Can I show my co-author the final version of an accepted publication I reviewed?

No, you cannot. Until the paper is publicly available you cannot show it to anyone nor even acknowledge its existence. The only slight exception I would make is that if a colleague was going to pursue similar/identical research, I would tell them they might want to contact the author. I would assume that this would result in my identity as a reviewer being revealed.

Your options are:

Submit your manuscript as is, but add the citation as soon as it become public.
Reveal your identity as a reviewer and ask the author for a preprint.

Option 1 is reasonable since you believe the existence of the paper is not critical to your paper. Option 2 is okay, but remember the reviewers of you manuscript will not have easy access to the cited material.


Is it okay to disclose papers under review for feedback on the review?

As you say, it's part of the process of getting a PhD to learn how to conduct peer reviews, and working off templates and examples is only so useful.

I would however say that maintaining the confidentiality of the review is paramount.

Were it my own paper that was being reviewed, I'd have no problem with it being discussed 1-on-1 with a student and their supervisor, or within a small, lab-group setting. Wider distribution than that would start to make me a little wary - essentially, the wider the circle, the harder keeping the review in confidence becomes.

Another technique is to review already published papers or pre-prints as if you were peer reviewing them. This is commonly a format for journal clubs, and helps you learn the process in a way where confidentiality isn't a concern.


What to do if the corresponding author is presumably dead?

You could contact their institution (or its successor), explain your issue and ask if you can access its archive. There is at least a chance that supplementary information or even a specimen preparation can be found there. Obviously, going through an archive can be a big effort.


Can I mention interest in two somewhat different research areas in my SOP?

Stop calling it an interest when you have publication proving expertise. I'm "interested" in the Real Housewives show. You need to find a better set of verbiage. You are at the edge of the field in two areas but it remains one field. Let the professors fight over who gets to work with you. Let them fight over who gets published with you. You need more than one vote to get in, so get all votes. You are accomplished in two areas of one field. Show that you are young and scrappy and willing to do the work and they will put you to work wherever they see fit. I'm wondering if current students "do their own thing" or basically apprentice on professor pet projects and publish for the professors. See what has been published. They want someone to do the work and keep the school top tier, but they don't need any competition later, right? Focus on what an honor it would be to be mentored by them at such a great place. They have to actually work with you and sit for office hours with you, so be that guy who gets the work done between meetings and isn't needy yet takes all suggestions and is deferential.


How comes over 25% of retractions fail to explain the reason of the retraction?

One reason is that it can be a face saving technique.  Sometimes there are suspicions of fraud or other misconduct that are difficult to prove, or the authors strenuously disagree with each other about who had responsibility for something or exactly what happened.  Instead of fighting about the explanation, the editors and authors may agree to retract the paper while giving only a vague reason that everyone can agree to.  This is not ideal as far as scientific clarity goes, but sometimes finding the truth is genuinely difficult, and even when it's possible it may not be worth the effort.

As a general heuristic, if a paper is retracted with no clear reason, then the reason is probably not good (or at best it's complicated or debatable).  After all, if there were an explanation that sounded good and was clearly true, then why wouldn't they include it?


MLA: in-text citations from one work - do I need to restate the author every paragraph?

You do not need to include the author's name in every citation, as long as you make it clear that you're only using one source.  I say this based on the MLA guidelines found here.
Specifically, you should look under the section "In-text citations: Author-page style", which states that the author's name doesn't need to be cited in the parentheses as long as he/she is mentioned in the text.


Students leaving a new lab - have I made a wrong choice?

The main result of  a PhD program is not a PhD thesis, it is a PhD-level scientist. In other words, you.

Your PhD is about you learning to be a researcher. It's about things you pick up from supervisor and the lab: research methods, writing styles, professionalism, passion, attitude.

The postdocs in the same lab may have different goals than you, different experience, different needs and expectations from/towards PI. Their decisions are their own.

For the sake of example, let me exaggerate a bit. Imagine you also had a  college student in your lab, and your PI happened to be a great college teacher, spending a lot of time explaining some basic maths to the student. The student would probably genuinely  benefit from this, but as a PhD student, you could feel yourself a little bit overlooked.  Is not it what your postdoc colleagues might've feel at the moment? Is it possible for a PI to be equally perfect for all members of the lab? To what extent this all-round excellence matters for you?

Maybe, reflecting on these questions helps you to find the right decision. Good luck.


Axis naming for multiple parameters in one graph

You should use the singular, "Position Angle," because an axis is  interpreted as referring to each data element individually.

In order words, at time 0.4, the red line is not at approximately "60 angles," but is at an angle of approximately 60 degrees.


In a research statement for PhD admissions, should I start with the context, or directly with the idea for my research?

Now my question is, which is the best way to format the proposal?

Different writers could balance these issues in different ways.  The key is moderation: you have to give enough context to make your proposal understandable, but you also shouldn't go overboard (it's a terrible idea to start a research proposal by saying "Since the dawn of history, transportation has been one of humanity's greatest challenges. The wheel and axle were a great advance...").  If you never mention until page 5 that you even have new ideas, then readers may give up in disgust before reaching that point.  On the other hand, too little context can be just as bad, since the proposal will do you no good if it's not understandable.  Unfortunately, there's no universal rule to decide the right amount.

One strategy is to look at the introductions to the research papers you've found.  If your introduction is briefer or more abrupt, then it's not reasonable to expect anyone to follow it.  If anything, a research statement should generally be accessible to a broader audience, and that may mean somewhat more background and explanation.

It can also be useful to cycle between background and new material.  For example: brief introduction, brief description of your new idea, longer account of context, more details on new idea.

Given that you are writing this for a specific professor, it's worth asking him/her for more guidance.  If you phrase it too generally ("How do I do this?") it might give a poor impression, but I think it would be safe to ask a question that shows you are seriously working on it.  For example, "I'm thinking of organizing my proposal like this: [Insert one or two paragraphs about your topic and how you plan to arrange the proposal.] Does that sound like what you had in mind?  If not, I'd be happy to rethink the organization."


How should feedback be given for "silly mistakes" on an exam

First, notice that students will typically be able to tell which of their mistakes were silly and which more significant.  So for silly mistakes you don't need to write feedback other than to circle where they went wrong, and indicate the number of points taken off (or granted).

For a more serious mistake you can write more detailed feedback.  Sometimes feedback here isn't necessary, either, other than to write, "see solution."

Second, you can figure out what types of errors and what frequency of errors you want to bring the grade down from A to B, from A to C, etc., and decide how many points to remove based on that.

More importantly: what's a well written exam like?  Example: I'm asking them to solve this eigenvalue-eigenvector problem.  If the student has a vague idea what is being sought, I want him to get one point.  If he sets things up well but doesn't know what to do next, he gets two points.  If he follows through well but for whatever reason didn't quite get to the perfectly correct punch line, he'll get 3 points.  Perfect, complete answer: 4 points. (This is just an example of the point distribution.  You might end up with a different scoring structure.) In short, the scoring should be integral to the exam design from the beginning.

Most importantly: as a TA, you should be getting special guidance from the professor for grading a midterm exam.


How were people able to graduate with a PhD at a such young age in the past?

There are several issues:

Your examples are somewhat biased, since you've selected researchers who were not only brilliant but also prodigies.  By contrast, Riemann finished his Ph.D. dissertation at the somewhat older age of 25, and Weierstrass didn't start his research career until he was 39 or so.  Brilliant researchers are more likely to get an early start than average researchers are, but the correlation is far from perfect.  Focusing on prodigies gives a misleading picture.
There are plenty of prodigies today (Terry Tao, Noam Elkies, Akshay Venkatesh, Erik Demaine, etc.).  If they occupy a smaller fraction of academia, it's probably because academia has grown enormously even relative to the population.  The faculty in the top departments today are stronger on average than a hundred years ago, but there are many more departments nowadays, so the average professor is overall probably not as talented.
The amount that's known is steadily increasing, so getting to the 19th century research frontier takes quite a bit less time than getting to the 21st century research frontier.  This is not as relevant in very new fields, but finishing a Ph.D. in algebraic geometry in two years is a more impressive feat today than it was a hundred years ago.  This increase in knowledge doesn't translate perfectly into an increase in time to degree: people also compensate by specializing more and then broadening later in their career.  However, the obstacles to a quick Ph.D. are certainly increasing over time.


How should I stay in professional contact with former supervisors and/or colleagues?

The easiest way is to keep working on projects with them. If that ship has sailed, then the next best way is to be friends with them on social media, which is to say, be friends with them in real life. Barring that, you have to work to communicate with them on a regular basis about topics relevant to your shared interests: go to conferences and strike up conversations with them, share interesting papers with them via email (i.e., "Did you see this new paper from prof X? What'd you think?"), propose joint projects and write joint grant proposals, etc. It's not hard, but it does take active work.

People definitely do this, and I think it's one of the best ways for a new post-PhD researcher to get experience writing grants and proposing projects if they haven't gotten that experience already. That being said, it's also hard. You're supposed to be striking out on your own and establishing new frontiers. Your old colleagues are either doing the same thing or using the slot you left to pay new students/postdocs to continue the work you left behind. It can be challenging for everyone to strike the right balance.


Should I include interviews transcriptions in my thesis?

Quite honestly I doubt that anybody would go and read that appendix. What I would do is that once the thesis is approved and put in the online repository of the university, you could add this appendix just as an online document and refer to it in the main thesis. That way if anybody wants to access it they can.


How do I judge a conference's trustworthiness?

Financial reliability is going to be related to scientific validity. Definitely agree with JonCuster's comment that long-standing conferences (e.g., annually recurring events with a history of substantive organizers and programs) are more trustworthy. Some new conferences are hard to evaluate; this will depend more on who exactly is organizing and whether your network trusts them. Otherwise, this general list could help.

https://libguides.ucd.ie/publishing/predatory

  The conference has an overly ambitious title
  The technical programme is broad. Very broad.
  The language on the conference website is…off
  Renowned organisations are sponsoring a low-profile conference
  The organisers’ contact details are missing, or aren’t quite right
  Another conference with a suspiciously similar name already exists
  The conference or its organisers have known associates
  The organisers are charging higher-than-normal fees
  The conference is unusually frequent

Caltech Library’s list of predatory conferences:

  https://libguides.caltech.edu/c.php?g=512665&p=3503029


Advisor associated with the U.S. Army want their name removed from the text of a published article

This seems like an unreasonable request to me. The copyright to the text rests with the publisher, and the "moral rights" with the authors of the paper. I don't think anyone who is mentioned in the article has a legal right to request removal from the article. Certainly, this would morally require consent from the authors.

In general, I do not think that there is a legal right to not have one's name mentioned unless that violates state secrecy rights (think, the name "Valerie Plame" appearing in newspaper articles about the CIA). If the local newspaper mentioned my name in the context of the local cycling club, then this seems to me to be a fair use of their journalistic priviledge that I can not reasonably challenge.


I would respond to the editor that:

Our paper was submitted on DATE.  Paper A was published on DATE.  Both works show that XYZ.  The publication of A in the well-known Journal of W is evidence that our work is important.

Most editors are decent people and will realize that the prior publication of A is not within your control, nor is it something you overlooked.
Do revise your manuscript to clearly compare your work with A.  In the manuscript, you can state that the paper A was published after your initial submission, if you wish.
Publishing multiple papers that independently get the same result is good for science and should be rewarded with publication.


I believe a publisher is infringing copyright when reproducing a figure I created. What can I do?

You attempted to use a crayon license, that is, modify the terms of an existing well-established license to better suit your needs.
This is frowned upon, because it can cause legal complications. In particular, the license CC-BY-NC 4.0 license that you attached to your work states

The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed.

or, in other words (human-readable version on their website)

No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.

The CC folks officially forbid you from using that name and logo if you do modify their terms:

Can I change the license terms or conditions?
Yes—but if you change the terms and conditions of any Creative Commons license, you must no longer call, label, or describe the license as a “Creative Commons” or “CC” license, nor can you use the Creative Commons logos, buttons, or other trademarks in connection with the modified license or your materials.

So it is going to be difficult to argue for your additional restrictions in court. They are likely to be void. For legal purposes, we can assume that your work is licensed under an unmodified CC-BY-NC 4.0.
Notice 1 still stands, because the CC license allows you to specify your preferred name and wording for the attribution (and it seems to me that they complied with it in the book). Notice 2 is void. Notice 3 still stands, because the license only covers non-commercial use.
So Elsevier is infringing it because they are using it in a commercial work, right? In principle yes, but you wrote that you had an exchange with them and essentially authorized them to use it in the book under the terms listed in Zenodo. We would have to review your full conversation with Elsevier to see what you really wrote to them.
Disclaimer: IANAL.


Should one cite during university exams?

In most technical university exams, there is no expectation of citations since the concepts are typically "textbook-level" material and thus established as part of the "common knowledge" of a subject.  Such information is rarely cited in the scientific literature, as it taken to be part of the shared background knowledge that has been so accepted as to no longer require explicit crediting.  For example, Newton is almost never cited when discussing basic physics.

In a literature or similar humanities course, on the other hand, the subject of an exam may explicitly be discussion and analysis of ideas presented by others. In this case, one would be typically be expected to at least informally cite the people whose ideas are being discussed, e.g.:

  Rawls' theory of justice, while more sophisticated than the simple utilitarianism of Locke, is considerably more difficult to comprehend"

Full formal citation, however, is typically both impractical and not useful within the scope of an exam.

Where business courses fall on this spectrum will depend on the course: when discussing case studies, I would expect informal citation to be appropriate, whereas an operational research and statistics course would more likely fall into the technical end of the spectrum where there are no citations.


What's the impact of former university's transcript on PhD application?

Every field (chemistry vs. mathematics vs. history) is different and every PhD program at different universities you apply to is different. Also, who serves on the PhD admissions committee may change year-to-year.

Yes, many top-tier programs will look at your GPA. How much weight will they use to judge your application is variable. I can imagine a situation where the five professors on this years admission committee decide to stress class grades for incoming students.

Yes, many program will seriously consider any research you do, even if you never published anything. Simple being involved in an processor's research laboratory will most likely give you an advantage. I can imagine a situation where the five professors on next years admission committee decide to stress undergraduate research in incoming students.

My point is the following: You can't predict what will get you into a PhD program because it may change year-to-year.

What I would do: It would be nice to find a way as an undergrad to research something, but I wouldn't stress about it being publicly published. It may be enough to have a strong undergraduate thesis, similar to a senior-project, that shows your research ability. That with a good recommendation letter from one (or more) professors you work with will be the building blocks of a strong application.


Critiquing or commenting on someone's talk

X, being an expert in the field, can presumably find ways to communicate their opinions to the speaker, publicly or privately, if they wish to do so.

Often, opinions communicated between experts will be much more complicated and mixed than a simple like/dislike. "I agree with you on points A, B, and C, but I think point D is contradicted by Y's research. I'll send you a reference." is much more likely than either extreme.

If you just heard X talking about point D and Y's research, you could get the impression X disliked the talk. If you just heard X talking up points A, B, and C you could get the impression X liked the talk. Neither impression would be fully accurate.

Unless X has positively authorized you to speak on their behalf, you should not do so. If asked directly, indicate that you are unsure and, as suggested in a comment, encourage the speaker to talk to X directly.


Switching from one area of graduate study to another?

In general, transferring to a different department requires a fresh application. While many departments will be sympathetic to applications from students alresdy at the university, they will still require all the formalities associated with a new admission.

However, the procedures vary wildly from place to place, and you must check with your local institution (if you have one already).

Other factors that can mitigate or complicate this process: if there's a standard procedure for doing this, if the two departments historically are comfortable with movement back and forth, if the departments are in the same college/school within the university, and so on.


Is it ethical to reject an article after acceptance?

The process is unusual for sure, but without seeing the reviews and what exactly the editor and you wrote to each other, I can't say that it is unethical. The acceptance of the article may, for example, have been conditional on improving language issues. This may or may not also have been stated in the reviews that suggested acceptance "subject to improving the presentation" or similar wording.

In the end, what you describe is an editor deciding that this improvement in presentation or language is apparently not forthcoming, and so the conditional acceptance was turned into a rejection. I'll note that you state: "And even more so because the rejection wasn't for the quality of my paper nor the fit of my article...", but that is exactly what it sounds like: the quality of a paper is not only a function of its scientific contribution and originality, but also its organization and ability to convey its meaning accurately. I have certainly rejected papers that may have had sufficient content for publication but were written in a way that made it impossible to understand or follow the arguments.

Obviously, I cannot say whether that is what happened. We lack the information for this. But in the end, I do believe that it is upon the author to present the material in such a way that it is understandable. Papers that fail to do so, even if their content is good, should be rejected.


How to publish new results for a paper under review?

There are three basic routes that you can take for close incremental improvements of this sort, depending on timing and the complexity of the work to be described.  They are:

If the improvement is relatively simple (could be fit into the existing paper), and is completed before the camera-ready deadline of the conference, then the best thing to do is to incorporate it into the current paper when you revise for the camera-ready version.  This type of improvement is generally acceptable in conference publications.
If the improvement is complex and impactful enough to deserve its own paper, write that paper and reference the current paper as "submitted."  If both are accepted, then the timing is likely to be such that you can change the citation to the final venue and date for the camera-ready of the second paper.
If the improvement is both too late for the current camera-ready and too small for its own paper, you can either incorporate it into an extended version of the original paper to be sent to a journal (I've done this several times myself) or else can post a brief technical note in a non-peer-reviewed but respectable and archival venue (e.g., arXiv, a tech report at your institution).

For your particular case, it sounds like option #1 (incorporate into the camera-ready) is likely to apply, but #3 may also be a reasonable path.


In medical research, what is the relative value of confirming old work vs. new discoveries?

Note, I have a physical/computer sciences background; things may be different in life sciences.

  I have the idea of experimenting with the role of some gene in an autoimmune disease but no one has done that work before. Is it good to pursue this?

Yes! Doing novel things will get more attention than revisiting old things (though both have value).

My concern here would be whether you, as a lone, beginning student, have the background and resources to do something completely novel. Normally, one's first study is done under the close supervision of a mentor. I'm a little surprised your supervisor is "turning you loose" like this.

  When I write it up, how will I do citations?

Presumably parts of the methods you used have been used before (perhaps for other diseases), and someone has studied this disease before. So, you should cite any past work, even if it's not a direct hit to what you're doing.

But, this is sort of what I meant above -- it's good to have a mentor to help walk you through this process for the first time (or first several times) -- getting novel, publishable results with no supervision and little experience seems like a very tall order.


Evaluate the effectiveness of a set of CS lab exercises for education

You are adressing a topic which (in my humble opinion) is one of the most difficult ones: How to measure effictivenes of teaching methods.

The only good way is to have a control group (and make sure they are large enough, randomly asigned, subgroups represented equally, et.c). In most practical situations this is just not feasible. (I have the same problem at the moment).

What I plan to do (so it is just an idea, not proven to be correct - fedback is wellcome!):

ask students who did the class twice how they liked the new format and whether it helps them in learning
Compare outcome.

I think 2.) is the one we should aim for since the ultimate measure of successful teaching is compentent students leaving the university. Since it is hard to measure their competence late in real life situations, the only thing we can do is measure their perfomence by tests / exams. So I'll compare the results of my current group with the one from last year and look for failure rate, attendeance at test, ... Given that your tests are comparable, this gives at least an indication.


Typically, Turnitin is set to find similarities that are 3-4 words long at a minimum. So, is there a way to make minor edits so that your statement is slightly different each time? You can also ask your professor if it's okay to reuse your problem statements. Then, even if Turnitin flags it, your professor will know that they are still your words and ideas, since you discussed it ahead of time.


Finishing incomplete degree after a decade to switch to industry

If you want to be in industry, go to industry.  Stop taking new degrees.  At least stop for a while.  Go work.
If you are in the US, take the FE/EIT, now.  Start racking up time to get your PE.
"Engineering" is awfully vague.  Mechanical, electrical or what?


Percentage of PhD's in mathematics with no publications

I sent an email to Professor Krantz mentioning the present discussion and asking him whether his numbers are "supported by published or rigorously gathered data, or your own observations, or are simply meant rhetorically".  Here is his response, posted here with his permission.

Summary: he does not appear to have data at hand to support those numbers, but he believes they are accurate.

  Dear Nate,

  Your question is a good one.

  Certainly my statement is well supported by my own personal
  observation---after forty years in the business.  But I have seen
  sources even recently that say pretty much the same thing.  I'm sorry
  that I can't say what those sources are.

  You can think about the matter this way.  The vast majority of
  academic jobs in this country are at what we call comprehensive
  schools.  And those are places where teaching is the thing.
  Generally speaking, people don't do much research there.  They have to
  publish a paper or two to get tenure, and those papers tend to be
  fairly close to the thesis.  But then that's about it.

  A lot of other people get jobs at the National Security Agency, or Los
  Alamos, or another government think tank.  Generally speaking,
  publishing is not the thing there either.  Sometimes people publish in
  special classfied government journals.

  Other people get jobs at Microsoft or Hewlett-Packard or what have
  you.  And publishing is not the thing there either.

  Those of us who are lucky enough to be in math departments at true
  research universities are definitely in the small minority.

  I believe that, at the time I wrote those words, I consulted some
  people at the American Mathematical Society and they had data to
  support what I was saying.

  Feel free to quote me to others if you wish.

  Best,

  Steve Krantz


Is it rude to request a read receipt when emailing the professor?

Unless you have reason to suspect that emails are not being delivered successfully, email receipts are pretty much useless. Here's why:

Not all email clients support read receipts - Mail on OS X doesn't, for one prominent example. If some of the previous emails you sent requested a receipt, and it wasn't returned, obviously either the prof's email client doesn't support it or he didn't bother clicking that button.
Unless the receipt is returned, you can never be sure if the email was read or not.
Unless the email is replied to immediately - which is unlikely if the reply will take some effort - it can easily be forgotten about. Receiving an email receipt is no guarantee that you'll get a reply.

If you have no response to an email after a reasonable period of time ("reasonable" can vary between 3 days and a month or more, depending on what is required), just send a quick reminder email.


How should I approach job materials for a lateral move entirely for two-body reasons?

I would tell it like it is:  You have a two-body problem and a 2.5-hour commute that you need to solve.  As soon as you say those words, everyone will understand.


Why do tenured professors at high-ranked universities move to lower-ranked universities?

There are many reasons that people change institutions. I was tenured at an R1 institution and moved to a "high research" institution because I wanted to live in the area where the second institution is located. Although my current institution has a lower research ranking, it is the state's flagship school, where my former institution is not. So, I actually get more resources, better pay, and our students are more prepared when they start college, compared to my prior institution. So, your assumption that a higher ranked institution is better is not always true.


Why don't papers have their titles as a filename?

The filename is some sort of encoding that is compatible with the database in which they keep the papers, it might have a real world meaning or not. It is optimized for their own processing. I seriously doubt that they use a flat file system to store the documents.

But in general, trying to use a paper's title as a file name won't work anyway, since some characters that might occur in a title aren't accepted in filenames on every operating system. Colon and slash, for example, are problematic. There is also the problem that a paper might need to go into the database during the acceptance/review process in which the title of the paper isn't finalized.

In addition, while we like the titles of papers to be unique, that isn't always the case. So, some disambiguation needs to be done.

What you have, actually, is a reference to the paper that represents its "identity". This is similar to a pointer or reference in a programming language. The thing referenced can change arbitrarily, but its identity doesn't. This help guarantee that they don't lose it.


Professor uses academic employees to write proposals

If I understand correctly, you (as a postdoc) developed a research proposal, your professor submitted it under their name, and the project was funded. Then you were sidelined --- you will not be a PI on this project and you will not even take any role in it. This is a terrible experience and I am sorry to hear it happened to you.
The professor's behaviour is wrong. Even for German academia, notoriously famous for being professor-centred and often exploiting young researchers unfairly, this is probably beyond what can be considered normal.
Now, what can probably happen if you expose the story? Likely, not much. There are two issues here:

It is impossible to verify reliably who was the author of the proposal. Even if you show the time stamped drafts, it only proves that you typeset the material and prepared it for submission. Your former professor may say that they explained you the main idea and asked you to type it. It's very hard to prove authorship.
Even when evidence is quite convincing, most academics and academic administrators won't pursue an established professor for a single case of academic misconduct, if it does not directly hurt the University. Ideas are stolen very often, but such stories rarely made headlines, so most administrators won't bother dealing with them. Of course, there are exceptions, when even a single problem can unexpectedly grow big and eventually cost academic their job (there were several such stories recently related to hot topics in political/social discourse). But as far as I see quite a few professors made their carriers by borrowing ideas of others and making their students and postdocs to do a lot of their own work.

So, what can you take from this story? First, you know that you can develop a winning research proposal. This is a sign of a great researcher! Not many people can do it in their postdoc. This is something you should be proud of, and this skill and dedication is something no-one can steal from you. If you decide to leave this story behind and focus on what's ahead, I hope you will be able to repeat this success and now get the full credit for your hard work and creativity.
Good luck!


How should I use a footnote reference inside a figure?

I suggest that you add your remarks to the figure caption. Its purpuse is to help making the figure understandable. A footnote reference in the figure can easily be overlooked, so I would not recommend it.


Acknowledge funding institute, sending and hosting universities

I think that you should distinguish acknowledgements from affiliation.  You should also generally act generously with acknowledgements, because giving acknowledgements doesn't generally detract from anything as long as you're honest about them.

So, in your case:

Your affiliation is University A.  If you are at University D by the time the paper hits camera-ready, then you might add that affiliation too, as a dual affiliation.
You definitely need to acknowledge the funding support of Institute C.  You may also want to acknowledge University B if the organization has given you support (as opposed to just individual faculty members).  For example, if the department loaned you facilities for doing your work, that would definitely merit acknowledgement in my book.
Other people who helped significantly with the project (except within normal non-scientific job duties) should get co-authorship or acknowledgement.  Thus, a hosting faculty member at University B should appear in the paper, but the IT person at University B who fixed your computer would not.


In a thesis, which comes first - Abstract or Acknowledgements?

You should check the guidelines from your university. I'd assume that they would have requirements for the order. If not, I always prefer the acknowledgements should come first, that way the non-scientific stuff is out of the way.


Can a supervisor extend the paper and change the order of authors?

If the paper was submitted without your knowledge and agreement, this is a serious problem. All co-authors are supposed to know about and approve a paper that they are listed on before it is submitted.  This would be an ethical breach by your supervisor.  I would at least raise it as a concern with them.  This is something that you could potentially raise with others, as well, such as someone else at your instutation, or even the journal.  Consider the consequences before you do anything, though: it's likely to have a major impact on your relationship with your supervisor, and therefore your PhD studies.

Beyond that, the situation is much more of a gray area.  Clearly the way things were handled, particularly the lack of communication with you, was not optimal.  But it's not so clear that it was "wrong" beyond that.

The PI directs the research of the group and has the authority to decide that someone else will now take the lead on a collaborative project.
It is a judgment call who should be first author.  If the other researcher made a significant contribution and put together the draft of this paper, they may have a legitimate case to be first author.  At least, it may be ambiguous enough that it would be hard to challenge.  Also, someone might feel that the first author on this paper should be the one who did the most on the revision/extension rather than the one who did the most overall.  After all, you already got first author recognition for the primary piece of work on the conference paper.  In a series of related papers that build on each other, who did the most recent work may be considered most relevant to authorship position.

Don't be too quick to assume intent. Your talk of the supervisor keeping things "secret" implies intent to sneakily do this behind your back.  I wouldn't necessarily assume that.

Perhaps your advisor is just poor at communication/management, and this was an oversight.  This is quite common; many professors are not good at managing a group of people.  Even submitting the paper without your knowledge may be an oversight (it shouldn't happen, but it does happen).

The advisor might even think they are doing you a favor by taking some work off your shoulders and getting something done that has been delayed.

Talk to them and make them aware of your concerns and see if you can arrive at a constructive solution.  It may be too late to undo what is happening here, but hopefully you can agree on a better way of working in the future.

If, after attempting to discuss this, you feel that your supervisor is acting in bad faith, you may want to escalate the situation.  But only do this as a last resort.


No luck with postdoc hunting after PhD. Will things change with a major paper out?

Think about it this way: What would make things different after your paper is out?

You'd be a person who has published a paper in a prestigious venue.
More people will read about your work (in that paper and through it, elsewhere)

No. 1 will likely help to some extent - perhaps even enough to secure a post-doctoral position. But I think the key is no. 2; and publishing a paper is just one way to get people to know about your work and its importance. If you have a clear idea of what you want to be doing, you don't just "submit applications". You talk to relevant researchers in groups which could use your expertise and input, and make a pitch - for a collaboration, for a visit, and possibly for employment. The fact that you made 20 applications makes me guess that for most of them were somewhat generic: You noticed a posting and mailed/email your application. Try to find a researcher who would not pick you among applicants, but rather just offer you work because s/he believes you would help their lab and their research.

Sorry for being a bit vague - I'm from a different academic field; but I think my point is valid for life scientists as well.


How to find an appropriate journal to submit to when working in a new, unfamiliar field?

Having had experience with this type of problem myself, I agree with the suggestions that you have been given in comments: the best way to figure out where to publish is to look at where the papers that you are citing in your related work are being published.

There is an additional challenge as well, however, which is that as a newcomer to the field, you are likely to have a more difficult time getting published because 1) you have not yet established credibility in this area, and so people will justifiably view your work with more skepticism, and 2) you are likely to be insufficiently aware of key concerns and points of debate within the community, which can get you into unnecessary trouble with your reviewers.

I would thus recommend a "publish early and often" strategy: rather than trying to send a major manuscript to a top publication venues immediately, start by sending a couple of more restricted manuscripts to less difficult but still respectable targets.  By doing this, you can gain experience with the community's expectations and start building your reputation as a good practitioner in the area, both of which will later help you to be able to publish in higher impact venues.


How do I change schools/advisors without making my advisor angry?

This is the answer to everything, but talk to your advisor.  If he is, as you say, very nice but hands off, you should talk to him.  Express your concerns, that you really feel you need a more hands-on approach and that right now you feel like you are floundering.  If you're honest and direct without blaming him, asking for help, he may change his behavior or work with you to find a better fit.  Either is good for you, but you need to talk to him.  He knows he's being hands-off, he just may not know that it is not working for you.  You need to communicate that.


How to credit a photo taken by someone else in my publication?

Credit lines for photographs should be displayed conspicuously with the photo or in a footnote on the same page. In general, it should look something like: "© Ansel Adams 2015" or "© 2015 Ansel Adams". Alternatively, if the photo was given to you for general use, use something like: "photo courtesy of Ansel Adams".

Some guidelines for citing images in various formats are posted here: University of Cincinnati. Near the bottom of that website there is a short section with advice on photo credit lines.


Including a future conference presentation in graduate school applications?

If it has been accepted then yes, include it, but mark it somehow (... abstract to be presented at ...). If it has been submitted, but not yet accepted, then you can include it under the heading of "work in progress".

But there is no reason not to include such things. As you say, deliverables are important. But so is showing some continuity in your research trajectory.


Date of publication vs. date of current version

Many journals offer an "early access" or "preprint" service, in which articles are made available online directly after final acceptance but before copy-editing and typesetting (i.e., before adaptation of the article to the journal's format and paper print requirements). The date of publication is the date when the article is first made available online.

After typesetting is done (which may be a few weeks later), the online version of the article is updated with the typeset version. The date of current version will be updated here, but the date of publication will still be the date when the preprint was made available.


Interpretation of a PhD degree in a very broad, interdisciplinary field

I completely understand your feeling. I can tell you that many other people in this field feel the same. This has nothing to do with how smart or how good they are. This issue also bugged me a lot, but I can offer some insights:

Bioinformatics/computational biology is really huge and you cannot be an expert in all aspects. Even if you look at senior scientists in this field, I do not think there is someone who is an expert in all subfields. You simply can't master all the physics, math, CS, chemistry and biology at an expert level - even in a much longer time than a PhD.
You can still have a huge impact without being a super-expert in every subfield. Just look at some of the research published in top journals. The reason is that you will have knowledge and a way of thinking that people restricted to a single field may not have. From personal experience, I can say that this is a significant advantage for asking certain types of questions and coming up with certain ideas that single-field specialists won't come up with.
After a while you will realize that you actually are an expert. Maybe not in the sense that you know everything about everything, but you will see that you can give good advice to other people, foresee potential problems, and so on. In addition to knowing a lot about computational biology, you will become an expert in things such as quantitative modelling, applied machine learning and "big data" analysis (I hate that term), skills which are very useful in a wide range of fields.
The fact that you cannot become an expert in everything doesn't mean you should neglect learning. On the contrary, you should constantly try to expand your knowledge in all related fields. And yes, it can be more difficult than learning only one subject.
Finally, in the end you will be working on a specific problem in a given biological problem with a given set of tools. That problem is what you really need to be an expert on.


What are the pros and cons of applying for graduate study in multiple disciplines?

The main issues against such a path are the time and expense involved in doing so. Effectively, you have to complete two different sets of testing requirements, and you'll need to write two very different sets of essays. You'll also probably need to get different letters of recommendation, as the emephasis for different fields are probably not likely to be similar. If you apply to US schools, there is also the cost of applying to the additional schools in the other discipline.

Since you're an international student, it isn't likely that you'll be asked to fly in for interviews, so that wouldn't be a big drain on your time.

As for the pros, if you aren't sure which path you want to pursue, this will definitely give you more options. But other than that, I can't think of a "real" advantage to splitting your efforts in such a manner. (I guess one other exception is if there's a special "dual master's" program at one of the school's you're interested in; however, this requires reviewing the information available from each school.)


Is copying paragraph structure plagarism?

It's not "plagiarism" because you are copying a standard format. That is known as scenes a faire in fiction, but can apply to Academia. This is not only allowed, but encouraged, because you are conforming to a "formula."

You should be worried if you were copying an unusual or original format. That's not the case here.


What is the relative importance of the parts of my application?

It is a very closely run issue, and as stated above can vary by school, but in general, the order goes:

Letters of Recommendation
Personal Statement
Transcript
GRE scores

If for some reason you don't get into the program of your choice you may consider applying to a U.S. Master's degree program that will get you up to speed, and make your application much more persuasive. Many schools offer 1 year masters in a variety of subjects, which are valuable in themselves, and are easier to get into for international students.

Letters of recommendation tell the committee a lot about you as a person, which is very important, since they are stuck with you for 5+ years. People coming from outside the U.S. are better off getting letters from scholars who have attended university in the U.S. because it is frequently difficult for U.S. scholars to weight the relative merits of courses, research and so forth from outside the country and someone intimately familiar with the U.S. system can help them parse that by making comparisons to things current in the U.S. Coming from the U.K. (or Australia, New Zealand, Canada, Germany and a few others) the systems are similar enough that the assistance is minor, but perhaps worth it all else being equal. Above all else make sure that your letter writers can speak in depth about you as a scholar and don't go for fame over substance.

The personal statement serves essentially the same purpose, but it shows the committee what you want to research while at the institution. The title "personal statement" is misleading, however, because you should treat it as a research statement. The biggest challenge students everywhere, but especially from overseas where different academic traditions may prevail, is completing a dissertation as a major research effort. Schools need to know that you have at least some idea what creating original scholarship means, and why you think going to their school is valuable to you as a scholar. They don't care about the time your dog died, and it inspired you to be a better person.

Courses show that you have the basic understanding of the topic, although unlike British or Continental programs, almost all U.S. PhD.'s include significant coursework, which will get you to where you need to be to write your dissertation. Grades don't necessarily compare across systems, and the committee knows that, but as long as you have done well and are prepared for the program.

GRE in almost every case is just a way to winnow out the thoroughly unqualified. FYI, most maths intensive disciplines (Math, Economics, many natural sciences) at top schools will not even consider you unless you have a perfect quant score (currently 170, formerly 800). Most schools don't hide their cutoffs, and if they do an e-mail to the department secretary will usually find it out for you, so don't waste your money applying to places you will never get in because you don't clear this obvious bar.

Finally, I highly recommend the book Succeeding as an International Student in the United States and Canada by Charles Lipson.


Informative article about physics and quote on "physicists don't care about precise numbers, they care about trends"

I do not agree that physicists are more concerned to obtain a qualitative analysis than a quantitative one. However, your question is not about my believes, so ...

Einstein: "If I can’t picture it, I don't understand it."
Dirac: I don't know the exact quote, but he said something like: "In order to understand a differential equation I have to be able to predict the limiting cases, and not solving the actual equation".

You will find the exact quotes in the internet.


Is my GPA good enough for top-tier graduate schools?

The 3.6 looks a bit weak, but there's lots of other relevant information that's not in your question.  For example, a poor grade in first-year calculus wouldn't matter so much if you have solid A's in more advanced courses; on the other hand, solid A's in calculus followed by lower grades in more advanced and theoretical classes would be a serious problem.  Also, letters of recommendation are very important in graduate admissions.  If you've done a research project and your supervisor writes an ecstatic letter about the quality of your work, that can compensate for lower grades in some classes.


How do I politely decline a research grant?

Let's be clear here. Based on your account I'm getting the impression that, with a reasonably high level of confidence, there is no way for you to "politely" decline the grant. The very action of declining will reflect poorly on you and show you to be an unreliable and difficult to work with person, and is likely to upset your PI and the funding agency who went to the trouble to evaluate your application. So, it's not about the "how". It's the action of declining that is by its nature impolite.

You may feel this is unfair. You may feel that you were given inaccurate information at the time of submitting the grant that led you to make a decision you now regret. You may very well be right on both of those points. In an ideal world you would simply explain what happened and everyone would agree that it makes sense for you to decline the grant. However, in the world we actually live in, I'd say accept it, do the work, use it as a learning experience and move on. And congratulations for getting the grant, it obviously says good things about you and if you do a good job has potential to benefit you in the future in many ways other than the measly stipend.


Long hyphenated surname – what to do when I begin publishing?

As other have commented, the length of your hyphenated surname is not problematic at all: keep it and don't worry.

Fun fact. Uh, well, it took me years to discover that Lennard-Jones was actually just one person and not two, and that the Hanbury-Brown-Twiss experiment was devised by two people and not three, Hanbury Brown (no hyphen) and Twiss. For  Jaynes-Cummings, instead, I tought they were two and they were actually two - amazing! But I would count this as a minor inconvenience, which actually taught me not to make assumptions on surnames (and, as suggested by E.P., this popular page discusses other false assumptions).


Can I count on "future works" ideas in a paper to work?

How to make sure if it will work or not?

The reason why it's in the "future work" section is that no-one knows because it hasn't yet been done (and it's easily possible the original authors never will try it). "Future work" ideas can range in feasibility from wild speculation to simple, almost-guaranteed-to-work extensions that just need a bit more manpower or computer power to finish.

This is a good topic to discuss with your supervisor as soon as possible. You should be asking questions such as:

How feasible might it be for these ideas to lead to some useful conclusions?
What if it doesn't work? How soon will we know, and what alternative paths are there?

Of course, some ideas are much easier and more feasible than others.  There's no way to know for sure but to try the idea yourself (after making sure that the problem is not already solved in later literature). Because dead-ends often go unpublished, it might even be worth contacting the relevant authors to ask if they attempted to follow up on their future ideas.

It's a courteous thing to do especially if theirs is a recent publication: if the original authors are still working on the problem, publishing the solution first might annoy the other researchers. Though whether to proceed anyway (and give them notice that you're working on the idea as well), stay silent, or offer to collaborate, is a dilemma that's off-topic for this question.


Would it be a good idea to drop out of my Bachelor's program and look for scholarships to restart abroad?

Different countries in Europe have a different opinion on what constitutes "old" for a student. There are countries where 23 would still be quite young.
You may want to have a look into whether programmes in the EU or USA would allow you to transfer (part of) the credits for courses you already passed. Some programs will, some programs won't. If you find a program that allows this, it might make your journey substantially smoother.


Can I share my results published results/research on my personal website or Medium blog post?

In most cases, yes you can, but you should ask your university if they have rules regarding hosting on websites/blogs with research products. Some places for example require that such a site is university hosted, can not be hosted abroad etc.

Should you do it? Absolutely, with the proviso that you should publish your paper first, or together with the code. With scientific results becoming more and more complex, it is often necessary to have access to various codes, for the purpose of reproduction. If your code is useful, it can also be quite profitable in terms of citations - remember to require people to cite your paper when they use your code.
Note that there are several journals (depending on your field) that actually specialize in publishing manuals for such public codes. CPC is a prominent example for physics (https://www.journals.elsevier.com/computer-physics-communications)


Don't read too much into the nomenclature of journals. Some of them are very old and the names are just traditional. The purpose of some may have evolved over time a bit but not the names. Each different society may use its own naming conventions as may each commercial publisher.

Nobody has looked at the whole field and tried to rationalize it. And even if they tried, the traditional names would stick.

But Bull. AMS is explicitly for expository articles, not the latest hot topic research. Therefore its "reputation" is different in kind from that of Trans. AMS, though both are high quality.


Should I list conferences I attended on my CV?

In general, you can put pretty much whatever you want in your CV (unless there is a template, in which case deciding what to put or not should be pretty straight-forward). The question is: what is the point of putting a piece of information in your CV?

Usually, a CV is used in the context of a recruitment process, where the point, in the end, is to give reasons to the recruiter to recruit you instead of someone else. Hence, a piece of information contained in a CV should be instructive, for instance by ensuring that you do have the proper credentials, or by providing evidence that you can be apt to the position you are applying for.

Perhaps attending conferences is something relatively rare in your field, and you have attended more than the average PhD students? In that case, listing all the conferences you have attended could indicate you are very interested in keeping up with recent advances in your field. It could also show that you enjoy travelling. Perhaps you have secure internal or external funding to attend that conference (i.e., the funding was not automatically given)? That's also good evidence. You could list them if it provides evidence for an aspect that you are willing to emphasise in your application.

On the other hand, if the conferences you have attended had nothing special, or do not help emphasising any particular point, then you might want to keep the space in your CV for something else.


You could mention self funding or not. However, it is important that you give some indication of why you are interested in this person and what it is in your background that might interest him/her in you. Mentioning past research projects in the same specialty would be helpful. Your statement is fine, but only as an opening.

In particular, you should investigate the background of the potential supervisor, including publications and past students. In mathematics, for example, the Genealogy project can give you information about where the person fits - advisor and students. For famous people, even wikipedia will give you information.


How can I tell if I have simplified my talk too much?

I definitely hear where you are coming from.

In my modest opinion, a good conference talk is not necessarily the one that lets me understand the technical contribution (I can read the paper for that), but the one that lets me understand

The importance and/or hardness of the problem studied
What were the key new ideas
Why they worked and when can I expect them to work

If I got this from the talk, I may be able to recall the result or the technique in the future when I have a need for it.

Of course I am not saying there should be no technical detail, the key idea may be the way a theorem was proved, but I believe any technical content should not be gratuitous.


Can a graduate school change its decision, from rejection to acceptance?

The typical process that happens in graduate application selection is that you subdivide applicants into three groups:

Accepted applications: These are your first choice of candidates, and you offer them a position. This list need not be ranked.
Waitlist: These are the applications you think are good enough to accept, but not so good that you want to make them an offer right away. You rank this list, and go top to bottom as people who have previously been offered a position decline.
Reject: These are the applications you think aren't good enough to succeed in the program. There is no need to rank these candidates because you don't anticipate ever tapping into this pool.

The point I'm trying to make is that the rejected applications are candidates you don't think are good enough to succeed in the program. You're probably going to ask what happens if everyone declines and you're out of names on your waitlist? Well, then you just don't make any more offers. That's because you've previously decided that the ones on the "Reject" list aren't good enough to succeed.

The only thing that's worse than not being able to fill all graduate student slots is to fill these slots with students who you believe will not succeed in the program. That's a sunk cost: you're paying for people who aren't good enough to do the job they're paid for.

So, under the assumption that all universities work on such a system (which I think is, in essence, the case), there is no reason ever to turn a rejection into an acceptance.

(Now, has it ever happened? Almost certainly, given just the sheer number of cases. Does it happen on a regular basis? No.)


Can I conduct psychology research involving my restaurant customers without their explicit consent?

What does your advisor thinks of that?
What does your ethics committee thinks of that?

Because, as far as I know, every and all experiments that remotely involve humans need to be approved by an ethics committee.

I'm from computer science but I had a few experiments involving people and that is usually the rule...

And remember, each country has its own set of laws, make sure you know yours!

Apart from that, my first impression was "bad idea". Even if it is, by some weird loophole, legal, it is not very ethical, at least IMHO...


What is the role of a teacher (of mathematics) at university?

I'm a student. I have always wanted to be a researcher/scientist cum professor all my life. The following are the qualities I would like to be instilled in me (and a few which didn't turn out the way I expected from a teacher) as a teacher at a university level. Note that some of the points are applicable for teachers in general and some specifically for math teachers.

(The following are in no order of preference)

One of the most important things that a teacher must do is to use the blackboard and more than you use a powerpoint. There is some kind of magic related to using the board for math. One of my professors used to use powerpoints for his classes, and most of the time students (including me) fell asleep.
If in case you do want or have to use powerpoints, then make sure to create animations like the ones here. One of the fascinating things about those animations is how perfectly it fits to capture a person's attention.
Encourage students to use online resources like OCW MIT. When I was in my university (graduated this year), neither did I have internet connection, nor was I aware of such a resource online. Encourage and suggest MOOCs from Coursera, edX, etc. which might be relevant to your course. It is not necessary that they should register/complete every single course or resource. Give them two or three options and ask them to pick one.
Make it an active class. And make it fun too. I learnt a lot from Gilbert Strang and Mehran Sahami. Be enthusiastic in class, that will help students get out of their tiredness. You can also toss out chocolates like Sahami does when students answer/ask questions.
Solve problems in class - either all types of the same level (easy/medium/hard) or one type with all the levels, going from the easiest to the hardest. The point is to make sure they understand the problem solving process. In addition, solve example problems from the textbook or handout and for every example problem, give them a problem to solve either in class or as an ungraded homework. This makes sure they are actually doing something in a math class rather than just trying to consume the knowledge passively.
Make sure the subject you're taking can be related to other majors and fields. Most of the technical subjects have some variation of mathematics being used in them. Take Calculus. It is used everywhere, even when we think we don't need it. I always thought it was used only in continuous domains, mostly in physics and not at all in any other fields. I was mistaken. You don't have to make this a mainstream for your class. Maybe as an ungraded homework or just a casual mention when the relevant topic comes up is enough to keep the spark up.
Go a bit beyond the syllabus. I know this will be hard, but, just a bit will be enough. It may involve deeper concepts, real world applications, etc. That is up to you to choose. Personally, I have always found it beneficial for me to learn a bit more than what is needed so that I won't be caught off guard during exams. This also helps students if they wished to pursue higher levels of the course possibly leading to research.
Have a review class before exams. Walter Lewin's lectures had reviews for midterm and the finals. It sort of helps to review everything in class rather than spending extra time apart from the newer material to be learnt the day before exams.
Inform students exactly how many hours they'd need to spend on an avg outside class. I wound up with terrible time management because I had no idea how to allot the required time for each course. This led me to focus on subjects I loved and got better grades and subjects I didn't find interesting for which I didn't spend time - and I flunked in them. Huge mistake.
Use standard textbooks, especially the ones which have 4 and above ratings on amazon. Ask students if they liked a different textbook, and if it is a better suited one, then switch. Don't use textbooks which you find personally attractive.
If it is not a problem with your university rules, make sure attendance isn't compulsory. There will be at least one or two students who might find attending lectures boring. To counter that effect, make sure you deliver incredible lectures that makes students feel want to attend rather than have to attend. In my university 80% was mandatory and I found it a huge waste of time for most of my classes.
Make sure problem sets contain all levels of problems. It helps students to practice properly. This increases confidence. In addition, don't pick problems from the prescribed textbook. Just pick another textbook and give them the problems to solve. For math, I'm sure there are numerous books and resources online.
Identify the distribution of students in your class. There will be one/two/a few gifted students in your class. Maybe conduct a simple quiz at the end of week 1 or 2 to find out who they are. (I find it hard to explain it in words) As a teacher, you will know who these people are. Now, chances are that they might be bored if the class feels too easy. In this case, add extension problems which are very very challenging. These can be ungraded, but interesting to solve. These gifted students will always go out of their way to solve them. This ensures that their skills don't rust away with time. Another horrible experience of mine.
Rehearse for every class you take, fully. Practice. If it is a 50 min lecture, give a 50 min lecture to the empty hall. Walter Lewin used to do this for every lecture he gave (he quoted in an interview somewhere on OCW or YouTube, not sure where).

These are the ones off the top of my head. Hopefully, these are enough.


Is it possible to join academia with a structured PhD?

In practice the distinction is gradual. Some structured programs don't function as well as advertised, meaning that the PhD students are pretty much left on their own, while some advisors of individual PhD project are very structured. Sometimes individual PhD students can participate in (parts of) a structured program, etc. etc.

In the end if you get a PhD, then you got a PhD regardless of the type of program. No one will know, and no one will care one way or another. In practice a well functioning structured program is beneficial as the students tend to learn more and the network of a given cohort in such a program tends to help as well.


How much of a role tuition revenue plays in underwriting research?

Much of my answer here, holds in this case. It's basically impossible to tell. If a new professor gets a lighter teaching load in their first year, is that "underwriting research" even if the professor's nominal work distribution is 1/3rd teaching, 1/3rd research, and 1/3rd service/admin?

Professors are paid to teach and research and serve internal university goals. How much they do each of those day to day is hard to tell. Now, that being said, if a professor fails to bring in grants to cover their summer months, I doubt many universities would indefinitely provide for them out of general funds.


Continuing with a postdoc with my PhD advisor, but have not got any official offer letter. Should I be worried?

No, you should not be worried. It is perfectly normal for official offer letters to be delayed.  Ask your supervisor if they submitted the necessary paperwork.  Ask HR what needs to be done.


How to calculate the rate to pay a recruiting agency for new students?

This is the only reference to their compensation I could find. In the UK case, average compensation/student in 2013 was about £4,300, which is about 50% of maximum annual tuition UK universities can charge to EU students (a limit that apparently does not apply to internationals) - all data as presented in the linked article. As other comments mentioned, and they seem ubiquitous, I'd request a sample of their standard contracts to get a better idea. This site seems to have decent traffic. Like all related links I could find, it rings all kind of alarm bells, but maybe you find it of use. For the U.S. case, someone put together some legal advice which you can download (as all this strikes me as fishy, I didn't dare to, so unsure if it's useful). I would definitely talk to your own school's legal counsel before taking any steps.


Will my chances of obtaining a student visa in Canada be reduced if I mention I applied for permanent residency?

The real question here is whether you are required to mention your permanent residency on your student visa application. If it is not required, I would refrain from mentioning this issue both in the application and during the interview as temporary residentship (e.g student visa) expects you to plan on returning after the agreed upon period. However, If you are required to provide such information in the form or are asked about in the interview, I would STRONGLY encourage you to provide the honest answer. Being dishonest in your application or interview can easily lead to your Visa being rejected. Bear in mind that your residency application is an officially submitted document and can easily be recovered if the Visa administration office seeks to look for it.


When to use academic titles in presentations in Europe?

If I understood correctly, you live in a culture where flaunting one's title(s) comes across as a bit crass; at the same time, you wonder if mentioning your title on the first page of a powerpoint presentation might increase your credibility when you are presenting to certain audiences.  (Did I get that right?)

You may be able to get the idea across in a more subtle way, that people would not interpret as bragging, on the first or second slide, as an acknowledgment.  For example, you could acknowledge the mentorship of Prof. XX in the YY Master's program at ZZ University.

That's just an example.  Does it give you some ideas?


I suggest stating the date ranges during which you were registered as a student, as well as the degree date:

SomeUniversity September 2012 to March 2014 and January 2018, MS SubjectX 2018.

That will presumably match up with the employment section of the CV that will show work during the gap.


How would I cite multiple authors from an online forum?

Starting with the principle that the goal of a citation is to make it as simple as possible for somebody to find the particular reference, I can see two ways to approach this publication:

Treat it like a journal special issue or chapters in a book, where there are multiple articles bundled together under one editorial title.
Treat it like a single multi-author article.

In this particular case that you have linked, it seems that none of the contributors have titles for their individual sections.  That means that you can't readily separate out the individual contributions.  I would thus recommend citing it as:

  Alice Waters, Jim Hightower, Eric Schlosser, [etc], "One Thing to Do About Food: A Forum." The Nation, 11 Sept. 2006. Web. 01 Oct. 2014.

Then you simply to who you are quoting in the main text like you are already doing.
If they had individual article subtitles, you could do:

  Singer, P, "Singer's Article" in "One Thing to Do About Food: A Forum." ed. by Alice Waters, The Nation. 11 Sept. 2006. Web. 01 Oct. 2014.

Without the secondary titles, though, listing Alice Waters as editor makes it sound like she's the editor of The Nation not the forum.

[Note: I think my style may be slightly off from your required format - the key point is the person/title pairings]


Is it necessary to understand every detail of a research paper?

I would posit that there are three general levels of depth to which you need to understand a paper:

Understanding context: For anything related to the work that you are doing, you need to be able to understand it well enough to explain how it relates to your work, and why it should or should not be directly compared.  This is the "general idea" level that you describe.
Direct comparison with other work:  For work that is closely related to your own work, you will likely need to be able to make a direct comparison, possibly even by running instances of the other work on the same problems.  Here, you need to understand at least well enough to correctly apply the other work and to make a cogent comparison of the relevant qualitative and quantitative attributes.  You'll probably need to understand most of the paper for this, but not necessarily all.  For example, you might not need to understand the proof of an algorithm's correctness, but would need to understand its uses and performance characteristics.
Building on top of other work: For work that you are actually making use of in developing your own work, e.g., by using it as a component or by extending a prior technique, you need to understand it very thoroughly indeed.  This is the level at which you really do need to understand everything in the paper.


How to explain a bad grade to a delusional student?

My first question to you would be

  Did you lay out the assignment expectations and how the grade would be determined when you gave the assignment?

If the answer is "yes" (and I expect that it is), I would use that as a starting point for explaining to the student why he/she did poorly.

That aside, it seems that either (1) the student didn't understand what was expected (regardless of the question above), and/or (2) the student isn't prepared for the type of work required, and/or (3) the student had a bad day.

It sounds to me like the answer is firmly #2, as repeated attempts to improve the grade hasn't worked.  Given that you've already spent a good deal of time with the student, it might be time to have a heart-to-heart discussion and say that it is time to stop thinking about that grade and to move on.  Obviously, you need to do this diplomatically, but (as they say), to make an omelet you need to break some eggs, and sometimes a firm and diplomatic "get over it" is appropriate.  I would pose the following questions to the student:

Do you have a clear set of goals that you are working on for the class?
Do you know what other grades are going to be part of the final grade for the class, and do you have a plan for making sure you are ready for each assignment / talk?
Do you conduct practice talks with other students in order to get constructive feedback? (if not, you should!)
(If the problem is English language skills) Have you sought out on-campus help with your writing or speaking skills? (this is available at many larger universities in the States)

Depending on how much time you are willing to devote to helping the student improve, you could also offer to sit in on any future practice talks to give pointers and feedback.  Likewise for written work -- you could offer to pre-read assignments.  This is a slippery slope, so tread carefully.  You want to avoid having the student see you as an always-available tutor, but there are times when providing such support is just part of the job.

Finally, I would stress to the student that one bad grade does not make or break a student, and it is better to make mistakes while in school than later when they might mean more in the bigger picture.  School is about learning, and you learn from mistakes.


Is it ethical for students to be required to consent to their final course projects being publicly shared?

The red flag here is that the instructor is requiring students to sign away a legal right they have. What gives them the right? A university may reasonably make such a requirement as a matter of university policy in a few situations where that makes sense (e.g., as someone mentioned, it is standard that PhD theses are made public). But the instructor’s mistake and clear point where they are overstepping their authority here is their assumption that they can set arbitrary rules that have nothing to do with the educational goals of the course, and that students must follow as a condition of getting their grade.
We have
seen
this
before unfortunately.
US universities simply don’t endow their instructors with such absolute-ruler powers. In fact, as someone who was a department chair and experienced the administrative side of running a university, I can confidently say it would be very undesirable from the university’s point of view to give individual instructors the authority to make students sign legal statements whenever the instructor thought it was a good idea. To put it mildly, some instructors are less sensible than others and probably should not be trusted with these sorts of powers. Nor is this a recipe for consistent policy-making.
To be clear, an instructor can set rules on where a student sits during an exam, or impose deadlines for homework submission etc, since such rules are necessary to accomplish the goal of teaching and testing the students. But at the end of the day the instructor is required by the university to assess the students’ performance and assign grades, and may not hold the students’ grades hostage to arbitrary conditions that make the instructor’s life easier or help them teach future classes, showcase their teaching achievements, or otherwise achieve other goals tied to the instructor’s self-interest.
To summarize: yes it’s unethical, and violates the “don’t be a jerk” policy, and probably other ones.
Edit: I was asked to spell out the specific ways in which the instructor’s behavior is unethical. They are:

Coercion: the instructor is coercing students to agree to give up their legal and moral rights to control what happens to their project work, where this does not provide them any legitimate educational benefit tied to the course.

Abuse of power: the instructor is using their power over grades, a technical power they are given by the university but that’s supposed to be used only for the specific purpose or assessing the students’ work, to coerce them to behave in such a way. This seems pretty clearly done for the instructor’s personal benefit.

Violation of employer’s trust: the instructor is violating the trust their university puts in them to use the authority the institution is giving them only for specific purposes and in specific ways.

Note that versions of these sorts of behaviors are illegal in many countries. For example using the power of your office to benefit yourself has been the reason for many holders of political office to be sent to prison in the US, and for a president to be impeached. In this particular case the behavior is probably not serious enough for these laws to apply, but the principle is the same.


How to ask graduate program coordinator, if i got funding?

Two things here:

It is never wrong to ask your question from the person at the university about something, which your are waiting for, or wanting to know. They are there to help you, in fact it is their job to do so.
Never dance around the topic, ask what you want to know. This is because it will save your and the person time; and of course with clear a subject.

I would write the following:

Subject: Fellowship Outcome

Dear <name of contact>,

Could you please let me know if I did qualify for the applied fellowship?
Also is there any available funding for me to come to the campus?

Kind Regards,
X


should I include offer letter from a different institution in my application for a faculty position

I think that it would be unwise to include a copy of an offer in another application.

But whether you inform them of the existence of an offer is a bit more subtle. I doubt that anyone will rush to hire you just because you have another offer. They will evaluate you on other things as usual. So, at best, mentioning the offer initially gets you nothing.

However, later in the process if you need a decision and they are delaying making it, you can let them know that you have a deadline. Whether that helps or hurts is also subtle. Whether it is wise, or not depends on the nature of any relationship you have been able to build with them. In the absence of any relationship, it might hurt more than help. It is easy to just cross you off the list unless they are very interested and have few other interesting applicants.


Would a retired researcher mentor a postdoc with his/her own external funding? What about one without external funding?

I'm sure you'll find people who are "retired" (from administrative duties, from chasing the next funding proposal) and still are hard at work, while others just want to stay at home and look at the lake in front of the window.

If one of them would take you on as mentoree (made up word, I know) is anybody's guess. Perhaps they retired in part to be free of having to deal with pesky students. Maybe you are so outstanding that you lure the hermit back into active work.


Applying for assistant professor position, teaching statement required but I have no teaching experience

I do not have any formal, class-based teaching experience

The way you wrote this suggests that perhaps you have some informal teaching or tutoring experience.  If so, you can write about that.

You have years of experience observing teachers at work.  Think about what made the good ones effective, and what the bad ones did wrong.  You can use this analysis to create your draft teaching philosophy.

If you do not get this particular job, and you decide to continue applying for teaching jobs, then I suggest you get some teaching and tutoring experience under your belt as soon as possible.  It's okay to volunteer -- as long as you treat your volunteer teaching as seriously as you would treat a paid teaching or tutoring job.


How old can references or sources in a thesis be?

References can be as old as they need to be to cover the material.  I had some that were more than 30 years old. But if all of your references are "old," people are going to want to know why.

You must also be sure you cover the most current research in your field.  A few in my own dissertation were for material published in the same year as my own work.

The link given in the comments and the revised question seems to be directed toward undergraduate research assignments, and the "ten years" reference is a part of an example assignment, not a requirement given by the Shapiro Library. The key idea in the link is that references must be "somewhat current."

For a thesis or dissertation, one must cover the field, including both early and very new research.


Should I put an apostrophe to indicate a plural or past tenses?

The Cambridge guide to English usage by Pam Peters has a long discussion on the usage of the apostrophe in the case of plural nouns. For what concerns your example, under the section Apostrophes, it says:

  Single letter in lower case still usually mark the plural with apostrophes, as in Dot the i's and cross the t's

The purpose is that of highlighting that you have the plural of a word composed of a single letter. However, under the section Letters as words there is the following remark:

  Yet even the apostrophe is unnecessary if italics are used and the plural s itself is in roman.

Though the above remark is probably meant for ordinary text, in mathematics variables are commonly typeset in italics, and I think that the above remark can be applied as well.

According to the above, I'd say that the apostrophes in your first example cannot be considered wrong, but they are actually unnecessary.

In LaTeX, I'd then write
your first example as

if we combine the $x$s and $y$s

Instead, in the past tense of your second example the apostrophe marks the elision of the letter e, and in this case it is required: xored -> xor'd.


Applying to a top-program, but for a sub-field that program is not strong in

There is no way to know. Some departments may rank candidates independent of their desired specialty while other departments may weight who the applicant wants to work with (and who wants to work with the applicant) heavily. For departments who give weight to the sub-field, the department might be trying to strengthen a weakness or only accept students in areas they are strong.

I am not really sure why the departmental politics matters. Trying to deceive (in a mild way) the admissions committee is not likely going to be advantageous. Your strongest application is going to be to talk about the area you are most excited about. Further, if you get accepted based on a falsely expressed interest in A, you may not be able to switch to B later.


Is a higher amount of literature cited in an essay generally seen as better?

The quick answer is yes. Pertinent literature is meant to support your position and build your story. The amount of literature cited usually reflects how deeply and how comprehensively a topic was examined. However, I should say that the literature cited must be highly relevant to be considered as a valid one. It will not be a good practice to pad the cited works to simply give an impression of in-depth research. Experienced readers of academic work will be able to tell if the amount of literature cited actually helps your cause.


How do you balance producing results with learning new skills?

A common fallacy I observe in students I supervise is that they think they need to spend some time "learning X" before they can use X productively in their research.

If you are doing research, the most efficient way to "learn X" (where X is a programming language, methodology, or subject area, that may be of use in your research) is almost always to learn it by immediately applying it directly to your research.

In other words, I tell my students that if they are "taking time off" to learn something before starting to use it in their work, they are doing it wrong.

I would give the same advice to you: instead of taking time off to learn a new skill, start applying it to your research right now.  You might be a little slower than usual for a couple of weeks (because you aren't comfortable with the new skill yet), but you'll still be making forward progress on your research, while learning the new thing.

Edit: This applies even more if the thing you are learning is a fundamental skill, and not an "extra" technique. Fundamental skills include things like writing readable code, scientific writing, keeping good notes, etc. The best way to learn these things is to actively and consciously work on them as you do research. It's not generally effective to take "time off" to read some books, then go back to doing research and start practicing the things you read about.

If it's a new skill that can't be directly applied to your research, then you definitely shouldn't take time off to learn it. But you might consider spending time on it during intervals of downtime. You can't spend 100% of your working time on your primary research anyways (mental fatigue sets in at some point), so spend time learning the new skill when you need a break.


Should I mention an informal research intern in my CV?

You have scientific research experience relevant to the position you're applying for, so explain that experience in your application.
You can mention that you worked with graduate students and you could even ask one of them for a letter of recommendation. You cannot mention working with a professor, because you didn't, nonetheless, they may be willing to write a letter of recommendation that mentions that you worked with their graduate students and they could perhaps quote one of them for the details.


What is the actual difference between Graduate and Undergraduate texts?

The differences between undergraduate and graduate texts seem to me to be no more dramatic than those between high school and undergraduate texts, and I don't consider it especially problematic.  But there are some differences:

  Why are graduate texts written that way? Why isn't there a plethora of classic texts at the graduate level?

There certainly is, but there are also plenty of mediocre books.  There's nothing special about graduate texts in this respect. Classic examples of anything will always be rare and noteworthy, more or less by definition.

You should keep in mind that graduate texts cover an enormous breadth of material (far beyond the undergraduate curriculum), and the upper limits of their depth can be impressive.  Some books are written for very advanced courses aimed at senior graduate students specializing in a certain area.  Of course they won't be easily accessible, since the research community barely understands this material.  With luck, fifty years from now we'll have clearer expositions.  In the meantime, we should be grateful that the author at least managed to distill the research literature into a coherent textbook, even if it is not yet easy to read.

Other graduate texts are intended for introductory grad courses.  Certainly there are some bad books out there, but in my experience there are plenty of beautiful introductions that are accessible to students with a strong undergraduate background.  It may still take more effort to read them than a typical undergraduate textbook, the same way an advanced undergraduate book may be tougher than one aimed at first-year students, but that's not a bad thing.  The increased difficulty comes with corresponding rewards.

You can also find especially accessible textbooks.  For example, some graduate texts are written specifically to ease the transition to graduate school for students with weaker backgrounds.  They aren't necessarily advertised that way (to avoid putting off readers), but some books are pretty widely known to be less demanding than others.  They can be a great way to fill in any missing background or just get used to graduate texts.

And it's worth having many different texts available for the same material.  Undergraduate courses can sometimes be fairly regimented, with clear expectations regarding exactly what students should already know and what they need to learn now.  Graduate school is much more diverse.  One book may be entirely appropriate for someone with certain preparation, but utterly inappropriate for others.

If there's a subject you'd like to learn about, the best approach is often to ask for reading advice from someone who knows your background and tastes.  If you can't get personalized advice, you can always take a look at lists like this.  Once you have some candidate books in mind, it's worth going to the library and gathering copies of them as well as any similar books that catch your eye on the shelf.  Then you can spend an hour or two comparing them to see which might best serve your needs.  It's going to take you far longer to actually master the contents, so a couple of hours is nothing if it helps you find the right book for you.


What do publishers provide to authors in different disciplines?

In theoretical computer science:

Papers are written, illustrated, and typeset (in LaTeX) by authors and refereed by unpaid volunteers.  Some publishers give free journal subscriptions to editorial board members; a few pay a small stipend to the editors-in-chief of each journal; otherwise, editors are also unpaid volunteers.
Most journal publishers provide an online system to help editors track submissions and communicate with referees.  Conference publishers do not; most program committees use free systems like EasyChair or HotCRP.
Some journal publishers employ copy editors, who produce the final camera-ready paper directly from author-provided LaTeX and image files.  Specifically, copy editors correct (and invariably insert) spelling and grammar errors, and reformat the paper (especially the bibliography) to fit the publisher's standards.  For other journals and most conference proceedings (Springer's LNCS series being a notable exception), copy editors simply do not exist; camera-ready papers are produced by authors using publisher-provided LaTeX packages, except possibly for page numbers.
Most publishers provide electronic versions of their papers to subscribers.  Some publishers also provide extensive indexing and cross-referencing of their publication catalog.  Online-only venues are still relatively rare, so for most venues, publishers print, bind, and ship paper copies.


While the experience that individual has gained throughout the course of their career is the best indicator of whether an individual has earned the respect of their peers, my impression is that the PhD title is generally more recognized with the public at large (basically those unfamiliar with how advanced degrees are awarded within academic institutions). This is purely a social construct that isn't germane to the field of advanced study.

I see the issue as someone calling a chiropractor a "Doctor" even though there is no award of an MD, or not understanding that a D.O. and an M.D. are basically the same thing.

Now, some universities in Europe do not traditionally award a "PhD" because they have a different three letter acronym for their doctorates. That does not mean that the individual is any less accomplished, its just a different system than the one in the US.

Perhaps one way to explain it to your students is to note what other fields have a similar award. In law, there are Juris Doctorates and PhDs; and in art there are MFAs and PhDs. The primary distinction appears to be what you have already recognized, that one is more about application than research.

To be a bit snarky, there are some fields of study altogether that do not get much appreciation, education being the main one with the award of the D.Ed. I do see some eye rolling when that one comes up, but I've also seen eye rolling from guys in the so called "pure" or "hard" sciences and their opinions of anyone in the humanities or "soft" sciences.

As to directly answer your question, Yes, there are published articles discussing the "perception" of one degree over another. I took a quick stroll on Google Scholar and found a number of published, peer-reviewed articles discussing this very question.

Here is one titled, "Doctoral Differences: Professional doctorates and PhDs compared".


Does a tutorial type conference submission differ significantly from a regular submission?

Tutorials at conferences in my field (supercomputing/HPC) are half-day or full-day sessions where you and your co-authors get up and teach lectures on your proposed and (maybe) have hands-on sessions where the students can try what they learn. These sessions are usually on a special day either right before or right after the regular paper talks and cost extra for attendees. There are often honoraria for the presenters due to the level of work required to organize the sessions. The submissions tend to be much shorter than the papers, but they also include CVs for the teachers and sample lecture slides from related or prior tutorials or lectures. A tutorial would never be given as a poster.

Given that, perhaps you mean to present a paper or poster that would be more of a  "How To" guide. Which is to say that you don't intend to give a half-day or full-day lecture on your topic. Perhaps you don't intend to give any new results, but simply show how certain methods are applied to you field. This might be acceptable to your conference's program committee depending on what is asked for in the call for papers/participation, but I suspect some sort of novel result will be required.


Do invited talks given via video-conferencing have the same weight on a CV as talks given in person?

Why would you want to try to express it yourself as a "lesser" contribution? You give much of the same value, especially if there is some facility for interaction with "attendees".

One of the reasons for "paying" for talks is that the speaker may need to travel and deal (time and effort) with accommodation - the hassle factor. It also means time away from their normal work. The money given to speakers isn't considered "pay" for expertise in the normal sense and is often called an honorarium.

But the effort required to prepare and actually deliver the talk is just the same as if travel were required in addition.

And, given the current state of things, there are few other options than virtual talks. That doesn't lessen their value. It is just what we need to do now. Just as travel was once required for such talks prior to the internet.

If you mark them at all, I suggest that you do so in a very minimal manner and certainly not separate them out from talks given in person.