What happened if the third author made extensive changes for galley proof without letting the editor, first and corresponding authors know?

I think you can relax - this isn't that big a deal.

You can contact the editor / publisher and say there has been a miscommunication between the authors, and you need some more time to sort it out and make sure that everyone approves the edits.  I imagine this sort of thing must happen all the time.  In the worst case, the paper might have to be postponed to a later issue, which is a little annoying but still better than having some authors be unhappy with the final version.

  I particularly concern that this is very unacceptable behaviour

I wouldn't say that - more of a minor error or misunderstanding.  Yes, the other authors should have been more careful about seeking everyone's approval, but under time pressure people sometimes make shortcuts or false assumptions.  Just sort it out and ask them nicely to pay more attention in the future - don't let something this minor ruin your working relationship with them.

  Will this have any impact on my other papers?

That seems extremely unlikely.

  Is making 30+ changes considered extensive changes?

The number of changes isn't really relevant - it's about quality, not quantity.  Do the changes significantly affect the content of the paper, such that a reviewer might need to reconsider whether the paper can still be published?  Changes such as paraphrases and added references shouldn't reach that level, even if there are a lot of them.


Is re-using an idea from a research proposal considered as self-plagiarism?

No: You can re-use ideas from research proposals which you haven't executed upon, i.e., ideas that you haven't advanced (e.g., because the research proposal was rejected or that part of the proposal was never addressed or ...), they're still fresh ideas.


Should I (assistant professor) call undergraduates by first name or Mr/Ms

It is disrespectful to demand more respect from your (adult!) students than you give them. So you should either both go my first name or both by last name. At least this is true in by culture (Central Europe) - I would think it is the same in Northern America.
So, unless it is a cultural thing everyone does in your area to call younger people by their first name, by respectful and call them as you want to be called.


How to deal with impatience when starting off in research?

From what you describe, i.e. preferring learning by doing rather than first getting strong theoretical foundations, you seem to be more a hacker than a academician.

From Hackers and Painters by Paul Graham (whole essay is about this difference):

  The fact that hackers learn to hack by doing it is another sign of how different hacking is from the sciences. Scientists don't learn science by doing it, but by doing labs and problem sets. Scientists start out doing work that's perfect, in the sense that they're just trying to reproduce work someone else has already done for them. Eventually, they get to the point where they can do original work. Whereas hackers, from the start, are doing original work; it's just very bad. So hackers start original, and get good, and scientists start good, and get original.

In my personal case, impatience brought me from academic science to startup world and data science What I do or: science to data science. If I had know about my psychological traits, I wouldn't have dove into the academic world (it's not only about intellectual skills, but also patience... and ability to deal with hierarchy).


What's the difference between 'research topic' and 'research area'?

A research area is what a research topic is placed into, but is much broader than the scope of the topic. For example a research area can be human physiology, computer science (as you mentioned) or even relate to a specific field within these broader terms such as cardiac electrophysiology or machine learning respectively.

A research topic would be a specific question, hypothesis or problem you wish to investigate and answer which is under the scope of your research area. That is to say, my research area is in neuroscience/neurophysiology and my research topic is investigating the mechanisms of neuronal communication, as an example.

You would want to say topics that interest you which relate to a certain problem that you may be aware of, whereas in the research area you would want to outline your inclinations towards a particular field of academia.


Who is responsible for detecting plagiarism in a PhD thesis?

The problem is that the PhD system is designed for people who intend to become researchers.  For these cases, plagiarism is not at all a common problem.  You are expected to published your research, and you will not have a successful career unless it is widely read and cited.  That gives lots of opportunities to get caught, and the penalties for plagiarism are a huge deterrent.

To the extent you find plagiarism, it's generally people who do not want a research career, but instead view the PhD simply as an obstacle on the road to a teaching (or other) career.  Probably the community should scrutinize these sorts of theses more carefully, but it can be hard to work up the energy to do so when most of them are OK, and when these theses really don't matter much for the research world.

The German politicians are pretty much the worst case scenario.  In the US, the stereotypical case is educational administrators.  Typically, you have a distinguished person who starts to feel the need for a PhD.  Perhaps it's because they associate with academics and feel looked down upon, or perhaps it's because an academic endorsement would make the public value their expertise more.  This student is very smart and accomplished, and nobody suspects them of any dishonesty.  However, they are also very busy, often working on a PhD while pursuing other projects as well, and academic research is not a priority.  At some point, they succumb to pressure and start taking shortcuts.  Probably it starts with small things, but the shortcuts gradually grow larger.  They rationalize that the thesis doesn't really matter anyway, because they have no intention of following an academic career track.  After all, they have the knowledge and experience, and they deserve the PhD title, so what difference does one document make anyway?  Meanwhile, the advisor probably doesn't spend that much time working with the student, and has no reason to suspect anything.  The advisor really ought to be extra careful in cases like this, but that would seem like an insult to the student, so it's easiest just to trust them.

So my take on this is that plagiarism is not as widespread as news stories might suggest.  It's just particularly likely to happen in cases where it would attract media attention.


Academia vs. Industry for Machine Learning

Other engineering disciplines can have a vaguely similar pay gap, especially when comparing with a top industry job as you describe (and doubly so when comparing living in SF to a college town)
A common argument is for the freedom offered in an academic job. Another is that industry jobs are often more boring. I think there is also something to be said for being able to potentially "leave your mark" in academia in a way that isn't necessarily possible working an industry job. Lastly, I'll point out that some cultures think very highly of professors, in the same way US culture tends to think most highly of doctors.


Do PhD students sometimes abandon their original research idea? If so, how do they cope with it?

Not only does this happen frequently to PhD students, it also happens occasionally to experienced researchers.  Many research projects are embarked upon in a somewhat speculative manner, where we do not really know what the answer to a question will look like until we get there.  Sometimes we get stuck and cannot get the answer to our research question, sometimes we get the answer but it is so trivial that we realise we were thinking about the scope of the problem incorrectly, and sometimes we get the answer and we then find out that others have already figured out and published the same answer before us (which is something that does not always show up in your initial literature review).
It is less common for experienced researchers to completely abandon projects, because we have pretty good a priori judgement of what will work, and we are also good at salvaging work if it does not turn out as planned.  Moreover, many academics tend to put unsuccessful projects "on hold" and come back and think about them periodically to see if they can be changed in some way to give fruitful research.  During my own PhD candidature and my subsequent research career as an academic, I have started and done work on several topics which I have subsequently "put on hold" or altered to such a degree that the initial topic was essentially abandoned.  I have had other topics where I did a whole lot of research, even wrote up a paper, and then subsequently found that I had merely rediscovered results that were already in the literature (under a name I was not familiar with).  I also have probably ten or twenty started ideas sitting around and stalled because I have encountered some roadblock that may or may not be fatal to the future of the project.  As you will see from some examples below, I have had some absolute doozies.
Mine have come about because I did initial literature reviews that were flawed, and I didn't realise that my research ideas were things that were already well-developed in the literature (under technical names I was not familiar with).  In terms of how you cope, well, you look at the silver lining --- often these aborted projects show that you are "on the right track" in terms of your ability to come up with interesting ideas, even though these do not pan out into publications.  If you are developing projects that are good enough for other researchers to "take them" then that means you are on the right track.  (In my case, other researchers were nefarious enough to steal my ideas and complete them decades before I was born!)  It is depressing when you think you have a great idea and then it turns out not to lead to anything, but you look on the bright side --- it is better than having no good ideas at all.

Some (kind of embarrassing) examples from my own research career
Rediscovering the theory of identifiability: When I was in the first year of my PhD in statistics I came across an interesting problem that I thought would be a wonderful PhD topic and I spent many months solving it and writing up an academic paper for a journal.  I was extremely happy with my paper and thought it would be a big deal, since it seemed to me that I had developed an important concept that would be a great addition to statistics.  A couple of weeks later I got a desk rejection from the journal, and the editor was kind enough to gently inform me that while my paper looked very interesting, and was well written, my ideas "look a lot like the theory of identifiability" (a term I had not heard of at that time).  Using this new term I did another quick literature search and discovered a huge literature; my own paper had essentially rediscovered an important mathematical/statistical concept that was already developed and published in about the 1950s-1960s.  I had managed to get through my undergraduate degree without hearing this term, and so it had not shown up in my initial literature search, and my supervisors also did not alert me to it when I showed them what I was working on.  So, I have the "distinction" of being one of the discoverers of the theory of identifiability (never published), which I discovered about fifty years after its original publication!  It was depressing at the time because I had done a lot of work on it, but now I look back and laugh about it.
Rediscovering the theory of constrained optimisation via penalty functions: This one came a bit after I had finished my PhD, when I was an early career academic.  I had done a bunch of work on constrained optimisation (Karesh-Kuhn-Tucker method, etc.) and I had thought of an idea of an alternative way of doing constrained optimisation that I thought was novel.  Again, I tried searching for it in the literature, but I used the wrong words so it didn't show up.  (I think I was calling the method "optimisation via augmentation" which is not its standard name.)  I spent my Christmas holidays working on a paper on my method, and was happy with how it developed.  When the paper was almost finished, by accident (when looking at another problem) I found a reference to a paper that led me to another paper that alerted me to the literature on optimisation via penalty functions.  I had a look at the papers I had found and boom --- another project destroyed.  From memory, this stuff was done in about the 1970s, so this time I was a mere forty years late to the party!  In this second case I did not submit my (almost finished) paper, so it sits on my computer as a fun little reminder of my Christmas rediscovering penalty function methods.


Where can I find a list of Marie Curie fellowship-funded projects?

You can find EU funded projects in CORDIS. For example, a list of all Marie Curie individual fellowships funded under the Horizon 2020 programme can be found here.


Wrote a paper, supervisor couldn't respond

No, publishing it in any form without all authors (and their consent) is misconduct. But you don't yet know that you are being blocked, and I doubt that you are, since it is pretty rare.
You don't say how much time has passed but if it is less than, say, a month, there may not be any problem. People have other things to do. Email gets lost or misfiled. Lots of things might cause this "issue" for you.
But you might be able to discover, by contacting the department whether the professor is available or if there is something causing the delay. You might not learn what it is, but you might be assured that it is just a delay. Illness happens, for example as do family issues, travel, and all the rest.
But some third party might be able to give you some assurance if not the actual reason. And it might just be patience that is needed.


How does one approach a professor to volunteer in his/her lab?

Whenever approaching a faculty member relating to research, I recommend that early career students offer them a resume/CV and some concrete example of research interest (a question about a recent paper, how you heard about the lab and why it interests you, demonstrating drive by reaching out to the current lab members, etc).

In the email, state your discipline, the research requirements, any potential references they may already know (like your advisor). Ask for a meeting with a specific length of time (10-15 min) with a clear objective (to get a tour, hear about the research, get more involved in the lab,etc ), and if you don't hear back within a week -- follow up.


What are the advantages and disadvantages of making the review content public?

I believe that there are many sides to this, but overall I think that the "sanctity" of blind review should be maintained. In either case, I think that at most, one can allow access to the review content, but not reveal the identities of the reviewers, nor the review scores.

While it is true that one can sometimes guess a reviewer's identity from the content of the reviews, I think that this is not an issue because

It's still a guess, and more importantly
If your review potentially reveals your identity (say by you unnecessarily suggesting all of your papers as ones that should be cited), then it's a bad review, and the practice should be discouraged.

Review scores are often useful to weed out clear accepts and clear rejects, but become really hazy when talking about borderline cases (see further comments below).

Having gotten that out of the way -

Pros of publishing reviews:

It encourages more careful reviews: if I know that my reviews will be public I'm encouraged to make sure that they're more careful.
It discourages abusive and unprofessional language in reviews. Ad hominem attacks in reviews do happen, and are a bad practice.
It encourages editors/program chairs to select reviewers who do a good job. I've seen reviewers submitting a single paragraph; this is not ok.

Cons of publishing reviews:

It encourages reviewers hold back and not write scathing/overly gushing reviews even if they truly feel strongly about the paper.
It may render papers less readable, as authors would rely on the reviews to clarify what they should have (as Buffy mentions)
Reviewers will worry about their identity being compromised, and thus early career researchers may not want to review at all/write very positive reviews.
It may cause community dissent: interdisciplinary communities host several small sub-communities, each with its own publication norms and acceptance thresholds. This is already a major issue, that will be further exacerbated by revealing reviews (this may be a pro, not entirely decided!).

I think that one of the main reasons I'm against revealing reviews is because the review process, unfortunately, involves a lot of random luck. As the NIPS experiment shows, PCs can widely disagree on a lot of papers. It is important to note that there is general agreement on what are very bad papers and very good papers, but a significant chunk of them are borderline cases that could swing either way. I think that showing the reviews for borderline cases might be a bad idea, as it would cause a lot of dissent in the community ("why did my paper, with one weak reject, one weak accept and one accept, got rejected but my paper with better scores got accepted?"). I think that the "clear accept" papers can be easily listed with their reviews; the others? Not so sure...

Overall, I think that presenting reviews might be good in some cases and should involve the informed consent of both the authors and all reviewers. However, I worry about it becoming a norm. Paraphrasing a bit, review decisions are like sausages: it's better not to see how they're made.


Internships for PhD students (e.g. in data science or programming)

Yes. Almost every PhD student in my (US computer science) department has at least one summer internship between admission and graduation.  In fact, most PhD students go through multiple internships.

Off the top of my head, I know CS PhD students who have interned at Google (Mountain View, Manhattan, and Shanghai), Facebook, IBM, AT&T, Yahoo, Motorola, Microsoft Research (Redmond, New England, and Bangalore), Disney, Zynga, Los Alamos, Sandia, Argonne, and Livermore.  Most of these places regularly advertise for interns on the web.


What to do if referees take a long time to upload their recommendation letters?

My experience comes with asking for recommendation letters with my PhD application, most of the times it was necessary to remind the referees about the deadline for submission; they're so busy that they easily forget about it.

Another option would be with resending notifications through the recommendation system; many of such systems allow for sending automated reminders to the referees thus eliminating the need for direct intervention with the busy professors!


Something like Colleague might work. Something like "informal advisor". It depends a bit on how much room you have to detail it, as well as the closeness of the relationship. If the person has a good, independent, reputation, then something like that should do fine. At some future point you might be asked to expand on it.


Almost all grad students feel under-appreciated by their mentors at some point.

Your adviser sounds like a top notch A-hole. Unfortunately, to be a successful researcher in academia, most institutions look at (in order): the quantity of grant money being generated, the quantity/quality of research publications, and how many PhD students you generate. In other words, most research faculty consider the needs of their PhD students last.
Therefore almost all grad students feel under-appreciated by their mentors at some point. What keeps most grad students going through the 'tough times' is they enjoy the subject-matter they decided to go to grad school in. What I recommend is:

Have you began work on a thesis paper? If not, I would consider the door wide open to a change of departments / research groups. Especially if you don't have a passion for your work. Any future career path is going to be influenced heavily by your choice of research; why go down a path you know you don't want to pursue?
Finding a major professor who can simultaneously be your academic mentor and best pal is hard. You are going to need to pick a field of research you have a passion for if you plan on making it to the end. If finding someone you get along with is important to you, the easiest way to tell is to rely heavily on the next bullet:
When looking into another graduate course of study / department / laboratory, ask the current graduate students. This is going to be by far the most useful input: if at all possible, ask them about their relationship with faculty. Ask them about their workload. Ask them if they publish. Ask them if they feel supported. Ask them how long it takes.


What to do when the potential supervisor does not respond after initial positive response?

After waiting for on week, it seems reasonable to write another friendly reminder email to him. Calling might be an option but you may not succeed if he is currently out of office. Therefore I would rather write an email.


Is it possible to be admitted to a Master's program after not completing Bachelor's degree due to academic dishonesty?

I don't think there's much room for optimism. Offers of graduate admission are generally preconditioned on actually completing the previous degree. Moreover, having your previous degree candidacy terminated on account of academic dishonesty will make you "radioactive"; very few graduate schools are going to want to bring in someone who got suspended for plagiarism or cheating. (Given that the entire research enterprise hinges on being able to trust reported results, why would a school want to take a chance on someone who has already clearly violated those principles?)

[More generally, however: I do know of an economics professor whose PhD is in fact his only degree; however, the circumstances behind that are so unusual that they're unlikely to be replicated any time soon. (Basically, he followed a professor from Germany to the US while he was still an undergraduate in the days when the Diplom system was in full force.)]


How to establish collaborations with academics who you do not know where you contribute to their research projects?

Collaborations almost never start with a cold email in my experience. All of my collaborations have involved people from my former lab, people I met at conference, or an obvious opportunity where I had the data and they had the analysis tool. Anecdote aside, I think you have to have something the other side will obviously want: a dataset, a method, a tool; access to a site or species or specimen; something besides an idea. Lots of people have ideas. Lots of people even have the same idea. But in order to start a research relationship with someone you don't know, you've probably got to have something they want and vice-versa.


In what cases is Ethical Committee approval not necessary for a study?

The exact regulations differ per country, but prospective studies with human subjects almost always need approval.

Since you tagged your question with "Netherlands", the relevant law is the WMO = "Wet medisch-wetenschappelijk onderzoek met mensen". Any research that falls under this law requires approval.

  Research falls under the WMO if the following criteria are met:

  It concerns medical/scientific research and
  Participants are subject to procedures or are required to follow rules of behaviour

There is a lot of information on the website of the Central Committee on Research Involving Human Subjects (CCMO).

You can usually also apply for a waiver from the IRB (at least in the Netherlands). You submit a request with a description of your intended research and the IRB will review your plans to determine whether your research does fall under the WMO and needs approval, or whether this requirement can be waived.

From the description of your plans, it seems likely that you need approval. Not having approval would not only mean that journals won't accept your paper, it would also mean that you'd be doing something illegal.


Ethics behind using external excel freelancer to help with my thesis?

From what you've said in your question, it doesn't sound like there's a problem here. You said the information and the figures are your own, you've just had some assistance with making the data easier to work with.

It doesn't sound like what's been done is much different than if someone had pointed out that Excel already has a function that does what you were doing in a more streamlined fashion. Of course, this would be perfectly fine.

It's quite common for a student to have had the help of someone else in the course of working towards their thesis. This is particularly the case in technical matters like coding. You just have to make sure that you acknowledge their assistance appropriately (typically, by saying in your Acknowledgements that they provided assistance with your data). It's perfectly acceptable to get help from other people in your work. Seeking advice from people whose expertise is different to your own is an extremely common part of academic work. Where it becomes problematic is when you don't acknowledge that the advice came from someone else, and you (even inadvertently) pass it off as your own. I don't see that the fee changes this at all.

If you want to know for certain that this is acceptable then you should obviously ask your supervisor. Just explain the situation in full and ask "Is it okay to include this work in my thesis?" The thesis has not been submitted yet. So in the case that what you have done is inappropriate then no damage has been done. You would just ensure that the figures that appear in the thesis were not those that the freelancer produced.


How many choices of postdoc jobs a PhD student normally get?

There are really no answers to your question. It depends on so many factors:
* If you're from Harvard or Berkeley, your adviser is well known, and you've been doing excellent work, then you might get offers from essentially all places you choose to apply.
* If you're from Middle-of-Nowhere City College, worked on some obscure research topic that was started by your adviser 40 years ago and that nobody cared about at the time (and cares even less about today), and did not publish, then you may get no offers from any of the places you apply to.

In addition, it of course depends on where you apply, how many applications you send, whether you carefully choose your letter writers, if you have many/few publications, if you're willing to look overseas, etc. There is no generic answer to your question.


What is the difference between a "research plan" and a "research proposal"?

Neither a research plan nor a research proposal is a "super specific thing you need to know about".

A proposal, on any subject, generally includes things like objectives, background, potential challenges, and a vague schedule.

A plan often includes all of the above, in greater detail, as well as necessary resources, a specific schedule with milestones, and perhaps additional project specific elements (e.g. which programming languages you might use).


Why should I add co-authors on Google Scholar?

In general, I find the Google Scholar profile pages to be elegant and useful.

Some people choose not to add co-authors to their profile pages. You might not see any benefit. You might not want to play favourites (i.e., who is enough of a co-author to be listed; what if I forget to add someone, would they be mildly offended).

In general, random people will google you and land on your google scholar profile page. Seeing who your main co-authors are might be useful to such people to give them an understanding of where your work is situated and who you are working with. They can then also more easily explore the academic work of your co-authors.


How do I refer to myself in a postdoc application research proposal?

You don't mention the formality of the application - for example is this an application to a specific PI or program, or an application for a fellowship to a nonprofit or government institution?

I'd say the safest bet is to rely on extreme formality and refer to yourself as "the applicant." I see this all the time in proposals and use it myself when discussing prior work in grant applications. So I wouldn't characterize it as "forced," (inelegant might be a matter of opinion).

However, if it's not very formal (i.e. submitting to an individual professor, or department/working group) then simply using first-person "my" or "I", etc., might be fine and suit your personal style better.


Should I stop worrying and work on my current postdoc till I get something else?

Don't worry about gaps that are easy to explain, especially by something that will have affected everyone to some extend, such as Covid in 2020/2021 (and hopefully not any longer...).
Keep working on your postdoc, and keep applying to positions that are in your interest.
Besides that, it is totally normal to have a few months between two positions every now and then. I'd love to have such a gap by the way, to take a long holiday without having to explain anything.


How to prepare for attending first conference as an undergraduate?

I wish I had the benefit of this hindsight when I was an undergrad or even a master's student. It took a while for me to understand how conferences (at least in theoretical computer science) work. I speak from my experiences in attending top-tier theoretical conferences. It may vary in your case. But in short: most of what you'll learn will be outside of the talks.

To set your expectations right:

Don't expect to understand a lot from the talks. Reading those papers in advance might be even more boring unless you are already familiar with the background, or at least the starting assumptions, of the presented works. Seasoned researchers have a good idea of results being presented, i.e. the exact formal claim, and they attend the talks just to get a rough picture of the proof and techniques involved. It's like intellectual networking. Get an idea of who has done what and how. Maybe it's useful later.
Asking questions during the talks will be intimidating. As a rule, I always hold my questions for until a couple of slides later. It is always good keep abstracting the ideas presented, and not worry about the details. Details often don't get in the way of getting a rough picture, which is essentially what the talks are for.

Now, ideas for making the most from your attendance. In short: you are charting the territory of your future research, and getting to know the leaders and active researchers in that field.

There are always researchers who have a reputation for nice talks. Make sure you attend their talks. Sometimes, all you learn is how to give a good talk. Which is not to be underestimated.
Go with at least some interest area in mind. Make a rough plan of talks you'll go to. Reach out to presenters during coffee and lunch breaks. Just chat them up. Really. Everyone is waiting to distribute pearls of their wisdom and are happy for dedicated audience. Even better if your professor can help you identify his peers or their students in advance. Go up to them and convey your prof's greetings. Ask how they got to doing what they're doing.
Make friends among other research groups. Hang out with other (also senior) students. Learn about their work. Grab a few drinks together. It's quite likely you'll see them again and even collaborate.

I don't think you first conference would be about gaining deep technical understanding about anything. You would have succeeded if you could remember at least as much as you do after a visit to a museum. This visit will be about learning how the community works, who's who, and what beer tastes like in that city.


How to review a paper that is not related to my field, when my advisor has asked me to review it for him and I can't refuse?

I agree with all of @Nate Eldredge's comments.  If you have a good relationship with your advisor, you should be able to say "This paper lies outside of my field of expertise.  I don't feel qualified to review it; in fact, even to understand it at a basic level would require me to spend substantial time familiarizing myself with the terminology of a different academic field."

According to your comments, you do not feel comfortable saying this to your advisor.  So here is what I would suggest instead: do the reviewing together with your advisor, in person.  So for instance you could begin by saying "I started reading the paper you assigned me, and I have some questions I'd like to discuss with you.  When can we meet to talk about it?"  Then when you meet you can begin to engage with all the unfamiliar stuff and see for yourself how far away it really is from your interests and those of your advisor.  If it turns out that your advisor doesn't understand the paper either, I would try to subtly lead him to the conclusion that neither of you should be reviewing it.  If he tries to shove it onto you, reiterate that you are doing it but that you want to get his input.  If necessary, ask a question of the form "How would you handle this review job if you were in my place?" The point being that the advisor is in your place since he is the one who has been asked to do the reviewing.  To pull this off properly may require some verbal aikido.

The worst case scenario is that after all this your advisor makes clear to you that he doesn't care that neither of your have the expertise to review this paper; he wants you to do it anyway.  At that point he is asking you to commit academic dishonesty, and you will be in a tough spot: you will have to decide whether turning in a noncommittal review of a paper that you don't understand is the least evil.


Should I mention studying during high school in academic CV?

In my academic CV, I have included all my university education, which naturally includes my undergraduate degree.

I don't think it makes any difference that you started when you were 14. You came out with the same piece of paper as everyone else in the end up.


To answer with something fully external to your university:

Google Summer of Code

Google Summer of Code is a program that is about getting university students (undergrad or postgrad) contributing to open source.

Some open source project can be very technical/scientific.
I've mentored this year and last for JuliaLang/NumFocus.
Since Julia is a language primarily aimed at researchers, many of our projects are very technical.
The project I co-mentored last year was literally to implement and improve an algorithm from a paper.*

JuliaLang runs a bunch of AI projects each year.
I am sure the R and Python communities do too.

*Lagaris, Isaac E., Aristidis Likas, and Dimitrios I. Fotiadis. "Artificial neural networks for solving ordinary and partial differential equations." IEEE Transactions on Neural Networks 9, no. 5 (1998): 987-1000.


Include reference strictly at first occurrence, or in detailed discussion?

The best thing to do is probably to reference them in both locations.

Reference upon first mentioning is a standard convention, which helps your reader because it makes it clear that the term references something that previously exists, not something that you are introducing in this paper.
When you discuss again after a significant gap, you should cite the paper again, as discussed in this question.


the paper status was back from "decision in process" to "under review"

The question presupposes that the behavior of such an editorial system has a meaning. Granting that presupposition, my first guess is that the editor got the reviewers' reports and was about to make a decision ("decision in process") but then noticed that something was unclear in one of the reports and asked the reviewer for a clearer report ("under review").


What is a correct way for "marketing" non core PhD achievements on a CV?

I see no reason at all to leave any reasonable skill or ability off of your CV. Play a musical instrument? Won some medals in a sporting event? Program an android app? Have a black belt in a martial art? Add a section called "Other skills" or "Personal Information" and briefly list these skills. There are two reasons for this. First, it can help a potential employer think of you as a real person, perhaps someone they would like to know. Second, many skills can take years of dedicated practice to master; if you can master one such skill, then there is a good chance you can master whatever new skills may be required in the new job.

Here is an example from my life. Many years ago I programmed a video game (one of the old "text adventure" style games. I placed this on my CV, not thinking much about it. It turned out that one of the elder faculty conducting the interview had played that game and remembered it fondly. This alone certainly did not "get me the job," but anything that can smooth the way can be helpful.


Enroll in an online program such as Open University provides for PhD, or wait 5-10 years and enroll at a 'normal' school?

This question is very hard to answer without more about your goals (and what discipline you're thinking of) for getting a Ph.D.  Ph.D.'s are essentially vocational training for entering academia.  If you're really passionate about your subject and think a Ph.D. program is the only way to immerse yourself in it to the depth you want, that's legitimate, but then working full time outside your discipline, will make that pretty difficult.  You might want to think about whether there are ways of accomplishing what you want to without something that requires the commitment of a Ph.D. program.  The fact that you write "advanced coursework" is an enormous red flag: the point of a Ph.D. is not coursework, and in some disciplines there is very little of it.  The point of a Ph.D. is to do research, and that's much harder if you're not embedded day-to-day in a community of other people with the same goals (physical proximity may sound quaint in this day and age, but there's an enormous drop-off in knowledge transfer between different floors of the same building).

I don't like being so negative, but honestly in most disciplines, there are too many Ph.D.s and unless you go to the most prestigious schools, and build a very strong network in your discipline, there's a decent chance it will worsen rather than improve your employment prospects.  Ph.D.'s have a specific purpose, and at least your question doesn't make it sound like you've really homed in on how that will serve you well.


Allocating master student schedules to fit semi-commercial research interests

First, see if you can find some existing university policy you could use as a basis for a complaint.  The other place you could look would be in some professional societies for their ethics policies.  Your university would not be bound to follow ethics recommendation made by outside bodies, but still it could be a useful reference to help you apply pressure.

If there is no university (or government) ethics policy in place, then you can lobby for one to be created.  Look at some general ethics policies and try to draw something up as a proposal.

I don't know where in your university governance structure you could submit a proposal of this sort -- that could vary from country to country or even by institution.

Once you have a proposal or a platform, you need broad support.  It's okay if you don't have a ton of people supporting it initially.  As you become more public in advocating for your university to comply with its own policy, or for it to enact a policy, people will join you.  Be ready to catch them with at minimum a google group.

Hopefully you can get some faculty to join with you in advocating for some clear limits for the chemistry students' non-academic requirements.  Hopefully they will see that the level of excellence of the institution will go down if students are spending too much time on "production", and not enough time expanding their knowledge and creativity.

Point of comparison: in the U.S., graduate teaching assistants work 20 hours a week.  Based on my experience as a TA, I would say that it would be difficult or impossible for most mere mortals to make significant progress in the graduate studies if the work hours per week were above 25.


Underscore in place of author in references

Some citation styles allow you to use a long dash in place of an author name if the work you're citing has the same author as the preceding one. It's stylistic choice.


By asking for all of this information, it sounds like this professor is trying to write you a personalized letter, which is usually a good thing.  She's helping you out.
Therefore, it's completely reasonable to take option 1 and simply explain your bad grades to her.  I wouldn't go overboard here - she's not making a hiring/admitting decision regarding you.  But a few lines giving her some context for all the material she asked for is not at all amis.


Set clear objectives and deadlines as early as possible to force yourself into a practical mindset. Don't do it for your supervisor, do it for yourself. Try to funnel your thoughts and ideas into a confined key focus point .

This prevents you from procrastinating (which I consider to be a big threat in desk research).


Oral vs written exam - from a lecturers point of view?

There's really no universal answer, but it depends on the university regulations and on your willingness to listen to students for several hours.

To give a personal example, I've been running oral exams for about 20 years. My exams, which are for undergraduate students (2nd or 3rd year), typically consist of a written test (2-3 hours) plus an oral exam with a duration of about 30 min for the standard exam or 1 hour if the student prepares an optional part (e.g. the presentation of a scientific paper or a presentation on a lab work). If you fail the written test, you cannot take the oral exam. You can be failed also at the oral exam too.

For me, the critical factor is the distance between two exam sessions because, given the rules in my country, the students who failed in one session should be able to retake the exam in the next one. Typically, in my university, the distance between two exam sessions at the end of a course is of a couple of weeks.

So, in my case, the magic number is of about 100 students, 150 maximum. Of 100 students, typically about 70 students come to an exam session. Of these, about 50% fail the written test, which means that I remain with about 35 students for the oral exam. Assuming that 1/4 take the optional part, I need 9+26/2=22 hours for the oral exams, which can be done in one week, leaving some days for grading and for rescheduling students who can have unexpected issues (illness, other exams on the same day etc.).

The benefits of oral exams have been discussed at length in the answers to this question, and I really cannot overestimate their importance in learning. See also this related question.


Is it acceptable to contribute a poster to a conference without actually attending?

Without knowing the particular field or conference:

No, this it's not common to have a conference poster without presenter.

It often happens that poster are on display for the whole conference and nobody stand by their side to explain them and this may give you the impression that there is nobody there to present them. However, usually there is one slot called "poster session" where the presenters are supposed to be with their posters and the all other participants are supposed to walk around and get into discussions about the posters.

However, more importantly:

There may be a rule on attendance stated by the conference.

It may happen, for example, that if some poster had no presenter, the paper that belongs to an accepted poster will not be published in the conference proceedings (or removed from the online proceedings).


Is it good to write a Critical report on my own published research work?

This is one of the issues that are solved by preprint archives. If your work was on arXiv, you would just post an updated version there, and not worry about the published version, because readers usually go to arXiv. Probably your work is not on arXiv, or you would not ask the question. Then you might enquire whether you are allowed to post it there, and/or consider doing it for your subsequent works.


Publishing with/without advisor as new Master student

Don't be shy about pushing your work forward. The stage at which a person becomes able to do original research is not fixed. Some people are more advanced. Well done you.

Generally speaking, a single paper isn't enough of a benefit that it should cause you to burn bridges. So I suggest you scope out how the faculty in your department would think about such an idea.

Your option 1 could get some feathers ruffled. Your option 3 seems to needlessly delay your advancement.

I suggest you find some variation on 2. In the school I did my PhD there was a head of graduate studies in the department. You could ask that person for some guidance. Present it as wanting to satisfy both being a good member of the university as well as advancing your work.

It isn't necessarily the case your department will push you to have a co-author. If you have come up with the topic and done the work entirely on your own, most profs will agree you should publish it as the only author.

It's different if you have any kind of assigned supervisor. Even if it's a very distant and high level kind of thing. For example, maybe there is one prof who deals with all the masters students. In that case, you would still want to approach that prof and discuss how to proceed. Still frame it as wanting to be a good member of the university while also advancing your work.


Normally an un-tenured faculty member in the US serves on a fixed term contract, usually a year, but maybe more. It isn't that they have to fire you. They just don't have to renew your contract.

It is only after earning tenure that you have a continuing contract and need to be fired for cause. I strongly recommend that you get legal advice or go along


Emailing professor too early has any impact?

Any sensible professor would be happy to reply to a talented student with A+ results; and be more than happy to supervise one.

The only issue with the time is, sometimes the good professors at a university can't take more students to supervise; because they are supervising 5-8 students for their final year projects. So, as soon as you can contact the professor, the better.


My experiment supports a theory. Shall I contact the theorist attaching with my drafts?

This is a complicated topic and you should definitely ask your advisor. There could be all sorts of potential pitfalls, e.g. perhaps there are caveats/loopholes to your experiment, perhaps you only supported a restricted form of the theory, perhaps the theory had unknown parameters that your experiment helped fix, and so on.
Given the dangers, don't try to navigate this yourself. If it comes to contacting the theorist, your advisor is likely to know more about what to write, as well.


ePrint Archive for PhD Dissertation in the Social Sciences

You can always put a copy of your dissertation on your professional web page.  Google will find it.


Is it normal for a supervisor to never talk to you or give you any direction?

No, this is not standard.
One of the main purposes of a thesis is that you learn how to perform research.
While there is some learning by doing, without supervision you are very likely to at least do one of the following:

misunderstand the task or the topic,
miss some important existing work when getting familiar with the field,
make mistakes that could easily be spotted by somebody experienced but may cost you a lot of time or make a lot of your work worthless,
focus on rather uninteresting aspects and miss interesting discoveries,
produce bad writing (and thus having to rewrite it entirely before submitting).

This is probably the first time you work on a larger subject. Nobody can expect you to do all these things right on yourself. And even if you do everything right naturally, proper guidance could make you better utilise your talent.

I thus recommend that you do (if you haven’t done it already):

Talk to other students or the student union to get an idea what exactly is common at your institution.
Talk to other students in your advisor’s group about their experience. Perhaps the others have the same problem and you can address it together.
Actively seek feedback from your advisor.
Consult with your examination rules and the responsible people at your department for ways to switch your advisor, get your advisor to do more advising (ideally anonymously), etc.


In a faculty job search, when and how should I reveal my preferences?

I've served several years on the faculty recruiting committee for my (US, top 10) computer science department, including three years as the chair.  Protocols vary significantly between different departments, different searches, and especially different fields, so take my experience as a sample, not as a definitive answer.

Faculty hiring is best thought of as a complex multi-player game of three-dimensional chess, using invisible pieces that occasionally explode, where nobody knows who the other players are or what rules they play by, and nobody wants to reveal too much information.

  Question 1: How often are offers made before the end of the interview period (i.e., before all candidates have been interviewed)?

It happens, but normally only when one of the early candidates emerges as an overwhelming favorite, and that candidate has another offer with an inflexible (or already extended) deadline.  But nobody wants to be forced into this situation.  It's really bad form to interview someone for a position that doesn't exist.

Some universities allow limited gambling with slots.  A department might offer a position to candidate A, and then later make a second offer to candidate B for the same slot, under the assumption that at least one of them is likely to say no.  If A and B both say yes, then both A and B get jobs.  (I've seen this strategy go very "badly", with four low-probability offers made on the same slot, all of which were accepted.  Gambling was outlawed for the next n years.)

  Question 2: If a candidate expresses that a school is her top choice, does it make any difference to the hiring committee?

Especially at universities that (a) forbid gambling and (b) do not let departments roll unused slots from one year to the next, departments do balance the desirability of various candidates against the estimated probability that they will accept an offer, to minimize the risk of not hiring anyone at all.  (This scenario also tends to generate offers with very short and inflexible fuses, sometimes while interviews are still ongoing.)

But just telling us that we are your first choice probably won't help much.  We want to believe you, and we appreciate your effort in making that overture, but we don't really believe you, because lots of candidates have said that and then left us at the altar.  And even if it's true, you really don't want the rumor that that you prefer us to reach someone else.  Best to keep mum until you have actual offers.

On the other hand, evidence that we are your first choice is taken very seriously.   For example, if you receive an offer from somewhere else, especially from another top department, telling us in time to make a good-faith counter-offer is certainly better than not telling us until it's too late.

  In fact, can expressing this kind of preference actually hurt a candidate's chances?

No.

  Question 3: To what extent do different departments talk to each-other?

Not at all.  Different departments are competitors; sharing information is counterproductive.

We do, however, gather as much back-channel information as we can, for example by scouring our competitors' web pages to see who they are interviewing and when.   Sometimes I do hear rumors of the form "So-and-so is about to get an offer from X", but those rumors almost always trace back to the candidates themselves.

  one can easily imagine a situation in which lower-ranked schools don't make a candidate an offer because they expect she will get an offer from a higher-ranked school

Unfortunately, yes, this does happen, although I suspect more often at the interview stage than the offer stage.  See "minimize the risk of not hiring anyone at all".  Nothing you can do about it.  Let it go.

  Question 4: Do I just need to relax?

Yes, always.  I recommend building up an immunity to iocaine powder.


I work at Researchfish now but prior to that I was at one of the research councils (MRC). I have had an ongoing involvement in the system, and particularly in defining the question set/information collected. The main aim is to collect outputs against the relevant funding i.e. a paper should be associated with the award if that funding has in any way contributed to or supported the research or other activities to produce the paper.

So, with regard to your questions:
Do I put in work that was started before the grant and then was finished during the grant?
- yes, if the grant has supported some of the latter parts of the work whether in resource, salary etc.

Do I include arxiv postings?
- my understanding is that arxiv is for preprints, funders tend not to need to know about a paper until it is published, although there are some exceptions so you should check with your specific funder. If your funder does want to now about papers before they are published this will be done through the additional sections of questions, rather than the main publications section.

Do I include published work that was on the arxiv before the grant started?
- this is less likely, unless there is significant change in the paper between the preprint on arXiv and the published version. Again, please think about the funding.

I hope this helps, but your funder should be able to clarify this further.

Bev Sherbon

Impact & Evaluation Adviser, Researchfish


Is it OK for the supervisor to expect half of grant money which student got through his help?

No, this is not o.k. Moreover, depending on the grant we are talking about, this instructor's request may even be illegal, but it most certainly is unethical. From what you write, it appears that in fact the request is illegal. I realize that this may be difficult, but you may want to discuss this issue with the department chair.


DOI's are managed by Crossref.org.  For each DOI, Crossref's database has a redirect to the current location of that digital object, and the owners can move things around and update the Crossref database as needed.  When you follow a link to https://doi.org/<DOI>, the crossref servers redirect this request to the current location of that paper.  As mentioned in another answer you can lookup an article in the crossref.org database to see whether or not it has a DOI.

Recent articles have typically been assigned a DOI by the publisher, and most publishers put the DOI on the title page of the paper so it's easy to find that way.

Older articles were originally published without a DOI, but the publisher may have assigned one after the fact.  If the publisher has not already assigned a DOI, then JSTOR may have assigned a DOI to the article that will point to the copy of the article in the JSTOR database.  This is a service offered to publishers by JSTOR, but not all publishers use it.  Thus not all articles in JSTOR have DOI's.

It appears that the article you linked to has not been assigned a DOI by either its original publisher or JSTOR and thus has no DOI.  I can't find the article in the crossref database.  The "stable URL" that you linked to is probably the best way to link to the article.


Will my advisor regret taking me if I start slacking off?

Communication is critical here. If your advisor knows what you are doing and why you are doing it, there is a much better chance that he or she will be patient with a low rate of progress.

You can communicate in a number of ways. A sit-down talk is obviously the most straightforward, but you can back up the message by putting in face time time in the office or lab, attending all lab meetings and relevant seminars and departmental events, and so forth. You can even ask for advice on how to balance classroom and research time. Sometimes an A- and research progress is better for your education than an A+ to the exclusion of everything else. (See also the threads about the relevance of your PhD grades going forward).


Should I be worried of being accused of cheating?

I'm going to just guess here that there won't be any problem. If there were, you'd likely have been challenged when you left the room. I'll also guess that no one even noticed.

You seem to have a decent sense of what is allowed. If you are challenged, just tell it like it happened and your thinking about what you did at the time. No one but your instructors can judge, but I think the issue is past you. Probably fine to just relax.

But note, also, that none of my statements are definitive. Too hard to make firm statements from a distance.


It is generally quite difficult to provide too much bibliographic information, and this is no exception: while few will notice or care about the additional information, it will certainly do no harm.

As for how to format it: that depends on the publication venue.  Every publication style, however, has a standardized form for books that are part of a series (intended for those books where the series is important bibliographic information) and you simply need to comply with that standard.


How to handle an advisor who regularly gives me new work for my thesis?

I am planning to start my PhD study under his supervision afterwards.

Is he aware of that? If not, you should probably consider what the PhD workload would be, if you are already experiencing the pressure you describe with your master thesis. If he is aware of it, it is possible that he is trying to broaden your views in order to prepare you more for the PhD work and probably being a bit overzealous by doing so.

However, in both cases you shouldn't be afraid to talk to him about where to draw the line for your thesis. That is also an important part of graduation. Personally, I don't take much into account the "mood" of my colleagues when discussing important professional subjects. If you adviser is so unstable, that an objective discussion when he is in one of his moods is not possible, that is another and more serious problem. In that case, you should consider finishing up your masters and going to grad school somewhere else, or at least with another adviser.

As for what you should do, as I said, approach him about your problem and determine where you are with your work and what is the scope of your thesis. It is normal to draw the line somewhere and proclaim that that amount of work will constitute your thesis. Once that is down, you stick to it. As I understand it, you have your problem stated, so you can any other proposed problems delay with "My thesis is my priority right now, but I'll keep that particular in mind, and once I've finished my thesis, we can start working on that one."


At least in mathematics, the arXiv is a pre-print server --- papers are mostly eventually published, and receive DOIs then. In fact, the arXiv encourages authors to add these DOIs to the arXiv metadata when they become available.

I think it could be quite confusing for papers to end up with two DOIs. Given that the arXiv numbering scheme works quite well, and in practice everyone knows how to resolve handles of the form arXiv:NNNN.MMMMM, why add the complication?


Where to put state of research in thesis when it needs to be referenced in introduction?

General background is a normal component of a thesis, typically more so than in research papers in the field.

You should follow your supervisor's advice for two reasons:

They are an expert in your field, and you (should have) chose them as a supervisor for this reason. If you don't value their opinion, you have made a serious error in making them your supervisor.
They will be evaluating your work and will be the one (or part of a small group) deciding whether your thesis is acceptable.

  This really irritates me because I always discussed the state of research later on after giving basic theoretical backgrounds needed for understanding (this would not be possible when mentioning state of research in the introduction)

This statement makes absolutely no sense to me. This sounds like exactly what your supervisor is recommending: giving basic backgrounds, then discussing the current state of research.

  I also do not think that generalizing the problem so much that it is not needed to use basic technical terms when defining the research question is useful at all.

This might be your opinion, but it seems like your supervisor wants your thesis to be at least somewhat readable by someone not intimately connected to your field. That's pretty typical advice in an academic context, especially in a thesis.


What does "ad indicem" mean in a citation?

To be short, yes.

According to the post in English.SE, it means 'see the index'. It basically tells you to refer the index section and look for the topic that is discussed in the context where it is cited.

Note: This question was asked in both Academia.SE and English.SE to benefit both communities as there isn't a single standard dictionary that could be found online to define this term. Credits go to the original answer in English.SE for answering my post.


Creating video recordings of R Studio and R console

OBS Studio (https://obsproject.com/) worked well for me for another statistical analysis program. For the very basic editing afterwards (cut the time that the kids ran into the room out of the video, join videos together) the video editor that comes with Windows was enough for me.

Also see: I need help adapting my academic workflow to the COVID-19/coronavirus crisis – where do I start?


SpringerPlus asked me to review a paper already published

You should immediately inform the editor and let them decide how to proceed further.

If this is indeed a double publication, reviewing it is a waste of time for you, other reviewers and the editor. In the unlikely event that there is some good reason for this (e.g., the other journal is a scam), the editor should be able to find out quickly or already know about it and tell you.

As for your reputation as a reviewer: If you see something very suspicious, reporting it is the proper action and is a job correctly done.

You should also ensure the following:

The other journal is really a journal and not, e.g., a preprint server like the ArXiv.
The mail asking you for a review did not mention this fact.
The mail asking you for a review really came from a reputable publisher (and did not only claim this).


Would it be rude to put my professor's name in for a reference when they haven't responded yet?

You should absolutely NEVER list somebody as a recommendation without permission. Its asking for trouble.  Your deadline issue is YOUR issue, not your recommenders.  If time is critical, you should have mentioned that in your earlier email.  You should consider a followup email, letting him know that time is critical, or even stop by is office or call.


Citing work with a publication year in the future

Most journals take as formal publication date the date it appears on their printed version. The online version is considered a pre-publication.

Thus, despite how weird it may look, it is ok to cite an article from the future (as long as it is accepted and in press or the online preview). Journals with only online presence would not have this issue or the time span might be smaller.

What is probably important is to provide the DOI of the article (if available) as this will make it easier for people to find its online version before and after it has been published on paper.

Edit: Just to add that the citation and its details is decided/provided by the journal and not by you.


Is there anything that has been tried to stop publication shopping

A version of your suggestion 1. is implemented in my academic field (mathematics).

In mathematics authors usually pay dearly to submit to any particular journal, not in money but in time. Namely, an unacknowledged but hard to dispute stage of the refereeing process in mathematics is the part where the referee lets the submission sit on their shelf for N months.  It would be interesting to track the dependence of N on various factors, but based on my own experiences as an author (and okay, yes, as a referee!) I believe the median value of N to be about three months, with a higher mean.  Especially, when I submit a paper to a large range of reputable journals in my field, I feel that I am incurring a risk -- small, but not negligible; let's say 3-5% -- that the referee will wait a year or so before rejecting the paper with a wholly superficial accompanying report (say, one paragraph that does not make specific reference to anything in the paper past the introduction).

This makes it rather impractical to shop a mathematics paper around to a large number of journals at about the right level.  (If you send a less than excellent paper to a truly excellent mathematics journal, the chances are good that it gets bounced back to you quite quickly.  I have heard stories of the absolute top journals in mathematics keeping a paper for a year or more and then responding negatively...but then I have also heard of them doing this and then accepting papers that I would have guessed they would reject.)  This certainly works for me: I have submitted over 50 distinct math papers for publication.  Most often I step down in quality after the first rejection and always after the second rejection.  For me, having three or four journals consider the same paper feels like quite an ordeal....because it is likely spread out over several years!

Maybe this sounds sarcastic.  It is not intended to be.  If anything, it is a relief to think that there might be some good effect of the current endemic slowness of mathematical refereeing.  Because we have a thriving preprint culture, it is hard to argue that slow publication has a significant effect on the intellectual progress of the field.  If only the slowness were equidistributed, I think there would be little to complain about.  (But it isn't, and I suspect that my suffering is as nothing compared to that of some of my junior colleagues...In fact, just now I realize that while for many years now my papers have been treated better by top journals whether they take them or not, at the beginning of my career I had several papers languish in top journals for a really long time.  The rich should have to pay more, not less.)


If I am going for a second masters and my previous GRE score is expired, do I have to take the GRE again?

Not necessarily.

I applied to a top department at an RU/VH university in the United States, and asked to have the GRE requirement waived for exactly the same reason, and they waived the requirement, and then admitted me to the program.

Ask the admissions office/committee if they will wave the requirement.


How common is it for submitted papers to have minor errors?

That's what peer review is there for: to tell the author about the minor, but correctable mistakes in the paper.

The way I see it is that, of course, I spend a lot of time writing my papers and making sure that everything is correct. But pragmatically, you will have to come to terms with the fact that no paper will ever be perfect. There comes a point where you just have to take the plunge, submit it, and hope for the best.


Are there academic reasons to only use journal articles and books when writing?

If you build your work upon other people's work, whether it be a blog post or postage stamp, then you should cite it, otherwise that's plagiarism. This is especially the case if the work is a primary source of the research (which can even be the case for blog posts).

That said, there are some guidelines you can follow to get the best version of the work to cite.

Find the most recent or most authoritative/official version of the work. If the paper is an unpublished workshop paper, is there a corresponding conference or journal paper that was later published? Or is the work perhaps written up in a masters or PhD thesis?
Find the primary source. Is the blog post (secondary source) a distillation of some other paper (primary source)? If so, go for that primary source. Is the Wikipedia article (tertiary source) based on some well-known book or article (primary source)? If the report from an NGO is original research (primary source) then you should cite it. If not, determine what it is based on an cite that.


Are PhD studies in molecular science possible following revoked RN license due to drug use (fired, but no criminal charges)

I have no domain-specific expertise here, so take this answer with a grain of salt. But broadly speaking, having been fired from one’s job at some point in your life is not an obstacle to getting into a STEM graduate program in the US (and I’m sure most countries). I’m not aware that it’s even required to report such things in your application anywhere. And I’m not aware that PhD programs do background checks on their applicants. No program that I am familiar with does.
So yes, a job in health care involving care of patients may be more problematic, but at least a science PhD seems well within the realm of possibility.


(Although the question has answers in the comments, I'm providing an answer so that this question does not remain unanswered.)
Articles that are based on interviews with mathematicians published in periodicals of mathematical societies typically have the title "Interview with [interviewee]" and have the interviewer as the author (that is, the interviewee is not an author).
As an example, see Jackson, A. & Kotschick, D. (1998). "Interview with Shiing Shen Chern," Notices of the AMS, 45(7), 860-865.
The article starts with the note: "This article is based on an interview with Shiing Shen Chern conducted on March 4, 1998, by Allyn Jackson, with mathematical help from Dieter Kotschick."  Also note that aside from Jackson, Kotschick is also listed as an author of the article.  (See this.)


How to parse the question "How many hours did you take at the institution?"

In the US, university education is quantified as "credits" typically expressed as "credit hours" referring to 1 hour per week of instruction for a semester (so about 15-16 hours of face time). A course meeting 3X weekly would be worth 3 credit hours and is usually expected to involve an additional 6 hours weekly of work outside class. A 4 year bachelor's degree is about 120 credit hours.

I'd interpret this the same as asking for how many credits you took with that institution, expressed in an appropriate conversion to credit hours.


Can a promising graduate turn into a crank? How should their advisor react?

In my opinion, every smart theoretician should take a crack at the major open problems in their field, at least for fun. Often the key to "solving" such problems is to not actually bang your head through the same wall everyone else has been stuck by, but to change the perspective or cheat the problem somehow. Even if you aren't smarter than everyone else, perhaps you can think of an outside-the-box idea others haven't. And as John Conway put it, we aren't as smart as we think we are. If I remember correctly, he said this when interviewed about Fermat's last theorem, which was unsolved at the time.

Of course if someone actually is "smart" enough to continue in research, they will be able to tell if they have failed. And they will be able to make a rational assessment of risk versus reward in pursuing such a path where the likelihood of funding and career success would be low. Hence pursuing such problems isn't all that different from pursuing other very-high-risk ideas. Just a little farther out on the spectrum.

One situation where this risk-reward assessment breaks down, of course, is mental illness. A manic person might think they are superhuman, for example. And there are some professors that I really wonder about. But mental illness is beyond the scope of sites like this, and I'd note that people with diagnosed illnesses can still function normally (or better) and be very successful in research.

The short answer is if you can't prove (rigorousy) they will fail, you can't prove they are fools for trying.


Typically journal editors are volunteers. I suppose for some of the flagships (Nature, Science, Cell, etc.) they might have full-time paid editors, but your typical niche research journal editor doesn't get much if anything at all.


The paper of

E. W. Steinhauer - Die Nutzung einer "Schattenbibliothek" im Licht des Urheberrechts Einige Überlegungen am Beispiel von Sci-Hub

says that downloading is probably illegal and viewing it in your browser is in some grey-area (although making this difference looks like some law-people did not understand the technicalities at all).

But there does not seem to be one court case where one was prosecuted for just downloading such material.
So if you still want to access the publications this way, then I suggest to use the following robust solution: Use the Tor browser or even the Tails operating system. In the latter you could save material with questionable copy-right license status in an encrypted file-system, then in Germany the law is pretty robust (compared to the USA or UK) around the "Aussageverweigerungsrecht", i.e. no authority can force you to decrypt it.


Publishing a tech report or other non-peer reviewed paper as an independent researcher

It might be field dependent, but I have only seen technical reports published by companies (if similar to technical notes) and professional organizations (like TAPPI).

But nevertheless, peer-review aims at improving your work, giving it more credibility, as it has been reviewed by your peers and they concluded it is (in their opinion) valid, or rejecting it if it is performed poorly (not exclusive list).

So publishing in any place other than a regular journal might affect your work's visibility (I'm not sure the power of Google can bypass this issue) and your work's credibility (as I'm not sure I would consciously cite a work that is available only as a pre-print and not peer-reviewed).

As for the problems you present:

  Money. I'm currently not affiliated to any academic institution which    would reimburse my conference fees and publication costs. I
  would also like to provide open access, so other non-affiliated
  researchers can actually read my paper. This can be very costly.

I understand the issue here, but when I was in institutions that had no money to cover the open-access publication, the non-open access option was the only alternative. Unfortunately, you probably can't have the pie and eat it too...

I can't comment on conference fees, as in my field, conferences don't count as publications.

A middle solution could be to choose the non-open access option of the journal you select and publish a pre-version or even the accepted version of your manuscript as a pre-print with a link to the official (but not open access) pdf (you could ask the journal policies on this matter). In this way, you provide all the information through the repositories you choose, the manuscript is peer-reviewed, and the article is indexed and available for those paying the paywall.

  The topic. It's an interdisciplinary thing I write about, which doesn't really    fall    into the field of interest of the usual journals and their
  peer    reviewers. It's a bit of an in-between-the-chairs thing.

Most works in my field are interdisciplinary. You can usually identify the main field of the article and find a respective journal. In most cases, you can propose reviewers, so you can select ones from the different disciplines your manuscript covers. Each then can concentrate on the part they are more confortable to review, covering eventually all aspects of your work.

Finally, if you insist for a technical report, you might be able to contact a relative association or company directly and discuss if they are interested in your work and a publication under their technical reports (but I admit that I have no experience on this and I might be completely out of subject).


How to reference sources when I only took the ideas?

You should make it clear in the text who invented the algorithms, and cite next to the names, usually. Write something like:

  The XYZ search algorithm [1], works by...

  Foo et al. [2] propose an algorithm which...


Is it socially appropriate to ring up a professor whom you have corresponded with briefly by email?

I don't see any problems for you to call him.

If you want answers quick, this is the best way to achieve it. If you feel a bit uncomfortable calling him, then I suggest that you "ping" him with re-sending your last mail or that you ask him if he can reply from the previous message.

Teachers at my university, some have their phone number (Both private and work, though private is not mandatory) listed at the university website so that students can reach them outside of working hours if it's urgent.

So having students call them is nothing new and shouldn't be a problem.


Can a failed research become the object of research?

Meta-science/meta-research is the discipline that deals with studies that use the research methods to study research itself. Its currently quite en vogue, I don't know if you could make your study fit into this category.
Personally my two most successful papers are about what would have been quite mundane studies but anomalies in the analysis lead me to identify problems with the way data was commonly analysed across the whole field.


Ethics for trip reimbursement from multiple parties

I would imagine that there are jurisdictions where getting reimbursed for costs that you have already been reimbursed for is illegal. It is at the very least unethical, so I think that thinking about this is certainly the right thing to do.

If you make a trip that includes more than the bare minimum "getting there and back" in travel (e.g., a personal detour on the way home, staying for the weekend after a conference for sightseeing, etc), many reimbursing institutions require you to hand in the receipts for your actual travel, plus estimates of what the bare minimum trip would have cost. For example, you could have printed out a screen shot of looking up a flight that just gets you there and back. They will then reimburse you for the smaller of the two amounts.

Likewise, if you have a multi-stop trip, you can certainly ask to be reimbursed for an even smaller amount, as long as the total reimbursed amount does not exceed what you actually paid. How exactly you split the total is up to you, as long as no institution pays more than it would have if you had just traveled there and back. That's also ethical: if they invited you to a talk, they did so on the understanding that they will cover your travel cost to get there and back; if you are asking for less money (whichever those savings are split among all institutions), it's to their benefit, whether or not they get exactly half of the savings, or a different amount -- it's money they had budgeted for you, and are now getting back, nobody can complain about that.


Uncited general claims followed by cited specific claims – is this an accepted writing style?

Certainly general statements that are common knowledge do not require citation.  Particularly if the general claims just help to provide a framework for thinking about things (context), are reasonable, and are not truly needed for the paper.

However, different people have different opinions about what is common knowledge, or is reasonable, or is important (say in putting the work in context), and part of your job as a reviewer is to point out where you think citations should be added or assertions should be questioned.  The authors always have the option to disagree, but at least if you make a suggestion, they should think more carefully about the validity and evidence for such an assertion.  (cf. my answer https://academia.stackexchange.com/a/66329/19607)

In your example, you might ask for evidence that they "appear green to most people and animals," or just point out (politely) that that's a stupid statment.

As another example, here's something I wouldn't expect a reference for:

  The only known techniques to attack Problem A are Method X and Method Y.  Method X was pioneered in [cite 1] and Method Y was recently applied in [cite 2].

It's hard to give a reference for the first assertion, and maybe the reviewer will be aware of a Method Z and can point it out.  Or maybe there is a Method Z but it got neglected by the authors and the referees.  Or maybe the referee's not sure.  This is why some people might prefer to be more modest and say "The only techniques we are aware of..." but people write in both ways, and as a referee I wouldn't say anything unless I actually thought the authors were neglecting something.


Citing a collection of work (i.e. literature review) by 1 citation?

Do not automatically cite everything X has cited. You should only cite a paper you've read, and it will be assumed that you have read everything you cite. Author X could have made a mistake, misunderstood something or deliberately misrepresented something.

Whether it's worth tracing back every reference cited in X's paper depends why you're referring to it. If your paper describes an alternative model and the differences can be traced back to, for example, the data sources you've used, then you should go back to them, read them and cite them; ditto if your paper is a critical review of X's model. If you're simply using X's model out-of-the-box you don't necessarily need to go back and pick over every source for every parameter estimate.


Thesis writing style: when to italicize?

There can be specific exceptions for journals, which may have conventions preserved unchanged from the past, but the general principle is to be typographically simple while conveying the necessary information. Quotation marks are required to unambiguously indicate that a certain sequence of text is a literal quotation; the quote itself should then not modify the format of the text, thus should be roman when the original is roman, italic when it is italic, and so on. Thus, your first option would be the correct choice.


Alongside my book proposal, I included by mistake a chapter with some typos (just a few, but major).

I have never been in either pair of the shoes, but I will try to break this down: To me, it's better to lose a book deal because I reported an error in my proposal than to lose a book deal because a reviewer commented "glaring grammatical errors in the introduction."

I would suggest sending the corrected version to the editor with an apology, explaining what the errors are and invite the editor to decide if it needs to be delivered again to the reviewers. That way, you did your job as a responsible intellect, and the editor remains in control. And even the editor decides not to resend another version and later a reviewer found the errors, you're already covered from the editor's point of view. That's why I really see no harm reporting that.

Best of luck to your publishing endeavor.


PhD - unhelpful supervisor, how normal is it?

This is mostly advice beyond the scope of the question, but to try to answer the question itself, the entire situation seems horrific and unsustainable.
I don't think it is literally "normal", but I do think the situation is far too common. It isn't really you and it isn't really the PI,  but the entire set up from top to bottom. Only a few (and there are a few) doctoral students could thrive in such a situation.
However, along with the bad, there seems to be something good about the current situation or you would have fled by now. A salary is good and avoiding pandemic chaos is good, but I'm not seeing an obvious path, here, to a doctorate.
But, you are early in your studies (half a year). I'd suggest that you spend some effort looking for a better situation, preferably in the English speaking world unless you are fluent in some other language. Even if you were to learn the local language fairly fluently in the next few months, the time to completion in Europe is normally expected to be quite short.
Look at all the options. It would be hard to find a worse one, I think.


How to read and organize academic materials

If you search for "a holistic method on how to deal with knowledge in your life", perhaps the Zettelkasten method might be something for you.


can I not mention that I have will complete a PhD degree while applying for another one in another country

The comment of Jeff is worth considering. Do you really need a second doctorate to migrate.
But, under the circumstances, send a message to the new university stating that since your application, you were awarded a PhD, but, assuming you want to, that you still want to continue your application and enter the new program. Stress that the research proposal will be different if accepted.
Hiding the recent degree could come back to harm you.


I regret declining a PhD offer and accepting another PhD offer. What should I do?

I feel very regretful now.  ... Should I ask school A to accept me one more time or reapply?

If you prefer School A to School B, then I doubt anyone will begrudge you a new application to School A.  Since you have taken a deferred entry at School B, the inconvenience to them of having you leave is less than if you had started your program.  If you decide to re-apply to School A then you will need to decide whether you want to quit School B first, or hold on to it as a fall-back.  In the latter case, you will also need to decide if you will disclose your new application to School B.

I can't speak for others, but if I were your proposed supervisor, and you had not started your candidature yet, I would have no problem with you coming to see me and telling me that you want to apply to another school.  Even if you wanted to do this, but keep your existing deferment as a fall-back, that would be fine with me.  (We deal with ranked preferences all the time in student admissions, job applicants, etc.)  I would appreciate you being up-front about this, and talking to me about it.  It is an inconvenience to lose a student that has been admitted, but it is not a big inconvenience, and it is far preferable to having a student trying to grind through an arduous PhD program in a school where they are not happy even before they start!

Now, having said this, obviously that puts you on the radar as someone who might not enjoy it here if you end up in the fall-back position of attending School B.  If worst comes to worst, and you are rejected by School A, after disclosing your application to School B, you might have to have a talk with them about whether you still want to be there.  Nevertheless, you can cross that bridge if and when you come to it.

  Applying to other schools might violate the deferring rules of School B.

It "might".  But here's a pro tip --- PhD students are expected to be able to find documents and read them, so exercise those skills to go ahead and read the rules and see if this does violate the rules.  (I doubt it would; there would almost certainly be legal issues relating to restraint-of-trade if a university had rules preventing you from applying elsewhere.)


In what cases should I completely state a theorem I'm about to use?

For my taste, I'd "recall" the precise statement exactly when you need it, in the internals of your proof, as you seem to indicate. I myself have become ever fonder of a math writing style which does not require so much flipping back-and-forth to understand what's being said. (Especially the otherwise-precise quasi-Bourbaki of referring to things by some (necessarily artificial and meaningless) numbering scheme, rather than any sort of descriptive reference.)

In particular, for simply the statement (rather than proof) of a result, adding an appendix would make things harder to read for many people, and the people who already know the result would not gain much. Skipping over known things is easier than flipping back-and-forth.

That is, allowing your readers to read straight through seems to me the ideal. So, no, similarly, don't introduce all the notation at the beginning and then expect people to remember it. Sure, you could have an appendix for reference for notation, but it really should be explained when first used, ... in my opinion. That kind of thing.


Why do people sign their names with only their initials?

There are many reasons not to include a full first name.

You don't like or identify by your first name.
The journal format demands it.
You are trans-gender and have changed your first name, but not the initial or your surname.
You are a minority in your field and hiding your first name means hiding clues to your minority status and possibly increasing the odds of your work being taken more seriously. (Mostly, hopefully, this reason is now outdated.)


Editor's comments differ from those of reviewers

It's the editor's call, and since you have no right to get your manuscript published, you don't really have a basis to ignore the editor's request -- if that's what the editor wants, then that's what you likely have to give him/her.

That said, while the manuscript management systems most journals use typically give you a deadline by which you have to turn around revisions, these are not actually enforced. That's because if you need to, you can always let the deadline pass and submit your revision as a new paper -- if you mention in your cover letter that it is a resubmission of a prior manuscript, then it will go to the same editor and from that person likely to the same reviewers.

The better approach is to discuss the timeline issue with the editor. Email the editor back and state that you're looking forward to making the requested changes, but that you can't do it in the requested time. Ask whether you can get an extension, stating how much time you need. As an editor, I can't see a reason why that should not be granted.


Possibility to supervise a student abroad?

I was supervised remotely for my Master's dissertation, so yes, this can and does happen in academia. My situation was similar to yours: there was no one working in the field in which I really wanted to specialise at my university.

My supervisor and I communicated via email and had a Skype meeting once a week (this is the closest you can get to an in-person meeting, so I would highly recommend doing it, or at least supplement emails with phone calls). I also visited him in person twice during the project (relatively easy since we were both in the same country, about 5 hours apart by train).

In my case, it was very informally organised; the course coordinator for the dissertation agreed I could have a supervisor from another university and I had a second supervisor at my own institution who I updated regularly on my progress. There was some talk of my having to pay tuition fees to my supervisor's university but in the end this didn't happen.

However, depending on the specific rules and procedures of your or the supervisor's institutions, there may be formal paperwork to submit. There's probably someone you can ask about this, e.g. the department head or administrator.

Good luck!


All you can do is ask; the best outcome is they say yes, hear your talk and accept you. The worst outcome is they decline to meet you and then reject you, which is the same as if you don't ask and get rejected anyway. I don't think they're likely to reject you based on you asking politely to meet them.

Apart from that, my only advice is to try not to worry. I remember how stressful the PhD application process is. As they say, good things come to those who wait, but I'd add that good things come sooner to those who are proactive. Good luck!


How important is the thesis document for judges on the day of the thesis defense?

Is this document important for judges?

You are really asking the wrong question. Any official document that bears your name eternally is important for you and your future. You are a MSc student with probably small number of publications (if any) and a MSc thesis is an important milestone on your transition from a student to a researcher. It is also a quite large document (much larger than the typical scientific publication), so writing an excellent document at this scale is a valuable lesson even if you want to work in industry, where technical reports / documentation and deliverables are quite common.

Conclusively, you must always strive for excellence and always do the best you can. You must change your student mindset from "Would doing A would get me a better grade" to the adult mindset "Is this really the best I can do within the time constraints I have or could I do better?". So you should focus on producing the best thesis document you can (within your time constraints)  regardless of how lenient the committee might be on judging it.


How to cite spreadsheets or other documents for in-line citations?

I'm not sure how strict are Harvard Publication Style guidelines, but I would use the following approach. Since the name of the organization in question is used twice in the reference, I would use the second mention to introduce its abbreviation and then use that abbreviation as the author keyword. This approach still retains the accuracy of the information, but, at the same time, solves the problem (inconvenience) of having to cite in-text a rather long phrase. Using your example:

[Reference]

  SBJ/MIAC (2015) Population by Age (5-Year Group and 3 Groups) and Sex
  (as of October 1 of Each Year) - Total population (from 1920 to 2000)
  [Microsoft Excel spreadsheet]. Tokyo: Statistics Bureau of Japan,
  Ministry of Internal Affairs and Communications (SBJ/MIAC). Available
  from:
  http://www.e-stat.go.jp/SG1/estat/ListE.do?bid=000000090004&cycode=0
  [Accessed: 27 November 2015]

[In-text citation]

  The above-mentioned trend is illustrated by the data, recently
  reported by Japan's national statistics agency (SBJ/MIAC,
  2015)...

Note: Relevant webpages and documents I've used for this answer: this document and this page (the ABS example there is IMHO incorrect - ABS is not defined, so I have fixed it in my answer).


It is not normal in UK biology PhDs for a student to be completely abandoned with no help; particularly not at the beginning. As you become more confident you will be able to take on new areas and new techniques with minimal advice, but I would never expect a student to dive into complicated, expensive and potentially dangerous experiments without so much as a protocol.

I would do the following:

Ask your supervisor straight up if he knows where a protocol might be found for the experiment, or whether he sees designing the protocol as part of the thesis.
Find others in your institution, but outside your lab that might be able to help.
Find an online protocol or protcol in a text book and specifically ask your supervisor if he thinks it is a good protocol and if he knows of anyone who can go through it with you.
If all else fails, a UK institution will almost always assign you a second supervisor or advisor: go speak to them.


Article submitted and clearly referee cannot understand basic premise-What to do?

I understand how you feel, but what you propose in solution 2 does not sound productive. I try to see (after the initial phase of being dissapointed and annoyed) the reviewer as a potential reader of that journal who is gracious enough to spent more time on your article than most readers will. Apparently, my article wasn't clear enough at a point, and that is something that needs to be fixed. It is easy to think something is too basic it needs no explaining, but there are a great many such basic facts; many more than anyone can remember... I suggest you take the same approach.


Is it normal I haven't met my supervisor yet?

First off, no - this is not okay or normal. Advisors should meet their advisees on a regular basis. I'd say every other week is the boundary of reasonable (unless of course there are other circumstances like sickness, parental leave, long vacation or sabbatical etc.).
While there are mitigating circumstances (this is 2020 after all), your advisor has a responsibility to you which they need to be reminded of. If they are unable to supervise you for whatever reason, it's still their responsibility to let you know so you can seek alternatives ASAP.
Tell him a series of times that you are available at, as well as deadlines you'd like to meet. Just describe the times you are free during this semester and see when you can schedule video calls. Your advisor might be unready or unprepared for remote advising, but again - welcome to 2020! It's awful in academia now.
To figure out deadlines, work backwards from your desirable date of graduation - in order to graduate at date A you need to submit thesis by B, for which you'll need a first draft by C etc. Then present this to your advisor in the correct chronological order.
Good luck!


Specifying a preprint is "submitted", *to a specific journal*

No, do not specify the journal that you have submitted to.

Anyone can submit a bad paper to a prestigious journal. The sole fact of submitting your paper to journal XY can not be used to signal or suggest a certain quality of the paper or the author.
If your paper is rejected by journal XY you are forced to update your publication list and are in fact publicly admitting and documenting that your paper has been rejected by journal XY.