WS are each concerned with a different kinds of questions, and the language their respective practitioners use simply reflects this difference.

This is familiar to me, given that I've been on both sides of the divide (English Lit as an undergrad minor, cognitive science for my PhD). I got a glimpse of why it exists many years ago when I was in a course with a bunch of Lit Crit majors and we were discussing a certain poem by a certain contemporary poet. The Lit Crit people where pointing at a specific part of the poem and going "Is this an allegory for his lost love? Is this a metaphor for the senselessness of  war?", and so on. Then, in a youthful display of naivety, I said "hey, the guy who wrote this poem is still alive, why don't we try to get in contact with him and ask him what he means?". The lecturer leading the discussion looked at me very sternly and said "that is not the point".

That was very illuminating, I think. I'm sure that the poet in question had something specific in mind when he wrote the poem (and we'll never know what it was because he's dead by now), but the Lit Crit guys don't care about that. The intended meaning of the poem is irrelevant to them, what they care about is the meaning(s) that others might extract from the poem. In the same way, in the passages you quoted, the author doesn't care about the android in and of itself, but rather about how others feel about the existence and characteristics of the android, and how these feelings affect other feelings and beliefs we might have about related issues. That is what allows him/her to make judgments about fashion and other things.

In comparison, people in the sciences care about "objective truth" (for lack of a better term), not about how other people feel about stuff. If I write in a paper "stimulus A caused neurological response B (p < 0.01)", asking about the Marxist/feminist/whatever interpretation of this finding is about as pointless as trying to get to the "objective truth" underlying a piece of poetry.


At any point during studying, is it okay to just give up?

If you cram right up to the moment of the exam you will probably perform sub optimally. You will probably remember only what you studied last, not what you learned overall. Give your mind and body time to decompress before the exam. A day might be appropriate. Your mind won't quit working just because you aren't trying to drive it unmercifully.

In general, take regular breaks if you have a long study regimen such as for a qualifying exam. An hour or so every few hours. Use some physical activity to get your blood moving and to get  you breathing hard. Then you can return refreshed to study.

It isn't giving up. It is just using your capabilities more efficiently.

This sort of thing has been studied extensively.


How to add an accepted but not published paper to my CV?

Use the following entry in your publication list (with the correct titles etcetera swapped in, or course):
A. Mitoz: The essence of mathematics lies in an Painlevé property group. In: Proceedings of the International Conference of Computer Science 2021, to appear.


Are cover letters sent to referees and should you highlight the contribution of your paper in the cover letter?

It is also polite to write a cover letter, even if nobody asks for it. And the purpose is often to ease the process of finding the referees, so helping to do so by giving insights about the paper that cannot be write in the paper is a good thing.
If you mention potential referees, I guess it will not be sent to the chosen referees. Otherwise (in my experience) it is.
You don't have to praise your results in the cover letter. Just state shortly the results (say more than the abstract, less than the introduction). If you think that there are issues related to the paper, this is also the place to state them (conflict of interest, new way of considering something - which can hurt someone's feelings -, direct negative comment on related work, etc.). If you think that, because your paper is gap-bridging, you need reviewers from several fields, you should say it as well.


Where can I get graduate level "tutoring"?

I would contact the math department at your local university.

I would be prepared to pay them well, they have lots of responsibilities and demands on their time as it is and it can be quite a lot of work to work through an academic paper, not to mention the effort involved in compiling background material to essentially teach this material to someone else.

If I were a graduate student still, I wouldn't do it for less than around $75 an hour, because the time I would have to put in to give essentially 2 hours a week of this kind of tutoring would be closer to about 6 hours, so even then it starts to sound barely worth it.


Discouraged by advisor to take courses, is there a way to navigate through this situation?

Audit the courses that you like, i.e., take them without receiving a grade/credit for it. You might not even need to formally audit courses, most professors will let you informally audit them. But as mentioned by others, research takes priority.


Sending a full Transcript, or only a part?

I have just one advise: Be honest. Changing an official transcript to make you look better is not honest, and could get you into trouble.

Moreover, a semester without math does not necessarily look bad.


How to cite this quote "The whole is other than the sum of its parts" in an article

It sounds like you are effectively asking if it is OK to cite a secondary source, if the primary source is not able to be located or retrieved. This varies by publication style guides; for example, in IEEE secondary sources are (at least in theory) prohibited, though as far as I'm aware there are no Grand Inquisitors enforcing this rule, so if you do it I don't know that anyone would think that an adequate reason to suggest rejection of your paper...but I haven't tried it.

As you mention Psychology, I'll note that in APA format, the answer is: yes, it absolutely is OK to use secondary sources, so long as you keep them to a minimum. However, your use of the brackets makes me think you might be using an ACM/IEEE style, in which case you are not supposed to use secondary sources; either you find a primary source, or you simply do not cite it at all.

If ACM/IEEE is your style, I would tend to suggest you just say something along the lines of, "in the words of the Gestalt psychologist Kurt Koffka, the whole...". And then you just don't cite it, because it's clear you are using someone else's words, you don't have a primary source, and it would seem weird to me for a reviewer to object to there not being a citation to that unless your work absolutely depends on Kurt Koffka having said those words (which would make no sense in a field that uses ACM/IEEE).


Obviously, you need to see the contract, and preferably go over it with an attorney.  There may be a repayment agreement.  You don't know until you look.

As to whether you can leave this postdoc early, I recommend thinking about how public the info would be, and how your colleagues in your field would look at it if they knew about it.

Personally, I could never hold it against a postdoc if they left to grab a dream faculty position.  I imagine this happens with some regularity.  That said, I would personally think less of a person that accepted a two-year position with the secret intent of leaving after a year. An institution is making an investment in you, and you would be letting them down.  I would think of it as you entering an agreement in poor faith.

Needing to relocate for personal reasons after a year is a decision that only you can make. If it's important to you, you might consider honestly discussing your situation with the manager of whatever program you're involved with before you sign on the bottom line.  It may be fine with them.  They might even be amenable to some form of telecommuting! If you choose to do this, you should do it knowing that a revocation of the offer is a real possibility.


Does it look better on graduate school applications if I'm getting a M.S.?

I'd have to sacrifice some courses outside of math (like english, history, etc.) in order to take more graduate math classes (need 8 total).

In general more math or related courses instead of non-related courses would support your application better. For some context, these mandated non-degree courses are not globally agreed to be necessary. For example a 4-year math degree in US can have less content in math then a 3-year math degree in Germany. Essentially some degree programs can have "bloat" approximating around or above of 1 year work (8 to 12 courses). It is not at all obvious that these courses in necessary (as they are not mandated in a lot of places) and I have never ever seen any admission body / personal being even remotely interested in the existence or non-existence of a -very basic introductory to a discipline of humanities-.


Pedagogical advantages:

It is much easier to catch misunderstandings early and thus "rescue" an answer. After all, bad exam questions aren't that rare (bad as in: if the student has a very good understanding of the subject, they may be able to guess what topic the examiner has in mind).
Misconceptions can be corrected: while a written exam gives a snapshot of what the student understood or not, in an oral exam the examiner can ask the student to think again if the answer is wrong. Or can give a counterexample that takes into account the student's answer
In the end, an oral exam can be a discourse on a subject, which IMHO allows for better/easier grading.
Related: the difficulty can be adjusted during the exam according to how much the student knows.
Many oral exams I had had a "mixed" approach for deciding how deep into each subject to go: often 2 subjects were covered in depth (one by choice of the student, one by choice of the examiner) and a number of other topics touched. Particularly letting the student choose a subject of their liking (usually as the beginning of the exam) is not possible with written exams.

Practical consideration:

if only few students are to be examined, oral exams take much less time for the examiner.

Disadvantage:

If the examiner is somewhat off in estimating the difficulty of their questions, a written exam at least has the same questions for every student.


Any pointers for reading articles digitally (on screen)?

I have terrible eyes and this is a very real problem for me. Although I'm not an eye care specialist I can say anecdotally that there are a few things that have really made all the difference for me.

First: if you wear glasses, get the computer lenses. Usually they are some kind of an off yellow to cut glare. These really help to reduce eye strain.

Second: look away from the screen every few minutes. Try to focus on objects away from the screen that let you change your focal distance. I find that doing this for just a few moments at the end of every paragraph really helps.

EDIT: Use natural light if you can. I've found that turning my desk so that the ambient light from the window illuminates my screen has also helped me a lot. You have to be careful of glare but when I finally got everything situated it made a notable difference.

Third: media counts a lot. If you're going to use a tablet or eReader look for something that has front/side lighting. Many people like the new Kindle paperwhite but I prefer the Kobo glo. If you're looking for a more stationary solution then I highly recommend a good projector. Prices have come down quite a bit and you can now get an 'OK' projector for just a couple of hundred dollars. It will take a little bit to acclimate yourself to the new reading format but once you do I think you'll find that you like it.  I know that I do.


How to request a positive reference letter from my former PI who does not know me very well?

So, as suggested I'll try to expand a bit my comment. I will assume you did a good job in your work and that the reference you would receive from who actually supervised you will be strong.

In my opinion, you can ask for two recommendation letters. One from who actually supervised you, i.e. the Research Scientist.
The second, from the PI, as you feel this might help you. In the end, you formally worked for them, so it would also be strange not to have a letter from them.

I think they will gladly accept and can write a nice one even if they don't know you that well, but if you feel it's necessary you could suggest they consult with who actually followed your work, i.e. the Research Scientist, to have a better idea of your skills. I would mention this to the Research Scientist when you tell them about the letter, something like "I will also tell the PI to write one for me, but they might ask you some tip on what to write, if that's not a problem".

Good luck on the admission!


How should I cite a conjecture to which no written record can be found?

"Which of these are most widely accepted?" sounds like you're asking a poll-type question, which is not quite kosher for this site.  I believe that the situation is sufficiently unusual that there is no "standard" answer.  Nevertheless I will say what I think.

First of all I want to express some skepticism of the premise that the information that Conjecture (C) was made by famous, long-deceased professor E is an important to the extent that the work of the paper would be less interesting without it.  If Conjecture (C) had been well known to the community and many other people had worked on it and/or written about it, then its provenance would be key information: those who knew about the conjecture would make a clear audience for the paper and would vouch for the prestige and value of the work.  But if no one  -- or almost no one -- except S has prior familiarity with Conjecture (C), then the information that it is due to professor E becomes more of a piece of trivia / personal motivation for professor X.  If the provenance of the conjecture had really been a key motivation for X, then one wonders why X did not verify this before working on the problem.

Second I want to say that I think you are using "knows for a fact" in a way different from the way I would use it.  If S is "sure" about the provenance of the conjecture because he saw it in print once but now cannot locate that printed source -- then actually he is not sure, I would say.  Often someone thinks they saw a certain piece of information in print, but when they go back to check it turns out they did not remember it accurately.  In fact probably every working academic has had this experience more than once.  I'm sure S is great, but "S says it, and S can be relied upon" is not really convincing to me no matter who S is.  In a professional context, the things that one is "sure" about should be verifiable: if E is a famous mathematician, then it should be possible to get a comprehensive list of their publications, and then with sufficient effort one can look through all of them, including "obscure conference proceedings".

The way I would handle the situation is by first corresponding with S and making sure that S is completely comfortable with being attributed the claim that Conjecture (C) was first made by E: if this gets published, then S may get asked some questions about this.  If they are not comfortable I would go with something more mild like mentioning S in the acknowledgments.  If on the other hand S really insists that Conjecture (C) is due to E, then that is what X knows and X can put that in the paper in that form, i.e., something like

  Conjecture (C) was conveyed to me by S.  According to Professor S, the Conjecture was first made in a paper of E.  Unfortunately we have not been able to track down a reference."

I would also be prepared to get some questions about this from the editor or referee when you submit the paper.

Finally: have you asked about this on MathOverflow?  This would be a very appropriate question on that site: if the paper exists then someone ought to know how to find it, though you may not know nor even know how to find that person.  Even if the question does not get answered in this way, you (or X) can still point to it as proof of your due diligence in the matter.


Where to add citation when having several paragraphs from the same source(s)?

When you have such a substantial chunk of information attributable to one source it can be useful to start the text by simply declaring the source. This can be done in the following way (exact formulation can of course be changed; I chose Harvard style referencing as an example):

  The following [x] paragraphs follow Name (yyyy) unless stated otherwise.

The formulation can be changed to better blend in with the text by adding details about what the information is about  or why this source is good or should be repeated, or both. The "unless stated otherwise" can be omitted if you have no need to add other references in these paragraphs; I added it for completeness.


How to handle an advisor who communicates badly and puts me in a bad position as a result?

As an advisor who often thinks I'm giving clear instructions when I'm not :), here's one thing that will require a certain amount of pain, but might help long term.

You might have tried this already, but when you're given somewhat vague instructions by your advisor, try to spell them out as precisely as you're able to and repeat them back to him on the spot.

So your advisor says, "maybe you should try (vague idea) X, Y, Z".

You  say, "so you mean that for (vague idea) X I should try A, B, ??".

Your advisor might say, "no no, I really meant D" while frowning fiercely at you. But at least then you've managed to get something precise out of him.

Or (and this has happened to me), your advisor says "Hmm. you're right: X doesn't make any sense: ignore that". In which case you've successfully eliminated one unclear option.

The "pain" here is that your first few meetings might go quite badly while you both struggle to learn to communicate with each other. But I suspect that if your advisor is merely not thinking carefully enough about the ideas he's suggesting, this will force him to think more clearly about them.


Should all computer science courses from a reputable university contain programming?

No, computer science is much more than just programming. That's what makes it science.

Introductory CS course tend to focus on programming, but as you get deeper into the subject programming becomes less central. Thus many (maybe even most) graduate-level CS courses at top universities do not involve programming at all. (Of course, graduate courses on systems or security will still involve programming, but it's no longer universal.)

By the same token, assembly code, digital circuits, and semiconductor physics are all vital to how computers work in practice, but we don't expect those to be a ubiquitous part of computer science education. We are able to abstract away from the implementation details of how our Python script gets executed. Likewise, more advanced topics in computer science will abstract away from the practical aspects of computing.

For example, course in computability and/or complexity theory is unlikely to contain programming aspects. The reason being that these subjects focus on what is impossible to compute and such impossibilities do not depend on what programming language you use or how good you are at debugging. That is, these scientific questions require you to think more abstractly. Similarly an advanced algorithms course may avoid programming assignments because (i) it's assumed (i.e. is a prerequisite) that the students could in principle implement the algorithms and (ii) the algorithms are complex and it would take a lot of time to implement them with little pedagogical value.


Can an algorithm tested only on artificial data be accepted in a high rank conference?

But yet i couldn't find any real data to evaluate the algorithm on real problems.

There exist a good site on benchmark datasets in machine learning,  uci machine learning repository that you can use these datasets as well as the artificial tested data.

  So i was wondering if an algorithm with good mathematical support but no evaluation on real data has any chance to get accepted in computer science conferences like SDM or CVPR?

The answer is yes if your approach is backed by theoretical support. On validation of attained results, you should provide intuition about how your proposed approach works on a class of problems via the theoretical results if you have such ones'.


When are authors on publications in Google Scholar clickable

Some authors have published their Google Scholar profiles and other authors have not.  If you click on an author's name and the author has a profile, then you'll see that author's profile information.

You might think that Google Scholar would show you the list of all publications by authors with that same name, but there are so many name duplications that this isn't done.

If you have a public author profile, then it should be possible for anyone who accesses one of your publications to click on your name and get to that public profile.


What qualifies a paper/dissertation to received the status 'published'

The exact meaning of the word "publication" is dependent on context.  In some contexts, it might be understood to include only articles accepted in peer-reviewed journals or conference proceedings.  (Impact factor is not usually a consideration here.)  In other contexts, it might also include books, dissertations, lecture notes, arXiv preprints, and other documents that have been made publicly available.

So whether a dissertation should be "named as a published paper" depends on your audience.

For academic CVs, people often create two sections: one that lists peer-reviewed publications, and another that lists non-peer-reviewed writings.  This removes any ambiguity.  A master's dissertation would go in the non-peer-reviewed section.

If you are writing a resume for the business world, standards might be different.  http://workplace.stackexchange.com might be a better place to ask about that situation.


Would my paper be published if I missed the conference due to visa-related problems?

To be part of the proceedings, the paper needs to be presented at the conference.

I have seen two cases where the paper was presented despite physical absence of the authors. In the first case, the paper was presented by one of the authors via a Skype call. In the second case, a befriended researcher of the authors gave the presentation.


Is it plagiarism to copy-paste part of a figure from a cited work?

Yes, copying an image from another work without crediting that work is plagiarism. You may want to contact the editor and ask him how to proceed.


Paper in high impact journal duplicates work done a decade prior, how should I respond?

This is a very opinion-based answer, but ...

  What is the protocol for this situation?

Letting it go.

You say that the paper got published in a high-impact journal 4 years ago. It reproduces results from another well-known paper. It is pretty much guaranteed that you are not the first person to notice that. It seems unlikely to me that the paper is indeed perceived as "suspect and unethical" by your peers.

Maybe your peers value the "more concise" write-up? Maybe there is a subtle difference that you have not noticed? Maybe, for some types of (empirical) papers, having a reproduction paper that basically just confirms that the observations from the first paper are indeed general is a really valuable contribution (although not citing the first paper is of course very bad in this case).

If you feel the case is indeed bad enough that something needs to be done, you have two options:

Mail the authors of the first paper.
Mail the EIC of the journal.

However, realistically, the chance of retracting the paper based on a years-delayed decision that the contribution was not novel seems very small, as long as there was no clear case of unethical behavior or a significant technical problem with the results.


How to research about professors wisely?

Does that mean that I need to spend time to dig into their papers (actually beyond the internet), or just reading the descriptions in their website is enough?

I strongly suggest you at least look over 2 to 3 recent, important papers of this professor. Not only will this allow you to write a mail that has a higher chance of being taken seriously, it will also inform you whether this kind of research is actually what you want to be doing for the next few years. This will indeed take time, but frankly, you should be willing to spend one or two hours to look over the work of a professor that you consider working with for your PhD. You don't need to read their papers end to end. Just figure out what research problems they work on, what methods they use, and so on.

  I cannot only concentrate on some particular professors, I need to increase the chance of being accepted by, erm, spamming other ones.

Here's the thing: for me, if your mail even remotely looks like you have been spamming professors with applications, your mail moves directly to my "Will never be answered" mailbox. Seriously. I have a keyboard shortcut for that. I assume similar things are also true for most other people in PI-y positions. Avoid spamming people at all costs.

Edit:
I will answer Ooker's follow-up questions here as they seem related enough to me.

  "How likely is a professor to ignore an email even when the sender does their homework?"

Very likely. Cold mailing somebody about a position is always a long shot. The difference between doing your homework and spamming, from personal experience, is that the former has a small chance of success while the second seems completely pointless to me.

  "How many professors should I contact in order to find the best one?"

I am not sure I understand. Given that your success rate with cold mails will be very small anyway, you (a) need to have a fallback plan anyway (this can't be your primary strategy to get into grad school, right?), and (b) it seems rather unlikely that you will have multiple offers that you then need to choose from.


Is it wise to resubmit a substantially revised version of my writing sample that has already been submitted for phd applications review?

One of three things will happen, depending on how far past the deadline you are and on the application management system used:

The graduate school will reject it without forwarding it to the departmental admissions committee. See Plan B below.
It'll be forwarded as supplementary information rather than replacing the original writing sample. Some faculty will see it, some won't get that far in your file since these are usually last in the packet.
It'll replace your original sample.

You don't have much to lose, so why not send it in and see?

-=-=-=

PLAN B

If the graduate school rejects your submission AND you've already been corresponding with a faculty member who would likely be your advisor AND those interactions have been positive, then you could suggest to that person that you could provide them a revised sample to share with other faculty.

If I were that faculty member AND if I thought your candidacy were strong AND my departmental and university regulations did not forbid out of channel submissions, then I might accept it that way.

A lot of ifs with Plan B.


After my PhD supervisor left, I was assigned to a new PI who has little experience in my area

I don't understand why this sentence has the word "but":

  Once in a while X is talking to me through skype but now X seems to be mainly interested in authorship of the work we have done together and also a project we planned to do.

Without the "but," that would sound great!

In principle, your choices are:

Transfer to X's new institution
Stay where you are but continue collaborating remotely with X (with lots of email and some occasional phone calls and video conferences).
Allow yourself some travel to where X is for some in-person collaboration (this has to be done with consideration for X's schedule and preferences, of course).
Talk to the department head and ask for advice.
Talk to someone else in your department and ask for advice.

Another thing you can do is basically choose option 2 (and perhaps 3), but try to be more independent than before, so that you don't need to take up so much of X's time.  Here are a couple of tricks for doing that:

Have a dialogue with X in your mind, where you lay out a question, and then you imagine the discussion that would ensue with X, based on what you know of X.  This works best when you're almost asleep.
Rubber duck your problem with a good listener, as programmers do when they're having trouble finding a bug.  Walk the listener through the background to your question, and the question itself.  Often, going through this careful exposition with a human being who at least looks like he's paying attention will get you unstuck.


How to tell a faculty member that I don't need him on my thesis committee anymore?

I think you're making a bigger deal about this than necessary.  You enlisted Professor A to serve on your committee because you needed a fifth man, not because of any close research connection.  More recently, but still before signing any paperwork, you found Professor B, who does have a close research connection.

Just tell Professor A that!  Problem solved.  You don't have to dither about how to present this information: send it in an email or send it in person.  The information of the previous paragraph is sufficient: you don't need to dwell on your connection with Professor A as much as you did in your question.  (But by the way: asking about your progress at the copy machine is what I would call "friendly".  At least he knows who you are and something about your progress in the program, and he cares enough to ask about it sometimes.  That puts him ahead of the curve in many academic departments at many universities.)

What you do not seem to realize is that if Professor A has no close connection with your work, it is overwhelmingly likely that he was being friendly indeed by volunteering to serve on your committee anyway, and he'll be equally happy or, more probably, a little happier not to serve.  Since he is a senior tenured professor he has lots of stuff to do.  Serving as the fifth man on a student's committee is not nearly such a prestige job that his layoff needs to be sugarcoated.  He'll understand, and he'll be especially happy that someone with more relevant expertise will be taking his place.


Contacting professor for PhD in different research area than past experience: do I need to prepare a research proposal before first contact?

the answer depends a bit on the culture of your country and even on the individual professor you are adressing. If you would contact me, sending an e-mail containing more or less the question posted would be sufficient to get an invitation to talk about potential research topics and about how to proceed.

At least in my position, the answer is more dependent on whether I have an idea on how to finance your position - so if you have ideas about this (grants, ...), you should include such information.


Difference between private and public universities as a faculty member?

A few anecdotal observations. It must be said that these are trends, and exceptions to everything I say are plentiful.

As just-learning said, private universities tend to pay a little better. Also, they seem to have less faculty turnover (perhaps for this reason).
Public universities often have more BS committee work. For example, my university periodically mandates a lengthy process of "post-tenure review". Negative or positive reviews have no consequences, and therefore the process is a complete waste of time, but we have no choice.
At least among top-notch research universities, public schools are usually large, and many private schools are small. Large schools typically have advantages (big seminars, lots of courses that can be offered to students, etc.) and disadvantages (lots of grading, people can feel lost in the crowd, etc.)
A corollary to the above: public universities often influence their towns more, simply because there are more people working and studying at the university. For example UNC-Chapel Hill and Duke are excellent universities (public and private respectively) which are ten miles apart, and it is Chapel Hill that has the really outstanding K-12 school system.
Especially at public universities, there might be many clubs which are largely student organizations, but faculty members and others also participate in. Especially if you are not yet inclined to "settle down", this could be a huge positive.
The campuses tend to be different. Many private universities are surrounded by lush greenery, where at public universities it is more common that you can walk across the street and get something good to eat.
Sports culture is more prevalent at public universities (although it is also very big at many private universities). I am a bit of a curmudgeon, annoyed at the overwhelming football culture at my school. But those more laid back than me simply enjoy the games.
Student attitudes tend to be different. At wealthy private universities many of the students will be more optimistic, and more ambitious goals and dreams seem to be more common. The downside (from what I have heard) is that entitlement and grade-grubbing are also more common.
Public universities serve the public. My university enrolls a number of students from disadvantaged backgrounds, many of whom are the first in their families to attend college. I attended a graduation ceremony, and when many names were called there was a palpable and obvious joy on the part of large crowds in the audience supporting them. Witnessing this was a deeply moving experience.


Should you write university names out in full, or use the common abbreviation?

When the abbreviation is actually better known than the full name, go with the abbreviation. Otherwise, use the full name. That will render the last option you proposed (though it would be fine to write TU Munich as well).


How should I reference the institution in my grad school applications if I went to a satellite campus?

If the rules and regulations are the same at both campuses, I doubt that you need to make a distinction. This is especially true if you would have been welcome to take classes at either campus without distinction.
But the university has an official name. If the satellite campus has a different official name you could, and maybe should, use that. But the "expanded" name may just be a geographic signifier without any official distinction other than geography. But you can ask the university for advice, of course.
My former university has several campuses in various cities in the same geographic region of the state. There is no distinction in the degrees offered and it is the university as a whole that grants them. The diploma shows no distinction. Is that the case at your institution?


Lecturer giving automatic top mark to the first person to submit

This type of marking is a clear deviation from every set of marking guidelines I have ever seen. Intentionally introducing procedural irregularities is something that can get faculty in trouble. This is something that can and should be brought up to the director of teaching. If that fails you can talk to someone in the student union. You could also get in touch with the external examiners when they come to visit.

It is unlikely the director of teaching would reveal your name when discussing this with the lecturer. If you are really worried, drop a note in the DoT's mailbox with the module number, lecturer's name, and a description of the problem. The behaviour is easily verified so the DoT does not need your name to follow up. The problem with being anonymous is you will not know what happened.


Non-confidential student suppport letter for a teaching award

I can't see into the minds of the judges responsible for the award, but such letters might well be discounted. The problem is the possibility that the students were actually writing to solicit favors from you in the future - trying to "get on your good side". Actually, it is the perception that they might be trying to get some future favor.

You might suggest to the writers that they send letters directly.

In any case, the direct answer to whether confidential letters might hold more weight is yes, they might.

But if there are a combination of letters sent confidentially and not and they are consistent, then I doubt it would be a problem.

But IANAMR (I am nor a mind reader).


How should one select his or her citations when writing a thesis in STEM?

The general answer to all your questions is to ask your thesis advisor. (S)he will definitely be able to tell you what the customs for theses in your field, and in your university, are.

That being said, I had the impression that you may have some misconceptions about why, and how, we use citations in academic texts. Specifically, you claim that:

  There seems to be no guideline or rule to selecting citations.

I would argue that this is because one does not "select" citations as such. Rather, the literature that your thesis cites should emerge from the text you are writing. You build a scientific argument and then, at the appropriate points in the text, refer back the original text whenever you use a pre-existing piece of knowledge. Sometimes this pre-existing knowledge may be standard enough that a textbook is a good source, but it is not uncommon that you will need to refer to original research papers.

If those papers have been cited often or rarely so far is not the right question to ask. Instead, if your argument requires that X is true, you find the original paper that proves X. You don't cite a different paper that also somehow uses X because it is more often cited. If you are not aware of any research that actually showed X, you have a different problem - why can you reliably assume X to be the case in your thesis anyway? Your current approach of writing down results and then worrying about what to cite for them seems a little backwards to me.

  All in all I will probably have over 80 citations. Is this too much?

"How many references should I have?" is really the wrong question to ask. You use as many as you need. That being said, if you have very few citations of previous work in a thesis it is usually a bit worrying, as a lack of citations often indicates that a student is not aware of the scientific state of the art or, even worse, of good citation practices. Conversely, citing many previous works is not usually a problem for theses. Of course some upper bounds exist in practice, but 80 citations seems nowhere close to excessive even for a master's thesis. Note that mathematical texts tend to have fewer citations than other STEM fields, so this may have biased your expectations when looking through the literature.


Why are operations research departments usually separate from mathematics departments?

Choose from : history, habit, snobbery, tribalism ...

There is no logical reason for one choice of departmental structure over another. Just look at how often universities change their departmental structures.

If you bring some groups of people together in a named department then you are excluding other people whose work does in fact have a lot in common with the first group. Departmental structures are always compromises.

Most academics see the benefit of interdisciplinary work, but universities, on the whole, like the apparent orderliness of clear departmental structures.

As to the specifics of operational research: its history was in dealing with urgent practical problems in wartime. Its practitioners were applying mathematics, but were not pure mathematicians. Neither were they what many universities described as applied mathematicians, although in the natural meaning of the words they were, of course, applied mathematicians.

When I took a master's degree in OR in the 1970s, I was in the faculty of engineering. A very few years later, I would have been in the business school of the same university (with the same teachers).


Avoiding the double effort of academic research and marketable job skills as a math PhD

A math PhD will teach you a large number of completely marketable, industry-ready skills:

how to think logically and analytically

how to research challenging technical topics on your own, solve problems, and pursue difficult goals over an extended period of time, overcoming frustration and maintaining a good level of motivation

how to communicate your ideas effectively, in writing and in person (in particular, if you gain teaching experience while doing your PhD your presentation skills will end up orders of magnitude better than those of your peers who went into industry straight out of college)

and many other “soft” skills that are difficult to quantify and describe but are nonetheless extremely useful and important.

All of these things add up to a very attractive package for employers. It’s easy to focus on the “esoteric math” part of a PhD and conclude that it’s a “waste”. Will an industry job give you an opportunity to use your knowledge of Schur’s lemma or Brouwer’s fixed point theorem, or show off your familiarity with Radon-Nikodym derivatives? Probably not. But that doesn’t mean you will have wasted your efforts learning those things. Along the way, you will have learned to look at the world like a mathematician, and that, as it happens, is a darn useful skill almost anywhere you go.


Postdoc Letter of recommendation same school or different school

Opinion only.
I think the primary goal is to have the strongest possible letters. So I would opt for a very good local letter over an alright one from somewhere else. Only if the recommendations were similar would the geography matter for me.
You might be able to work your connection to the other writer into your cover letter.


Is using Mendeley to organize my files a good idea?

I've personally used this feature, and I really like it - though honestly, part of the value I get from Mendeley is that I stop worrying about my files and folders and just use the software itself most of the time. As I have it sync them up I'm not even really concerned with where it stores them any more.

My recommendation is just to copy-paste your directory of files to a separate area "just in case", then fire away. File naming is (was) a pet peeve of mine, and I really like to have the files nicely named so I can search them - then I usually also sync that folder to Google Drive so I can access my documents anywhere (phone, guest account, etc).

It's a useful and nice feature, but honestly I found less value from it than I expected precisely as I began using Mendeley more. I still use the feature, but the other things the program does make it almost redundant - but still nice and I'm glad its there.


Is it possible for an individual's TOEFL score to decrease between exams?

It is possible.

As an International student, I have taken TOEFL 4 times in one and a half year. Personally, I increased my score in every section at every exam.

However, it does not suggest you will always improve your score. The reason is simple. Assume you do not spend time on learning English regularly between two exams. In fact, your score is a random variable with constant mean and variance. You may have got 28 in reading last time and 26 next time.

If you spend a lot of time on improving English skills, you may still get a lower score in writing and speaking sections. For those secitons you can apply for rescoring service.


Absent a formal policy, is it rude to use a mobile phone to take notes in lectures and seminars?

Phones are not perceived as note-taking tools, making them undesirable in education and business settings. Laptops are tolerated in both settings, but don't expect respect. Tablets are perhaps the lesser-evil, especially when used with a stylus. Better still, specialised note-taking devices (not dissimilar to tablets) are now available. Paper will serve you well and set the best impression.


Add Everything to my Annotated Bibliography

I think it is somewhat misrepresenting the concept to call it an "annotated bibliography". That term suggests something formal, organized according to a specific, prescribed structure, but really all you're doing is organizing the resources you've encountered along with any thoughts you may have on them. The resulting compilation of information is for your use only, and so you should organize it in whatever way you find most effective. I do suggest using a reference manager, since it takes a lot of the tedious work out of organizing your information, but if you honestly find a Bibtex file or note cards or stacks of paper on your desk to be better for you, by all means, go for it.

Whatever organization you use, it should have a few key features:

Starting from your notes on a paper (or other source), you should be able to easily retrieve the information needed to cite that paper.
And the other way around: starting from a paper's citation, you should be able to easily retrieve any notes you may have for that paper.
Notes should be searchable, meaning that if you remember making a note about some topic or idea, but you don't remember which reference it was attached to, you should be able to find it (the reference) without too much trouble. This probably limits you to some sort of digital database, unless you have a pretty good memory.
You should be able to access the full text of a paper that you've read, given the citation information. If your citation information is complete, this is satisfied by the ability to go on the internet and download the paper.

A bonus feature, not really essential, is the ability to share your notes on a paper with others. Some social reference managers enable doing this over the internet, or try to (assuming your collaborators also use the service), but it's more frequently accomplished by conversations in the hallway.


Is it realistic to apply to a Master at MIT, Harvard, Yale, Berkeley, Stanford with a Bachelor of a German Fachhochschule?

tl;dr. I think it's unrealistic at this stage.

Note that the Masters degree in America is different than in Germany, in the sense that bachelors are typically longer and the Master and PhD are somewhat parallel in something called 'graduate school'. One question that arises is to what purpose do you want a Masters? Are you interested in doing research on the longer haul? Then it's a PhD you need. Are you mainly interested in the prestige?

My advice, if you are interested in doing academic research would be to already find a German university that will accept you in a Masters program (I don't know if it's possible...). You will be better armed to apply for a prestigious American graduate program.

More precisely about your concerns:

  my age,

It's fine, people start grad school later than that.

  nationality,

Nationality is a non-issue providing you are accepted in a program and have secured funding (see below). If anything it might take a bit longer for visa procedures, certainly not a killer criterion at any rate.

  university in Germany,

German institutions are generally highly regarded in America, the problem is not Germany, it's the type of your institution. A German 'university of applied science' (Fachhochschule) delivers vocational degrees. The focus is to give graduates a set of practical skills so that they can enter the workforce directly upon completion of the degree. It does not prepare you to enter a prestigious graduate school, whether in America or anywhere else. When applying, you will be competing with people who are far better prepared than you.

Top American graduate schools give a enormous importance to recommendation letters. It's already hard to find professors at German/Swiss universities who know enough about the American recommendation culture to write something competitive, I suspect few (none?) of the teachers at a Fachhochschule have experience in that matter.

  money situation?

You will need funding. For Masters you already realized how much tuition you will have to pay. Many student fund their studies with loans, and in the business schools it's common for employers to pay tuition. Departments sometimes pay tuition.

For PhDs, It's (almost) never the case that graduate students pay tuition out of pocket, that's also a reason why these programs are so competitive. Your potential adviser will have to secure hundreds of thousands of dollars to pay your tuition and stipend. For the reasons listed above, I think you will struggle to find funding, but it's unrelated to your current account balance.


How should a non-native English presenter respond to a question they did not understand?

Yes, it is appropriate to ask the questioner to repeat the question, prefaced by:

  "I'm sorry but I didn't understand the question.  Can you repeat it or rephrase it?"

If you still don't understand it, you might ask someone else in the audience to restate it or rephrase it.

Some people at academic conferences are not good at asking clear, direct questions, even when they are native English speakers with normal dialect.  I have asked people to repeat or rephrase questions for this reason, and I am a native English speaker.


Is the Nature publishing group's "Scientific Reports" journal well regarded?

My take: any journal that considers rigour and validity only, and not perceived impact, will be less well regarded than an equivalent journal that has a good reputation for rigour and validity and also considers impact.

On the plus side:

Page charges are normal for open access, and open access is a positive, so I don't think there's a problem there.
As a Nature journal, Scientific Reports inherits a little of the "glow" of Nature, which will lift its reputation relative to other journals that don't consider impact (e.g. Helyion and PLoS).
Nature journals employ full-time professional editors, which means that people submitting to Scientific Reports can also expect fast, professional review and editing. This help's the journal's reputation, too.

An impact factor of 5 is very high in many fields, but nothing to crow about in other fields. So I would expect this journal to attract higher quality papers from those fields in which 5 is considered a high impact factor, and lower quality articles from fields that typically have high impact factors.


Is a software developer entitled to participate to paper?

Based on what you say, I believe ethically you would be listed as an author on the grounds that data analysis in an integral part of research. At least, this is what I would do. I would do this trying to keep things professional even if personally I came to dislike the software developer.

However, in practice, it may depend on the contract you signed. If there was nothing in the contract, things get trickier as the situations seems already deteriorated. Is there anyone in the research group, apart from the IT engineer, that can vouch for your work and argue for your inclusion?

If you did not sign off the copyright to the software, you may have legal grounds for not having the research group use it (again, depends on the contract), although this would be harsh. An alternative would be to publish your own paper on the software, just as a data analysis tool if it is general purpose enough to be of use to others. That would give you even larger credit. Note however that most likely the software would need to be available free of charge to other researchers.

(As a minor point, I do not understand your first bullet point. If you are not on the paper, why is it important to you that the others interpret the results correctly?)


What criteria need to be matched to be able to distribute a research article openly?

Under what conditions you are allowed to distribute a scientific work are governed by the licence terms under which that work is made available. Most often journals or repositories of other research outputs will have clear indications regarding reuse, redistribution, etc. Often, all rights will be reserved by default and only certain rights for reuse/redistribution, if any, will be explicitly stated. If no specific rights are stated then you have no rights to reuse/redistribute.

In order to distribute a scientific work where no rights are automatically granted you are required to contact the copyright holder to request those rights.

This is one reason why Creative Commons licences were developed; so that authors of works can be explicit about what reuse rights they allow so users are not forced to individually contact creators to request rights.

Even when a work such as a dataset may not have copyright protection in the strict sense (e.g. facts), it may well have database rights protecting the specific compilation of the data into a whole. It is important to request permission, especially where you are unsure of the restrictions that might be in place.


Tax write-off for research-related expenses in the US?

I am not a lawyer and this is not legal/tax advice.

I believe you can deduct these as unreimbursed employee expenses.  For 2013, this was Line 21 of Form 1040 Schedule A.  Details can be found in IRS Pub. 529.  It lists a number of examples of expenses that would be deductible on this line, including:

Research expenses of a college professor
Travel related to your work
Tools and supplies used in your work
Subscriptions to professional journals
Dues to professional societies

There are a couple of major caveats:

Roughly, you can only deduct the amount that exceeds 2% of your adjusted gross income (AGI).  More specifically, you take the amount of your unreimbursed employee expenses, add the rest of your miscellaneous itemized deductions if any (see Pub. 529 for the list), and subtract 2% of your AGI; you can deduct the difference.  So this may only apply if your research expenses are fairly substantial, or you have other significant miscellaneous itemized deductions.  (Note that miscellaneous itemized deductions do not include the big itemized deductions like charitable donations, state taxes, or mortgage interest.)
You have to itemize deductions to do this.  If you don't have many other itemized deductions, you may be better off just taking the standard deduction.
Of course, you cannot deduct expenses that were reimbursed.

Note that you might also get good answers on http://money.stackexchange.com.


If I publish under a pseudonym, can I still take credit for my work?

Taking it that your asking about a nom de plume (aka "pen name") for reasons of conspicuousness, rather than for reasons of anonymity:

Yes, it is possible to publish under something other than your legal name.  A nom de plume isn't that unusual in academia, particular for folk with common names who would otherwise be unfindable in literature databases.

You need to make sure that your legal identity is sufficiently tied to your nom de plume, so that there's not going to be any arguing about it.

Some people adopt double-barrelled surnames for their noms de plume: others add a distinctive first or second initial. As long as its sufficiently close to your real name, that should be sufficient.

Note that this will entail your nom de plume effectively becoming your name for academic purposes: it's what will be on your email correspondence, your web page, your conference name-badges, and so on. You'll just have to do a bit of tweaking with university administration so that payroll, legal, and travel arrangements are all in your real name, not your pen name.


Should I mention that I was an athlete in a curriculum for a PhD application?

I would put it in your CV. I see several reasons for this: first it completes your CV and you are 'honest' with anyone you apply to. I don't know the sports you are in but if someone googles your name, s/he might end up finding you which in my opinion raises questions (if you did not mention it).

The second reason is that of traits and skills a semi-professional career as athlete gives you: persistance, discipline and so on. Yes, it may distract you, but this is why you have chosen to focus on one path. Be prepared to answer questions about this when you are interviewed. Focus on the positive aspects that this occupation has given you.

Third: I think it highly depends on your sport. Is it athletics, football, or something else (popular) it is perhaps ok. Something like Mixed Martial Arts raises other questions and might put you into a unwanted light (agressive, conflict orientated). Sports like e-sports are also still a problem. Many do not recognise them as sports at all, although they might indicate team and communication skills as well as reflexes.

So I guess you should reflect upon the positive and negative aspects of your sport and why it has formed your character into the person you are know. If you can answer questions about this relation in an interview setting, you are pretty well off I think.


How to obtain a fair recommendation letter from a professor who knows me via course, not research?

Visit the professor and explain your plans and your wish to have him provide a letter in a brief but structured way. Slip in some of your (positive) thoughts concerning his course and, if you were inspired by it, the importance of the course for your current interest. I do not think you can do more. If the person is not interested, I doubt you can do anything to change the view that would not be annoying in the end. It is possible the person has forgotten you but if you stood out even a little in the class, my bet would be the opposite. As I see it you only risk getting a no, and not much could be done to change that.


Is it appropriate (as a current student) to ask professors questions not directly related (but related enough) to course material?

As a former mathematician and academic, the interaction you describe strikes me as unusual. Certainly not the norm, and not in general what you should expect! Most of us, I suspect, learned most of the math we know via self-study, with the benevolent guidance of mentors as we went along. And as pedagogues we generally like helping people explore their interests in math, even when only very loosely connected with the matter at hand.

That being said, it is worth noting that university professors' time is pulled many ways, and in many cases their formal incentives are not at all aligned with spending their time opening the minds of random students on random math topics. At research universities, their career success depends on research productivity, and they may have little time for teaching to begin with, and helping students learn outside of the curriculum may not be high on their priorities. At more teaching-focused colleges, one hopes the desire to help would be strong(er), but teaching and administrative loads may be higher and they may feel their time is limited. In either case, if others are waiting for office hours they may feel those whose questions are directly related to the curriculum take precedence; and if their office hours are poorly attended (perhaps for a reason....), they may start feeling entitled to be using that time for lecture prep or something else unless someone comes with a directly relevant question. In my opinion, they shouldn't, but they may.

The basic advice of "find someone else who is less of a grumpster" applies. Beyond that, whether with this individual or someone else you approach, there are certainly things you can try to increase the positive response you'll get for "extracurricural" questions:

Make an appointment / "ask whether you can ask" and indicate roughly what you want to talk about, and recognize you know it's past the curriculum itself. Be willing to come another day.
Demonstrate enthusiasm and curiosity, avoid projecting entitlement. Professors want to stimulate the former, but we're pretty jaded about people who come across as if they feel they have a right to answers to whatever level of detail they feel like, or get irritated that the question they asked has a more complicated answer than they were clearly hoping for.
Do some reading/research beforehand, and indicate you have done so. There is a shift from highschool, where you are taught, to university (undergraduate and graduate), where you are being helped to learn. Show you are making that shift!

All of the above may well be things you are/were doing, and you just have a grumpy professor. Sorry about that. But I'm summarizing them anyway, since any academic or ex-academic will have stories of students whose keenness was infectious, as well as those whose non-stop, entitled questions were a pain in the neck!


Why don't high-ranking journals go solo?

Many journals are publishers' own products, "going solo" makes no sense. It's like asking why Gmail does not segregate from Google. In some cases, professional societies hire publishers to take care of their official publishing organ, I imagine your question relates to these cases. Otherwise, there have been cases of the entire editorial board leaving for another journal, I've heard it happened to a Frontiers journal over concerns on quality, but in this case the journal is still there, just edited by other people.

Running a professional-level journal is not trivial and there are reasons to favor established organizations, commercial or not, to handle that part. These include administration, secure web hosting, a long-term back-up strategy, typesetting, distribution, submitting accurate and complete article metadata to third parties like Pubmed or Web of Science, printing when applicable, etc. and of course finding the money to do all of these.

For many editors, it's a pretty straightforward decision to outsource these hurdles to a specialized organization, be it for profit or not, especially if there is an ongoing issue-free relationship going on for years.


How to get free programmatic access to citations counts for a given paper?

If you are an R user, you can use the scholar package. This package allows you to analyze data from Google Scholar and obtain citations, publication list and even perform predictions of the h-index. An example R code:

library(scholar)
id = "xJaxiEEAAAAJ" # Isaac Newton's id
cit=get_citation_history(id)
barplot(cit[,2],names.arg = cit[,1])


If your thesis was accepted and you have your degree, there is no "action" that can be taken against you. You can, however, produce a new publication giving the "missing" background of your original study.

Even better would be to extend your work, and maybe your model and explain in a new paper the new work, encompassing the old.

Just be careful to cite the old work, especially since it has been "published" on the website. That will probably make it impossible to republish that, but makes it even more possible to derive new work from it.

But any "blame" for missing parts is not yours alone, being shared with your advisor and any committee that accepted the work. But, in fact, I don't think there is really any blame to share. Move on. Do even better work.


On citing common knowledge and giving credit to the 'right' authors

First, the definition of "common knowledge" and I think this answer by Ben Norris from the post that Stephan Branczyk posted elucidated that pretty well (https://academia.stackexchange.com/a/2196):

  If the statement/concept/idea that you think you want to cite is covered (without citation) in the introductory undergraduate textbook(s) on the subject, then it is likely common knowledge in the field.

So next step is to search more than one sources about that specific examples or specific numbers. If that book is the only source that came up with that example/number then you can cite from that author(s). You give credit from where you found the information. It is better to cite than not and might trouble you later on since it will give an impression that those numbers/examples are from your own findings (and which someone might cite that example from you). Because again, 'when in doubt, always cite'.


Is it suspicious for a conference abstract submission to be subordinated to registration?

€500 is within the normal range for an international conference, but the mandatory subscription before getting the notification of acceptance is indeed a bit suspicious.

However there are some conferences which work in the following way: pretty much any abstract submitted is accepted (except if out of scope, I guess) and is supposed to be presented at the conference. The selection process happens when a subset of the abstracts are accepted for publication as a full paper in a journal issue. I'm not very familiar with this setting myself, but I assume that it might make sense for such a conference to make sure that the authors attend and present their work even if it's not selected for the journal issue.


What are the non-academic job prospects for a PhD in probability?

The main industry job for anyone involved with probabilities nowadays is called

  Data Scientist

(also called applied statistician which, in turn, is basically applied probabilities).


Publishing a preprint while having another related work on review

I wish to [publish] a preprint (that I've already written) immediately because...What should I do?

Make the preprint available.

  I fear [publishing] this preprint [is detrimental to the ongoing review] of X

I don't see why this should be the case. How can any result that builds upon X be detrimental to X? Surely such results are favourable to X, since they'd show that X is useful?

You could cite the preprint in X, especially if it helps address reviewer's concerns.


What provisions exist to handle scooping when there are multiple reviews of research papers?

After writing to a number of journal and conference organizers, KDD and IEEE responded by saying that putting up a document on arXiv and then submitting the same document to one of their conferences or journals is ok. IEEE officially mentions it here. There's also a nice answer here.

UPDATE:
As of 2019, KDD no longer allows pre-prints on ArXiv due to their double-blind policy.
As of 2020, IEEE started their own archive named TechRxiv, and they still allow pre-prints on ArXiv and TechRxiv.


Keyword tagging across scientific papers making it searchable

You could look into a noSLQ database. ElasticSearch or SOLR come to mind immediately. Most cloud services also offer their own flavors of this(DynamoDB on AWS for example). The solution could be designed to retain the original content, your notes (both searchable also), and your classification system. Most of these systems should have plugins to import various file formats directly.


How do I politely ask a convenor to not publish my name on the conference website?

From both an ethical and a practical standpoint, you don't. The ethical reason should be obvious (and has been stated in comments); you are lying to your employer about leave, and asking the conference organisers to be complicit in this (presumably without their knowledge). If you want to take sick time when it's not permitted, that is your risk to take, don't ask others to shoulder that for you.

From a practical standpoint, you should really ask yourself if hiding your name in the conference proceedings is in your best interests (relative to the chances of your employer discovering via Google what you were up to). I will presume you are going to this conference to begin/advance/change to an academic career. Reputation is gold in academia, and by concealing your activity, you are actively hurting yourself and reducing the profile of your work. If you don't care about the profile of your work and your academic footprint, then why go to a conference? They are expensive, and there are much nicer things to do with your time on a transcontinental trip.


Proposing current postdoc supervisor as a Marie Curie mentor

This should not be a problem. I know of (at least) one MSC global fellow that did just that. Just make sure to explain why this would be the best place in Europe to complete your research proposal (which you should do regardless of which lab you chose).

The only way I could see this speaking against you of this person was also your PhD advisor.


I feel like I'm in a wrong place, should I quit my PhD?

I am so sorry that graduate school is taking such a toll on your psyche. Please believe me when I say that you are not at all alone in feeling this way, and I agree with Buffy that this largely sounds like imposter syndrome -- something that even the top academics fall trap to.

In regards to your cohort, here is my advice, regardless of whether or not you change programs: remember that there will never be an even playing field. All of you have different backgrounds, strengths, areas that need growth, goals, and research interests. There is absolutely no way that any of your cohort members check every single box. With small cohorts like yours, it is difficult not to compare (especially if your program has set up a culture of competition). However, these comparisons can be detrimental to your psyche because you are only seeing part of the picture: what your cohort members publicly present. It could very well be that you are the strongest of your cohort in areas like grant writing, interacting with certain groups of people, or even a personality that others like to be around (a major factor that might sometimes get overlooked), but you are so early in your program that only time can reveal this. Wanting to succeed in academia is half the battle; if you have this, no matter how much or how little you are bringing with you into the program, you will find your fit. There is a reason you have been selected that might not be particularly clear to you, but it was clear to the graduate admissions committee, and it helps to shift your focus from what you think you lack, onto what your strengths are/what you offer that your cohort cannot.

In my own cohort, each of us offers something different. I highly respect the intellect of all of my colleagues, and when I publicly state this, some seem surprised and have even admitted that they had not recognized x as a strength of theirs until they heard it pointed out to them. Though I cannot guarantee you will get your a-ha moment, I can guarantee that early academia makes it very easy to forget the qualities you possess that have gotten you to where you are now. There have been occasions that your cohort members have lauded you or even felt jealousy, but since this knowledge is not explicitly expressed, you are understandably feeling as if you are not "enough."

Another thing to remember - your required classes are only one small part of your PhD. You will need to learn interpersonal, research, professional, administrative, and teaching skills, many of which can be learned but the extent to which you succeed cannot. These are skills you will need no matter the school that you choose, and it is often expected that you will accumulate them on your own (with some help from your program, however it is not necessarily your program's responsibility to walk you through them). It is so very likely that despite not coming in with the same knowledge or strengths as your colleagues, you will be stronger in certain aspects of the PhD track than others, and hopefully, you will be provided an adviser who can help you assess these strengths and weaknesses with you. For me, creating an Individual Development Plan (IDP) helped tremendously.

In regards to changing programs, are there programs that allow you to enter with an adviser? If you are not provided with this adviser, is it still possible for them to be on your committee? In my program (based in the U.S.), admission is heavily contingent on the adviser you choose and committee members are just as important. At your current institution, is it the norm to meet with professors you are interested in working with, to get a better sense of what they are about? Despite the program seeming to be restrictive on academics, perhaps there are faculty members that do not feel this way and can become allies to you. Find allies within the department, let them know the surmounting stress you feel, and gain their advice. Assess whether or not you feel comfortable talking with your graduate chair (if applicable). How accessible is the person you wanted to become your advisor, and how much time do they have for their students? How many students do they have? What are they even looking for in students - is it more based on research interests, or is it on grades? I believe that no matter the discipline, it is often the prior; since you are in a PhD program, you will be there a while, and your position in the department can change for better or worse at any moment and thus should not feel set in stone.

If all else fails, know that people do change programs to find a place with a better "fit." Finding an institution that fits your needs might take time and visiting many different institutions you had not previously considered when applying. It sounds like you have learned a lot about yourself in this process, and if you are adamant in choosing a new program, there are people in your institution that will support you and help you with this; hopefully, in your department, but at the very least, within the graduate school, academic advising, career advising, and graduate success initiatives.

Your questions regarding how to approach the situation when reaching out to schools is not easy, but it sounds like the problems you are having can be voiced in a manner that speaks about department "fit," which the right school will understand. I am unsure how you chose your current program, but speaking in person or on the phone with prospective schools and advisors is really what solidified both mine and my adviser's choice to work together. Perhaps explaining your problems with your particular program to other program's graduate coordinators might put things into perspective and allow you to see how other programs stack up on the idea of PhD flexibility.

On your qualms about speaking up affecting your funding - is your funding contingent upon your timely progress in the program? If so, keep focusing on that while sifting out your personal feelings about the program in the background. Focus on passing those exams. Take extra initiative to get to know your department, so they can get to know you personally and your POTENTIAL rather than your current knowledge. People in your department may talk, but the extent to which they have control over your ability to stay in the program funding-wise may be minimal, and letting them to get to know you outside of hearsay will be instrumental in making a good impression - a REAL impression of you.

Changing programs or not, you got this. I cannot emphasize enough that programs care more about your potential than how well you are doing in these classes, because academics can be taught but your willingness to learn cannot. It sounds as if you are more than willing to learn and more than capable of showing your value to your program (or to a different program that might fit your needs better). Best of luck!


What are the benefits of serving as a reviewer, initially as a PhD/PostDoc and later as a faculty member/research scientist?

The primary advantage of peer reviewing is that you are ahead of the researchers in your field by a margin of several months. Second advantage of getting a bad paper for review is that you get an idea "what to avoid" in your own future work. Most people do not realize this because it is not a paid service, nor there is any public acknowledgement on the paper. Several journal editors have mentioned to me that they have difficulty inviting reviewers. I asked an editor of a pretty good review-type journal and he mentioned that at times he has to write to 10-12 people and only a few respond. It is a also common complaint among editors that people from certain countries don't commonly accept peer review requests because the academic promotion is based on paper publications rather than article reviewing.

In short, we should accept review requests, if we feel we are qualified to do so, as a service to the community as well for your own education.


Plagiarism and Authorship in a Translation

Publishing a translation of your own article is not plagiarism, or any other kind of misconduct, as long as it is clearly identified as a translation.  Usually this means that the first page of the article says something like "Translation of [original title], published in [journal, volume, date]".  The editors of the new journal should be aware that it is a translation, not a new paper.  The publishers of the first journal should also give permission (this may be legally required if the author has transferred copyright to them).

The author should not try to "count" the translation as a separate paper, or otherwise mislead people into thinking that they are two independent papers.  For instance, his CV should show one paper as a translation of the other, or list them together as a single publication.

However, translators are not normally credited as authors, unless they have made an intellectual contribution to the text of the paper, beyond simply trying to translate it faithfully and idiomatically.  Likewise, the translator should not try to take credit for the translated paper as a publication on a CV, etc (unless as a separate section from papers they authored).


What kind of citation can be used in a paper?

Whatever you use, cite it. If it is only a Tweet by a ten-year-old, cite it.  If it is a hallway conversation with your colleague, still cite it.

But do not expect your readers to believe it is reliable, or that it is from a peer-reviewed paper.


Why publish a research paper when a blog post or a lecture slide can have more citation count than a journal paper?

It's not fair to only look at the peak of the distribution. For an apples-to-apples comparison, you need to compare peaks to peaks and averages to averages.
The two sources you mention are both in the field of machine learning. If we assume that they correspond to the blog/lecture notes sources with the most number of citations (i.e. the peaks), then we can conclude that these venues can generate at most ~700 citations. If you compare to the most cited machine learning papers, these 700 citations are minute. For example putting "machine learning" into Google Scholar yields:

Scikit-learn: Machine learning in Python (journal article) -- 14919 citations
Data Mining: Practical machine learning tools and techniques (book) -- 34724 citations

What about averages? I don't know what the average number of citations a blog post or lecture slide gets, but I'd guess less than one, since many blog posts don't attract comments. The average number of citations for a journal article however is easy to find - just look at the impact factor. Putting in "machine learning journal" into Bing, I get journals such as Machine Learning (IF = 1.855 as of time of writing) and International Journal of Neural Systems (IF = 4.58). Clearly the average journal article gets a lot more citations than the average blog post or lecture slide.
tl; dr: What's the point of studying machine learning instead of playing soccer and earning hundreds of thousands of dollars a week? The answer to that question is similar to the answer to this one.


Publishing code in order to improve my chances to be admitted to a CS graduate school

It sounds like you have a portfolio that should be a part of your application to university or a job or anything. Furthermore you're saying that the working product is a better testament to your skill than the code itself. This is also fine.

The only concern I see is how much work you will require on the reader of your application. If you link to a YouTube video, also include screenshots. If you link to a GitHub profile, consider writing up some basic statistics on the activity or health of your activity there.

Regarding where to publish code, don't overthink this. Github is popular, but a Dropbox file, a Google Doc, a file sharing service, or anywhere else you can post a file will do.

I do not know the proper channel to submit a portfolio or the proper format. This situation is probably documented in the application instructions however, so you should be able to find info there, or reach out to a recruitment officer for how to proceed.

EDIT regarding where to post - actually a .zip file or similar may be problematic since they tend to look like viruses to people, who don't want to open them. Github or a competitor may be the best choice since the source code is browsable in their web UI. It is best practice to include a software license whenever you publish (literally "make public") code, even if you think it is unusable. I think the MIT and Apache licenses both amount to (IANAL) "do whatever you want with it, just don't sue me."


How to think about journal-hosted preprints, or "Just-IN" manuscripts?

How different can the final published "copy of record" version be from the "just-IN" version?

By as much as how just-accepted articles can differ from actual published articles (this is in all likelihood what the two types of articles are in this case). Copyediting is done, figures are moved, author corrections are implemented. This last part can be quite substantial, e.g. if the reviewer recommends acceptance but has a few extra (optional) comments that the authors agree with. The central arguments presented by the paper are not likely to change, but the presentation might.

  To cite the "just-IN" version I would use the DOI. Given that this DOI will later point to the final version, am I potentially misleading readers if the two versions turn out to be significantly different from each other? (If I instead were to cite the arXiv version, should it exist, at least the previous versions would be available to future readers.)

Because the central arguments presented by the paper are not likely to change, you can safely use the DOI of the just-IN version. In rare cases, this might not work, e.g. if you say something like "See Jane Doe et al [ref] figure 3" (since figure numbering might change), or if you're citing Jane Doe et al for something that isn't their central claim, e.g. "It is well known that dark matter exists [ref]" where Jane Doe et al isn't a paper about dark matter's existence, but rather its properties. But these exceptions are quite rare, and you should be able to safely cite as-is.


I've received interview for faculty position at one school but am interested in another school

He is probably trying to be professional and separate you as a student and you as an applicant. I wouldn't bring it up to him. You clearly already have a leg up since he told you about the position in the first place. He also probably already knows that you are applying to other places (since people generally apply for jobs before graduation).