How can I properly attribute unpublished data gathered by someone else when using it in my masters thesis?

In my opinion, stating in the introduction "the data were taken in the such and such experiment prepared and run by A.Becede" would be enough. It's not unusual to analyse data from someone else's experiments, especially at MSc level.
Just as a tip, in my field when we cite something unpublished, we cite it as:
"A.Becede - private communication"
or
"courtesy of A.Becede".


Can departments sanction students who do not take sufficient precautions to protect their work?

Can a department in the US punish a student for helping other students cheat even if the student is not taking the class where the cheating is occurring?

I don't know what you can do legally, but morally I think it would be wrong to try to prevent the student from making his/her coursework from past years' courses public. Making the work public could help the student market themselves to prospective employers, and has multiple other benefits for both the student (ego boost, impressing friends, fulfilling an altruistic desire to provide a useful internet resource they worked hard to create, gaining valuable experience using github, and more) and the internet (people from all over the world could download and use the code). Who are you and your colleagues to say that your selfish needs of not having such code available for download online because it facilitates cheating by your colleague's students are more important than the needs of the student and others who can genuinely benefit from the student's work? I think your premise that the student is doing something wrong is simply incorrect.

  If so, what should be done? If not, might there be anyone at the school that can do anything?

Yes, something could be done; you and your colleague could free yourselves of the harmful mindset of trying to control what your students are doing with coursework they worked hard to create after they finish taking your classes. As Massimo Ortolano suggests in the comments, stop taking the easy way out of giving the same assignments year after year and then blaming others for how easy it is for your students to cheat, and instead put in the work to give original assignments.


Why do math journals' aim and scope provide so little information?

No information is probably better than misleading information. Any journal can talk about accepting "outstanding contributions", or whatever, on their homepage, without actually having high standards in practice. If you want to know how good a journal is, their aims and scope is not a good place to look. Either go to some independent source (e.g. Scimago journal rankings) or (more work, but perhaps more reliable) have a look at what they've been publishing and try to get a feel for how strong it is.
Most mathematics journals, however, will be specific about which areas of mathematics can be published, or at least, as specific as they need to be. A journal that specialises in a particular field will usually say exactly what parts of that field they like (and don't like). Here's a random example:

The research areas covered by Discrete Mathematics include graph and hypergraph theory, enumeration, coding theory, block designs, the combinatorics of partially ordered sets, extremal set theory, matroid theory, algebraic combinatorics, discrete geometry, matrices, discrete probability, and parts of cryptography.
Discrete Mathematics generally does not include research on dynamical systems, differential equations, or discrete Laplacian operators within its scope. It also does not publish articles that are principally focused on linear algebra, abstract algebraic structures, or fuzzy sets unless they are highly related to one of the main areas of interest. Also, papers focused primarily on applied problems or experimental results fall outside our scope.

The journals you mention simply don't need to say anything about areas, since no area of mathematics is off-topic for them. If the paper is of sufficiently high quality, they will publish it. However, it's worth bearing in mind that some journals which do in principle publish in all areas still have preferences making the bar higher in some areas than others. A good way to gauge this is to search for papers published in that journal on mathscinet in, say, the last ten years, and see what proportion of them have the relevant primary classification (this breakdown is available with the search results). For example the figures for Inventiones are:
Algebraic geometry (126)
Dynamical systems and ergodic theory (89)
Differential geometry (75)
Number theory (70)
Partial differential equations
(45)
Group theory and generalizations
(41)
Several complex variables and analytic spaces
(38)
Manifolds and cell complexes
(31)
Topological groups, Lie groups
(22)
Probability theory and stochastic processes
(20)
Global analysis, analysis on manifolds
(19)
Functional analysis
(14)
Commutative rings and algebras
(11)
Functions of a complex variable
(11)
Nonassociative rings and algebras
(10)
Statistical mechanics, structure of matter
(9)
Algebraic topology
(8)
Quantum theory
(8)
Associative rings and algebras
(7)
K-theory
(7)
Fourier analysis
(7)
Combinatorics
(6)
Convex and discrete geometry
(6)
Mechanics of particles and systems
(6)
Operator theory
(5)
Relativity and gravitational theory
(4)
Mathematical logic and foundations
(3)
Measure and integration
(3)
Fluid mechanics
(3)
Field theory and polynomials
(2)
Category theory; homological algebra
(2)
Special functions
(2)
Ordinary differential equations
(2)
Systems theory; control
(2)
History and biography
(1)
Linear and multilinear algebra; matrix theory
(1)
Real functions
(1)
Potential theory
(1)
Approximations and expansions
(1)
Abstract harmonic analysis
(1)
Calculus of variations and optimal control; optimization
(1)
General topology
(1)
Statistics
(1)
Astronomy and astrophysics
(1)
Information and communication, circuits (1)


Academic dishonesty -- math graduate school admissions

This is certainly not going to help your application for graduate school, and it can be fatal if it doesn't look like you've learned from it. I suspect the default position of most people is going to be against you, unfortunately.

If you still have time (i.e. years till you graduate), make sure to show that you can put the incident behind you. Don't cheat in other classes, but get good grades in them anyway.
If you don't have time, that's bad. You'll need to write a good explanation in your application.
You will be asked about this. There's a box in many graduate applications asking if you've ever been involved in academic dishonesty situations. Don't omit this even if you've put the incident behind you, because if you do, you are not reporting full facts and if discovered any offer of admission can be rescinded even if you've already matriculated (see the statement you have to sign at the end of the application).


Is it a good practice for teaching assistants to sit in the lectures?

I have seen TAs do this, but generally don't ask my own TAs to do it. As you say, it's a (very) time-consuming way to solve the coordination problem. I personally prefer to just sit with the TAs for a few minutes (< 30 minutes) every so often to coordinate, which in my experience has been completely adequate. Of course this means that I have to invest a little of my own time, but I find it completely appropriate to invest a few minutes of my own time every so often to save my TAs quite a lot of time - but of course your milage may vary with other professors. I certainly wouldn't find it strange if a TA sat in the lecture, I just don't find it necessary.

However, I do strongly suggest that the TAs take some time to go over the teaching material, so that they get a sense for what I am covering in the lecture, and how far I have gotten by the time their tutorial or supervision session rolls around.

Finally, we have also used a joint Slack channel where TAs can ask questions and expect a fairly immediate response. This has been useful for me to communicate if I, for instance, needed to skip a section due to time reasons, or if I felt through in-class exercises (or blank stares) that a certain topic needs deeper exploration in the supervision sessions.


How to avoid European bias in science history teaching?

[I want to] avoid giving the impression [...] that everything was discovered or worked out by white european men.

I'm not a science historian, so I can't really say if the impression is actually right or wrong. It seems counter-intuitive, however, that a small local fraction of the earth's population should have "worked out" science alone. That's puzzling enough to examine this assumption.

  I want to improve.

This is a great example for how questions from students can trigger a researcher to advance their own research and understanding. I'm sure there's a huge literature on non-western science history. Knock yourself out.

  But firstly, how should I respond

By admitting that you know little about non-western science history, and that, naturally, your previous knowledge and specialization have shaped the syllabus of your course. After asking colleagues and/or doing your own literature search (it doesn't have to go into any depth), you may feel confident enough to give some pointers to your students who want to read up on non-western origins of science. The main point here is to acknowledge your perspective (and you already did that) rather than to claim a "neutral" viewpoint based on unexamined assumptions.


How can I convince my department that I have the academic freedom to select textbooks and use multiple-choice tests in my courses?

As a current undergraduate student who recently attended a Community College I personally agree with at least requiring all professors to use the same textbook. It means that students from different sections are able to study together more easily than if the books and overall approach to course are different as I'm seeing in some courses at my current University. At least some Community Colleges allow you to change courses up to at least one week into the course with no extra fees, which means that if you find a professor doesn't suit your learning style you can change to another professor, but if you need to buy another text book that would become significantly more difficult for those students. This is especially important in a multi-course series like Calculus where its possible that you could purchase the textbook for the entire series for a fraction of the cost of purchasing the book for each course individually.

I know I'm probably in the minority regarding Ebooks as a large number of my fellow students in the time I spent at a Community College preferred them, but I always preferred a physical book as most Ebooks come with a subscription of some kind which requires renewal every semester for a significant portion of the cost of the book.

And as a final point regarding selection of teaching material, it seems that your department only requires you to use the textbook they decide is best and you are able to supplement your teaching materials with animations and MatLab objects as you see fit. This was a very successful scheme for my Calculus 3 professor as they were able to quickly show us what the concepts looked like as 3D objects in a way they would have been unable to on a blackboard.


It's a very free process. The reviewer can ask for it if they want (though they would have to keep it confidential). You can refuse if you want. The reviewer can, as a result, decide to give a poor review. The editor can decide to reject the paper on that basis.

In a few cases there might be a good reason that you would not want to share your primary data, but generally, I don't see why it would be a problem. In any case, many journals (at least in my field) require, or at least strongly recommend, primary data to be made publicly available upon publication.

If you are worried about being scooped, you are probably worrying over nothing. If a reviewer was to try to present your data as their own (very unlikely and difficult to start with), it would be very easy to demonstrate, through your documented submission, that the work was yours and they were stealing it.


Can I revise and use a part of my published paper in PhD dissertation?

If these published papers were part of your dissertation research, I don't see how there would be an issue. For example, at my University we were expected to submit and publish three papers for our dissertation. We then wrapped those papers into a single document, added an introduction chapter and conclusion chapter. My dissertation document was then published on the university website.
In my case I made sure that I did not use the publisher formatted final version of the papers. With the publishers I used, permission was not required for including in a thesis or dissertation. For example, I published some of my papers in IEEE journals. IEEE has a button on their site for each paper that you can click to get copyright permissions. It has a drop down that says "thesis/dissertation". All that they require if you are the first author is to include a copyright message to IEEE in your dissertation. Of course, the practice may be different in other journals, as the licenses will vary too.
I also made the choice to only publish my dissertation in the university's open access library repository as required by the university, and not in proquest's subscription repository of dissertations as that could result in monetization of another publisher's work.
In this example I gave, self-plagiarism does not apply because 1) you would be sure to acknowledge at each chapter's beginning that this is an already-published work, 2) the dissertation is a university requirement for graduation. Nowadays, many people are publishing their chapters separately and you are required to collate them into a single document for graduation. It wouldn't make sense to me to have to write an entirely new document to report the same findings in a more wordier manner. That would be a waste of time.


Career change for a mathematician - from academia to ...?

Rumors say that the financial industry hires Ph.D.s in math and physics, having found that those guys are smart in ways that matter there.

In the US, the largest non-academic employer of Ph.D. mathematicians is the National Security Agency.  But they hire US citizens only.  I do not know if there are similar opportunities in Europe.


Will low grades on my transcript ruin my chances of getting into an MBA program, even if I retake classes for course forgiveness?

You will have the opportunity to discuss your transcript in your Personal Statement when you apply. You may choose to discuss it or not, you may have a better story you may want to talk in lieu of it later in your life, i.e a project you worked on, an internship, etc.


How to respond to a perceived unfair editorial decision?

That is a frustrating experience that many (all?) of us were forced to endure at some point in our careers.

Fact is, a "major revision" is not guaranteed acceptance upon receive. Papers that are not rejected in the first round of review usually are close enough that they can be accepted after revision(s), but that is in no way guaranteed.

Now, in your case, the reviewer made promising remarks for the future, yet failed to act on them. It can be that they misjudged the first time, that they are inexperienced (perhaps the review was delegated to a student), that they had malicious intents, etc. This line of reasoning, however, is a dark rabbit hole best avoided. You have no way of knowing for certain what was up with the reviewer at the time and little benefit even if you did, so it's best to let that go.

The next point is the editor's decision, "decline and resubmit". Again, there is zero guarantee that the paper will be accepted by a potentially different set of reviewers. Usually, journals prohibit submitting the same paper again once it has been rejected. So, if it is a particularly important venue, I'd consider this a better thing than straight out decline. Another important point is that (at least in my field) for a resubmit after decline, a predefined amount of time is required to pass, e.g. 6 months, and a significant rewrite is expected. Practically, close enough to a new paper. If similar practices apply, it is probably easier to resubmit somewhere else.

Appealing rarely works without substantial proof of malpractice during review. In fact, you may have already gotten the best result an appeal can get you: the right to resubmit for a new set of reviewers.

Bottom line, the lost time and the additional time it will take to resubmit is unrecoverable. You have the review feedback as it is, and you have your current and previous draft. If you feel that the reviewer's directions were misplaced, you can polish up the older draft and resubmit. My advice would be to try to get the best out of both versions, take into account any remarks the reviewers had, do a thorough proofread of the paper, and resubmit at some other venue.


What are good methods for determining course instruction workload equivalency?

Actually, most universities I've heard about specify either courses or numbers of “contact hours” per week. It is the job of the department chair (or executive officer or equivalent) to make sure everything is properly distributed within the department, so that one faculty member isn’t teaching only 300-student lectures while another faculty is only teaching specialized seminars for 10 students.


Is it fair that a PhD student should be allowed to review a research paper?

Yes, it is fair.

The quality of reviews written by highly experienced researchers is low.
Many manuscripts have obvious flaws that should be spotted by the inexperienced.
Reviewers are (in theory) supervised by the editor.
Novice reviewers are more enthusiastic than experienced reviewers.
If the paper cannot be understood by a PhD student, it will not be useful to very many people.
PhD students may have more specialized expertise because they work on fewer projects, as compared to senior researchers (per @nayrb)

Of course, it depends on the individual PhD student.  Some are better prepared to review than others.


Why there is no enforcing body in validating contributions?

Actually the "enforcement mechanism" is the entire academic community. Papers, for the most part are written by specialists, often for other specialists. Every reader can make a judgement about both ethical concerns and contributions. Every reader can criticize any paper that they read.
One problem with a "centralized" scheme is that the expertise is so varied that it would take a gigantic organization to do so. That "gigantic organization" is the entire scholarly community.
Moreover, as to contributions by individuals in joint papers, that is probably best left to the authors themselves. Most journals insist on some form of agreement among authors in this by asking them all to "sign off" on the paper.
And your judgement about what is a "minor" contribution vs a "major" one might well differ from mine. But this is because there is so much variation in the kinds of contributions: time spent, "effort", key ideas, writing, organization, creation of the enabling lab, ...


Is this website that claims to provide paper writing services real and legal?

Typically such paper-writing sites are "legal" in the sense that they say that the essays written serve only as "example" and are not to be used for assessment. Of course, you know, the clients know and the company knows that this is highly unlikely, but unfortunately, there is no way to legally enforce the academic integrity that such services undermine.
Maybe it will change in future, but for now, all that remains is for students to undergo a viva or to be examined under controlled conditions. Under Corona conditions, the latter is difficult to protect from cheating, either, at least without significant breaches in privacy (discussed in other questions on SE).


Is it common to delay the start date of a postdoc?

It is very common to negotiate the start date. All of the postdoctoral researchers I hired or was involved in recruiting came at different times than advertised. Most funding bodies allow you to defer funding for a few months. For instance, EPSRC allows up to 3 months delay for start of projects. Also, most funders allow a so-called no-cost extension, meaning you can extend the end of the project without losing the money.

Just apply and in your cover letter say that you would be available in October, for instance.

Source: I am faculty (engineering) at a UK university and have been involved in recruiting 5 postdoctoral researchers.


General guidelines for how to include a figure in a scientific paper?

Though the question refers to "including" graphs, the issues seem to be matters of labelling and presentation, which are part of graph design as a whole. The following are "the principles of graph construction" from William S. Cleveland's excellent if dated "The Elements of Graphing Data" (Wadsworth, 1985).

CLEAR VISION:

Make the data stand out. Avoid superfluity.
Use visually prominent graphical elements to show the data.
Use a pair of scale lines for each variable. Make the data region the interior of the rectangle formed by the scale lines. Put tick marks outside the data region.
Do not clutter the data region.
Do not overdo the number of tick marks.
Use a reference line when there is an important value that must be seen across the entire graph, but do not let the line interfere with the data.
Do not allow data labels in the data region to interfere with the quantitative data or to clutter the graph.
Avoid putting notes, keys, and markers in the data region. Put keys and markers just outside the data region and put notes in the legend or in the text.
Overlapping plotting symbols must be visually distinguishable.
Superposed data sets must be readily visually discriminated.
Visual clarity must be preserved under reduction and reproduction.

CLEAR UNDERSTANDING:

Put major conclusions into graphical form. Make legends comprehensive and informative.
Error bars should be clearly explained.
When logarithms of a variable are graphed, the scale label should correspond to the tick mark labels.
Proofread graphs.
Strive for clarity.

SCALES:

Choose the range of the tick marks to include or nearly include the range of the data.
Subject to the constraints that scales have, choose the scales so that the data fill up as much of the data region as possible.
It is sometimes helpful to use the pair of scale lines for a variable to show two different scales.
Choose appropriate scales when graphs are compared.
Do not insist that zero always be included on a scale showing magnitude.
Showing data on a logarithmic scale can improve resolution.
Use a scale break only when necessary. If a break cannot be avoided, use a full scale break. Do not connect numerical values on two sides of a break.

GENERAL STRATEGY:

A large amount of quantitative information can be packed into a small region.
Graphing data should be an iterative, experimental process.
Graph data two or more times when it is needed.
Many useful graphs require careful, detailed study.


How do I judge a professor's quality while choosing a PhD?

Disclaimer: My answer rather aims at underlining that judging which Professor is the best for you depends on your long-term objectives.

You might want to choose your supervisor for two reasons. They sometimes do not align (i.e., it's either-or).

Choosing a Professor for during the PhD: You might want to choose a good supervisor for the time you are PhD student. In such case, you are looking for someone who has already supervised PhD, has time, has research focuses aligning with your research topic/motivations, etc. This will ensure you have a "nice time" during your PhD, with enough support and guidance. Talking with former PhD students might help. Note that in this case, the institution (in terms of courses, funding, support, etc.) matters too.
Choosing a Professor for after the PhD: However, sometimes, what you focus on is the next step. It may vary from one field to the other (I don't know about math at all), but I know first-hand that sometimes, what matter the most for getting the position is recommendation letters (more precisely, who wrote them). Having the right (meaning "well established and acknowledged, with large network) connexions helps you getting visiting PhD/PostDoc positions more easily. Don't get me wrong: you won't get those positions if you are not doing good research. However, when you have reached a certain "enough good" level  (except in some rare case where you're extraordinarily brilliant), my opinion is that the quality of your work matters less than who recommends you — for junior researcher position, at least. So in such case, working with a Professor that has an above-average impact factor, published in renowned journals, and, most importantly, have "sent" PhD students in prestigious institutions (what they — the Professor — can easily do because their best buddy is PI there) and "landed" former students in cool positions is what you are looking for. Even if they might be less good mentors during the PhD. So track where are currently working their former students.

In both cases, look for a Professor that is interested in what you are doing.

Remember also that it's just like houses or spouses: there is no such thing as a ideal positions. You want to find the best "good-enough PI" that would accept you, even if they are not perfect in some aspects.

Finally, please consider that you are choosing a position that will significantly impact your life for the next 3–6 years. Don't neglect your personal needs/requirements (a very good position is not worth anything — in my opinion).


What are the responsibilities of a Program vs. General Conference Chair?

Conferences in theoretical computer science like the ones you mention typically don't have general chairs. They have a local arrangements team for organizing the event, and program chairs to manage the review process.

Many conferences in CS outside theory have a general chair because they have many more activities. The general chair might be in charge of selecting

The workshop program chair
The posters chair
The tutorials chair
Publicity (and social media) chairs
Treasurer
Local arrangements

And so on. The general chair can be viewed as being in charge of everything except the technical program and then delegates.

But this may vary even within iterations of an individual conference.


After long time without, three review invitations in two weeks. Coincidence, or do editors share lists of helpful reviewer names?

The journal editor (in chief) may not, but boards of editors have overlap and word does often spread that "X@Y is prompt, conscientious and fair."

Or it could be random entropy.

I wouldn't give it much thought. At best, you are being thought of as a good reviewer. At worst, it's a random quirk.  Choose the interpretation that makes you happiest.

--
p.s. If you're feeling overwhelmed, it's entirely ok to tell a journal that you have to decline. Respond as soon as you can so that they can move on. Quick declinations (and referrals to potential other reviewers when possible) are also signs of good, conscientious colleagues. And I'm a strong believer that the good karma from these unrenumerated acts of conscientiousness will help in the long run.


Withdrawing from course in a PhD Program (i.e. W on PhD Transcripts)

I withdrew from a class when I was a master's student: no one has ever cared why I did. I was later accepted into multiple PhD programs and a post-doc.

I would have a prepared answer for why you withdrew from a class. "I withdrew from Ballistics 782 in order to better focus on my research. I produced two papers that semester."

If you ever think you would have a chance to go back and complete the course in another semester, withdrawing is even less of a risk. One W will matter little in the long run. (And likely even in the short-run).


Not knowing the details of your project, I'll offer some general suggestions.
In a sense, it seems to me you're asking two problems:one question is how to read papers, the other question is how to compare methodologies.

As far as comparing methodologies, the key concept in my mind is that of a "metric" or some means of judging/ranking methods. In CS, for example there are many such metrics: computational complexity, run time, stability, theoretical results regarding convergence, etc. Metrics often are often context dependent, meaning that different classes of users may have different ways to rate/rank a method. An algorithm may give an exact answer, which to a theoretician may be great, but if the algorithm can't function in real-time, another use may prefer another method that gives an approximate answer but quickly. So know who is going to use the methodology often helps you understand what metrics are really significant. So two thoughts to keep in mind are the methods you learned in class for judging how good an algorithm was and also who is going to use the algorithm (what are their concerns/needs and which methods best addresses
them).
A suggestion in this regard that will also help you with your paper reading is to look at what the authors of each paper say are the advantages of their method. In the introduction every author will give a reason why their method is "better" than the other (existing) methods.


Can I add a baby as a co-author of a scientific paper, to protest against co-authors who haven't made any contribution?

There was a similar case in 1975, when an American mathematician and physicist, Professor Jack H. Hetherington of Michigan State University, added his cat as a co-author. Apparently, a collegaue who had reviewed his manuscript, had pointed out that he had used "we" and "us" throughout the manuscript, but this was incorrect as he was the sole author. so, instead of typing out the entire document once again (those were the days before Ctrl H), he decided to speed up the process and added the name of Chester, his pet cat as a co-author. However, to disguise the fact, he put "FDC Willard" as the name, with FD standing for "felix domesticus" and the C for "Chester." And Willard was the name of Chester's father.

However, these days, with so many regulations in place, I'm not sure if it would be ethical to include your baby's name. If however, you choose to do so, I would suggest you inform the editor and mention this in a disclaimer somewhere within the title page, so that readers are not misled about your intent.

Another well known case is the paper "In a fully H-2 incompatible chimera, T cells of donor origin can respond to minor histocompatibility antigens in association with either donor or host H-2 type." by Polly Matzinger and Galadriel Mirkwood in The Journal of Experimental Medicine, 1978.
As Ted Anton described it in his book Bold Science, "Refusing to write in the usual scientific passive voice ('steps were taken') and too insecure to write in the first person ('I took the steps'), she instead invented a coauthor": her Afghan Hound, Galadriel Mirkwood. Once discovered, papers on which she was a major author were then barred from the journal until the editor died and was replaced by another.


Multiple choice exams certainly do get used in math, by many people and at many places. (At the university I'm at, we use them for the calculus sequence, and then move to short answer exams after.)


What are the main differences between undergraduate, master's, and doctoral theses?

In a Bachelor or Master thesis, you have to show that you are able to apply the knowledge of your field to solve a typical problem in your field.

In a PhD thesis, you have to show that you are able to extend the knowledge of your field to solve new problems.

The distinction between a Bachelor and a Master thesis may be a bit subtle. Generally I think a Master thesis should show a significantly greater level of independent working. While for a Bachelor thesis your advisor could tell you which methods to use to solve a specific problem, for a Master thesis you could be expected to choose the methods on your own, and maybe adjust existing methods to better fit the problem at hand.

These are the principle differences I see, but of course its also depending on the specific student. A good Bachelor thesis can be better and include more independent work than a bad Master thesis.


Dr. ‹First Name›: a good nickname or a "professional cancer"?

Going by "Dr. FirstName" is just confusing. If people aren't familiar with you, they will think it is your last name. If they do know you, it doesn't seem more casual, just odd.

It depends on the context and culture, but in the US it is standard to go by either "Dr. LastName" or just "FirstName." Like Solar Mike mentioned, a shortened form like "Dr. Initial" is sometimes used for students to refer to you.


Permited peer assistance in PhD and MSc thesis

In my opinion, none of your numbered items (1-4) is acceptable. As for the two bullet points above, they must be carefully circumscribed:

You can of course get comments on your manuscript from your peers. This should not include solving your problems for you or writing parts of the work.
Some technical work may be performed by someone else: chemical synthesis of a compound you are using, specialized analysis of some samples etc. Each instance should be clearly specified: in the text, in the legend of the figures obtained this way etc. The reader needs to see clearly the distinction between your effort and that of other parties.

All this is codified in the saying: "Credit where credit is due". However, this principle is applied slightly differently to a thesis and to a journal paper:

A thesis demonstrates the ability of its author, who is assumed to have done all the work contained in it. That is why any external contribution should be indicated.
A paper's main goal is to present a scientific result. It is therefore less crucial to know "who did what", although some journals (e.g. PNAS, PLOS One) do require it.


The reason to do a postdoc is because you want to continue to do academic research.  This might be a short-term goal, or a long-term goal, or exploratory (you're not sure what you want to do long-term).  The latter two are the usual reasons.

Lots of people go into industry after doing postdocs (either because they decided they prefer that or couldn't find an academic job they wanted), so that's no issue.  Keep in mind that it's generally easier to go from academia to industry than industry back to academia.

How long it takes to transition from post-doc to a permanent faculty position depends on the field and type of job you want.  In math, 3-4 years (1-2 postdocs) is normal before getting a permanent research job and 0-3 is common for moving into primarily teaching jobs.

As for "success" rates from postdoc to permanent faculty, I think they're reasonably good, say over 50%.  I quoted some relevant data from the AMS in this answer, though I don't think the right data is there to give you a precise number.  If you take into account that a large fraction of these people want to leave academia, the success rate should look quite good.


Applying for masters again, will the application be evaluated on the basis of undergraduate/Bachelors or the most recent postgraduate grades

The admission committee will see your entire record.  It is up to them to decide how to consider and weigh the various parts of it - different people will feel differently about this, and there is no way to know what the sense of the committee as a whole will be.

If you had special circumstances that affected your grades, you should address them in your statement of purpose or cover letter.

See also:

How do you get a bad transcript past Ph.D. admissions?

Should I mention a "math depression" I went through in my letter of motivation?

Applying for PhD after a poor master's


How can I deal with claims of technical difficulties for an online exam?

Unless we somehow want students' grades to reflect the quality of their home Internet connection, the quality of their hardware, and their tech savvy (or their families'), there is not a sane alternative but to take seriously essentially all claims of technical problems. No, it it not really possible to "prove" technical problems, nor is it reasonable to try to insist that people with technical limitations be astute enough to document the tech problems!
Yes, from a traditional enforcement-oriented viewpoint this is "impossible". Yes, indeed, so, manifestly, that traditional adversarial viewpoint is not really (meaningfully) sustainable in plague times. So, indeed, what instead? Very context/culture -dependent, to begin with. Are classes gauntlets to be run [meaning adversarial situations in which one proves virtue by survival]? Or do we want classes to be fundamentally educational opportunities, and helpful to the students [as opposed to skeptical and adversarial]? In plague times, at least, what are viable (and useful) goals?


Does 'securing letters of recommendations' count as one of legitimate reasons of going abroad for one semester?

No, you shouldn't mention securing letters of recommendation in your personal statement.  It sounds a little too mercenary, like you are more interested in bureaucratic outcomes like letters than you are in actually learning.  It may hurt the feelings of faculty from your home institution who read it, and it's not really what the other institution is looking for in a personal statement.

On the other hand, you're right that this experience could really help in securing compelling letters, and I think it's sensible for you to take this into account in your (private) decision making.  If you currently attend a strong research university, then getting letters from an even stronger research university probably won't help much.  However, there are many students at teaching-focused schools that don't send many students to graduate school in any given field, and very rarely to the top departments.  That makes it harder for faculty to write strong letters of recommendation, because the comparison group is not so good: even if somebody writes "this is the best student I've seen in 20 years", it's not clear that this is in itself a strong enough statement.  (It's still possible to write a compelling letter if the recommender can offer enough concrete, impressive details, but it makes writing the letter harder and requires the recommender to know the applicant really well.)  If a faculty member can easily compare you with lots of students attending a range of good to great graduate schools, that makes it easier for them to write a useful letter.

So if you're studying in a department that rarely or never sends students to the graduate programs you'd like to attend, then it's very much worth trying to get a letter from someone who has a broader perspective on the applicant pool.  Otherwise it's not so important.  But either way, you shouldn't mention it in your personal statement.


How to Find Peer-Reviewers Who Aren't Busy (During the Summer)

You're not being asked to find reviewers who are willing to review your paper. You're only being asked to suggest reviewers. There is no guarantee that any of the reviewers you suggest will actually be the one(s) who review your paper.

Therefore you should not so much identify people who have time as you should identify people who can review your paper. If you're still concerned you could identify people other than the superstars, but suggesting superstars is fine, because the superstars probably know others who can review your paper (so they can suggest someone).


My Department head is very condescending - anything I can do about it apart from leaving the new job?

Department chairs should solicit feedback from students and they should insist that teaching practices be based on evidence.  That's normal.  But it sounds like this department chair is using these mechanisms to be a bully.  That's bad.

My advice would be:

Document everything.
Consult your university's omsbudsperson.
Study up on your institutions procedures.  There may be something that keeps the department chair accountable, such as an election.  We do not know your institutions specific regulations.
Develop good relationships with the dean and other faculty in your department.  The chair often has little power on their own.
Look for a new job.
Keep in mind that department chairs often have no training for the job and may not like being chair.  Do not be surprised if they are bad at their job.


Do medical journals require the authors to upload their raw data in addition to the manuscript?

Some examples of policies (note: excerpts are all very brief, I've included them mostly just to indicate these journals all have policies and that none require all data to be shared, more detail is available at their websites; I included a bit more from The Lancet since it was mentioned in the OP; I made some formatting changes to display better on StackExchange):
JAMA

For reports of randomized clinical trials, authors are required to provide a Data Sharing Statement to indicate if data will be shared or not.

NEJM

The International Committee of Medical Journal Editors (ICMJE) and, therefore, NEJM require investigators to submit a data-sharing statement (2018) and register a data-sharing plan when registering a trial (2019). NEJM has not yet formulated a policy on which types of data-sharing plans are acceptable.

The BMJ
BMJ journals have three tiers of data sharing, marked by journal here.
As a general statement, they write:

We encourage you to make available as much of the underlying data from your article as possible (without compromising participant privacy), but at least the minimum data required to reproduce the results presented in the associated article.

And The Lancet's own policy:

From July 1, 2018, all submitted reports of clinical trials must
contain a data sharing statement, to be included at the end of the
manuscript. Data sharing statements must indicate:
• Whether data collected for the study, including individual
participant data and a data dictionary defining each field in the set,
will be made available to others (“undecided” is not an acceptable
answer);
• What data will be made available (deidentified participant data,
participant data with identifiers, data dictionary, or other specified
data set);
• Whether additional, related documents will be available (eg, study
protocol, statistical analysis plan, informed consent form);
• When these data will be available (beginning and end date, or “with
publication”, as applicable);
• Where the data will be made available (including complete URLs or
email addresses if relevant);
• By what access criteria data will be shared (including with whom,
for what types of analyses, by what mechanism – eg, with or without
investigator support, after approval of a proposal, with a signed data
access agreement - or any additional restrictions).

Summary
Medical journals tend to encourage but not require sharing of data, and it is now standard in most major journals to require some sort of statement about data, either mentioning how data can be obtained or why data cannot be shared. Peer reviewers can also request further analyses or less abstracted data during the peer review process.
Raw data in particular are quite an issue for medical research, because aspects of the data involve the private and often legally protected health information of individuals. Journal policies avoid conflict with these protections or else important research cannot be published there.
Even anonymized data can potentially be revealing and may not be as anonymous as it seems.
Overall, there is a move towards more open data policies, and you'll see from these examples (both quoted and in the linked pages) that they refer to updates in just the past few years.

Rocher, L., Hendrickx, J. M., & De Montjoye, Y. A. (2019). Estimating the success of re-identifications in incomplete datasets using generative models. Nature communications, 10(1), 1-9.


Practicality of attaining a law degree despite difficulty remembering facts?

How well do you remember films?

I had a similar problem, though not as bad as you describe. I found it helpful to think of each seminal case as an old black-and-white movie with a dramatic scene as judge's read their verdicts. I forget dates, but I remember the meanings and that proved much more important.

Side note: A law degree is (typically) a very field-specific endeavor. If you have a good reason to pursue it, then I wish you the best. But, just in case you've never heard this before: unless you plan to practice law somewhere, law school probably doesn't make good sense.


How much research experience or publications are required to get into a good PhD program in USA

I think you should focus more on the quality and focus of your research than the amount. If you are researching a concrete topic, and have 1-2 solid works dealing with it, then you are golden. Make sure you explain the value of these works in your research statement/essay. That would be more or just as important as the resume, because it is an expression of you as an individual.

Other people will tell to go down the bullshit path and sprout several pieces that milk the same research but add little to the field. Some schools will buy that, but others will not differentiate you from the rest of students. You can also try this approach, but it may be even more time-consuming than the first.

Reading your question again, it is better that you engage in research before applying. Perhaps you can contact a professor and work with him, or a PhD student at your university, or find a research institute in which you can put in some time.


How can I force a journal to withdraw a paper?

This sounds like a strange situation, in which something isn't adding up. It seems to me that one of two things is going on here:

This isn't actually the reputable journal that you think it is.  It might be a "look-alike" predatory journal, or a formerly-good journal that has been hijacked, but in either case they are trying to scam you.
Something is deeply confused within the editors, and they've decided to publish despite the fact you've told them that you will not be paying.

In the first case, you definitely don't want your paper there, and in the second case maybe you'll get a free publication for some strange reason. The problem is to distinguish between the two cases.

Accordingly, I would recommend proceeding by writing an email something like the following:

  Dear Editors:

  As you know know from our former correspondence, we are unexpectedly unable to pay the publication fee for this paper. We are confused as to your current plans for the paper, however, and request a clarification.  Which of these two is your current plan for the paper?

  The paper is withdrawn, and we will submit to a different venue.
  You plan to waive the fee and publish the paper free of charge.

  Please let us know promptly, so we can plan the next step with this paper. If you do not reply within one week, we will assume the paper is withdrawn.

If they are predatory, they'll probably try to either stall or else try to tell you they're going to publish it and you have to pay.  Ignore such threats, even if they bluster about taking you to court. You are the author and nobody can force you to publish a scientific paper against your will: if they try, they will simply be exposing their own fraud.

If they're real, they'll probably answer one way or another --- or fail to, in which case you would be quite reasonable to assume the paper is de facto withdrawn and take it elsewhere.


Are there any reasons or benefits for the very long process of reviewing grant proposal?

The processes for grants and papers are very different. Once the editor or programming committee has reached a decision, there’s not much left to do.

Grants are much tougher. After the decision by the panel has been reached, there are several additional levels of bureaucratic approval that must be secured before a grant can be formally awarded. It’s these latter stages that lead to the extended time between submission and decision.


Does an acceptance of an abstract mean that I will definitely be presenting at the conference?

The practices vary significantly by field, but unless it is a very unusual case, having your abstract accepted means that you will be presented in some form or another.  It is not certain, however, whether you will be making an oral presentation.

In some meetings, having your abstract accepted means that you are definitely going to be getting up on stage and presenting.  In others, it means that you will definitely not be presenting, but will be given a chance to stand next to a poster in a distant corner of a giant room where nobody will realize that you are even there.  Most are somewhere in the middle, and you cannot know where it will fall on that spectrum without asking the organizers or looking at information from past conferences.

In all cases, however, it is reasonable to approach your advisor / department to ask about travel support.  Whether you can get full support depends on their policies and finances.  If you cannot, many conferences also have student travel grants or opportunities to work as a conference volunteer in return for having some of your costs compensated.


Should I send a copy of a closed-access paper requested on academia.edu?

I'd send the article.

I am not a lawyer. However, it's quite common for people to send me e-mail messages requesting reprints of my papers. The Academia.edu and ResearchGate websites have mechanisms to request a reprint of closed-access papers for similar reasons.

Now I think it depends a bit on the journal. The chemistry (ACS) journals that I tend to publish in, allow 50 reprints in the first year, and unlimited reprints after that point. So far, I haven't run into trouble with exceeding 50 requests for a paper in the first year. I'm happy to e-mail PDF reprints or handle them - in my case through ResearchGate.

Your mileage may vary (i.e., depending on the journal). Personally, if the journal expressly forbids sending such reprints, I'd find a different journal for my work.

In my opinion, blocking such infrequent requests for reprints impedes scholarly work.


Should I include journalistic articles in my CV?

I have written a couple of articles for 2 different daily newspapers. In them, I have discussed the issues of my academic field. Should I include them in my CV?

Yes, certainly, as long as you clearly separate them from your academic publications.  Strictly speaking, they are form of publication, so it wouldn't be lying to list them together with your research papers under a vague enough title, but this would be a very bad idea.  It would come across like you are trying to make your publication list look longer by inflating it with non-academic publications.

[If the newspaper articles had nothing at all to do with your academic work, then mentioning them probably wouldn't make sense.  However, it sounds like they do.]

  If so, under what title? Is press release appropriate? What is the most common and accepted term?

Definitely not press release, since a press release is something else: it's a document given to journalists to inform them about a possible story they could write about.  Occasionally newspapers publish lightly edited versions of press releases, without gathering much more information, but this is considered bad reporting.

I don't think there's a clear standard for how to list this information.  You could list it in several ways: outreach, other publications (if you have a "scholarly publications" section, say), writing for the general public, etc.


Actually, there are often many "facts" that really aren't. It is a fascinating research question to dive into the internet and libraries to verify the origin of something taken as a fact. This happens in every field and especially with pithy "quotations" that appear on calendars. Just for fun I like to look for the true source, in one instance I came up with five different supposed authors! This is also why you should reference your facts: So that others can verify that you are stating it correctly.

In the area of machine learning you can use the ACM or the IEEE digital library to dig around and look for a source. There are no shortcuts, this is research :)


How much knowledge is expected of a PhD applicant as compared to a postdoc or a research assistant?

I will only attempt a partial answer here as your question is a bit convoluted. Doctoral students on the first day, are expected to know less than a post-doc or research assistant on the first day. But they are expected to know relevant things. How your specific case would be judged would be up to a specific judge (i.e. a potential advisor).

But note that universities (as opposed to commercial/industrial labs) have a dual purpose. It isn't just to support the research interests of the current faculty, but to also educate the next generation(s) of scholars and researchers. Without that second  purpose there would be no need for graduate students at all. But then scholarship would end in a generation or two.

Universities are long term contributors to the future and take the role seriously, both in research and teaching.

The other links in your question seem to be pretty good for answering your other concerns.


How to get pornographic movies for scientific research purposes?

I really don't get this. This is a little like the Movies Classification Board or the Classification & Ratings Administration feeling awkward about asking to view the movies they are going to rate.

If you are developing an algorithm for detecting pornography, why would it be awkward to request funding to acquire test resources? This is an entirely legitimate application, that has huge potential, both economically and socially (note: use of bold inspired by OP). There are many researchers all over the world working in similar fields. Clearly, at some point you will need to discuss your work with your PI, and presumably, they are already aware of the work you have been doing in the previous 6/9/18 months, and perhaps already requires justification against existing research funding.

Whatever the case, your work will need to be approved by, and comply rigidly with, your institution's ethics committee.

There are also a number of steps you could consider before committing to viewing full-length extreme hardcore films. In making some suggestions, I'm going to make a few assumptions:

1 Your definition of a pornographic movie is one classified as
"mainly concerned with sex", and involves extreme nudity and acts of
sexual behaviour.
Your algorithm looks at exposed and interacting body content in some way, and does not work on quality of script and acting (otherwise daytime soapies will bring up many false positives)
Your algorithm looks at small fragments of movie clips, and not the entire 60/70/90 minutes worth, or however long these movies go for.
Your PI knows what you've been spending your previous doing, which is most likely already associated with existing research funding.

So, some suggestions

Acquire a number of movie trailers; these are usually freely available for all types of movies, and typically run for about a minute. Contact the various movie studios directly if you need to.
Speak to your national Film and Television archive body. They are likely to have a number of suitable media to preliminary early test procedures on. Various bodies exist.
Speak to other researchers in this field. There might be a good standard set of images/movies that can be used to determine baseline effectiveness.
Go to your local friendly adult shop and check out the "specials" bin.
Finally, and not the best approach to take, look at the internet. I'm guessing if you typed in the right combination of words, you'd get unlimited supply of short, copyright-free videos, to use both as a test group and control group. But I stress, this needs to be done in strict accordance with your institutions policies for network and    computing use, and therefore should be approved by your PI and ethics committee.

However, whatever approach you take, the summary is: talk to your PI.


You should keep a research notebook, regardless of whatever other system you have for notes. The format of the notebook is up to you; it can even be public (see Carl Boettiger's as an example of an electronic lab notebook). it can be created in programs such as an iPython or Jupyter notebook, or even a more specialized program such as Findings.

If you choose the pen-and-paper route for your research notes, and want to have the added flexibility/security of taking your notes with you (and also because it's good practice to do so), you should consider getting a scanner and making regular backups. You can then import these into a product like Evernote, Onenote, or MacJournal,
If you are using LaTeX, your options are somewhat limited, as most of the major tools for notebooking really don't support "live" LaTeX. Then you'd be better off using something like Aquamacs as a holder for your "notebooks" (LaTeX documents), and then using one of the above packages (or something like Papers or Paperless to organize the resulting PDFs.


What is the importance of TOEFL and GRE?

My experience is with US admissions in Computer Science at a productive albeit mid-tier graduate program. Both tests were required (TOEFL only for English as a second language speakers) and both tests are used for reasons to disqualify someone rather than admit them to the program.

My grad department would get about 500 applications for about 15 slots per year. About half of those were from totally unknown schools in China or India and were rejected out of hand, just because we had no idea about the quality of those students. Of the 250 remaining, about half of those had substantially deficient transcripts- things like missing or woeful TOEFL and GRE scores. The remaining roughly 120 applications were looked at by the graduate admissions committee, and then they picked about 30 high quality candidates and circulated those applications among faculty who were known to be looking for new students.

You'll notice there are two distinct types of decisions there. The first two phases were looking for reasons to disqualify people. The third phase was looking for good reasons to pass people along to final consideration. My guess is that virtually all departments would only use TOEFL and GRE scores in this way.

In other words, a bad GRE score can hurt your chances, but there's little difference between an acceptable GRE score and a great GRE score.

TOEFL might be a little different- our experience is that even people with good TOEFL scores might be atrocious language speakers, so our department always arranged in-person interviews via Skype or similar as a way to assess language proficiency. A great TOEFL score definitely didn't mean anything other than an acceptable score, because the in-person interview was the actual test of proficiency. I will note that we had much more stringent language expectations of Asian students than those from Europe.

Another thing to consider- I was told flat out by the University graduate admissions department that I would not be accepted with my GRE score, which was 20 or 30 points below their guidelines. The actual department I applied to didn't care. They were far more impressed by my independent study and selection of a challenging senior project than they were concerned about GRE scores.


Should I quit my PhD - workload, self-esteem and social life

I don't really want a degree.

There are many good reasons to get a PhD. Probably lots of people get say, bachelor's degrees and master's degrees, because they just want a degree, but the number of people who get a PhD just for the sake of getting a degree is (in my opinion) lower (for example, you might want to teach at the university level, see answers here). This is partly because a PhD is in some sense harder and more time-consuming that bachelor's/masters degree, but also that the degree isn't really the point of a PhD, see for example, this answer here by Pete L. Clark. To very briefly summarize, a PhD is a way to 'learn how to learn' and the stuff that you learn is a lot less important than the process of obtaining said knowledge. So your statement that you 'don't really want a degree' worries me a bit. I mean, the degree is not the point, and wanting a PhD is not at all the same as wanting a degree in general. Why did you apply to PhD programs? What was your motivation? What are your goals?

  I just want to get married, and have
  weekends and evenings off, and chill out and play board games, and
  have nice conversations with friends, and have time to exercise and
  eat good food, and partake in hobbies, and read books and play
  computer games and watch movies and write a novel or two.

Don't we all! Anyway, you know, you can do these things as a graduate student. This is easier/harder depending on your exact circumstances/stage of graduate career, but certainly doable. I recently graduated (with my PhD in mathematics), but in my graduate department on Friday nights a lot of us hung out at the grad student bar and then repaired to the department lounge to play boardgames often to the early hours of the morning. Some of us came in to work over the weekends, but not all of us. Anyway, even while physically in the department, we would visit each other's offices and goof off fairly regularly. Okay, for us goofing off also often involved talking about mathematics, so it wasn't entirely a waste of our time. In any case, chilling out and nice conversations with friends occurred throughout the workweek as well. In the first few years of graduate school, I did a really good job of eating right and reading and such, since my time was a lot more structured, and I was able to plan relatively well. Much of my department were regulars at the gym, and quite a few of us were spotted running on the jogging track (some of us were/are pretty good at this stuff: for example, one of did quite well in the Houston marathon and a current student is doing some awesome Crossfit things these days). During major exams, or thesis-writing, or trying to get a paper out, these things got a bit harder of course. Aside from fitness, many of us did well with hobbies. Some of us were hardcore gamers – we even had an informal Magic the Gathering tournament periodically among the grad students; others enjoyed cooking – the rest of us enjoyed the food they would bring in to share; I enjoyed jigsaw puzzles – for a while we did jigsaws in my office, where others in the dept would drop by to puzzle for a bit when they needed a break from work; one of us was in a band, others in in/formal choirs and such; I and some others were involved to various extents in students organizations; and so on. Some number of us got married while in graduate school (not me personally), and one of the students in my cohort had a child as well. How did we do all this stuff? We had an advantage in being mathematics graduate students, since we are not tied to a lab as our counterparts in the rest of the STEM fields, and we had the advantage of being in a department with supportive faculty (who sometimes joined us for weekly boardgames and graduate student bar hangouts) and awesome fellow students.

The most important part of the above list though, were the awesome fellow students. I was in a small department, so it was natural for us all to hang out together, but perhaps you're in a large department where this is harder. Try to find some fun fellow students. They are possibly feeling much of the same things that you are, and if they are in your department they possibly share your interests. If you don't know too many people (if this is your first or second year in the program), organize something – a movie night at your home, a potluck, or a boardgame night. You might be surprised at how many of your fellow students also want to find someone to chill with.

The second most important thing is time management and prioritization. Figure out what's important to you, and then figure out a way to do it. You might have to be very disciplined and focused during the workday so you can run in the evenings, or play boardgames every weekend. But, if there's one thing I learned in grad school, it's that the number of hours you work is not as important as the quality of work you are getting done. You might end up spending less time overall on work, but if you're happier in general, you will probably do better work in the smaller amount of time. For example, I absolutely need some time every week that I can be at home by myself watching TV, probably with multiple cats napping on me. This might seem like wasted time to the outside observer, but really it's time that I need to recharge so that I can get actual work done at other times. That's just the way I work.

  I like my research, and I like my advisor,

That's really great. I mean this sincerely. The opposite is sadly far too common.

  but I feel like I work a
  lot harder than my friends in industry, and I'll be putting my life on
  hold for at least the next two years, while I'm finishing classes and
  qualifying exams.

Well, to be frank, it is possible that you are working harder than your contemporaries and that you are putting your life on hold, but that doesn't have to be a bad thing.

Lots of people have lots of life-changing stuff happen in their mid-20s. For example, it seemed to me for a while that everyone that I knew in my age group was getting engaged, married, or having kids. I decided to count in 2013 and here is what I found

51 people I know got married i.e. about 1 wedding per week.
31 people I know got engaged i.e. about 2.5 engagements per month.
19 people I know had a baby i.e. about 1.5 babies per month.

(The count is with multiplicity, that is, if two people I know independently get married, I counted two weddings. There were no twins/multiple births that I'm aware of.) That's pretty intense!

These are all cool people and I wish them all the luck, but I don't want to be getting married and having kids just because all my friends seem to be (I mean, what an odd story to tell your grandkids someday).

Again, yes a PhD is hard work, hard work that doesn't ever get compensated for in any 'real' way. But the point of the PhD is not some eventual reward, the point of the PhD is really just the process of the PhD. Most likely I will never make the same amount of money as my friends with MBAs; they will probably have fancier job titles than me, and depending on where we are in the world, they might get more respect and power as well. But (forgive me) a PhD craves not these things. If you want prestige, power and such things, a PhD is not the right way to go at all.

If you're getting a PhD chances are that you have somewhat different priorities than the average person (which is fine, just as the average person's goals are also just fine). My friends who are younger than me have much more seeming grown-up lives true, but they are on a different track than me, and it doesn't really make sense to compare.

  Frankly I don't feel like I can survive the next
  year, and just the thought of staying here for the next few months
  makes me depressed.

This is concerning. Please consider talking to someone directly. It's great that you asked AC.SE this question, but we are after all strangers on the internet. Talk to someone you know and trust. Your university probably has a counseling center. Talk to your advisor/mentor.

Graduate students are often discouraged and depressed (I was no exception, see here), for example, see this article. The 'usual' discouragement often passes, but it is not uncommon for us to have undiagnosed mental/emotional health issues. A trained professional is a much better person to talk to about these things, and I hope you will consider doing so.

  The problem is if I wasn't a PhD student, I'd just be another fat ugly
  loser with no social status, and nobody would love me or think I was
  valuable.

This seems very unlikely to me. From just this question itself I see that you enjoy reading, and playing boardgames and video games, and enjoy good food and hanging out with friends; from this I see that you have hobbies and interests, and enjoy people. You asked this question, from which I gather that you can be introspective and that you are giving actual sincere thought to what you want to do with your life. This is all from this one question. The poster of this question seems like an interesting person to me.

Some of us are fat and some of us are less than conventionally attractive. Each of these things comes with barriers that one has to overcome. Conventionally attractive folks have their own set of hoops to jump through too. Yes, there do exist people in the world who think 'this person is overweight/stick-thin/different race than me/unattractive/the opposite gender/something else and therefore I do not value them', and those people can go f* themselves. There are enough of the rest of us too though.

  I wouldn't be taken as seriously when it came time to apply
  for jobs, and people would think I was stupid or at least not any
  better than someone with a bachelor's degree.

That's kind of a judgmental statement about people with bachelor's degrees. Anyway, all of this depends on what kinds of jobs you're applying for. There are some jobs where having a PhD would actually hinder you (see here).

  At least now I can apply
  for internships and get interviews. And because I am a PhD student at
  a top school, people assume I'm smart,

This is also a worrying statement. It's possible that I'm misinterpreting your statement, but in case I'm not, please look up imposter syndrome, it's distressingly common in academia; in short, this is a phenomenon where despite much evidence to the contrary, someone is convinced that they do not deserve the success that they have achieved (also see this question).

  which also helps me find dates,
  even though I'm obese, wear glasses, and dress poorly.

If you think that wearing glasses is hurting your ability to date, you could wear contacts. Similarly you could try to dress better (I recommend the show 'What Not to Wear'), or try to lose weight.

  It puts me in a
  different "league" and if I quit I'd have to go back to dating losers
  who only want me because they can't find any other girlfriends.

The people I know that are single do not all look alike, or dress alike, or all have poor vision. There isn't much that's common to them than the fact that they are single. You seem to be saying that if there were two individuals who were identical in every way except that one is in a PhD program that the grad student version would get more dates – I simply do not buy this. I might be willing to accept that this would be a true of a man, but I absolutely do not buy it for women.

If you think someone is dating you just because they can't find another girlfriend, please dump them. Similarly, if you think someone is dating you just because you are a PhD student, please dump them just as fast.

  Also if I quit my PhD, I would never be able to come back,

I know this guy who was a PhD student in my department (mathematics) in the 60s, didn't finish, left with his master's and was teaching in community college. He kept doing math on his own time though, and he came up with something cool, enough that a faculty member he had been in touch with got him back into our program and he eventually got his PhD in 2011. He is an inspiration. (See here for more such stories). So, yeah, I disagree with this statement.

  and what if
  my new job ended up sucking, or I couldn't even get a job?

Yeah, it's possible. But it's possible that you couldn't get a job with a PhD. Or that the earth is destroyed tomorrow to make way for an interstellar bypass. But worrying about this will not help us in any way.

  I do like
  my work, and I'm glad I get to do such interesting stuff, I just wish
  there was less of it.

You know, reading your question, it really seems to me that it's not that there's too much work, but more that there isn't as much fun non-work in your life right now. I would really suggest trying to build a social circle among your fellow graduate students, not only for having people to do fun things with, but also for people in similar situations to talk to. I know that for me it was really helpful to talk to my fellow students about my doubts and concerns, because we were all in the same boat. It sounds like you are very concerned about dating, so for what it's worth, lots of graduate students I know dated other graduate students.

While on the subject of dating, please consider whether you're giving too much thought to it. It is nice to have a partner that you can talk to, who will support you and care for you when needed, but finding such a person doesn't need to be take over your life. I strongly believe that successful relationships are composed of people that are also happy on their own and in their own skins. Perhaps it might be worthwhile to work on your own happiness for a while before seeking out a partner, particular since when having self-esteem concerns it is very easy to find oneself in abusive and/or unbalanced relationships.

I would also recommend that you give some serious thought to what you value most in your life and what you want to do with it. What are you looking for? What is your dream job? It will probably help to talk to someone directly about such things too. You said that you like your advisor, so they might be a good person to talk to. Most of us that have been through graduate school have dealt with these things to some extent.

Depending on this self-examination, you might decide that a PhD is not for you. This is fine. Or, you might decide to stick with it. This is fine too. With the caveat that you're doing it for the right reasons. Some of us hang on to PhD programs with this notion that 'quitting is bad'. That's a poor reason to stay in a PhD program. On the other hand, if you truly enjoy doing what you're doing, and you want to keep doing it for the rest of your life, that's a great reason to hang in there. If you want to stay in the program so that some hypothetical someone might deign to date you, that's a poor reason to stick around, and also such a person clearly isn't worth your time.

Getting a PhD can be hard work, probably harder work than your contemporaries are doing in industry (I speculate, I've never had a job in the real world). It is rewarding in its own way though, to some people. This isn't a value judgment. Math makes me feel like a complete idiot almost all the time. The remaining 0.01% of the time is pretty good though, and that's enough for me. Mostly this makes me a masochist I think, but that works for me. But it makes perfect sense for it to not work for everyone, and honestly these other folks are probably better adjusted anyway.

Lastly, your last paragraph makes me think that you're worried that you're making irreversible decisions. You're not. If you choose to leave your PhD program now, you can still come back to get a PhD (probably somewhere else). If you started your PhD with the goal of being in the academic world, but decide later that you want to be in industry, you can still do that. If you want to start back from scratch and work in sociology (say), you can still do that too. These things might require some work, but they are all still possible.

Best of luck in your decision-making! I'd like to reiterate, pretty much all of us wanted to quit at some point, and pretty much all of us wondered why we were doing it. You're not alone!


Sending a paper to a conference with indicating that it is a preliminary version

In my field (one of the social sciences), where conference papers are usually regarded as work in progress that at a later stage will be send to a journal (as opposed to computer science, where 'publication in a conference' often is the goal), it is not uncommon that people include a statement like "Work in progress, please request most recent version from the authors before citing". I've done that several times, in fact.


What are financial prospects for a postdoc as compared to a PhD student without funding?

So is my financial situation going to depend on if I can secure a
  grant for my research as a postdoc or I should expect to receive a
  salary?

The question is not getting a grant or getting paid, it is getting paid by the institution you work for or getting your salary from a grant giving institution.

  How many postdocs do get paid?

(As far as I know) All of them. Depending on the country you are talking about it may even be illegal to employ someone without pay.
However, (as @virmaior pointed out) there are some "postdocs" in Japan that are not paid and have no work requirements. At least in Europe and the US this is not common and in most cases this is probably a bad idea for someone looking for a regular postdoc position (see my comment below).

  How likely is the success in either ways?

That depends on your field, the quality of your work, ... . We can not answer that but you can talk to your peers /supervisor about the job market to get an idea.

  [as a postdoc] I do not have to pay academic fees or any other fees to
  a university

Right.

One general remark: If you are not not getting a (paid) postdoc position or a grant you should try to find a job in the industry anyway. Finding a more senior position is usually much harder than finding a postdoc position.


What is the least amount of effort needed to ensure no copyright issue of using online pictures in lecture notes/slides

Use images that have a CC0 (public domain) license. That way, you can use them for any purposes even without having to attribute them to anyone.
For instance, use https://search.creativecommons.org/ and select the license "CC0":

Or https://free-images.com/ seems to be a search engine specifically designed for CC0 images.


How important is the publication venue for academic hiring and grant applications?

There is probably not a single truth here but I would make the following statements:

Having a good publication record is the basis for basically everything in academia. The question is then what is good? As a fresh PhD student citations will be near zero (I am guessing in most fields). Having publications in citation index listed journals is therefore a definite plus. Having several as first author is a must (see What does first authorship really mean? for a discussion) I would also argue that having papers not part of the PhD (even if not first authored author) is a plus since it indicates activity.

As a new post-graduate you need to improve the publication record as best you can. You need to show that you do your own new work but also be part of collaborations in some mix. Building a publication record takes time and will partly be up to your own efforts and in some way also by chance (you never know what opportunities lie ahead).

To get employed, you can basically only compete with a good publication list. Everyone knows this takes time and I am guessing all fields have their own "standards" as to what is a reasonable publication rate. In my field where papers are based on field investigations, 2-4 papers per year is considered acceptable, the longer-term average should be towards 3-5. The rate is thus an aspect that should not be over-looked.

Typically you will have a dip post-PhD because it takes time to build or get into a new environment and to start writing new papers. Having something on the back burner for that period may thus be useful to bridge the gap.

As a final note, the citations will be more and more important after a few years. In my field it usually takes a few years to start getting citations because the results will inspire someone to apply for money, go into the field for new investigations, and then write papers. In a lab or theoretical environment such response times may be lower so check with seniors in your field what applies. A good question to ask is perhaps if there are ways to promote ones work to increase citation records, I do not have the answer to that question.

Bottom line: publish in as good journals as possible. Good quality counts but a reasonable publication rate is also necessary. Citations will come with time.


How to cite a thesis/paper when it's not available online?

Assuming X is citing the reference Y whose content is unavailable, it is fine to cite Y just as done in X. It is better to mention it as a secondary source by stating that the concept mentioned in Y is as claimed in X. @jakebeal's answer to this post is most apt solution for this problem.

Some sources may inaccessible or totally unavailable (as in your situation) but they are cited nonetheless in the conjecture that the content they are assumed to provide are true. For instance, if an important method was proposed long ago and you wish develop on it, you ought to cite the original author of the paper (in addition to the standard books you refer), even if you couldn't access the paper yourself.


How to prepare enough material for my class?

It is a common misconception among beginning teachers (including me when I first started) and some experienced teachers that it is good to include more materials in your teaching.  However, since students have a limited ability to learn, it is better to keep the quantity of material within that limit.  Pick the most important stuff, and make it really good.  Then review as much as possible to help students remember.

When designing your teaching methods, start with objectives (e.g. improving students' TOEFL score), then pick your assessment (the TOEFL), then design the content (practicing things that are likely to be on the TOEFL).

When I teach, my challenge is getting rid of unimportant material so it does not distract students from the important information.


Is there any way to find changes between two revisions of a book?

There are several out-of-box tools that you can use to check the differences between two or more documents. I typically use the built-in merge feature of Mendeley that gives you a confidence interval when merging two documents. From that you can extrapolate if the documents are pretty similar or extremely different.


Applying for a PhD before or after finishing master's

As you already noticed, almost everyone applies during the last year of their master's. No one wants you to feel compelled to take a gap year between your master's and PhD. Since almost everyone is in the same boat as you, they will have a similar level of recommendations. This is expected! Your thesis supervisor should still be able to say some nice things about your research aptitude and potential. Apply now!


Can't handle the stress while being bombarded with questions during the presentation

In this situation, you're a presenter and you're getting bombarded with questions, is this right? Are people incessantly asking questions and not letting you answer, or do you just feel this way because you shut down in front of the audience?

First, relax, because as the presenter, you have the floor, and you should thus be in control of the room. This mentality has helped me in the past because if you're presenting, pending time limitations, you're the highest authority in the room aside from the chair/professor, and you're free to speak at your own pace, discuss things in your preferred order, etc. Others should respect this, and remembering this gives you power.

Pace yourself, and take time to think. If someone interrupts you, etc. tell them that you'd like to answer the previous question before you get to them. Stand tall, and crossing your arms behind your back helps posture to an extent, and try to not focus on one person in particular as you answer questions. Watching their reactions can be intimidating.

Just make sure to not focus on the people asking questions or how you feel about questions, but rather on how you feel about where you are in describing what you wanted to talk about.

Edit: If you don't have an answer, that is also fine, and never be afraid to say "I don't know". This is still part of the presentation, and that is what you have to offer. If you don't like not knowing it, ask the person asking the question if they can give you their information so you can follow up with an answer later.


Transitioning from PhD in biomedical engineering to software dev (have 5-6 software experience working for a team during PhD)?

I have been in both industry and academia, both as a software developer and lecturer, and here two points that might help you:

You Diplomas: You non-software related diplomas, does not hold you back on finding good software development jobs. It is how much you know about software development. In fact, you have a good story on saying that you are chasing what you like.
Choose Your Side: Ok, so you been involved with robotics, so probably you enjoy logic and reasoning more than shapes and colors. Therefore I would suggest to look into back-end development sort of things (e.g., Python, Java development), rather than front-end design and implementation.
Your CV: In you cv include any software development experience, even if it is by using an obscure software or programming language. Also, do not hide your academic past, simply explain that is what you did enjoy then and now you enjoy doing software development.


What is the procedure with regard to unfinished thesis if I am terminated from the program?

Departments generally do not terminate PhD students without letting the student's advisor know in advance. The fact that your advisor has not responded to you for 3 weeks, suggests the possibility that he/she is ignoring you. This is reasonable behaviour, if in fact your advisor was behind your termination.

As you are not currently in the US, you need to call your department chair and/or the chair of graduate studies and figure out what is going on. In my opinion, it is too soon to look for a new program or to start really worrying about your data.


Percentage of the world population with subscription journal access?

Perfect question! If anyone can provide such stats this would be amazing. :)

I would make the question a bit more specific. Let's assume I'm an author who wants to publish an article and have to choose between a particular toll-access journal and an Open Access one. We want to know what's the potential audience of both journals, measured by the number of scholars who can access the article, without differentiating between disciplines (for simplicity) and without considering non-scholars (they're hard to measure). The main question is how these two numbers relate to each other: the toll-access audience is 90%? 50%? 5%? ... of the OA audience? I suspect the value is closer to 5-10% for most journals, because there are something like 30,000 journals out there and most of them are not very presitigious and subscribed only by a fraction of institutions, esp. in developing countries. Being able to quote such a percentage value would make a powerful argument for OA.

So, one half of the answer is simple: potential audience for any OA journal is in the range of 7-9 million - that's an estimated global number of researchers, according to the STM Report 2015.

The other part of the question is more difficult: for a particular journal, say, Nature, what's the number of scholars who can access it through institutional subscriptions, and what fraction of 7-9M it is? Or, how many institutions subscribe to a given journal? -- I don't know the answers, but I think it should be possible to come up with some estimates by analysing subscription lists of different institutions and coupling these data with counts of researchers at each institution - if not globally than at least for a particular country. For US institutions SPARC may have some data, I guess?


What happens if a professor's interests shift dramatically?

Assume that the change is gradual, not abrupt. Alice will want to learn something about the new field so that she is able to do effective research in it. No new department is likely to accept her until this happens. She is also unlikely to completely abandon the old field due to the many constraints, both financial and ethical. Yes, she needs to see to the needs of her current students somehow, and may need to keep publishing in the old field if she wants good annual evaluations.

Once she has a few nice publications in the new area she can start to look for a new position. She probably doesn't need to get any additional degrees unless that is needed to obtain the expertise in the new field, but it would probably help her job search to have some formal qualification in the new field.

One way to get some expertise is to try to collaborate with experts in the new field, first as a junior partner. It is best, of course, if she has something to offer her collaborators, perhaps some research perspective from the old field.

For smaller jumps, of course, it is much easier. Many people switch back (and forth) between math and computer science, for example. This is true even though the basic research methodologies in those two are quite different. I switched from math to CS over a few years at a time when the institution I was at needed expertise in a developing field (long ago). But a person who switches here likely is able to use many of the ideas in the "old" field to enhance their work in the new.


When does it make sense to send more inquiries asking about review progress to PLoS ONE?

PLOS One are pretty good at hassling editors to get a move on (I know, I am one) and if an editor doesn't move on a paper, they will reassign it to a new editor. So I don't think asking what's happening will help.

The usual reason for delays is reviewers. You ask someone to review. They don't reply. They are reminded. After two weeks, you give up and try to find a new reviewer. You invite them to review. After one week they agree. Two weeks later  a reminder is sent. A week after that another reminder is sent. A week after that you give up and invite a new reviewer. We are at two months, and we don't have a reviewer yet.

The one thing that you might do to help is suggest reviewers. You might be aware of people who are working in the area that the editor may not know about (for example, because you have seen them present at a conference).


Is it appropriate to discussed a proposed method in the literature review or in methodology chapter?

First of all: There are no global rules or even guidelines as to how theses should be structured and how chapters should be titled. Whatever works in terms of intelligibility is allowed. The only thing that can happen is that your supervisor (or in rare cases, your department) has become fixated on a certain structure and insists on it. But we can hardly answer on this here.

Thus, in your situation, you have several options. The following come to mind:

Include your method in the literature-review chapter, but name that chapter “Methods for X” or similar, not “Literature review”. If the literature review contains things not fitting under that title, think of a better title or make a separate chapter for those things.
Include your method in a new chapter called “A new method for X”.
If your methodology chapter is strictly about how you compare methods, do not include your method there (and give it a better name like “Benchmarks for methods for X”). If it does however cover several different aspects, your method may fit there.

As I already said, whatever works is allowed. Thus the most important things to consider are things like what prior knowledge the reader needs to understand your description of your method, as this should obviously described beforehand. And those are things only somebody very familiar with your thesis can decide.


[paper review service] reduced [paper] size by more than 50% by taking out words phrases that they thought to be redundant and rewording sentences to be easier to understand by anyone.

A fifty percent reduction in paper length is an excellent improvement of your paper, because your readers have less to read. (Assuming what "they thought to be redundant" really was.) There's no need for any "sour feeling," appreciate the improvement and learn how to make similar reductions. (Note that reductions are far easier for someone else to make than the original author.)


Writing homework essay anonymously to avoid controversy

The point of an exercise in dissecting a contentious issue is not that you must agree 100% on the solutions to the issues by the end. The point is to find where you and the other members agree and where you and the others agree either that a) further research is needed or b) fundamentally different approaches are being proposed.

Your desire not to sign off unless you agree 100% with everything in the document essentially defeats the integrity of the exercise. You are allowing your (preconceived) stand to override the goal of finding common ground. Common ground is saying "We agree on these statements, we need more time on these statements, and we disagree on these statements."

So, first compile a document that presents the statements where you both agree, where you both agree that further research is required, and where you both agree that you both disagree.

Then, prepare an addendum. Present your views for the statements where you disagree. Invite your co-author to do the same.

Avoid using the addendum as a way to poke holes in the main document. The addendum should be of the tone "I FULLY agree with the presentations in the main document. I see issues however at the noted points of disagreement. My reasons are as follows: ..." Limit the addendum to a minimum (e.g. one page or even one paragraph).

Submit the document and the two addendum pages.


My PhD supervisor is against external collaboration. What should I do?

Since you wrote that you are funded by a project, I'd like to mention one possibility, without knowing whether that's really the reason or not.
Project funding, especially for more applied funding schemes (e.g., EU Horizon 2020), typically come with obligations, such as reporting, or having to work on certain problems that were promised to be worked on in the funding proposal. This is possibly a reason for why you are working on a topic that neither your advisor nor other group members can help you with: because it has been promised in the proposal for some reason.
Now as you mention your best bet to get support is by collaborating with externals. Scientifically fruitful collaboration is often quite dynamic: the actual research question addressed may change a bit during the collaboration, and in particular it may move away from what was promised in the proposal. From a scientific point of view, this is how great ideas are developed, but you end up getting results that your advisor (grant holder) does not know how to sell as fulfilling the obligation that comes with the project funding. Also, you may end up getting results that your advisor may be unable to use as a proof of competency for future funding proposals, which is important to maintain the flow of funding.
Both of these would be problematic for your advisor, which is why he/she may be unwilling to give up control over what you are doing by letting you collaborate with someone not under his/her control. Also, once a collaboration has been started, if would be problematic for your advisor to ask you to end the collaboration if he/she later gets the impression that the focus of the collaboration is not what he/she needs or wants - at that point your potential collaboration partner already invested time, which has to be respected.


Zero papers in first PhD year. Is this common?

In my experience (in environmental science), it is unusual for students to publish in their first year, and typically only happens if they are publishing work that was largely done before starting their PhD (e.g. from a research Masters degree).


For NSF proposal and grant purposes, do graduate students meet the definition of "investigator"?

Actually, the NSF, in its Grant Proposal Guide, does not actually define the concept of an "investigator." Instead, it chooses to define the different categories as "senior personnel" and "other personnel." Typically, postdoctoral fellows and graduate students fall under "other personnel."

Personally, in such matters, I would opt on the side of caution and just have the graduate students fill out the conflict of interest form. It doesn't take very long, and having it in place makes life easier for everyone.


I wouldn't turn down the position with your advisor out of concern for how it will look at your CV.  It's hard to know for sure what will trigger a negative reaction in any one specific person; there are a lot of different people on hiring committees so it's very hard to absolutely rule out the possibility.  But precisely because of that, you can't let the possibility of something looking bad paralyze you, since almost anything could.  Someone once pointed out to me that there are certain things on one's CV that "look bad" but only really to people who are looking for some excuse to knock you down; if you don't give them that thing to take a hold of, they will surely just find something else.

Furthermore, I think the possibility of having a CV that suggests a charmed path of continuous success is a horse which has already left the barn.  If someone is going to hold a postdoc with your advisor against you, they could also certainly hold being on your 7th year of postdoc, or whatever number you had done; certainly if there's a gap between the end of your current job and the next one, they can hold that against you.  I would take whatever path is going to give you the best short term chance to do good research; that's what your job search next year will be based on, not exactly what path you took while doing it.