Should I reveal academic misconduct on grad school application?

There is a difference between academic sanction and academic misconduct. Your question seems to confuse the two. Technically, if the question specifically asks for academic sanction, then according to your definition of a sanction as you say, you do fulfil that criteria and should mark it Yes.

However, the bar for academic misconduct is far higher and this sanction does not seem to fulfil it. Berkeley defines academic misconduct as -

  any action or attempted action that may result in creating an unfair academic advantage for oneself or an unfair academic advantage or disadvantage for any other member or members of the academic community

I can't see how you getting a zero and being sanctioned for a 5% assignment would lead to an unfair academic advantage in any way. The intent is to create an unfair advantage even if it is not technically illegal or against the rules. Remember though that college applications are the subject to much publicity in America at the moment, with high profile criminal charges led by the Department of Justice splashed across the media - New York Times article

Canada seems different, as they have a more comprehensive public system and no high profile media cases (not that I know of anyway), so the politics would be different. Such a minor 5% sanction for an assignment would not be gripping stuff. However, if you have to get a notary to sign your grad school application, then that would be a higher bar than if you just tick crossed it online. The legalities are complex and the motivation for the university or justice department to investigate an issue that seems outside the spirit of the law and more of a technicality would likely be minimal. Such a low acceptance rate of 8% will mean any reason to refuse your application would likely be significant. Good luck.


I agree this is not plagiarism if you make it clear that is an essentially verbatim extract from your previous paper.

However, it also seems unnecessary, especially if your previous paper is readily available online.  (And if it's not, why not?  Consider posting it to arXiv or your personal web page.)  In such a case, I would probably rather just refer the reader to the previous paper ("see Lemma 4.3 of [8]").  If you feel it's necessary, you can say something like "changing all occurrences of H to X", but I'd expect that a mathematical audience will just do that automatically without needing to think about it.


Arxiv equivalent for medical research article

To elaborate on the answer by ddiez: bioRxiv has been deliberately designed to fill the same sort of role for life sciences that arXiv does for physics, math, and computer science.  A key reason for this is the growing recognition amongst some practitioners in these fields that scientific communication is being inhibited by the long time to publication and pre-publication secrecy that is typical in life science fields---it is not uncommon to be hearing privately about work for years before one is able to read the details or cite it.  Overall, this is a very good thing: it improves communication, it reduces the chance of being "scooped," and it reduces the "all-or-nothing" pressure associated with targeting super-high-impact journals.

That said, bioRxiv is still fairly new, and the conventions for its relationship with journals are still evolving.  Some journals are very supportive and encourage authors to deposit in bioRxiv.  Others still tightly embrace the prior publication culture and consider deposit in a preprint repository a prior publication that precludes submission.  Check carefully what the policy of the journals that you are targeting with before you make a decision about whether to deposit.


Can one give a conference talk on a topic already published in a journal?

This may depend on your field and its customs.  In mathematics, it's totally acceptable and happens constantly.

However, if the conference publishes proceedings (only a few math conferences do), you should not publish the same paper in the proceedings.  Some people use the proceedings paper to write a "survey article" intended to give the reader a broad view of their work and other related developments in the field, but they would usually not consider this to be an original research paper.

In other fields, where a conference talk is considered to be like a publication it its own right, this might not be acceptable.


Unfairness and wrong accusations make the blood boil, not just yours. The more it is important that you cool down and stay polite and collected. Now accumulate evidence that supports your case.

The things you write here make a good start.

Bring the "legal cheat sheet" with you and explain that you wouldn't have to cheat in any case with everything that was on there.
document that you took extra courses which covered large parts of the material
offer to give a test (unlikely that they will take it up, but who knows)

The things would demonstrate that you have no incentive, and probably no need to cheat. Of course, you can say "hell" and "sh*t" and "fr*cking" and all these things, but what you need is proof which these pieces of evidence provide. Do you have other indications that support your statement?

What reasons do they have to assume that you copied from him? Is he usually better? Are you usually doing worse? Do you suspect he told them you copied? As Ran asks, did you help the other student? (because that can create a problem, too)


Interested in pursuing a PhD but I graduate in December. Do I have to wait an extra year to apply?

Certainly not. Most students graduate in the spring, but apply to graduate school several months before graduation. It is not expected that you will have your final transcript in hand when you apply. However, it is expected that you will have the transcript prior to the actual start of your graduate school studies.


My professor thinks I deceived her, but it was miscommunication on my part. Should I send an apology email?

Whether you can meet with her or not -- and I suggest you try, even if it were via Skype -- I would recommend sending her an email laying out your side. If you do receive a poor grade and you need to seek redress through some formal process, email is evidence that you attempted some explanation. The merit in your explanation is, of course, quite another matter.

Good luck.


What is the difference between "docent" (lecturer) and "Universitair docent" (Asst. Prof.) in the Dutch system?

"Docent" or "D" or "gepromoveerd docent" is a teaching-only position (or with a minimum amount of research time, like 20%), while a "Universitair Docent" or "UD" is someone who has much more research time (e.g., 40%).
Also, there are much more tenured UD's ("UD met een vast contract") than tenured D's.
After I finished my PhD, I was docent for a year (basically because I did not get an UD position), basically teaching a lot, then I became UD, and now I'm a tenured UD.

While there are some exceptions, a rule of thumb could be that a D-position is a teaching-only and often something temporarily, while a UD position is something that can be potentially permanent and involves research time.


How to answer a supervisor's email that includes and presents another professor to you?

It depends on what that new contact is for.

If it is for something completely unrelated to anything that you are working with professor A, then I'd suggest replying to both with a thank you message and then separately contacting Prof B.

If, instead, the work is, even sidely related to whatever you are doing with Prof A, add everyone in your emails. Transparent communication is key in any healthy relationship. If you are worried about spamming Prof A with relatively non-related content you can always contact Prof A separately and directly ask him if he/she wants to keep being CC'd in the email chain, there is no problem with that.

These Profs, they are just people, treat them like people!. Don't overthink it, as StrongBad says.


How common is it for academics to write fiction?

I am an academic and a professional writer. In my particular field of writing (interactive fiction), a large chunk of writers are academics, so it’s definitelt possible.

Most employers are not concerned about outside activities as long as they don’t interfere with your responsibilities. However, writing commercially requires a large enough time commitment that it will be very hard to conduct research at the same time. The most prolific and successful academic/writers I’ve seen either stopped writing or stopped being a research academic. A few are able to find a position where there writing is valued as academic research (such as Nick Montfort).

If research is an expectation for your position, then your best bet would be to take a more teaching-focused job or to work only a small amount of time each day and marketing your writing after you finish it in your own.


Is an undergrad travel grant relevant to a CV?

Giving a poster talk at a major conference is certainly important in your CV. If the travel grant to go to the conference was based on academic excellence, then it should also be included in the CV. If it was a lottery, or based on non-academic merits it might be irrelevant. Nevertheless, even in the latter case, it doesn't harm to put it on your CV as it shows some initiative and dedication.


Authoring unverified common-knowledge statements in papers about quality software-engineering?

This doesn't sound like the sort of thing for which it is meaningful to have a "first guy that said this" reference for, unless you are writing specifically about the history and development of modern coding standards.  And even then it's difficult or impossible to find a single, definitive source.  More than likely the ideas emerged dynamically from a whole host of forces and in multiple people/locations, rather than any one person who "said it first" and everyone else followed the lead of.  What is "good" and "quality" is largely a matter of convention and opinion, after all.

Having hundreds of textbooks and thousands of research articles that support it is more than sufficient to establish it as a common mantra, or whatever you want to call it.  If you can find a respectable book that is specifically about modern coding practice and its (historical) development, you could reference that as your support for the claim.  Otherwise referencing a few major, influential texts that make the same claims would be good, though you may want to be careful with your phrasing.  Citing them as proof this is the one "right" or "universal" way to do coding is arguably misleading and circular; saying that you take the same approach as those authors, however, makes no claims to objective truth and simply makes clear an assumption to the reader.


you cannot teach with a PGCE, you need to pass the Agreg or CAPES examinations, at which point you are placed at a school. New teachers have very, very little say in where they teach.

PGCE credits are loosely equivalent to masters credits, but my experience is that few universities will APL them in because it's effectively a professional training course. If you carry on learning at the same institution, they might have a scheme to "convert" the PGCE to an MA or MEd.


How can teaching assistants deal with grade disputes?

In the United States, the professor responsible for the course should take responsibility for resolving disputes (but not requests for corrections and clarifications).  There is an expectation that they will be heavily involved in grading, even if the bulk of it is done by teaching assistants.
In some cases, the professor may choose not to involve themselves in grading at all, and leave it up to teaching assistants to resolve disputes.  I do not agree with this practice, but if you are stuck with it, you can handle disputes by:

Using a rubric to grade.
Resolving all disputes using the rubric.
Refusing to compare the work of different students.  In the USA, comparing students' papers runs a risk of violating privacy laws.

Ultimately a portion of students will never agree with you about how you grade (they want to learn something different from what you are expected to teach) and this simply must be tolerated.


Since the limitations you describe are related to the coverage of the scenarios, I would describe them in the "simulated scenarios" section. If you really have a lot of content about these limitations, then it deserves its own section in the method chapter.

Then in the discussion part you can mention them again if relevant, e.g. "it's possible that results would differ if..." with a ref to the method chapter.

Traditionally the conclusion is a summary of your findings and a description of further work. If relevant you could mention "cover more scenarios" in the latter, but that's not where the explanations about the limitations should be.


Can I upload my open access publications on researchgate.net or academia.edu?

Maybe. But not necessarily. It depends on the exact terms and conditions of the open access paper: there are many different variants (Springer use more than one, as do many other publishers). It also depends on the exact terms and conditions of the site you intend to upload to.

So there is no general answer, beyond this:

Read and understand the licence on the paper.
Read and understand the terms and conditions of the site you want to upload to.
Work out whether they're mutually consistent, and whether you want to accept the T&Cs of the site you want to upload to.


Business School professors - how different are they?

I can address questions 1 and 2 (although for 3, all I know is that my friends say it is very different).

When you are negotiating over salary, your leverage is determined by the best alternative you have.  To keep from losing you to another employer, your job must offer a better combination of pay and benefits than anyone else (including benefits like job security, having interesting colleagues and students, having flexible hours and the ability to choose your own projects, etc.).

People in the humanities have very little leverage except from other academic jobs.  Mathematicans have more, because there are applications in industry or government, so they get paid somewhat more, but this leverage is limited by the fact that many mathematicians don't want non-academic jobs.  Computer scientists have a lot of leverage, and business school faculty have even more.

So basically it comes down to this.  Business school faculty often have expertise that is in high demand outside academia and could earn them a lot of money, and there's at least a stereotype that they care more about monetary compensation than some professors do (which makes sense, given their interest in business).  This means that to attract excellent faculty, business schools have to pay enough that job applicants would rather work there than in the business world.

In principle, this is no different from other departments: literature faculty also have to be paid enough that they don't leave for the business world.  It's just a question of how much that is.
This really depends on the subfield.  Business school faculty are certainly more likely to do outside consulting than scientists are, but there are no universal rules (some business school professors do none at all, and some scientists run their own companies).  Occasionally, a company will sponsor a university program according to some negotiated agreement, but consulting generally does not involve a pay-sharing deal.  Instead, the faculty member simply consults part-time for the company, without using university resources, and is paid directly by the company.  In the US, universities typically allow a certain amount of time to be spent on outside consulting, for example one day per week, with no special approval needed.


Is it possible to get a research grant without any degree as a person that has a self-learning mentality?

No.
Without a degree and a position at a university or research institute, it is highly unlikely you can get any kind of funding for research.
You can try to get a job at a company that does research in such topics (which requires who to have the background knowledge, not necessarily a degree), but this will also be hard to get.


Referring to individual chapters in a review of an edited volume

Cite them normally. At least BibTeX has a feature to refer to another entry (the book as a whole, in this case) in the entry for the individual article, giving something like 'A. N. Author, "Random ramblings", pages 111-123 in [reference-of-the-book]' in the bibliography.

For techniques/tools for writing papers, you should perhaps ask at TeX-LaTeX.


What can a student do to respond to faculty/administration decisions based on current political events?

As a student, unfortunately there is probably nothing you can do about the situation -- except to remind yourself that one day you might be in a position of power and influence yourself, and able to do things differently.

Things might be different if there were was a particular American professor you wanted to invite to campus for academic reasons. In that case I would express to your chair that you understand his concerns, but talk about what you hoped to gain academically from such a visit.

The immigration ban is strongly opposed by many American academics. If there iss someone particular you would like to invite, you might ask if he/she has done anything to fight the ban (e.g. calling one's senators, participating in protests, donating to the ACLU). In such a situation, your chair might be willing to reconsider.

That said, I would not recommend pushing the issue hard if at all. You are still a student, and as such you don't have a lot of political clout.


Famous professor at relatively unknown university for post-doc

Just opinion, of course, but I would suggest that a great professor at a small school, no matter its reputation, would be a huge asset. You will have a chance to work closely with a mentor that you wouldn't get to do as well at a larger place. I realize of course that size and reputation aren't necessarily the same.

But it is the letters you get from the professor if they are well known that can set you off on your career and, if you do get the chance to work closely, that association can pay dividends for a long time.

While a degree from a prestigious place has value, I think a postdoc with a leader of the field is a great asset.

And, of course, "relatively unknown in central Europe" is itself relative. Lots of people don't know about, for example Charles, and such, depending on where they are from.


What determines the copyright year for a publication?

You are not showing the location of publication, however in the U.S., while Copyright is established the moment the work is created, the only effective way to claim infringement is to have registered the work with the U.S. Government's Copyright Office (http://www.copyright.gov). The date shown is more than likely the date that they received confirmation of the copyright registration from the office.

Subsequent editions will also refile copyright, so you can have various dates or a range of dates shown. On Molecular Biology of The Cell by Alberts, et.al, the copyright page has the 2015 copyright for the sixth edition but also lists the 2008 date for the preceding fifth edition.

I have generally seen date ranged copyrights on software, so if you select About This Mac on an Apple Mac computer, the splash screen shows (c) 1983 - 2015.

UPDATE

Even though copyright exists from the moment of creation of the work, an important reason for official registration has to do with the damages that you can seek for infringement. The following is from the Copyright Office's FAQ

  Why should I register my work if copyright protection is automatic?

  Registration is recommended for a number of reasons. Many choose to register their works because they wish to have the facts of their copyright on the public record and have a certificate of registration. Registered works may be eligible for statutory damages and attorney's fees in successful litigation. Finally, if registration occurs within five years of publication, it is considered prima facie evidence in a court of law. See Circular 1, Copyright Basics, section “Copyright Registration” and Circular 38b, Highlights of Copyright Amendments Contained in the Uruguay Round Agreements Act (URAA), on non-U.S. works.


Is there data or research on the tradeoffs associated with revealing how a student's grade on an assessment compares to the rest of the class?

If you Google something like "pros and cons of ranking students" or something similar you will find several websites and other resources that deal with this topic.

Ranking students is common in education. The best examples are standardized tests that always include a percentile ranking (SAT, ACT, GRE, etc.). This is one form of norm-referencing, which is a common tool used in assessing. However, since standardized testing is nationwide, it is hard to be too competitive with the person sitting next to you during the exam, since you probably do not even know their name.

Within the classroom context, ranking could be detrimental if there is a higher consequence of the ranking. For example, only the top 20% will pass and the rest will fail. This could lead to some cutthroat behavior and really lead to a negative learning environment. If the ranking lacks deeper implications, students may not even pay attention to it.

In the end, whether or not to rank or not depends primarily on a person's philosophy of education. Some believe this is beneficial while other do not and there is empirical support for both positions. It is impossible to say that this should always be used or never be used.


Does it have any value getting a PhD in engineering after 45?

You can answer this with salary survey data.  Based on the data, it would be reasonable to assume a CS academic would earn $95,000/year a few years after their PhD.  This would rapidly make up for any lost earnings from not driving a taxi during a PhD, so we can determine that the answer is yes without figuring out the taxi driver's earnings or the PhD stipend.


Where can I find good examples of personal statements [BSc, MSc, PhD]?

I think you will be hard-pressed to find actual statement of purpose on the Internet. The one submitted to the departments are destroyed after the application process because of obvious privacy issues. Generally the applicants do not publish their own statements for several reasons. Your best bet is to ask some people you know that might have written one and can send it to you.

Another option is to have a professor or a postdoc help you with your draft because they have probably been in committees routing through these statements and will have a good idea if you are heading in the right direction. There are many ways to write a good statement, you should be able to write a statement from the general guidelines that you can find in the other  answers on this website. After all the statement is meant to test your capacity of developing your ideas and your writing style.


I work in a program for computational science, and we do online interviews with all of the qualified candidates for both our dual-degree (master's-PhD) and doctoral programs.

Because we are a rather broad program, we tend not to favor "quizzes" that test knowledge. Instead, we are looking for things like:

Ability to communicate in English
Enthusiasm for computational science (many people think we're a computer science program, instead of a computational science program!)
Match for the research interests of one or more of our institute members (particularly for dual-degree candidates)
Previous experience in computational science
Evidence of teamwork and ability to fit our program

There's no real way to "game" the system, at least in my interview, unless you want to invent an entirely new personality for yourself. That's because most of my questions are free-form after the first few, and will try to explore the answers you've given in greater depth. For instance, if a candidate expresses an interest in fluid mechanics, I'll ask what they've done, what makes it interesting, what they'd like to do in the future. If someone happens to express interest in my area (computational materials), things will go in yet another direction altogether.

The best advice is be yourself. If you try to come off as someone you're not, that will likely show up during the interview.


Fellow student doesn't share progress in joint paper for coursework - how should I react?

The first thing I would do is to try contacting your partner again. You've said you already told him that you prefer a more cooperative style, but perhaps you should can be clearer about this. For example, if you say "I think you aren't communicating well, I need you to cooperate more", this is ambiguous and could possibly be interpreted as an attack on his working style. Instead, you can try to give more concrete suggestions. For example, setting up weekly meeting times for both of you to sit down together and talk about the paper and what you need to do next. You could also suggest setting up a google docs or dropbox etc. where both of you have access, so that you can both edit the document and see the changes the other has made.
If this still doesn't work, I would consider the cost/benefit of the next steps. You can escalate by going to the professor, but this isn't necessarily in your best interest, even if you don't like working with your partner. You say that there are formatting/style issues, and broken references, but to me these sound like minor issues that can be fixed pretty easily. It also sounds like your partner is doing a lot of work on the paper, which is good because sometimes you might get a partner who does nothing or does everything at the very last minute.
If you do decide to go to professor, you should understand that if you can't fix the group, the professor isn't going to be able to either. Maybe if your partner is ghosting you the professor can force the two of you to sit in the same room together, but beyond that they can't do a whole lot. Your professor is also not going to grade you easier because you complain about the group to them. Really the only thing the professor can do is possibly give you the option of working by yourself for the rest of the project (but they won't necessarily allow this). But of course, then you'll be out of a partner altogether.


Interview for a faculty position after accepting a postdoc offer

My understanding of the norms in academia is that tenure-track and tenured positions are generally accepted to be rare opportunities, and that taking those if offered is the right thing to do. As such, it is perfectly acceptable to attend an interview for a tenure-track position, and to accept it if offered, even if one has already accepted a conflicting postdoc. In such case one should, however, be apologetic to the snubbed postdoc mentor, and do ones best to minimize the inconvenience to them.


How important is age in CS PhD admissions?

Age is simply not a factor in PhD admissions in computer science, at least in North America.  As Zenon says, age discrimination is illegal here.

However, being out from school for a significant period of time (say, more than five years) is a potential hurdle for PhD admissions, at least in my department.  We typically recommend that those students pursue a MS degree first, to refresh their academic background.  But since you're in an MS program now, that shouldn't be a issue for you.


Can I apply to other postdocs after accepting an unofficial postdoc offer?

Till I get any official letter can I apply to other places also ?

Depending on the laws in your country, it is likely that you are allowed to do so without breaking any law. However you should be very careful about damaging your reputation in case you end up committing to several positions.

In my experience, in academia an unofficial commitment can be trusted and official paperwork can take some time to be issued. This depends on many things obviously, in particular how much you trust the PI who offers the job.

Since you mention that your main concern is about having a backup plan, I would recommend inquiring with the future PI (or the administration of the future institution) about their administrative procedure. Why not also mention to the PI that you are considering other offers? This could motivate them to speed up the process. And in case you feel that they are stalling, then you have a good reason to look elsewhere.


Why do non-governmental organizations tend to publish non peer-reviewed "grey" literature?

I can think of a couple of reasons:

Peer review is slow. NGOs want their paper to influence policy now, not in one or two years from now.
Peer review journals have a different audience than grey literature. NGOs typically want to communicate with people like policy makers or journalists, and these are less likely to read peer reviewed journals.
Related to point 2: in order to effectively communicate with their intended audience they need a different style of writing and presenting their arguments than what is common and acceptable in peer reviewed journals.


Should I communicate to a researcher that I'll apply for a postdoc position is his lab in approximately two years?

Sure, why not?  Telling him you are planning to apply is not the same as applying.  He is not going to make an evaluation right now, so the drawbacks you mention don't apply.  You might also ask him what he regards as good preparation for working in his group.

The only part of this that looks bad to me is that you are planning in advance to do a second post-doc, rather than even try for a permanent position.  But I understand that may be the norm in some fields.


After getting a PhD at a low-ranked university, would it be harder to get a job at a high-ranked university?

Moving from a Ph.D. at a mid-ranked institution to a postdoc at a high-ranked institutions happens very frequently.  The easiest path for this is to have solid publications (extraordinary is not necessary) and a good relationship with both your Ph.D. advisor and the supervisor you do the postdoc with.

One of the important factors enabling this is that a strict ranking of Ph.D. programs does not make much sense once you get above a certain base level of quality.  Beyond that point, every program is extremely heterogeneous based on the particular professor.  Absolutely world class professors are often at "mid-ranked" universities, and people in their particular subfield will know it, and consider that university "elite" in their particular subfield.  It's just that you can't obtain this information from US News or other "generic" rankings.

An example: US News currently gives the University of Massachusetts, Amherst, a rank of #60 in the US as an Engineering grad school and #76 overall, but they have an extremely strong artificial intelligence group that practically dominates in some subfields.


Is it polite to ask for an attachment from the recipient?

There shouldn't really be any problem with this other than a bit of embarrassment. Just explain what happened and ask if it is still possible to have a copy back. Worth a chuckle, but no more. I don't see how it should affect your application provided that the institution is ethical. Humans make mistakes.


My advisor cited her colleague's papers in her own methodology even though she did not use those methods. Does this qualify as scientific misconduct?

The issue here is not citation, it is correct reporting.  If a method varies from the cited version, the appropriate thing is to say something like "Method from FrozzBozz et al.[73], modified by change of RPM from 3000 to 6000, growth media from LB to M9, and phase of the moon from new to full."
But did the method actually differ?
Now, there are definitely arguments to be made about the level of detail that is necessary and appropriate in protocol reporting.  For example, the details about how a sample is shaken may or may not matter, but are often omitted because people are often simply not very systematic about this.  Likewise, layout of samples on a 96-well plate is typically not reported, even though there are sometimes locality effects. Thus, many of the things that you are concerned about might be reported by one group but not by another.
The key distinction between reportable and non-reportable method details is whether a reasonable reader might expect them to have a significant impact on outcome.  In many fields, this is more clearcut: for example, an algorithms paper reporting the number of iterations required to solve a problem would not declare the system the algorithm is run on, but one reporting the time of execution would.  In biological sciences, however, it is often quite unclear and reasonable people have very different perspectives here.  Thus, the Ph.D. candidate might not even believe that they have meaningfully changed the method at all!
My advice it to start by approaching it from this perspective, in a non-confrontational manner.  Start by just asking for help in understanding the differences in method.  If they do not explain in a way that makes sense, then it would be appropriate to escalate to the PI that ultimately supervises both of you, and ask for help in figuring out what details of method variation are appropriate to include.  No need to get into accusations of lying at this stage, and you both might end up learning new things in the process.


Publish more research papers or advise dissertations?

Your question is largely a false dichotomy. For instance, there's no reason a paper written by one of your students can't involve collaborators at your institution or from other institutions as well.

So long as your students are publishing, and you're establishing a network, I wouldn't worry about trying to prioritize one over the other, unless your institution's promotion and tenure regulations have something specific to say in the matter.


Will excellence in professional career be considered for admission or financial aid

Professional IT skills have very little to do with graduate-level work in computer science. While such skills may lead to a positive letter of recommendation, it is unlikely that you will receive either admission or financial aid (in the form of a teaching or research assistantship) solely on the basis of your record as an IT professional. There may be exceptions to this (for instance, if your professional work is in a specialized area that maps closely to an existing research area at the school to which you are applying), but in general, but that would be more the exception than the rule.

In other fields, such as bioinformatics and chemistry, where "professional work" may be more similar in nature to ongoing academic research, this is more of a possibility—I know several people whose work careers did have an influence on their admissions to graduate programs.


Is it a good idea to submit a recommendation letter from a friend who is doing PhD at the university I am going to apply?

No, it is not a good idea to ask your friend to write a letter for you.

Recommendation letters for graduate admissions should be written by people experienced within the field, who know you well enough to form a clear opinion of your preparation and potential for graduate work in your chosen field.  In almost all cases, they should be faculty members with whom you have worked closely, or at a minimum, taken classes with.

Having your friend write the letter would be useless:

He is working in a different field and would not know what skills are needed in your field.
He presumably has little or no experience of research of his own, so will not have as good  a sense of the attributes that are needed for success in research in his own field, much less yours.
He is your personal friend and there would be doubts about his objectivity.  (Ethically, if he were to write a letter for you, he should disclose that relationship.)

The fact that he is currently attending the same institution where you want to apply is irrelevant.  That doesn't give his opinion any extra weight.

Beyond being useless, submitting a letter from your friend would lead an admissions committee to think one of two things:

You cannot find two faculty members who have a good opinion of your abilities, so you asked your friend instead.  This would suggest that your preparation is extremely poor and your application should be rejected.
You are completely confused about how the application process works and did not understand that a letter from your friend would not be helpful.  You have not done your research and probably don't really know what grad school would be like or why you want to go.  They are not likely to accept such an application, either.


Is it worth the risk to apply to REUs? How likely am I to be accepted?

I don't know where you are getting the idea that it is a longshot specifically for non-minorities. In general, REUs do have low acceptance rates for everyone. There are a lot of students who want to do them and not that many REUs.

Now, to answer your question: yes, being female will likely help somewhat, but it likely won't make a big difference. What will matter more is the GPA which will help out a fair bit. The previous research experience may hurt or help; at least in math some REUs try to admit undergrads without experience to spread them around, but that's not all of them  by any means, and for the most part it would be helpful. I suspect the situation in biology is similar.

Since you are a junior, you should already have some connections within the biology department, either your adviser or faculty whose classes you have taken. They can likely give you more personal advice since they know you better. But at least from what you've said to us, I suspect you have a higher chance of getting admitted to an REU than the average candidate.


How to cite a retouched image that originally comes from an ebook on archive.org?

You need to cite the book, as that vouches for the provenance of the image (including that it is of who it is claimed to be).

If I'd done that retouching myself, I wouldn't mention it as it doesn't change the content (it's effectively undoing some of the effects of scanning an old image).  A "(retouched)" might be appropriate, and certainly "(enhanced to show...)" if that was what you'd done.

If someone else had retouched images specifially for a paper I was writing, they'd deserve an acknowledgement, so here they deserve a mention.  I would cite the original still, but with a note (or the equivalent in your referencing style). Something like "(via https://commons.wikimedia.org/wiki/File:Cajal-Restored.jpg, retouched by user Garrondo)" should be sufficient for academic propriety (and should cover the CC requirements were that an issue).


I am hesitant with this question because the ethics of the fact that you are in a position of authority over them and what you do could affect whether or not they are published. The point of research is to advance the field, so by reading their paper, you have had a reactionary idea that will advance the field even more. So, I vote to mention it in the review and see if they pick up the idea, if advancing scientific progress is truly what you are worried about. If they don't do anything with the information then go ahead and develop it yourself.

Otherwise, you risk rejecting them for personal gain, on an idea that you said you haven't even implemented or tested yet, something that they have done.


How to show interest in a candidate when no positions are available?

This answer is about faculty candidates, not graduate student or postdoc candidates.  (I misunderstood the original question.)

First, be honest with the candidate, both about your interest and about your ability to hire.  Yes, we are very interested.  No, we don't have any regular faculty slots this year.  Yes, we would love to fly you out, have you give a talk, meet with some of our faculty and students, maybe have a chat with the dean, and see where things go from there.  Make no promises you can't actually keep.

Second, a lack of open slots does not mean it is impossible to hire.  Your college or campus may have finds set aside for "excellence" hires, or for cross-departmental research initiatives (like "clean water" or "computational science"), or for dual-career families.  Some other overlapping department may be willing to give you half a slot for a joint appointment.  Another faculty member in your department or college may have just unexpectedly retired, resigned, moved to administration, failed to get tenure, or died.  Your dean may be impressed enough (or encouraged enough by other senior faculty) to give you an extra slot just for that person next year.

Creating a slot takes a lot of legwork and a lot of political capital—you may burn a future slot even if the candidate doesn't come.  So they'd better really be special, and you'd better know that they'll come if a position is actually offered.

Yes, I have seen this work.


Is it appropriate to mention one's religion in an academic CV?

There are some situations where religion could limit someone's ability to do their job. For example, a Muslim professor may require prayer breaks, which could limit the times at which they can give lectures.

Religion should be mentioned only on a "need to know" basis, unless it's common practice to include it in the country you're applying to. Similarly to if you have a disability, you shouldn't mention it on your CV. It is more appropriate to explain such caveats in the cover letter, during a job interview, or prior to accepting the interview.

We should be judging people on their ability to do the job, not their personal beliefs. Such beliefs are only relevant if they interfere with their work. Unfortunately, particularly as a result of increases in extremism,  Muslim candidates in Western Europe are more likely to be at an unfair disadvantage, rather than being favoured for a position.


There is a really good document by Columbia University that explains how to read a paper (focused in science and technology). The key is to read firstly on breadth, getting the best information from the abstract, figures, tables and so on. And then in depth if you think that from the first diagonal reading the paper is worth the time to do so.


Edited volumes in bibliography: (eds) or (eds.)?

APA 6th edition uses "Eds." So there's at least one reputed style guide that abbreviates in the plural with a fullstop.


How to start research as an undergraduate CS student

The two options you give are not mutually exclusive.

In some universities some members of the faculty will have summer internships, you can ask staff about such opportunities. Since you are studying Computer Science the internships are likely to be somewhere between research and implementation.

If you are interested in research-proper or you are still finding out what interests you then it is also good to approach faculty. However, stating you are simply interested in research will not provide them with a way to help you. I suggest reading some papers related to a course you enjoy and start looking for gaps in the research, thinking of - very small - improvements you can make and - then - discuss with a member of faculty who may give suggestions on how to approach the problem and offer to look at any progress you have made. This second approach makes it much easier for faculty to help you.

This second option is not coming up with a research idea yourself, but instead finding a small gap and getting the advice of staff on where the research may lie (that you could feasibly conduct).

I must stress that it is important to be realistic about what you can do; faculty will be more receptive if what you want to do is manageable (i.e., you show them you're a grounded type of person).


Does your final-year GPA matter once you apply for graduate school during your undergradate study?

The linked duplicate question answers your query regarding applications in the US. This answer will address the UK situation.
In the UK, if you haven't graduated and got your final mark yet, your offer of a PhD place and funding will almost certainly be conditional on you finishing your degree with a certain grade. They may specify a certain GPA you need to graduate with, or the equivalent UK degree classification. Since the UK system is less finely graded than in the US, the latter scenario gives you more flexibility.
For example, they may state that you must achieve equivalent to a 2:1 (pronounced "two-one", aka upper second class) degree. In the UK this means an average of between 60% and 69%. Let's say your GPA is currently 3.5, which might correspond to 68%*, a high 2:1. However, in your final semester it drops to 3.3, which might now correspond to 64%, a middling 2:1. In this imaginary scenario, your drop in GPA didn't correspond to a drop in UK classification, so you would still meet the offer.
However, if they give you an offer in terms of your GPA (perhaps less likely), asking for you to graduate with a 3.5 and you drop to 3.3, then you have missed the terms of your offer and your place and funding will likely be rescinded.
Related to Jon Custer's comment, it's also important to note that in the UK the average grade tends to be weighted towards the final year, and first year grades almost never count towards the final classification. So doing poorly in your final year certainly looks bad from a UK perspective, as the final year courses are arguably the most important and have the biggest effect on your overall classification. While that may not be true for your own degree, the unconscious bias may still be in the minds of a UK admissions committee.

*Note that I have no idea how GPA would really be converted to a UK classification; likely the university you are applying to will have their own method of conversion that would definitely be worth asking about before you apply.


addition of physical address upon paper acceptance

Probably.  But only the journal can say and you should just ask them ASAP.  Worst that can happen is "no".

Edit:  removed non-SE compliant sarcastic remarks.


What are the cons of studying in a Ph.D. program that takes much time to confer the degree (about 1 year and a half or 2 years, after dissertation)?

Many academic positions after graduation are dependent on proof of degree completion, so this could potentially be a problem.  The NSF math postdocs, for example, require a signature from the school that you've completed your degree, and some positions explicitly require a copy of your transcript or diploma that indicate your completion of a Ph.D. program.  The institution where I completed a postdoc was in this latter category, and would only issue an informal offer (and not an official contract) until they received final documentation of my degree, which in my case took several months to arrive after graduation.  One practical problem I faced as a result was difficulty arranging for housing at my postdoc institution; most rental companies want to see their tenant's signed contract as proof of income.  I am also aware of tenure track jobs where the contract specified that the tenure clock only started after conferral of a degree.  I suspect some institutions would be willing to bend the rules a bit in unusual circumstances, but it certainly could be a problem.  (Note that this answer is based on experiences of myself and colleagues in the US.  I have no idea how this practice varies in other countries.)


Expected undergraduate semesters and requirements for graduate students

I have been wondering recently about how graduate schools and in general anyone who reviews my academic record views coops.

Coops are fantastic.  Especially for programs in computer science / applied math / data science, relevant industry experience is a strong advantage in graduate school applications.

  If the student takes more than 8 semesters to graduate, is it a problem?

No.  Nobody cares.  Even if someone on a grad admission committee noticed, the longer time would quickly be explained by your coop semesters and your change in majors.

  Should the student (if they can) extend their studies by an additional semester so that they graduate in the spring, or is a fall graduation equally acceptable.

Acceptable to whom?  If you mean graduate admissions committees, then I repeat: Nobody cares.  In particular, graduating in the spring is no barrier to starting a graduate program the following fall.  (Of course, you have to eat, but that's a separate issue.)

  Do grad programs accept students to start in the spring, or only the fall?

Some do, some don't.  Every grad program is different.

One last point: You mention coops, GPAs, and program reputation, but those are not the most significant bits.  Graduate admissions committees at top departments are primarily looking for strong evidence of research potential.  Assuming my quick Google search correctly identifies your university, you should have lots of opportunities for undergraduate research experience with world-class faculty.  Take advantage of them!  Start now!


Is it ok for an examiner to hide exam reviews

My personal view is that you should be able to get feedback on your exam, though that doesn't necessarily imply getting a marked-up copy of it. But that is a personal view and whether there are rules or not at your university, the personal views of your professors hold more weight than mine.

It may be that there is some fear that giving you this material will make future use of the questions impossible - security through obscurity.

But what is OK in one place is forbidden in others.

But you are more likely to be successful if you ask for feedback on your performance. It is hard to argue that you are not entitled to that.

I doubt that there is fear that you have been too harshly judged in the grading, but there may be a reluctance to do anything that might generate such a charge.

But, as you are aware, without feedback you have no way forward other than blindly guessing.

One possibility is that your grades are being reviewed by a higher authority and so there is a delay. If making a bit of noise has been effective in the past, you might be able to successfully call for a higher level review without seeming like malcontents.


When applying for a position, how do I best reply to a question asking for skills I don’t have?

First of all, do not worry too much about whether this is a strict requirement for the position.
This is something they have to decide (based on your honest assessment of your prerequisites).
Also, if you made it past the first stage of the hiring process, it is likely that this is not a strict criterion.

Additionally note that (depending on country, field, and individuals) job ads that ask for more than they can possibly get are sadly common and in this case it is no problem if you only have a subset of the skills they ask for.
Whether this actually applies to your situation is something you have to judge yourself:
How likely is it that somebody already acquired all the mentioned skills at your stage?
In particular if we are talking about a PhD position here, acquiring relevant skills on the job should be the norm.

That being said, when faced with such a question:

Answer truthfully. You don’t want to do a job you cannot do and it almost certainly ruins your relationship with your advisor if they suspect you were dishonest about this.
Is there anything similar you have experience with or anything that may facilitate you learning these skills? If yes, talk briefly about this.
Do you find the methods in question interesting? If yes, state so and explain why. (If no, you probably should look for another position.) It may very well be that you were asked this question just to check that you do not shiver with disgust in light of these methods.
If it wouldn’t be uncommon to have these skills at your level, explain why you do not have them. For example, if your past universities did not offer a course on them, state this.


How much of a share should I have in a startup based on my PhD research?

TL,DR: You deserve a large majority.  I consider 90% for you and 10% for your professor fair.

I finished my Ph.D. and co-founded a company based on dissertation work. I continue to work as a funded tech entrepreneur.  I offer the following insights:

From your situation, it sounds like no one else is remotely close to your level of contribution. If you leave, there is no business.
Equity should be determined based on real contribution to the enterprise.  You aren't being cruel or disrespectful by placing a value on what people bring to the table. At this point of the business, value equals cash or know-how. Do not award equity to someone who's really eager and ready to "work like a dog" (chances are they will fade in six months) without tying their effort to a vesting period -- they don't receive their equity until after a period of satisfactory work, quantified and agreed-to in writing.
As co-author of the patents, your professor is entitled to proceeds from the use of the intellectual property, but not equity. In this case, you are choosing to give equity in exchange for permission to use the patent.  Your business operating agreement should state that.
You need to check the university guidelines regarding use of the patent. Most likely, the patent is controlled by the university and you'll have to work out a licensing agreement.

When all is said and done, you need to have enough cushion to absorb dilution (if you bring on investors or high-level staff), yet retain control or a profitable equity position. I think a 90%-10% split between you and your professor is about right at this point. If you bring on the business student (they may be a nice person, but aren't providing a lot of value), I propose a 85%-10%-5% split with a vesting period for the student.  Consider awarding more equity to the student later if they work hard.

Good luck and remember: you have the know-how if people decide to make things difficult.  Walk away if needed.


Who should be provided as an academic reference for job applications?

Your academic reference should be a teacher you have taken a class from or worked with in another academic capacity like a research assistantship, an academic internship, etc.

For students very early in their careers who have only taken large lecture classes, this can be challenging. Some teachers of large lecture classes have concrete guidelines for when they will recommend students in these classes (e.g., I might have a policy of recommending any student who achieves more than a 3.7/4.0). You might look at your professors websites or ask them. The professor will likely review your work in the class before writing a letter so you will be wise to pick a professor of a class you did extremely well in.

Alternatively, you might be able to ask a post-doc or graduate teaching assistant that you worked with more closely with who is familiar with your academic work. I wrote these letters for undergraduates when I was a graduate student. Graduate student letters would be inappropriate for applying to a graduate program but should be just fine for intra-University programs and placements.


Data sets of questions asked in conferences

Such a data set probably does not exist, due to human subjects considerations.  While conference speakers are often asked to consent to possible recording of their talks, conference attendees are not generally asked for such consent.  Sometimes questioners do get recorded anyway, in those rare talks that actually are recorded, but they have certainly not provided any explicit consent for becoming experimental subjects.

Now, some researcher and their IRB might well be able to work out a way to build a data set from the decidedly biased sample of publicly available talks that happen to include questions. Doing so and then executing that project, however, is likely to be a rather large research and coding effort and with that much work the authors would certainly end up wanting to publish papers on it.

In short: if your literature search isn't turning it up already, then it doesn't exist.


Should I abandon any further higher education knowing that I was dishonest as an undergraduate?

Sounds like you have had some insights to your past behavior, and understand what you did was wrong - that could serve you will in future situations where you might be tempted to game the system. That experience could be a positive rather than a negative.

You escaped any consequences, and I don't think it's productive to think about hypothetical situations where you didn't, especially for something that is at least a few years in the past.

There are lots of good reasons to not enter a PhD program. I don't think you've found one here, but you should think about what goals you would have as a PhD student since a PhD is unlikely to advance your career unless you want to enter academia. You'll need a lot of internal motivation to get it done. Focus on those things rather than dwelling on your past indiscretions.


Is it appropriate to compare students to other successful students in a letter of recomendation?

This makes the letter of recommendation more personal and shows, you really want to support her. It makes a difference to all the other "this student has good grades and is always on time"-letters. So go ahead!


How do I prepare for a postdoc position with requirements in working with the theoretical basis of the software, which I have never worked with?

Three quick thoughts:

Discuss it with your advisor. They might know of more suitable positions, or have field-specific advice.
During your PhD (and before), you should have improved the skill of learning things on your own. This will be useful in a postdoc or maybe an industrial position. Just don't be afraid to use it.
It seems you have some time left before the defense. Use it to start learning the software and skills you need. Consider starting a new research project where you'd have to use these methods (nothing like learning by doing!), or just reimplementing an existing paper.

Good luck!


How to choose between multiple math postdocs offers?

nagniemerg is absolutely right that at the end of the day, your results will be much more important than a name on your CV.  I think being at a prestigious institution is very useful for getting a first look at your application (which is a f***ing valuable thing, as Rod Blagojevich would say); if the rest of what's there doesn't stand up, getting that look won't help much.

That said, I would think carefully about how sure you are that institution Y really will provide a better research environment.  Prestige tends to correlate (far from perfectly) with having an active department with a lot of seminars and visitors, which can often be more valuable than day-to-day contact with a single advisor.  Having higher-quality students and colleagues can make you a better researcher.

I also think there's a lot to be said for the uncertainty of life.  Maybe you'll go somewhere and whoever you were going to work with will get a job somewhere else, or have a baby, or go on sabbatical.  Maybe you'll start a collaboration with someone you don't even know exists yet.  It's all very hard to predict, and on some level you have to go with your gut.  You could do a lot worse than just going with the most prestigious option, but if other factors seem to point another direction, I don't think you should just ignore them.

EDIT:  I wrote this is a bit of hurry last night, and I realize it might be a bit unhelpful. However, it's honestly quite difficult to say anything general, and you indicate that senior mathematicians who know you and know what your options are cannot come to a consensus.  To me this indicates that probably you will not be able to conclusively figure out where is the better choice.  This is not to say it doesn't matter, but once the uncertainties are sufficiently large, one might as well flip a coin (or at least flip a coin until you get the answer you want).


How can a professor who has signed The "Cost of Knowledge" pledge review papers without having to recant?

Sounds like he's sticking to his moral principles, which is the best anyone can do. Maybe he could evangelize his opinion more to increase the impact of his crusade, but that's about it.

I disagree with the insinuation that he may be doing his field a disservice, since moving away from the ancient publishing model is a good thing for any field in the long run. Besides, it's not like he has left the field; just a small part of its publication scene.

Just because nobody seems to be following him (yet) does not mean he failed in any way.


Presumably, your master's thesis was graded by academics other than your supervisor. Since your supervisor read it and checked it on multiple occasions and considered it excellent. In particular, your supervisor advised that your analysis is more than enough (as opposed to weak and insufficient, as remarked by your graders). (I don't understand what is meant by: that is definately his comments [since] he is the only one on faculty to specialise on this topic. Firstly, what comments? Secondly, non-specialists can evaluate your work.)

  Whom and how do I address these issues?

It seems your supervisor is on your side. I suggest meeting with them and discussing your grade. Assuming your supervisor believes your grade is unfair, they may be willing to champion any appeal and guide you through the process.

Beyond your supervisor, you need to follow whatever appeals procedure your institute has in place. I strongly suggest seeking the advice and support of a friendly faculty member, preferably someone you know reasonably well and someone who either knows the procedure well or is well-connected enough to find someone who is.


My admission is revoked after accepting the admission offer

I would recommend the following:

Contact the other universities and ask if they might still be
willing to admit you (this might be the easiest way out). If the
answer is negative make sure to keep their answers for the later
points.
Write to the university that revoked the offer stating (in a
friendly tone) that you turned down other offers due to their offer
and that this situation leaves you (and them) is a suboptimal
situation. If the result of point 1 was negative then add this
information too. Ask them for a solution. If the mistake was made
just on your application then they might consider admitting you to
avoid a law case. If they wrongly offered to all applicants (e.g.
software bug) then they will not be able to do this.
If point 1 and 2 do not lead to anything then write to them a second
time threatening with a law case in order to cover your damages
caused by their mistake. But still in friendly words along the lines that you would prefer not to etc ... (Many people in the comments below suggest to skip this step and go for the lawyer right away "Never threaten to sue. Either do it, or don't").
Get a lawyer to discuss further actions.

Other points to consider:

How long was their offer there? If it was just there for 30 min it
might be different to being there for days and they decided to revoke
weeks after you accepted.
Was the offer conditional on anything?
Assume you win with the help of a lawyer - do you want to spend the
next 4-5 years of your life in this environment? I am not saying yes or no - it is just something to consider.


Should I publish in a journal that appears on Beall’s list?

Beall's list is grounds for high suspicion, not a ban.  In the case of this particular journal, it looks like not a very good journal, but not an obvious scam.  Google Scholar finds a number of articles with moderate citations, and on first inspection they don't look like metric gaming, so it looks like it wouldn't be a black mark on one's record.

Bottom line: probably legit, but if you've done good work isn't there somewhere better than you can publish it?


Two professors declined to write LOR for me because they are busy?

There's a chance they're trying to avoid writing the LOR because they don't think they can write one that's good enough to help you.

If an instructor can't write an LOR they think will actually help a student based on what they know to be the truth (even if only because they don't think they know you well enough), most instructors will try to encourage the student to go to someone else.  No one likes writing a bad reference.  But they also struggle with how to do that without hurting the student's feelings.  Some just won't tell you the bad news directly and they may foot-drag and hope you go away or they may make silly excuses about being busy or whatever.  That's spineless and it's not right, but that doesn't mean it doesn't happen.

So, if you ask someone for an LOR and they don't seem to want to do it, you should probably just ask someone else.


Is it acceptable for a student to hire a tutor to explain and fix homework mistakes?

We are allowed to share solutions etc, as long as each student's
  doesn't just copy but understands what he/she writes.

This is the only information we have about your instructor's policies, so this is the only answer we can give to your question. It's OK to hire a tutor for help with the homework, as long as you don't just copy but understand what you write.

It's also possible that your instructor intends different rules for paid tutors than for cooperation with your fellow students. However, we would have no way of knowing that from the information provided in your question.

There are also general expectations about plagiarism and originality, and these are ethical norms that you're responsible for understanding and following, regardless of your instructor's policies. Your description of your working relationship with your tutor isn't specific enough to make it clear whether you have a problem here or not. As JeffE has pointed out, "fixing" your mistakes might entail plagiarism, if it means that what goes on your paper isn't actually what you wrote yourself.


Can you still distinguish yourself at a second-tier grad school?

First, I think it is important to recognize that the definitions of "1st tier", "2nd tier", etc. are not so universally defined. World or national rankings of universities are substantially based on the opinions of department heads. The differences between the #1 school and the #20 school may not be that large.
Professors also move from "2nd tier" to "1st tier" schools all the time based on demonstrated research output. Therefore, it is possible to improve your value to hiring committees with more productivity.
Now to analyze your 3 options (which I think are fairly comprehensive): I think all 3 have some impact.

Departments often hire faculty with new expertise, meaning that no one at the department is an expert in that subfield. If they are not expert enough to evaluate individual papers directly, they may use as a proxy the quality of the journals which papers are published in, or the ranking of a school at which the student graduated from. However, I think this has the least impact because the quality of an individuals' research publications can usually be assessed separately from the ranking of their alma mater.
"1st tier" universities often hire the most productive faculty and have the highest expectations for promotion and tenure. Faculty at "1st tier" schools may have the best research abilities, skills, or ideas and share these ideas or skills with their students resulting in their students also becoming more successful researchers.
"1st tier" universities can pick the most promising new graduate students, which includes students who had the best combination of ability, skills, and motivation in undergrad and going into grad school. These students are likely to continue to perform at the top.

To answer your question directly, I believe that a student at a "2nd tier" school could certainly distinguish themselves sufficiently to be hired at a "1st tier" school. It happens infrequently because the students at "1st tier" schools have the advantages of being advised by top researchers and being top students when entering grad school.
Nevertheless, distinguishing yourself for a faculty job is hard at any school. I know many PhD alumni of "1st tier" schools who left academia.
Finally, not every school can be "1st tier", and professors at "2nd tier" schools can still do good work in research and teaching. You may want to consider whether you prefer being a professor at a "2nd tier" school to an industry job.


If you aren't still a student (or faculty) you can't use your previous university. But "Independent Researcher" is really enough. Affiliation is there for identification purposes primarily.

But you should probably not  use your current address. It is likely to change and become useless. But it might also attract spammy mails that never go away.

Some might list "none" or "unaffiliated", but "Independent Researcher" seems better to me. It isn't uncommon, actually.


Can journals decide to refuse previously approved publications conditional to minor revisions?

Yes, most journals require revisions to be submitted within a certain time limit as specified in the editors decision letter, typically 3-6 months. Failing that, the paper will be considered withdrawn and any re-submission treated like a new submission. However it is also possible to ask for an extension of the revision deadline, if one can provide good arguments.

Of course, I don't know the details of your case, but you should be able to find out from the journal website.

I also strongly advise you to contact your co-author (preferably in person rather than via email) and enquire about the state of the manuscript and their plans for resubmission.


If an assumption proves to be false, is the research then meaningless?

The answer is not necessarily, for two reasons:

It may not actually matter. There are many assumptions that get made in research that are probably not true, in retrospect. Some of these are known to be false from the outset (in my field, it's the assumption that people mix randomly). Said assumption may not actually have all that big an impact on the final outcome, either numerically, or often as importantly, in the subjective takeaway from the project (Should I do X or Y? The difference between X is twice as good and X is 2.17 times as good doesn't really change that you should do X).
You learned something - presumably from actually doing the research, but also about the importance of critically evaluating your assumptions. This is a good thing, and at the high school level, probably the most important.


How can an undergrad from a country with little 'international' research improve his chances of being a "good fit" for a top PhD program?

Ok, good question, but let's eliminate the phrase, "noting the difficulty/impossibility in doing any ground-breaking research especially as an undergraduate here?"  This actually applies to almost the entirety of the undergraduate population.  Very few undergraduates work on ground-breaking research projects -- and, if they do, their role on the actual project is unlikely to be the intellectual driver.  They might have done some lower-level work under the supervision of the principal investigator (PI).

So, your question is really about how to improve your chances of acceptance in general.  That really depends on the discipline, and it really depends on the program to which you are applying.  Every program has a unique admissions committee that will review applications and assign different levels / weights to factors they consider important in making admissions decisions.  Thus, certain programs may place a lot more emphasis on GRE than other programs.  Some programs might consider letters of recommendations to be very important, which other programs may consider letters of recommendation to be of little importance (since most letters of recommendations are cherry picked from the possible letter writers).

That said, your task is to tailor every application to the programs where you are submitting an application.  A general snowball approach where you submit the same application everywhere is an alternative strategy, but one that I advise against.  Learn what those programs value most in their admissions decisions, and tailor the application accordingly.  Of course, it is hard to figure out what they value, so you have to do a lot of researching -- e.g., any published data on the current and previous cohorts?

Good luck!


What is the difference between Ph. D programs with coursework and those without it?

It seems to me that there are several advantages; none of these are suitable for every student. It's up to you whether enough of them apply to you, to make it worth doing a taught PhD:

A PhD with a bit of coursework in the first year will help those who
are crossing over into a discipline that they're not already deeply
embedded in: it will give you some hand-holding through the things
you'll need to know but don't yet;
it should (if taught well) also teach you some extra research skills;
it will give you some indication as you progress as to how well you're doing, compared to how well you should be doing if you're going to finish
it will allow you to explore different aspects of the field, to help you finalise your thesis topic
it may, depending on the country and institution, give you an intermediate degree at the end of the taught section, such as an MRes, which will count for something even if you then don't go on to do the full PhD
it lessens the culture-shock for those going straight from fully-taught study to a research degree.


Is it standard to ask for an "equal contribution" footnote in a 60%-40% scenario?

I don't think there's a common standard for how to settle this after the fact, at least not one spanning all fields where author order matters. But my rule of thumb would be this:
If your estimation of your coauthor's contribution exceeds your estimation of your own contribution by more than the (likely also estimated) margin of error of your estimates, then you probably shouldn't ask for equal contribution. If the balance is too close to call, or the contributions are too difficult to compare (which is often the case in a theorist/experimentalist collaboration, for example) then sure, having a discussion about it is appropriate. (Just be open to updating your estimates based on the discussion.)

You could also consider including an "author contributions" statement in the paper to clarify who did what.


Dipl.-Math. stands for Diplom-Mathematiker. It is a German academic degree and equivalent to a master’s degree.
Before Germany adopted the bachelor/master system, a Diplom (diploma) was awarded to students after finishing about five years of study and writing a thesis.
Almost all German universities now award bachelor’s and master’s degrees, but at some universities, students can choose to have their degree called Diplom after completing a master’s program.


Applying for a PhD - how and when to broach the fact that I have previously left a PhD program

For a variety of reasons you should reveal it early as part of your education in the CV or other materials. But you don't need to give any reason there. Just that you were in a doctoral program (and maybe ABD) from such a date to some later date.

You are probably required to give transcripts of all educational endeavors, and it would be a lapse to omit any.

There are a lot of reasons for leaving a doctoral program and only of a few of them reflect badly on the student. Not passing comprehensives might be a negative and being expelled for ethical lapses would certainly be. But those are only a few of the possibilities, including just becoming disillusioned with the program or with an advisor. Money. Family. Medical.

But later, in an interview, you will probably be asked and then is the time, IMO, to give reasons.

And, if you think the experience strengthens your case, then, in a Statement of Purpose you could say how it supports your future goals.


Recommendation Letter Request: No response

I am not in your field. But from a faculty's perspective, the lack of response does not necessarily entail that the professor is unwilling to write a recommendation letter for you. A faculty's life is much busier than you think (this is something I did not know/agree when I was still young and crazy); it is possible that the professor forgot to get back to you and/or that s/he is currently out of touch. If I were you, I would wait for a day or two and would send a polite email telling the professor that you decide to seek for help from from another person due to time constraint (and this is exactly what you need to do in order to ensure that the universities you are applying to receive all of your application materials on time and to give another person sufficient time to work on your recommendation letter).


I grade exams together with a colleague but disagree with their grading. What should I do?

Have each person grade different questions, not different students.

Consistency in grading is important, and it is unfair to the students if their grades depend substantially on the allocation of their work to a grader.  For this reason, if you must split grading duties with another colleague for a particular assessment item, it is best to split the grading duties for the questions rather than splitting the grading of the students.  So, for example, one person grades Q1-3 on all papers and the other person grades Q4-6 on all papers.  That way each student is graded by the same person for the same question.  (Logistically, each of you should grade your questions on half the papers, then swap.)

It sounds like this ship has already sailed, and you have made the rookie mistake of splitting grading for the students, with different people marking different students.  It also sounds like you have tried to discuss this with your colleague, but you have exhausted attempts to change his grading.  In that case, even if your own grading style is superior to your colleague, adapting to his grading level for this assessment is probably a reasonable second-best option, simply to maintain consistency of the level of grades awarded.  In future, try to avoid the problem all together by splitting grading over questions instead of over students.


I found a trove of Computer Science Masters thesis unprotected on a respected uni's website

If you feel it's incorrect for them to share the links in public, you could contact the webmaster and question their process. They possibly should disable the file listing at the directory.

Nevertheless, it's possible that for some universities access to theses is provided free of charge for other researchers to access, and you probably found the location where all of them are stored.

I don't think access should be disabled to the files individually, but indeed it is my opinion that the file directory listing should be private. They probably have a website with descriptions somewhere else, that link to the files.


Am I supposed to add the name of a surgeon who had no contribution?

My take from your description is that the surgeon gave you his clear permission to publish without his name attached -- in the form of a written text message. Assuming that the wording in the text message is unambiguous, there ought to be nothing for you to worry about: He's expressed his opinion, and you're free to proceed.


What are the differences between a presentation in academia and a presentation in industry?

The comments above are correct--you're probably pitching to the wrong audience, and your presentation skills are probably not as good as you think they are. To put it undiplomatically, the great majority of (STEM) presentations in academia are horrible, but after a half-decade or so of grad school you become inured to this and recalibrate your expectations. You've probably noticed that a genuinely engaging and accessible academic presentation is often judged to be less deep and interesting than an incomprehensible one. This is not going to be the case in a business environment.

The key difference is that the focus in a business presentation is on utility: You're not just trying to convey information, you're trying to be useful to your team and to the company. What are the people in your audience going to do with the content of your presentation when it's over? They want usable information, and they want it quickly and efficiently. Here are some ways to do this:

Include a "30,000-foot view" and (metaphorically) keep it in sight throughout the presentation.
Keep the narrative of your information focused. That is, make sure it's clear why each piece of information is relevant to whatever point you're trying to make.
Leave detailed background explanations to follow-up questions.
Be parsimonious and efficient in your flow of information. Pictures are generally better than words.

I'm assuming you're in a role where you process and produce data, so that your reports and presentations are informative rather than persuasive. But many of the same principles would apply if you are trying to convince your audience of something.

A final remark: People who give business presentations practice them. You probably have access to tech for recording a video of yourself, or at least a screencast with audio of your presentation. Use it.


Should I agree to review papers as a postdoc?

Yes, reviewing papers is an integral part of your job now, and a very beneficial one at that!

It's true that the first papers you will review will take you quite a bit of time, but it's a sound investment (unless you consider dropping out of academia next month). You'll improve your reading and ability to read between the lines. It will help you gain a wider view of what others are doing in your field, because it will force you to really go through the paper in depth, not just skim over it as we are so often forced to do when a paper is not at the core of our own research.

Moreover, it will give you invaluable experience when you write your next papers, because you will be able to put yourself in the reviewer's shoes! You will see better what could be problematic for a referee in the presentation of your work.

As for whether you should list it on your CV: yes!


PhD (at Oxford) vs staying at in the industry (Facebook) for a ML student?

You must make this decision - no one else can make it for you. Things to think about:

Uninteresting jobs are bad. If you can't see your job getting more interesting, then say 5-10 years down the line there's a good chance you'll get so bored your performance starts suffering, and then you might get fired.
You know the industry very well since you have a first-hand insider view. What jobs do you enable by getting a PhD? If they're more interesting jobs (do you actually know they're more interesting, or do you just think they're more interesting?) that you will never be able to do without a PhD, that's a powerful reason to get a PhD. On the other hand, it's conceivable that you'll be able to do those jobs without a PhD simply by staying put, acquiring more experience, and doing well. You'll know better than anyone else.
Do you have a significant other or a family to provide for? If so, what do they think? Remember that usually, once people experience a luxury, going back to a less-luxurious lifestyle is typically a big no-no even if it was previously acceptable. Even if you can accept it, your significant other / dependents might not.
What does your current manager or other senior colleague think (if you trust them enough to talk to them)? Just as important, are they willing to rehire you after you graduate?
Is it actually economically better to do a PhD? Run some calculations. If you stay put, you earn $X this year, $X + [increment] next year (if you have one), etc. If you go to Oxford, you earn $Y for 3 years where Y < X, but then after 3 years you earn $Z where Z > X. How many years does it take before the second option exceeds the first, if it exceeds the first at all? The fewer years this takes, the more attractive the PhD becomes.

These things are too intricate to say more, unfortunately. As above, you must make the decision - no one else can make it for you.


Is all research connected via citations?

When looking at the paper-is-cited-by-paper binary relation in an undirected manner: Is all research connected to each other or will there be clusters?

First, it's possible to have an unconnected paper. Unlikely, but possible, to write something that has no citations and is never cited. This is clearly an edge case, but you did say all.

Second, all research can connect, but there can still be clusters. The two are not mutually exclusive - fields will cluster, presumably, but there will then be some links between fields. My suspicion, from personal experience, is that these papers will be methodological in focus primarily.

  In other words: Is there a way from a, say, computer science paper to a chemistry paper by walking along the citation graph?

Third, yes, you could get from a CS paper to a Chemistry paper. I know this because I can trace that tree in my own work, and the work my work cites. The path isn't even all that convoluted or exciting.


My results are different from my original poster title now. How I should prepare the poster?

Of course you shouldn't pretend that the result is still significant, when you know now that it isn't. As you have noted, that would certainly be unethical.

Prepare your poster using the results that you believe are correct now. If anyone asks about the difference between the poster and the abstract, just explain what happened. (You aren't the first to make a mistake and catch it later, nor will you be the last.)  You can also email the conference organizers to find out if they can update the poster title and abstract (online at least).

Occasional mistakes are common in science, as in everything else; don't stress about it too much, just learn from it for the future. It's great that you caught it now, before your poster presentation, so that you can correct it.


reprinting permission of an instrument image on a website

You almost certainly need a copyright release in the form prescribed by your book publisher.

Track down the manufacturer's public relations office; one or two phone calls should be sufficient to find the right people. They will be very happy to supply you with pictures and the necessary copyright releases.

If you use these instruments in your own lab and they are at all expensive, or you have a lot of them, there will be an account executive (i.e. sales person) assigned to your institution.  That person will likely be ecstatic to help you get what you need.


First of all: Don't Panic!

If you search for Bad Grade on this site you get a lot of questions from students in a similar/worse situation. In this case I can just talk for me and for my case and let the other questions talk for themselves: I'm currently a PhD-student and I've gotten among others one B, one C and even one D in courses during my masters. In the end nobody cared because I've written an really good thesis and (at least here at my university and group) that's way more important. So focus on what's ahead of you.

So all in all it is of no significance (or at least should not be).


Can I publish a source code containing potential copyright violations that someone gave me at a university (updated)?

With the caveat that I am not a lawyer, the answer is "no".

You have:

code A, which is GPL-licensed
code B, which is a derivative work of A and not GPL-licensed.

The GPL license requires that all derivative works are also GPL-licensed. As B does not carry the GPL license, it is a copyright violation and (depending on jurisdiction) it is probably illegal for you to distribute it.

If the changes needed are small, your simplest way forward would be to take code A, and modify it yourself as needed to make code C, while keeping it GPL-licensed, and release that.

EDIT: As noted in the comments, it is possible that A had two licenses: The GPL, and another license granted specifically to the author of B which permitted them to change the names and redistribute without GPL. This seems very unlikely, but you should consider the possibility if considering accusations of any sort.


How to provide codes to reviewer without making it public

As others have mentioned, some venues offer an option of submitting additional material.

If not, you have two options.

Include your code as a single file into your submission in the PDF/A-3 format. (I do not recommend this option that much, though, since special software is required.)
Put your code on a public site as a password-protected archive. Most compressors such as zip and rar allow you to encrypt and compress.  Put the archive on a public site but give the password only along with the submission. E.g.

  Bibliography

  [S18] Smith, J., Example codes, 2018, http://www.example.com/example.zip, protected with the password example_password.


What to do when you find someone else is working on the same masters research

Masters projects generally do not aim to produce top-quality original research, rather they give masters students an introduction in the art of doing research. So the fact that two people at two different institutes are doing more-or-less the same thing does not matter. It would only become a problem if

One student plagiarized the work of the other.
The two students collude, reducing their workload to produce one thesis that will be submitted twice.
Both students tried to publish their work – whoever gets in first will receive the credit and the other will possibly not get published.

Even in the last case, it is not unheard of that parallel submissions of the same results by different parties occurs. Sometimes it is worth publishing both, especially if they approach the problem differently. I have heard of one case where the editors asked the two parties to produce a single combined paper.


Difference between publishing textbooks and publishing research for acquiring tenure

I have spoken with a few people who have written textbooks. The universal advice they have given is never write a textbook until after you have received tenure.

In general, you get very little or no credit for writing a textbook, as it doesn't really help in any of the major "checkboxes" for tenure—research, teaching, and service. In addition, the time that you spend working on the textbook can generally be put to better use in writing grant proposals or working on peer-reviewed manuscripts.

I know from personal experience, when I was a graduate student, that there was an assistant professor in my department who spent all of his time working on a textbook. He let his research languish, and ended up with a textbook but no promotion to associate professor.


Reference on availability of source code used in computer science research articles?

Here's a relevant study on computer science systems research that addresses your first question, "What percentage of research articles are provided with their source code?". The study is described in a tech report:

  "Measuring Reproducibility in Computer Systems Research." Christian Collberg, Todd Proebsting, Gina Moraila, Akash Shankaran, Zuoming Shi, Alex M Warren. March 21, 2014.

The authors of this study observed the following protocol to determine code availability:

  We downloaded 613 papers from the latest incarnations of eight ACM conferences (ASPLOS’12, CCS’12, OOPSLA’12, OSDI’12, PLDI’12, SIGMOD’12, SOSP’11, VLDB’12) and five journals (TACO’9, TISSEC’15, TOCS’30, TODS’37, TOPLAS’34), all with a practical orientation. For each paper we determined whether the published results appeared to be backed by source code or whether they were purely theoretical. Next, we examined each non-theoretical paper to see whether it contained a link to downloadable code. If not, we examined the authors’ websites, did a web search, examined popular code repositories such as github and sourceforge, to see if the relevant code could be found. In a final
  attempt, we emailed the authors of each paper for which code could not be found, asking them to direct us to the location of the source. In cases when code was eventually recovered, we also attempted to build and execute it. At this point we stopped — we did not go as far as to attempt
  to verify the correctness of the published results.

Here is a summary of their findings:

Total papers examined: 613
Papers that appeared to be backed by source code (not purely theoretical): 515

Of these 515 papers, 105 were excluded from consideration so that the resulting set of papers had no overlapping author lists. That leaves 410 papers, with results as follows:

Papers with link to source in the paper: 85
Papers not in above category, where source was found via web search: 65
Papers where author shared source following email request: 81
Papers where author declined to share source following email request: 149
Papers where author did not respond to email requests for source:  30

More details of methodology and results, as well as all the data and other materials used in this study, may be found at this web site.

There is an "Anecdotes" section appended to this tech report, which I think you may find very interesting, as it relates to some of the other points in your question. It documents the author's struggles to get authors to give up their source code :)


How do I abbreviate the titles after my name?

This varies between countries.  My impression is that listing titles after the name is more common in the UK and Australia, and there may be fixed conventions as to the ordering, but I can't address that.  What I can deal with is the U.S., and my advice in that context is simple: don't do it.  In the U.S., if you list one title ("John Smith, Ph.D."), you'll look a little pompous and like you are overemphasizing your degree (leading to questions like "Gee, is that Ph.D. still his proudest achievement?" or "Does he worry people will think he didn't get a Ph.D.?"), and if you list more than one it will look ridiculous.  In particular, don't list titles after your name in academic job applications, CVs, signatures for letters of recommendation, etc. that are being sent to the U.S.  Of course, conventions in other countries may be different.


Have you considered submission to a journal? As reviewers are not identified, it is reasonable to trust their judgement that the paper is "okay", and of course "okay" at a top conference in CS could still be quite good, especially as it's within the top 15%. Although perhaps the top-tier journals would render a similar judgement, there may be a venue where it is appropriate (I'm not familiar with the computer vision area), and you could publish without an excess of additional work.

Alongside this you can (usually) always put a preprint on ArXiv, few journals or conferences take issue with this now, which allows you to make it available in the meantime, regardless of what else you decide to do with it in the future.

However I would definitely not include the reviews. Although there is no rule against doing so, particularly as the reviewers shouldn't be identifiable, it contributes nothing to your research - the reader should be assessing the value themselves. The inclusion of reviews would only indicate that you want to boast about your work, or that you want people to accept it because someone else said it was good.


My advisers did not want to be coauthor of my accepted journal article

There are a few different situations that could lead to this:

Most plausible case: Your supervisors determined that in accordance with the standards of your field, they do not count as coauthors.
Different fields have different customs concerning whether supervisors are assumed to be coauthors of papers resulting from the supervised work. If you worked independently and your supervisors agree, then being a single author on the resulting paper will always be reasonable. Since you mention asking them only at submission stage, it does sound as if their involvement is limited.

Your supervisors really ought to be coauthors by the standards of your field, but declined to give you an (unfair) advantage or similar.
This is problematic from an ethical perspective. Having another persons consent still doesn't allow an academic to present their ideas as ones own. A carefully worded acknowledgement might work.

Your supervisors declined because they are aware of flaws in your paper, and don't want to be associated with it.
While one would hope that peer review would spot problems, there is no guarantee that it does. If your supervisors are aware of any major flaws, it would be your ethical responsibility to find out and either fix the paper, or to withdraw it if it is unfixable.

The manusscript is sound, but your supervisors are under political pressure to not associate themselves with the results. (pointed out by nick012000 in the comments)
Probably no ethical concerns about you publishing here, unless the political pressure is there for very good reasons.


Is reviewing papers moving away from voluntary community service?

I will address your three questions directly, and in-line:

  "Is this a general trend in the research community, i.e. is this
  happening in other domains as well?"

I have never seen this before, and never heard of it. Everyone else that answered and commented, except for one person, has said that they have not seen it happen in their field either. The one person in the comments that did see the trend was Franck Dernoncourt, who says that it's definitely a trend in NLP (which probably means Natural Language Processing, not Neuro-Linguistic Programming). So, it is not a "general trend", but it is happening in some fields (such as yours and Franck's).

  "If yes, does this imply a change in the peer-review paradigm? For instance, as a researcher should I stop doing "free reviews" in order to keep my reviewing time for mandatory reviews?"

My answer is "no", but even if it were "yes", I do not see how that means you should "stop doing free reviews". The vast majority (by a long shot) of peer-review is still done for free.

  "If no, are there other solutions being tested to the problem of ever-increasing papers/reviewers ratio?"

I have never seen any other solutions tested. The peer-reviewed conferences I submit to, such as QIP (Quantum Information Processing) keep an extremely high standard for who is able to review. There is a committee of reviewers who are selected because they are recognized world leaders in their sub-fields, and each of them reviews several papers. Forcing any random person that submits a paper to review a paper, would lower the standards of the reviewers, and hence the standards of the conference.