Assessment of an IT-related extended abstract

Is it customary/obligatory to publish the source code for prototypes in academic papers/abstracts?

No. Most academic articles (in IT) do not include the code. Some rarely do have a link to a link where the code and source materials can be downloaded.

  Are scientific paper references not a requirement for an extended abstract and by some degree an indicator of the quality of the paper?

It depends on the reviewer. Some would look at the number of studies referenced to make sure that sufficient background research and literature was conducted (been through that one). Some may look closely at the quality of the references (although I haven't experienced this sort myself). Some only expect the relevant concepts too be attributed, even if only 3 or 4 items are referenced.

  How would you assess the abstract in terms of project execution, accurracy, tracability?

If the underlying novelty is focused so as to improve performance of an existing system, then a simple line about the increase in performance metric/accuracy with respect to the state id thee art will do. Statisticians are not to find of bare accuracy. There are many other measures for This, but a simple mean+_std. dev. ought to be a better alternative.

If the novelty lies in the application itself and not any performance measure, then this'd line would not be necessary. I'm not sure how the traceability aspect would come in an abstract.

  How would you interpret "code exchange not necessary"?

Sorry, but that's a question for your instructor.


Wordiness of paper titles in life and medical science journals

When I wrote my first paper, I read this book about scientific writing: "Scientific Writing = Thinking in Words" by David Lindsay.

The author of the book highlighted that article title should be as explicit on the content of the article as possible, as it is the first element any potential reader will read. As today the amount of available articles is growing faster, the skimming step in the article research is becoming more and more important and a good, self-explanatory title is therefore a key element in article "success".

As an example, the author strongly discourage the use of non-explicit title such as:

  XXX as an effect on YYY

and advice to use something more like:

  Increase in XXX induce a decrease in YYY

which directly tells the reader what is the article about and the what is its main finding.

In conclusion, do not be afraid of wordy title.


Optimal structure of cover letter for PhD application submitted directly to PI

I would say you are waiting too long to explain why you are interested in the research group. Your motivation for writing and taking up the faculty members' time should come much earlier in the message—I'd recommend no later than the second paragraph.

I'd also suggest that you might also want to consider sending the message to the Oberingenieur or Akademischer Rat of the faculty members' group; he or she may have a better idea of what vacancies are currently available.

Finally, "cold calling" does not get a high response rate; if there isn't an active opening, most potential advisors won't really respond unless they have to.


Statement of Interest for Ph.D. admissions

The primary difference between a statement of interest (or purpose) and a thesis proposal is the specificity. A thesis proposal outlines a specific project to be pursued during the thesis research, and will usually be written at some point during the process. However, in many cases, this is done after the graduate student has been accepted and joined a particular research group, rather than before admission has been granted. When asked for at the admission stage, it's usually in cases where the assignment to a particular research advisor is done at the outset of the doctoral program.

A statement of interest, on the other hand, simply details the kinds of problems or research areas a given student would like to pursue as a graduate student. This is usually asked for in admission cases where the decision is being made at the departmental level, rather than the individual faculty member level. A student is not specifically committing to a particular project at this stage—nor does the department necessarily want such a commitment.


How can I find out if someone really holds a doctoral degree?

You could ask the candidate to provide written consent for the university to verify his degree. If he refuses to allow verification of his CV, then he's probably not someone you want to hire, regardless of whether his doctoral degree is legitimate or not.


If an IRB approved a study, does it need to be mentioned in the papers that results from the study?

It depends on the journal. For example, the Journal of Multicultural Counseling and Development instructions for authors state:

  appropriate institutional review board (IRB) review and approval should accompany all studies involving human
  participants or research material derived from human participants. This information should be clearly stated in
  the Method section of the manuscript. In addition, the manner in which informed consent was obtained from
  the study participants (i.e., oral, written, online/electronic) should also be stated in the Method section. If the
  study was exempted from IRB approval, that information should be indicated in the Method section. Failure
  to provide this information in the manuscript may result in the manuscript being returned without review.

Nature takes a different approach and does not require the IRB approval to be mentioned in the text (and may not even allow it), but does provide a checklist, that the author must complete and is provide to reviewers, that deals with IRB approval.


Fast is great! Just be warned that it means editors will like you and send you more requests so you’ll have to learn to say no.  If you also say “no” quickly and suggest alternatives, then you’ll still leave a good impression with the editors.


Are special issues of a journal more highly cited?

It might be pertinent to consider that the journal editors will undoubtedly commission their special issues in subjects that they consider to be 'hot topics', with the aim of boosting overall citations and of establishing their journals in those areas. So there's an element of selection going on even before you consider whether a community might respond more favourably to a paper just because it's in a special issue.


Affiliation when I have already resigned and am currently unemployed

I would still use the affiliation of the institution which paid you during the time you worked on this paper. If however, the majority of the work was done after you resigned, I see no problem in using "Independent Researcher" or "Freelance".

I faced this problem when switching institutions. Typically papers published during the transition were written by the old institution and paid for by the new. I use the new affiliation as my first and include the old as the second affiliation.


My potential future PhD supervisor ask me to peer review a paper

Maybe it's a matter of question formulation, but I find this to be a very peculiar request and would be equally confused as you seem to be even if I wasn't busy with other stuff.

Specifically, you're not qualified to review a paper, yet.

If he's asking your analytical opinion on a paper, kind of like a journal club style dissection of the content, then sure I guess that's no big deal. But if you are given a manuscript, written by someone else and submitted to a journal, I find this request unrealistic and even unethical.

Also, in a way disagreeing with the previous answers here, I don't think it's a reasonable request even if you were given the article in a more relaxed, journal club-like format. Because you are supposed to learn to read and understand the scientific literature, it's part of your training as a PhD student. To use that during the recruitment process, as a test is a bit unfair in my eyes.

  that was my first feeling actually, that he was assigning me some of
  his work while I am still in the application phase. The paper is
  anonymous and I am asked to peer review it for a journal publication.

The above alone, would even deter me from considering to start there. I think it might be worth thinking about what kind of work environment you want to get yourself into for the coming 3-X years of your life.

But again, it's possible that I misunderstand something in the OP. Just my two cents...


Responsibility to new PhD students regarding bad environments

I see no ethical quandary whatsoever in revealing your own negative experience / suspicions of systemic problems within an academic department.  It would be easier to argue that some ethical obligation cuts in the other direction: i.e.,
people should be informed about what they're getting into.

You don't discuss your current status in the academic community. Of course complaining about people who are in a network of your peers and superiors could have some risk to you.  (That's basically always the case.)  But that's not an ethical concern.  The need to be "loyal" seems a bit misplaced here.  Yes, loyalty is good, but it cuts both ways.  Some people / an institution had a chance to treat you well, and apparently they really blew it.  They can't reasonably ask you to deny or minimize it.

I will say though that complaining is tricky.  The problem with people who are bitter enough to complain is that...well, they sound bitter.  In particular, your description of this nameless department sounds a bit cartoonishly bad to me: I couldn't recognize it in the context of any of the academic skullduggery I have seen in real life.  For one thing, you almost seem to be saying that the
department faculty takes an active interest in crushing the dreams of students and postdocs.  To be honest, I am skeptical: crushing students' dreams can be hard work, and we are terribly busy.  For another, you imply that this department is viewed as exemplary and the terrible treatment and terrible placement of graduate students is totally ignored by your academic community.  Really?  In my circles (mathematics, US) departments are ranked in large part on how how well they service their graduate students: percentage of students who get through, time to degree, good placements.  Some places have a reputation for being "nicer" than others, but even a "not nice" top department does a better job of placing its students than a mediocre one.  Or so it seems to me, anyway.

So if you really want to complain effectively, I suggest you take the time to make your complaints factually based.  Can you assemble (in a solid, honest way) statistics to show that the department you talk about is bad for students?  People will take that a lot more seriously.


How is publishing in JoVE (a "video journal") perceived?

Based on our work with them, it seems to be a high quality publication. We published a JoVE article last year and several of the protocols we use in the lab are adapted from other JoVE articles. So it seems effective in its mission. The video format really works for certain protocols, and it may make it easier for people to reproduce your work (thereby getting you more citations).

That said, there is the price tag to consider, and the editorial process is extensive and time consuming (you write an article, then go through normal peer review, then work with them to turn it into a screenplay, then get everyone together with the videographer they provide, etc.). So I would say that if your method does not specifically benefit from the video format, there isn't an advantage over a conventional methods journal.

As far as how it's received, I haven't noticed any differences from any other small journal.


How to formulate good problem statements in CS research

Have you tried the following:

  Turabian, Kate L. A Manual for Writers. Chicago: University of
  Chicago, 1987. Print.

It's a very nice book and is applicable to CS (unlike many other research methodology books).


Shifting to unrelated field after postdoc? Neurobiology to linguistics

Disclaimer: I know nothing about research in neuroscience or linguistics, so my answer is about a general person who finished a PhD in topic X and wants to switch to topic Y.
I would go for options 1 or 2. Option 3 is generally not a great idea. A PhD means spending several years on starvation wages, and a good chunk of that would be spent rehashing things you already know, like research methodology, how to explore data and so on. A postdoc allows you to explore whether your true passion really is linguistics. Treat the postdoc as you would a PhD - you have two years to write a thesis (well, not really write a thesis, but get enough results to fill one). Postdocs are often given much more freedom to explore their interests so you could build your knowledge on the topic while not having to do like a decade of PhD studies.
I would suggest a fourth option: would you be able to get a faculty position in neuroscience and then start exploring your dream at your own pace? Faculty members are masters of their own fate (to an extent, certainly more than PhD and postdocs). You can decide that you want to change your focus, and as a faculty member you may actually find it much easier to do so.


What tone to use when talking about oneself in statement of purpose?

There is a difficult tension to balance here: one the one hand, you don't want to hide your light under a bushel.  On the other hand, the people reading the application will have seen a lot, and will probably be pretty good at detecting somebody puffing themselves up and will not be impressed.

Two useful strategies for approaching this:

Follow the writing strategy of "show, don't tell".  If you've done something awesome, don't tell that you were awesome: "I made important contributions to the study of newts."
Instead, show the thing that you've done: "I studied newts under Prof. Coolness as a junior, and our paper on how newts prefer turn clockwise under the full moon was recently accepted to the Journal of Arbitrary Herpetology."  Give the reader enough evidence that they can conclude awesomeness for themselves.
Once you've got a draft written, ask a trusted professor to look at it and check whether you've left anything important out or are overinflating yourself.


This really depends on the country, the institute, and its specific rules. If you're concerned it would be worth speaking to the TA about it as they would be 1) more aware of the rules and 2) probably more likely to suffer if it goes wrong.

I know in my institution in England, I was told when training to be a TA that it's fine as long as you're not directly marking their work. The advice was you can go to the course leader and say 'I can't mark the work of student X because we're dating'. But I've heard in the US generally rules are a bit stricter. And I'm sure rules differ across the UK too.

I'd say in any case, transparency is the best option here. If you try to keep it secret to avoid consequences, the consequences may end up more severe.


Alphabetical Order for Authors in Computer Science

In theoretical CS, alphabetical order is the norm - see the relevant wikipedia entry.


Honesty of advisor when determining an adequate research project for thesis

I would like to start by reinstating an already made comment: it is hard for anybody to look at this kind of mild conflicts without biases. The student who replaced you certainly had to replicate some of the work you have done, and most likely has been exploring and wandering in other research direction.

That being said...welcome to the academic world. Not all advisors are able to mediate their own best interest, with their students/postdocs best interests. Let me be more precise, and talk in economic behavioural terms: it is always the advisor's best interest to get as much work as possible from any person working for him. He/she lives in a highly competitive world battling with few resources to stay ahead of the competition. However, any supervisor needs to balance his/her need to get the most work out of his/her research group, with the need to build a positive reputation in offering a working environment that compromises reasonably between being treated fairly, and having the opportunity to grow in a career while working hard. Failure to do so will cut his/her stream of future students/postdocs into his/her group.

It seems like your advisor did not quite strike that balance - especially about the unpaid work. Unfortunately, that too is all quite common, especially in universities/countries where funds are lower than in the average US institution.
Just take it as a learning experience, and try to learn the most out of it.


In principle, age discrimination is illegal in the US and various other countries in the world.

In practice, there are a lot of apparently legal ways to get around age discrimination (e.g. discriminating based on experience, work history) and I have heard of first-hand accounts of supposedly illegal discrimination at various institutions throughout the world.  There are a number of employment lawyers who go around arguing these kinds of cases.

However, at least in the US, being good and well-known is an inoculation against much of this discrimination.  Ultimately, if you are successful and active, at any age, you will be hirable.


Who evaluates Marie Curie Intra-European Fellowship proposals?

You will find details on the evaluation process in the Guide for Applicants. The evaluators are experts (=researchers) in the field. They will be matched to the proposal according to their profile and to the abstract and keywords. They will for sure be in the general research area, but might not be in the exact same field of the proposal. It is (at least, officially) not possible to find out who evaluated the proposal afterwards, but you can find a list of former evaluators here:

http://cordis.europa.eu/fp7/experts_en.html


Do peer reviewers generally care about alphabetical order of variables in a paper?

Let a be the number of math-heavy papers I have read that use an alphabetical order to introduce all their variables.  Let b be the total number of math-heavy papers I have read.  Let c = b - a be the number of math-heavy papers I have read that did not use said ordering.  Then c = b.


Applying for postdocs / lectureships - sorting bad advice from good (UK, mathematics)

My advice would be:

write more applications

Academic job hunt is a gamble. Boosting your CV does improve your chances, but it is still a gamble. There is no security in this game and no guaranteed strategies. Places which seem to be a 100% match can reject you without an interview, and places where you barely meet the role specification can shortlist you. There are often more criteria than are written in the job specification and there are often several competing agendas each Department wants to fulfil.

A few months is not enough to publish your  best piece (review process may take years). Speaking at conferences may help, but realistically even if a professor will love your work and would like to hire you, they may not be able to do it immediately, unless they have funds to spare (very rare and unlikely situation in the UK). Organising a conference takes more than a year.

tl;dr:  polish your CV and application pack, submit more job applications and (if you have time) prepare a Fellowship application, e.g. to EPSRC


Are all math majors expected to get a perfect score on quantitative reasoning?

At Texas A&M, we typically admit graduate student applicants with quantitative GRE scores down to somewhere between 160 and 165. So your 167 is totally fine, in fact I would say it's in the top 1/2 of those we accept. No need to worry.


Time between on campus interview and tenure track job offer

Unfortunately, there is no clear and well-bounded answer.  In general, however, you should anticipate the time to be on the order of months.

To understand why, consider these typical components of process:

After your interview, a number of other candidates may be coming to interview.
Once all of the candidates interview, the faculty needs to decide who they want to hire. This may happen in multiple stages (e.g., first a search committee triages down to the top candidates, then the full department chooses between them).
A formal offer is prepared for the top candidate and negotiated amongst the department and any other involved university organizations (e.g., HR, deans, centers, etc.).
The candidate has some weeks to decide whether to accept the offer, possibly including more negotiations and revisions to the offer.
If the candidate says no, things begin again with offer preparation, negotiation, and decision for the next candidate.

Every one of these steps is likely to take on the order of weeks, so you can see how it can easily add up to multiple months.


Does department receive funding for each PhD candidate

This makes me wonder whether the department receives money for each PhD candidate to finance the department, so that the PhD candidates number and years spent there are of essence.

(Context: I'm familiar and have first-hand experience with the German system.) There is no direct flow of money for each PhD candidate. However, the number of graduated PhD students is seen as a performance metric for both departments and professors, and professors might receive a certain salary bonus for scoring well on that metric.
A rational reason for keeping around the candidates longer than necessary might be that she wants to squeeze more work out of them, including papers. There might also be other, non-rational reasons.

Is there anything to be done to get out of such situation?

Walk away. The advisor seems to have little to offer except for the dangling carrot of an eventual PhD degree; however, for a person that values their time as an asset that could be used for other things, that's probably not worth it.


Is it possible to find out which author got the most citations in a specific scientific discipline?

"Most cited papers" in a given field/period is fairly easy through something like Web of Knowledge; it's a few clicks to find out that both Scopus and Web of Knowledge list this as the most cited paper in chemistry in 2014, for example. (Tellingly, they only agree on three of the top five...)

Doing this for authors is more challenging, though - the Google Scholar registered authors method suggested above is effectively an opt-in database and so there's no way of telling who's not in it. Scopus has fairly good author-citation indexing but I'm not sure if it's set up to answer this specific question.

A couple of studies with similar questions:

Abramo et al looks at a defined set of researchers (all Italian academics) and shows a way to identify the most highly cited authors within them - basically just WoK citation counts. Robust but tedious, and you probably don't want to start with a list of "all astrophysicists"...

Another approach is to pick the most highly cited articles in your field (assuming that the bulk of citations are in these, not the long tail) and look at the authors of those papers. See, eg, Choi et al, which is "the most cited authors of the 250 top papers in the field", or Uthman et al, which looks at the authors of the top hundred medical reviews.

You could combine these - pull out, say, the fifty most cited papers, look at their authors, and do full citation counts on these using WoK. It seems likely that the most cited authors overall will be an author on one or more of the top papers.


Clear colormap for figures when printed?

UPDATE:2

Use perceptually uniform color-maps when possible. I suggest to use this nice toolbox in Matlab (colorBrewer) or to use the new perceptually uniform colormaps from python matplotlib (also available in Matlab).

Matplotlib's new colormaps look like this:

UPDATE:

If you use Matlab, and you have access to Matlab R2014b or newer, use the default colormap: parula. They designed it so it is a good colormap, not only for b&w printing but also for correct data visualization (i.e. it doesn't add features due to the choice of colour, as jet does)

Explanation: http://blogs.mathworks.com/steve/2014/10/20/a-new-colormap-for-matlab-part-2-troubles-with-rainbows/

Parula looks like this:

Original answer

Use the "hot" colormap. If you use Matlab this is one of the built colormaps. I believe than in numpy and other languages you also have this colormap included.

You can see in the image below, how the commonly used "jet" , the "hot" and a "gray" colormap are seen in grayscale. It can be seen that the "hot" colormap is quite good both in colour and grayscale.


How not to be like a rolling stone in research?

As a young researcher who is just trying to find his research path which I want to stay in, how should I make sure that this is the topic I want to do research in my whole academic life?

You can't. The world will progress, funding will change and your interests are likely to develop as well.

  How should I stop my interest to learn new topics disturb my research productivity in future?

There is inherent trade-off between focused work on a predefined topic and an open-ended mind-wandering. The current climate in academia seems to focus on productivity, which (in my opinion *) is not good for any non-incremental progress.

But as long as you find enough time to publish good papers, I wouldn't bother about not being focused enough (publishing requires you to focus, whether you like or not).

  How should I overcome my desire to do research in many research fields and work on different research topics and stick to just one or two research fields and read papers and books only related to the research topic which I want to work on in long period of time?

Don't take a narrow (and, I think, common) definition of productivity as sticking to a narrow field and never wandering around. If you read a research-level book on another field (not just  - its first chapter) then it is not shallow.

* Piotr Migdał, There are no projects like side projects (on Albert Einstein, John Bell and John Carmack)


How to test (admitted) grad students before hiring them in your lab

What tricks/procedures do you use?
I am especially looking forward to King Solomon's cutting the baby in half type of creative solutions. Perhaps PI can ask the student to do an impossible task and see how long it takes before the student says he/she thinks it is impossible.

You're contemplating starting out a long-term, intense professional relationship with this person. "Tricks" like this are dishonest. Dishonesty is not a good way to begin such a relationship.
The situation is similar to an ordinary job interview. In a job interview, it's not just the employer who is judging the candidate. The candidate is also judging whether the employer is someone they'd want to work for. Manipulative interview techniques are a flashing red light telling the candidate that this is not an employer who respects his employees.
Another thing that a job candidate is looking for is an employer who will support him in his long-term professional growth, rather than treating him as a labor commodity who needs to be productive from day one. This holds even more for a student getting started in a PhD program; the reason universities claim that grad students are not employees is that they're supposed to be focused on learning, not on acting as cheap labor.
In the usual case where the student does a rotation in your group, that's the opportunity for each of you to see if you're a good fit for the other. It's meant to be an experience that helps the student to learn and grow, not one that produces a lot of research. Part of what the university is paying you to do is to provide these opportunities for these students to learn and grow. If, by the end of the rotation, the student has shown a lack of aptitude, then you've provided the service you're being paid to provide.


How to use results/ideas from a paper I reviewed?

You can't ethically do anything based on ideas from this paper until it is made public (by the authors as a preprint, or by the publisher).  In particular, before that point you can't refer to the paper, you can't use the ideas without referring to it, you can't publish or otherwise disseminate results based on it, and you can't discuss it with other people, including your collaborators.  It can be really frustrating to know something important and be unable to tell anyone else for the time being, but there's no way around it ethically.

The reason is that submitting a paper for publication is not considered to release it for other use or dissemination until it is actually published.  The people involved in processing and evaluating it (most notably the editors and reviewers) have an ethical obligation to keep all information about the submission strictly confidential and not to use it to gain any personal advantage.  Once it is published of course it can be treated the same as any other paper, and in the meantime the authors can choose to make information publicly available via preprints or talks (in which case others can follow up on this information as appropriate), but nobody else is authorized to release any information before publication beyond what the authors have chosen to share, or to use it for any purpose other than reviewing the paper.  Otherwise it has the same ethical status as using material you stole off the authors' desks.

There's no reason why the research community has to work this way in principle, but it's the system that has evolved over time.  (Note that as recently as the 1930's, famous physicists were not all in agreement as to how peer review should work.)  It's possible that in the future we will move to systems such as submitting for publication only after releasing a preprint.  That seems to be the trend in some fields, but we haven't yet made a full transition if we ever will, and the community's ethical principles still offer protection to authors who choose not to distribute their paper before publication.

Nobody signs a non-disclosure agreement when reviewing a paper, but the ethical principles are well established.  Deliberately violating them would be a serious form of misconduct, which could easily be career-ending if it was more than a minor or technical violation.

Pete L. Clark asks in the comments whether referees are allowed to prepare follow-up papers, as long as they don't distribute them before the original paper becomes public.  I.e., does the "you can't ethically do anything based on ideas from this paper" really mean you can't do anything, or just that you can't disseminate anything yet?  (Let's assume it's a single-authored paper that is not discussed with anyone else in advance.)  My interpretation is that nobody can stop you from thinking a little, and you may not even be able to stop yourself, but actively working on and writing a paper of your own would be abusing your position as referee.  There probably isn't a consensus as to exactly where the line is for what's strictly forbidden, but either side of the line could still look terrible.  If you want to publish work you began thinking about as a referee, I'd strongly recommend against doing it so quickly that's it clear you had to have known about the original paper in advance.


Is "get passing grades and follow voraciously your curiosity on the side" a good strategy for graduate school?

The passage you have shared refers specifically to a baccalaureate degree:

  The edge, I realized, isn’t in the package of what was on the official program of the baccalaureate... but exactly what lay outside it.

In a PhD, coursework takes a backseat to research. In research, there is no such thing as "get passing grades"; there is no meaningful threshold at which your research is considered acceptable, only a continuum of poor to exceptional. At the end of your PhD, your prospects on the job market (especially the academic job market) and the impact you have made with your work depend on how close you are to the "exceptional" end of that range, not just having achieved some minimum requirements and earned a piece of paper that says you have a degree.

Furthermore, PhD-level research requires a level of depth and focus that is not typically present at the undergraduate level.

That's not to say you can't have broad interests, and you can even leverage your broader interests to improve the quality of the work you do in your primary field. But a strategy of planning to undertake a PhD and put minimum effort into your PhD research while doing other things on the side is not a winning strategy for most people. Instead, you should try to use your curiosity for your PhD research. (Also see: Can I slack off and get a PhD?)

In fact, later in that same chapter, Taleb describes how his curiosity and drive to understand probability led him to specialize in that and focus on that to the exclusion of everything else:

  When, at Wharton, I discovered that I wanted to specialize in a profession linked to probability and rare events, a probability and randomness obsession took control of my mind. I also smelled some flaws with statistical stuff that the professor could not explain, brushing them away—it was what the professor was brushing away that had to be the meat. I realized that there was a fraud somewhere, that “six sigma” events
  (measures of very rare events) were grossly miscomputed and we had no basis for their computation, but I could not articulate my realization clearly, and was getting humiliated by people who started smoking me with complicated math. I saw the limits of probability in front of me, clear as crystal, but could not find the words to express the point. So I went to the bookstore and ordered (there was no Web at the time) almost
  every book with “probability” or “stochastic” in its title. I read nothing else for a couple of years, no course material, no newspaper, no literature, nothing. I read them in bed, jumping from one book to the next when stuck with something I did not get immediately or felt ever so slightly bored. And I kept ordering those books. I was hungry to go deeper into the problem of small probabilities. It was effortless. That was
  my best investment—risk turned out to be the topic I know the best. Five years later I was set for life and now I am making a research career out of various aspects of small probability events.


On the other hand, it seems really awkward to demand that someone acknowledge me - it seems like a faux pas even to admit that I noticed.

Don't be embarrassed to ask to be credited for your work. If you're not willing to stand up for yourself as a professional, others may not do it for you!

An acknowledgment is entirely appropriate to recognize your contributions, which are technically useful, but not necessarily rising to the level where it is directly tied in to the goal of the final paper. To ask for it, I would ask the first author:

  I think my bug fixes helped you carry out the research. Do you think you could mention my contribution in the acknowledgments of your new paper?

This makes it clear what you want and why you think it's useful. An acknowledgment is "free" in the sense that it doesn't dilute the author list, and there's no logical reason why you couldn't be accommodated.


It sounds like you angry that the other students were "cheating" and got admitted to the PhD program while you were honest and were passed over. To add insult to injury, the professors seem not to care. Though you don't seem to have a clear goal in mind, I would suggest that it is to (a) achieve justice, and (b) not be handicapped in your final exams.

To the first goal, you should certainly report your experiences to the graduate director or another competent person. Even without proof, if they hear enough rumors, they will investigate, and things may be better in future years.

Without proof, they are unlikely to do much. There is so much reasonable doubt. In particular, are you sure that the other students are  blindly copying solutions? At the graduate level, using solutions when you get stuck or to check your work may be appropriate (and student collaboration is encouraged)

Your claims about the exams are more worrying. Are you sure that the other students have exams? Are you sure that the professor knows this?

If the professor might not know, it is fair to tell him.
Without proof, the professor may not believe you (or may not care) -- as you say, he may just assume you are bitter and looking for someone to blame.
You can provide proof by naming names. But you seem not to want to do this, and I don't blame you -- this could open a whole can of worms (i.e., questions about your integrity for not having voiced your concerns sooner).


In my mind, I see the Linux source code as a single bibliography entry (possibly with its official kernel.org repository as the source URL). You can refer to the different files in the text as \cite[Version~4.1, \texttt{drivers/android/binder.c}, Line~18]{Linux}.

EDIT: suggested kernel.org instead of github, as pointed out by bdsl, sebleblanc and Bruno.


Background: In Australia, PhD theses are examined by at least two external examiners; they must be more than an arms length away from the student or supervisors; e.g., no previous collaboration or have worked recently at the same university. Critically, they must be internationally recognized experts in the student's subject matter.  The examiner reports are then deliberated upon by a committee with members drawn from across the university; this means the award of a degree is not done at the school or faculty level.

The examiners serve as independent auditors of the quality of an Australian PhD thesis.  They certify/vouch that an Australian thesis is at an international level.  They do this by presenting a report that justifies that a thesis contains 'significant contributions that extend the state-of-the-art'.

To achieve the said claim for an oral exam, Australian universities will need to either hold video conferences or fly examiners in.  The former is an admin nightmare; e.g., different time zones, getting all involved people to attend/agree, etc.  The latter is too expense.    Now imagine doing the former or latter for hundreds of theses every year.

Having said that, at my university, oral defense is an option that can be requested by an examiner.  This is only for very exceptional cases and rarely granted.


One by one:

In the past, when journals were published in paper, the journal would collect a certain number of papers / pages and print them all together to make an issue. It's no different from e.g. reading a magazine or newspaper, "issue X". Each year the issues are collected into a volume. The practice has persisted. When you check a reference you might see, journal X volume Y issue Z, which tells the reader where to search for the paper referenced.
Impact factor is a metric for how many citations the journal's papers get. It's calculated by number of citations received in two years divided by the number of articles published (with some subtle details). In general the higher the impact factor is the more prestigious the journal.
You don't have to submit to an open access journal. Many subscription-based journals can still accept open access papers for a fee (the so-called "hybrid model"). You also don't have to wait for a call for papers - journals are usually always looking for papers; the call for papers is when they have a specific topic they want to focus on.
If your paper is within the scope of the journal, the journal should consider it. Whether or not the latest issue is relevant is not important.
Nothing in particular - your paper gets considered as normal.

It sounds like you are unsure what open access is as well. Open access is when the author pays the publisher to publish the paper, and the publisher makes the paper free to read and access. Subscription is when the author does not pay the publisher, but the paper is behind a paywall and any reader must pay the publisher to access them.

What to do: submit your paper to a relevant journal. You don't have to wait for an invitation or call for papers. If you are submitting to an open access journal, check with your supervisor or librarian if there are funds to pay for the article processing fee. This varies from journal to journal and publisher to publisher. I checked the EURASIP Journal on Wireless Communications and Networking's charges for you: £905/$1420/€1155 for each article accepted for publication.

Good luck!


What does it indicate if a professor from other departments is included in applied math department?

Affiliate faculty are common in many university departments. This indicates faculty who have a departmental home (faculty line, voting rights, tenure and promotion line, office space) but for a variety of reasons are given courtesy appointments (sometimes called in the USA as 0 FTE appointments) in another department. This may be because they teach a crosslisted course or occasionally sit on doctoral committees of the other department, or occasionally just for the academic lulz (ie, they requested an affiliation and there was no reason to deny it).

Affiliate faculty rarely occasionally (depending on discipline and university) serve as chairs of doctoral committees and similarly are rarely/occasionally (depending on discipline) given students in that department to supervise. Their ability though to sit as members on committees is useful if you were to want to do a project in geophysics (in this case) but otherwise you can ignore them.

Note that this is different from faculty with dual appointments where their faculty line is split (0.5 FTE in one department, 0.5 in another). They have voting and advisory rights in both departments.

FTE = Full-Time Equivalent, the essential counting unit of faculty lines.
A department with two full-time faculty and two joint-appointments would
have 2*1 FTE + 2 * 0.5 FTE = 3 FTE

TL;DR: Don't worry about affiliate faculty. Focus on the core faculty and their strengths when making decisions.


How to cite own unpublished work in text and reference?

When citing unpublished work that is still under review, it's best to leave out the potential publication venue, saying only:

  Authors, "Title," under review.

(or the appropriate equivalent in the citation style that you are using.  The reason for this is that venue doesn't matter until they decide to accept your paper: you can get your most terrible work rejected from as fancy a journal as you like.

When possible, it is indeed appropriate and useful to provide the unpublished material as supplementary material for the reviewers.  You need not worry about copyright for this, however: there is a distinction between "supplementary to be published paper" and "supplementary material for review only," and you just need to make sure that the under-review material is labelled as being for purposes of review only.


In choosing between MD-PhD and PhD, how should I factor in the expected age at which I'll start my career as a professor?

According to the NSF's report, the median age of a PhD recipient is 31.6 years old. That means you'll only be a little older than a typical graduate.

This age shouldn't be shocking considering in the US it often takes 10 or more years of college to obtain a PhD, so that means that most people will be late 20s or early 30s if they never went to industry or didn't graduate early.


Professor Matters for Independent Study?

In some ways everything matters, but probably not as much as you think. Probably not enough to worry much about it. A lot of things will help you, but working hard and gaining skills is pretty high up the list.

I'd suggest that rather than trying to game the system, find courses (including independent studies) that will make you well educated and well rounded. There are fine teachers without a huge reputation. There are terrible teachers with a great reputation. There are all of the other combinations as well.

Study something meaningful with someone who can help you learn it well. Work hard at it. The rest will follow.


How to find book titles in other languages?

Arguably the most complete resource would be the UNESCO's Index Translationum, a database of translation from 1979 onward.

There you should be able to search more easily, selecting desired language and inputting a keyword from the title or an author.

There is also a list of references hosted by Michigan State University's Library Guides, which offers a few hard-copy guides for consultation, however these are more restricted by field (mostly having to do with works of literature).


Paper published in peer-reviewed student journal that appears to have shut down. How should I present evidence of article publication?

In the (rare) event of you requiring proof of your publication, you ought to still hold the email communications that connects to the Publisher as evidence; especially the 'acceptance for publication' and 'confirmation of publication' letters.

Your issue volume and number look like it's a relatively new journal to which you've submitted your paper. I sure hope that it isn't a predatory one.


Am I being taken advantage of by working on a committee member's research with no payoff?

Yes, you should discuss the issue of authorship. From this description, we can't tell you whether or not you are being taken advantage of. In general, whether authorship is appropriate depends on the intellectual content of your contribution.

To discuss the issue, start by saying "I'd like to discuss the issue of authorship on this project." If you'd like to be direct, you could then say, "I have committed a lot of time to this project. I am under the impression that my work is substantial enough that I might qualify as an author on papers arising out of this project. Under what circumstances would you consider including me as an author?"

If you'd like to be less direct, you could instead ask several questions about your committee members' philosophy on authorship. "What sort of contributions do you believe qualify for authorship on a project like the one we are working on together?"

If you don't like the answer (the person refuses to make you an author), then you need to set some boundaries in a professional manner. "I'd like to continue to contribute to this project. However, since there is not a possibility of authorship here, I am sure that you understand I need to prioritize my other work. Going forward, I can commit to X. If you need more help than this, I think we should revisit ways I could be compensated or qualify as an author."


How should I cite a specific section of the LabVIEW online documentation?

It's generally best to provide the location of the cited material in such a way that, should a reader need to find it, they can do so without searching extensively. The pages you are citing are in two different locations (the first is a tutorial on the site and the second is essentially a section from the 2012 version of a manual) on the LabVIEW site so it likely makes the most sense to cite them separately from each other. There's always the potential issue of resources changing location and links breaking, so include other identifying details where possible, like page names and edition dates.


Is it inappropriate to use school-provided remote learning tools to pursue friendship or relationship with another student?

For already established contacts, there should not be any problem. Same when you ask a group of known and new people (e.g. the general group chat), whether they want to do something together (which might not be the best idea at the moment, but I hope you get what I mean).
Contacting specific people that are not your friends might be a different story, especially if your approach might not be desired. If you go this way I would be very careful in how you are approaching someone, especially if it is, or can be perceived as such, of romantic nature. One way to go could be to start out with asking if the other person is okay with being contacted by you for private matters at all in this system.
However, I would suggest to try social media instead. Or ask common friends/acquaintances for a contact - the way we did it before social media existed. Again, of course, nice and respectful.


A high quality contribution but an annoying error is present in my published article

It is probably best to do all of that. Contact the editor and ask if a correction can be published (letters to editor, ...). Put out a corrected version somewhere visible.

But also, don't obsess over it. Perfection is rarely attainable in an imperfect world with imperfect humans.

The sort of error you mention is very common, actually. Once you write something it is difficult for you to read it as incorrect. Often your mind "reads" what you think is supposed to be on the page rather than what is actually there. It is notoriously difficult for people to proofread their own work.

Ideally, the review process should have caught the inconsistency, but since it wasn't caught, others glossed over it also as immaterial to what your arguments are.


If I don't participate in research in first couple of years of PhD , how much am I losing?

I think it's better to be involved in research from the beginning of a PhD program, but I've seen plenty of programs designed to discourage starting research until the student has passed the qualifying exams. Both models can lead to good PhDs and good careers afterward. You appear to be in the enviable position, assuming you can sustain it, of being able to save a substantial portion of the salary from your day job so that when it comes time to start some research, you can do so with your own funding. If the project goes well, and you are good at research, you may be able to complete your dissertation more quickly than someone who has to work on a funded grant which has deliverables other than your thesis.


Estimating postdoc salary with "30% ruling" in the Netherlands and is postdoc a "scientific" position?

Normally PhDs and Postdocs from abroad would be considered for the 30% ruling, simply increasing your net salary by adding 30% of your gross salary to the net salary. Concerning the salary, normally it would be around 3.1k I have colleagues who are postdocs and their salary is in that range. HR can help you in estimating the net salary and after your friend employee, HR will handle the process of 30% Ruling after being accepted by the municipality.

  Dutch tax legislation provides a special facility for employees attracted from abroad who possess a special expertise that is scarce or cannot be found on the Dutch job market: the 30% ruling. Under this ruling, the employer can provide up to a maximum of 30% of the gross salary to the employee as a tax-free cost allowance`

For more details:https://www.utwente.nl/en/products-services/product/p339189/30-ruling#introduction

I hope that would be helpful.


How handicapped am I in graduate admissions if I graduated from a lower tier university?

You don't mention what field you're in. At least in the social sciences at my R1, we look at various factors. The admissions committee knows that people have to choose the college that they went to for various reasons other than just academic excellence.

One of the factors that I look at is trajectory. Someone who went to a public high school, then a community college, and then transferred to a public university, with perhaps middling grades the first year but then quickly ramps up to stellar grades by the time they graduate is very interesting to me -- much more than someone who got all As at a good school but doesn't seem like they pushed themselves very hard.

With the portfolio that you describe for yourself, I'd say you wouldn't be eliminated in the first round, but you'd struggle in the second and third rounds to stand out. How you stand out is up to you. I'd work on a stellar statement of purpose -- one that strongly articulates why you want to go to graduate school to study what you want to study.

Again, this is in the social sciences at my school (a large private R1), your mileage may vary.

Part of this is because brilliance by itself isn't enough for grad school in the social sciences. Perseverance and autonomy and the ability to get knocked down and get back up are also critical.


Statistics on readership and posting habits for academic blogs

I think it's interesting to consider the relative value to society of blog posts relative to more traditional forms of content distribution, such as book chapters, text books, journal articles and so forth.

Obtaining Benchmark statistics

RSS counts: Many blogs, particularly popular ones, show their RSS subscriber count. You can use the Explore Search feature in Google Reader to search for blogs you know. This returns the number of Google Reader subscribers. This is less than the total reader count, but it can give you a rough ball park.
Page views: Some blogs occasionally post their site statistics. Alexa can provide a very rough estimate of the popularity of a site.
Comments: It is straight forward to look at other blogs to get a sense of how many comments they typically get.

My rough rules of thumb

I've been blogging since 2008 and have kept an eye on RSS feeds and page views over timeon my own blog. I've also picked up information from other blogs that I follow.
My main observations are that it takes time to produce content, get indexed by Google, obtain RSS subscribers and so on. These would be my rough benchmarks for academic blogging. In the fields that interest me (e.g., psychology, statistics, R) I can think of specific blogs that fall in to one or other of these categories. This helps to inform the benchmark. Anyway, these are just my casual rules of thumb; of course, they aren't anything definitive.

RSS subscribers:

0 to 10: Not popular
10 to 100: Just getting started
100 to 500: Moderate levels of popularity
500 to 1000: Relatively popular
1000 to 10,000: Popular Blog
10,000+: Superstar blog

Annual Page Views

0 to 1,000: Not popular
1,000 to 10,000: Just getting started
10,000 to 50,000: Moderate levels of popularity
50,000 to 300,000: Relatively popular
300,000 to 2,000,000: Popular Blog
2,000,000+: Superstar blog

What does a page view mean

It is a little difficult to know what a page view means in terms of achieving broader blogging goals. Only a proportion of page views correspond to a person reading the entirety of the page. And only a proportion of those page views have any meaningful impact on the reader. In order to get a sense of what these proportions might be, I reflect on my own browsing. For example, I might be searching to diagnose a software error, do a tutorial on something, or get a review of a product. It might take a few search results to find what I'm looking for. That said, perhaps something between 1 in 10 and 1 in 2 search results provide useful results.

In summary, even if only 1 in 20 pageviews helped someone in some meaningful way, if you're getting a hundred thousand page views per year, that's still 5,000 instances of people being helped.


Bonus Quizzes to entice students to read their syllabus?

I'd avoid setting summative assessments (i.e. for course credit) on topics other than the subject material you expect the students to learn. Doing so might come back to bite you, even if you keep the relative contribution to a final grade as low as you are suggesting.

Perhaps you could spend half of your first lecture rhetorically asking the sort of frequently asked questions that get your goat, while at the same time navigating your course webpage, to show where a student will find the answer to your questions. After  reading out five or so of the most commonly asked questions, the students will get the message:- the answer is likely to be on the webpage. Look for it.


Formulate a version of your thesis without the problematic results. Write it up, at least as an outline, but probably more completely. Analyze it.

But also consider the fact that the results that aren't as expected might invalidate some expectations and lead to a different result. If that is the case, it may be that the "odd" results are pointing you to something important. If so, write that up, instead. Analyze that version.

Then give either or both versions a good look and see how it appears to you. Do you have any results of significance that will carry you to your degree? The next step is to show this work to your advisor and get whatever feedback you can from them. Point out that you have dropped one aspect or changed the focus, but that it holds together, assuming you judge that to be true.

Then take whatever advice you get from the advisor. I suspect you will be told it is fine to proceed, but if not, work out a plan for completion with the advisor.

In general, "not as expected" is a research opportunity, not a setback, but you can probably be successful on one of the two paths.


Which citation style is the most concise and has the least impact on word count?

Coming back to this question when writing a grant with very strict word limit, I discovered that the most concise citation AND bibliography style must be the Science (without titles).
Example:

  1.R. Hisakata, S. Nishida, A. Johnston, Curr. Biol. 26, 1911–1915 (2016).

You can find the citation-style-language csl file in the official csl styles github repository, that you can download and use in Zotero, Mendeley, RefWorks, etc.
If you're an EndNote person, see the style file in the most popular answer to this ResearchGate question


Is it bad to copy and paste from your SoP to other questions on a grad school app?

Well, eventually this is an opinion poll but I would predict the odds is at your good side. I've been reading many application packages in a graduate school and situations like yours do not bother me for the following reasons:

The statement of purpose is supposed to be the best thought out piece of your application. For that reason I think it's sensible to reuse the materials.
You have slightly revised the passage by adding some contents to the beginning to make the whole answer stand alone fine. That shows thoughtfulness.
Some committee members may even advocate for you for being able to include some crucial information in the statement of purpose without being asked.

So, I don't think it's a deal breaker. If you want to tackle this kind of situations more confidently, provide a shorter synopsis in the short answer, and note that a detailed description of the leave is included in the statement of purpose. This would improve the coherence between the application components.

Good luck.


Do journal titles need to be included in a brief literature review in the introduction?

Your advisor may be referring to or be inspired by the following:
All journals I know require you to use a complete citation¹ in the rare case that you want to cite something in the abstract of your paper (example).
This makes sense as there are some cases in which people only have access to the abstract and thus a stand-alone citations are desirable.

However, this does not apply to the introduction (of any kind of work) and I would not see any good reason for it. Moreover this has the following problems:

Unless you use this citation style throughout your thesis, it would make your citation style inconsistent, which is confusing for the reader.
It interrupts the regular text flow and thus makes the text more annoying to read.

Whether this is worth starting a quarrel is something only you can decide as it depends on the influence of your advisor and the risks you are willing to take. Most importantly you should find out the opinion on this by whoever will actually read and grade your thesis. If your advisor has some influence but will never read your final thesis, you could change the citation style just before printing.

Either way, you can ask your advisor whether he has any other argument for this other than his own opinion (but again you are taking a risk here, only you can evaluate). After all, he might give bad advice to other people in this regard – or we are all missing a good reason for this advice.

¹ Containing sufficient information to uniquely identify the cited work, usually author, journal and year, sometimes also the page number, but usually not the title.


Should I mention in an email to a professor that they are referred by another one?

The letter is fine, but I'd actually suggest that you replace this:

  I have asked prof A about studying with him, but he has kindly refer you to me since he's on leave next year.

with something like the following:

  Prof A has referred me to you as being a good fit for my research interests.

There is no real need for the rest of it, and might be inferred without saying it directly.

But, your original is fine, also. Good luck.


is it good for academic path if I publish too many papers in arxiv

No, you shouldn't just submit to the arXiv instead of journals.

Articles in the arXiv are not considered published in the traditional sense, and they are not peer reviewed.  In fields that use the arXiv, papers are typically submitted there and to a journal (but you can do this only if the journal's policies permit it, so you should check if you aren't sure).  The role of the arXiv is then to provide access to preprints before publication and "green open access" to published papers.

You don't have to submit an arXiv paper for publication, and occasionally people use it to distribute papers they don't intend to publish (and for which they aren't looking for publication credit).  But you should be careful to avoid getting a reputation for putting mediocre papers on the arXiv.

There have been a few high-profile cases of great arXiv papers that were never published, like Perelman's work on the Poincaré conjecture.  However, you can't get away with that when starting an academic career (unless you are revolutionizing your field).  If you just submit papers to the arXiv and not to journals or conferences, it will destroy your career.  They will count for far less than published papers, and search committees will wonder about all sorts of explanations.  Are you profoundly eccentric?  Do you have no idea how academic careers work?  Are your papers just not good enough for journals?  Is there something you are hoping nobody finds out via peer review (e.g., that you plagiarized or rediscovered something already known)?  Basically, everyone will make uncharitable negative assumptions, in addition to considering the papers themselves as worth less.

The question you've asked is a perfectly reasonable thing to wonder about, but I find it a little alarming that you've basically proposed career suicide with no indication that your advisor has warned you.  This suggests that talking with your advisor more about career issues could be helpful, or attempting to find another mentor if your advisor is not so helpful.  Academic career paths can be narrow and demanding, and good advice is essential.


The rule of thumb that I generally use is that if any portion of a work has been supported by a particular grant, then it counts as part of the outcomes of that grant.

Typically, in reporting on outcomes, one is asked not just for names of papers, but also for some sort of narrative of the work, in which it is simple to state what work was done, much as you just did.  If for some odd reason the funding agency only wants you to list papers and nothing else, then I would think that it is incumbent upon them to understand that they may not be the sole source of support for some of the items listed.


I discovered a mistake in my application after being accepted to a master's program. What should I do? Will my offer be rescinded?

I doubt that it would be rescinded if you tell them what happened and apologize. But failing to tell them might lead to some future charge of fraud, which could be grounds for expulsion. It might depend on how prominent the minor is in the application materials.
It is possible that the error was already noticed and dismissed since your transcripts show your coursework. So your informing them is just "In an abundance of caution, ..." statement.
No one can guarantee an outcome (other than the university), but errors happen. It might have been a bigger issue had you named Math or CS as a minor since that might have been a part of the decision to accept.


How is an online article referenced if there is no obvious author?

There are probably several answers depending on the situation and on the standards in your field.

First there are papers published in journals with no authors that are referenced as:

  Anonymous, yyyy. Paper title ...

In some cases an organization can be the author. this is true for, for example, governmental organizations, NGO's etc. In these cases the publications are offically published. References would be listed under the organization (often abbreviated) such as:

  WMO (World Meteorological Organization), yyyy. Publication title ...

To reference online material is always a bit more complicated but I guess the anonymous author can be used and the source organization listed as the "Publisher" such as the The Guardian in your example. The point is that the source is known but not the author. If you have a lot of these sources there will of course be many "anomymous" floating around in th etext and reference list which may be awkward. In such a case you may consider using the organization as author.


Are there journals with the same "great big debate" format at Behavioral and Brain Sciences?

Although I haven't seen this format in particular (and I'm a neuroscientist, maybe I should be paying more attention!) it looks like Open Peer Commentary is also a phrase used by other journals, so searching based on that phrase may help you find journals in other fields relevant to your interests.

A less-formal approach that is somewhat similar is "post publication peer review", although at least in my experience these venues have not really taken off. PubMed Commons, for example, was discontinued after a pilot. These formats allow for online comments on published papers, but not in a curated format like your example.


Many published articles cite "In press" articles forever and it's not an issue.

You could, however, publish a preprint (on arXiv, on PeerJ, on ResearchGate, etc). This will allow you to have a DOI for the unpublished article. You need to be very careful: not all journals allow preprints (I do not know about conferences), so it could jeopardize the publication of paper 1. You have to verify your signed agreement (if you have one) or ask.


E-Mailing supervisor during Masters Thesis - How often and how much?

There is no standards about contacting your professor.

I think the proper answer to this is : ask your supervisor about it. Only he can tell you what he expects of you and how available he is. If you keep your email or contact with him civil and polite, their is nothing more to do.

Depending on how many student he has to supervised and his working habits, he might tell you whether he prefers emails or meeting, or if he is able to make extra meetings with you should the need arise.


How can I proof-read my own work more effectively?

From Google:

Proof-read:

from hard-copy
backwards
aloud
a few days after the last revision
after revising the text for clarity and brevity
line by line, covering the remainder
double-checking small words ("if") and proper names
looking for one type of mistake at a time
looking for mistakes and idiosyncrasies to which you are prone (using the search function or even more sophisticated).

Helpful links:

Proofreading and editing tips
Top 10 Proofreading Tips
"Proofreading", from The Writer's Handbook

On motivation:

schedule enough time to divide the task into small chunks and take breaks
reward yourself after completion of each chunk
listen to music
have a nice cup of tea
you have the soon-to-be published result of your hard work in front of you. Indulge in some pride as you go through the paper.


Traditional, subscription-based publishing, with self-archival of pre-prints, works well.

That is probably the major reason why other models stay confidential, or are plagued with dishonest behavior (like author-pay, "gold" OA).

The other aspect is that such initiatives are typically pet projects driven by a few enthusiastic individuals. Sometimes their institution tells them to do what they are actually paid for. And when they leave their institution, stop their academic career for a reason or another, or retire, there is no real incentive to find someone to take over.

Side note:

  Of course, this reduction of editorial (and other) overhead takes the
  wind out of the sails of the "who is going to pay for it" argument.

Not really. In the "green" OA model, somebody is obviously paying for archival. It might be invisible to most authors, but institutions have to decide to allocate a portion of their budget to maintain these databases. As for formatting, it's payed via the salary of researchers who spend time on such a task instead of on research and teaching. Highly educated scientists having to worry about font size, picture format, placement of floating objects and 'overfull hboxes'... The cost of knowledge, indeed.


Is it common to make seniority distinctions between coauthors of a paper in math?

This is uncommon. However it seems less unusual to refer to something one of the authors did, e.g.:

  In a previous result [2] by one of the authors, it is shown that ...

or:

  This builds on prior work of the first author [3], namely, ...

As  Andrés E. Caicedo says in the comments, I would assume that this is just a way to refer to one of the authors, similar to the above statements. That is, this is not a way to imply that they are more important, or contributed more to the paper. (If anything I would assume the senior author contributed a little less :) ) It may be a small gesture of respect, formality, or acknowledgement to the mentor of the work, but nothing more.

  In my mind there was always the implicit assumption that all others contributed approximately equally to the paper

Yes, this is indeed the implicit assumption. Moreover, referring to an author as the "senior" author does not really contradict this.


Lack of mathematical work during PhD and coping up with the requirements of postdoc positions

If you have the knowledge, but not the "qualification" in those areas, make sure that your letters of recommendation say that. If you don't have the knowledge, it might be a bit easier to improve Python skills than math skills.

Alternatively, you might be able to get someone to tutor  you in the math area and make sure your advisor and other recommenders know to mention it in the future.

A third option is to focus your statement of purpose and other application materials on your knowledge of these things, rather than just listing courses.


how reference a translation of an already translated text?

STEM texts

In STEM texts, the main goal of providing the reference is to give attribution to ideas. Thus, the reference acknowledges that Alice wrote De Nihilo in 47 BC.

  As Alice has pointed out long ago (Alice, 47 BC), nothingness does not exist.  ...  Alice, De Nihilo, 47 BC, Rome, Manuscript Publishing.

The secondary goal is to point the reader to the available translation, in case he wants to verify the source himself. In your case, this is the German translation Bob made.

  As Alice has pointed out long ago (Alice, 47 BC), nothingness does not exist.  ...  Alice, De Nihilo, 47 BC, Rome, Manuscript Publishing = Alice, Über Nichts, 1987, München, Hanser.

No one cares if you made your own translation into English; readers value ideas first.

Language studies

In language studies, you are likely interested in how exactly the same idea was expressed, maybe to the point where you are pointing out differences between several translations. Alice and Bob deserve separate mentions now. If you have taken the effort to translate De Nihilo into English, this deserves to be published, say, in appendix A of your work.

  Alice is genuinely worried by the nothingness conundrum (Alice, 47 BC), but Bob's German translation fails to convey this emotion (Alice, 1987). My English translation (appendix A) seems to resolve this problem.  ...  Alice, De Nihilo, 47 BC, Rome, Manuscript Publishing.  Alice, Über Nichts, German translation by Bob, 1987, München, Hanser.


How to tune algorithm performances in computer science papers

It would be dishonest to do this without mentioning that the algorithm was tuned differently. You ought to specify what the tuning changed and how this affects the results of the algorithm.

You should also list accuracy results for the fast algorithm and speed results for the accurate algorithm. (Your probably also want some numbers for middle of the road tuning too). Not listing the "bad" results isn't dishonest, but it's bad science. If you didn't include these numbers, I'd expect your reviewers to bring it up and ask for them.


There are three different sorts of bibliographic entries in your situation, I think: suggestions for further reading (for the students), acknowledgement of your sources, and historical references. One should acknowledge one's sources, whether or not it "helps the students". I think it will help them in the larger sense of perhaps slightly better appreciating how human knowledge is advanced and organized. Including historical references helps people understand the timescale on which things happen.

Even with "well-known" relatively elementary results whose origins have faded into obscurity, you can note that you learned these things from various textbooks yourself... not that you came up with it all yourself, for example. You could tell the textbooks you studied from.

Even if that information is not "tested-on", I think it sets a good model for the students.


Lack of available reviews on scientific papers

Usually the issues pointed out in a review have been corrected by the time the manuscript has been published, so old reviews wouldn't really be relevant to the online version.

Critiques of published articles are sometimes prepared, if one thinks the issue is significant enough; they're usually published as "Comments" or "Responses" to the article in question. However, since they're normally also peer-reviewed, they won't simply be appended to the article, but instead have their own independent status.

As for the reason why more articles don't have reviews and commentary associated with them—it takes a lot of time to do so, and that's time that can be used to make progress in one's own research. And there isn't much incentive right now for such efforts.


What do I do about my lab head misattributing my grant proposal?

Is what they're doing ethical?

Being a chief investigator on a grant does not necessarily imply that you are an author of the proposal.  Proposal a writing can even be outsourced to a third party.

In order to determine if the proposal is ethical, it would be necessary to read it and read the funding agency's rules, but if it's unethical it is probably not for a reason you have stated.

  What can I do if I don't like it?

Probably nothing, except ask the lab head to change their course of action (Is it too late?).  If the university paid you to write the proposal, it very likely belongs to the university.


Article based on thesis and co authorship

If this is the case, what he is doing is not morally correct. You can refuse his request and thank him inside the acknowledgement part of your article for helping you. An author of an article should make some major contributions to the work, even if he is not writing any part of the article. Minor contributors should be mentioned in the acknowledgement section.


Where can I find descriptions of arXiv categories?

From the arxiv.org home page, click on detailed description for the discipline that you need (everything except physics has one). For instance, the one for computer science reads:

LG - Machine Learning [...]
Covers machine learning and computational (PAC) learning. Roughly includes material in ACM Subject Class I.2.6.
CY - Computers and Society [...]
Covers impact of computers on society, computer ethics, information technology and public policy, legal aspects of computing, computers and education. Roughly includes material in ACM Subject Classes K.0, K.2, K.3, K.4, K.5, and K.7.


Mentor added his name as the author and changed the series of authors into alphabetical order, effectively putting my name at the last

Speaking from a field where author lists are always alphabetical: This will do you good in the long run! If you follow this convention, you will never have to argue over authorship order - take a look at the amount of questions on this site dealing with exactly this question, and be thrilled that you have the option to simply exclude that from your life.
Since I am in such a field, I also know what people do on their CV: they explain what they did for the study. You can write that you did the experiment, the analysis and wrote the first draft of the paper. This will be more informative for a hiring committee than any amount or author-list ordering principle you can come up with.


Addressing Professor in email with half-typed name, how to deal with the mistake?

Forget about the mistake. If you want you can apologise in the next email. First names are more than enough for most academics unless you are culturally inclined to be very formal with a professor of the same back ground.


Are generalized recommendation letters bad?

First, as wsc says, you should not be uploading the letters yourself.  Usually there's someone in your dept. who can accept letters and send them out if there's no way for the letters to be uploaded directly.

Second, senior letter writers already spend a lot of their own valuable time writing letters for dozens of people.  Asking them to write separate letters for dozens and dozens of applications for each person is completely unreasonable.  In Math for research jobs in the US, letters for job applicants are not school specific.  (Though they do usually say "postdoc" or "tenure track position" since obviously a strong postdoc candidate would often be a weak TT candidate.)

(For teaching letters for liberal arts schools my impression is that the situation is somewhat different and some specialization may be expected.  But I don't have first-hand knowledge.  Of course, for those letters, it's less likely that one person is writing 50 letters a year.)


Is it appropriate to reply every time to a professor's "thank you" email?

Email exchanges need to end at some point.
If the professor's email is a simple receipt of correspondence, then I don't think there's a need to reply. However, if the professor has initiated a larger email then a reply is probably appropriate. See these examples:

Thanks sent as a form of receipt:

  Student: Hi Professor Smith,
  I've run the analyses you have suggested (see attached),
  Cheers,
  Mike

Then the professor replies:

  Pofessor Smith: Thanks for that

In this case, I think there is no need for the student to reply "You're welcome".

It wouldn't be a big problem, but it would be mildly distracting for the professor. Email exchanges need to end. The professor's "thank you email" was already a confirmation email indicating receipt of your original message.

Thanks sent by professor as part of a larger email initiated by the professor

Imagine the professor sends you an email that provides detailed information that also includes a thank you.

  Professor Smith: Hi Mike, well done on your work in the lab the other day. You did a really good job of fixing that equipment. I really appreciate it.
  Cheers,
  Professor Smith

In that case it might be appropriate for the student to reply: "you're welcome".


Interpretation of "GRE subject test is required, but your application will be considered anyway"

This is certainly poorly and confusingly worded, but I think I can explain the reasoning based on similar issues I've seen with other departments.  Here's my interpretation:

The department expects every applicant to take the GRE subject test.  However, they know that every year a small fraction of the applicants screw up and don't manage to register in time to take it in the fall.  It's impossible to take the test at the last minute, so at that point there's no way to fix the situation.  The department doesn't want to automatically reject these applicants, for exactly the reason you mention (what if someone's the next Terry Tao?), and they are worried that if they list the GRE as an absolute requirement, then the university administration might force them to do that.  On the other hand, they also don't intend to offer applicants the discretion to decide for themselves whether taking the subject test would strengthen their applications.  They want everyone to take it, with the possibility of forgiveness for outstanding candidates who screw up.  These goals get combined into the confusing statement that it's mandatory but your application can still be considered without it.

I don't know how the Harvard math department evaluates applicants with no GRE scores, but I can tell you how my department does.  We're a little happier if we see an apologetic note about how the applicant intended to take the test but failed to do so in time, but of course we know such a note proves nothing.  Our default assumption is that the applicant was worried about doing poorly, so we start asking questions like "How badly would we guess they might have done?" and "Would we have accepted them anyway, even with low GRE scores?"  If the application is otherwise fantastic, then the chances of acceptance remain good.  However, these are the cases in which we would have cheerfully made excuses for low scores (maybe the applicant just isn't good at standardized tests or had a bad day), so nothing is gained by skipping the exam.  An otherwise marginal applicant with no GRE subject test score will be rejected, and a strong but not fantastic applicant will be at a disadvantage.

So my best guess as to what the policy means in practice is something like "if you don't take the exam, we'll be annoyed at your irresponsibility and we'll evaluate your application with a presumption that you wouldn't have done well on the exam, but we'll still consider admitting you."  This means you have a strong incentive to take the exam if you can.

  On one hand, it seems possible that they would want to "consider" applications without the GRE subject test, in that they receive the admission fee and that they can discard the application with very little time and effort

In a typical U.S. department, application requirements and graduate admissions decisions are handled pretty much entirely separately from application fees.  For example, many people on the committee won't even know offhand what the current application fee is or where the money goes within the university.  In particular, whoever wrote the policy about GRE scores probably wasn't thinking about application fees at all.


Can a research publication have a bad impact on your career?

First, regarding your comment that “if [the paper] was so bad it would not have been published”: in my experience, pretty much anything is publishable, it all depends on the journal. Don't overestimate the field: there are journals out there that publish absolute crap. And that is not only my opinion, e.g.

  in many cases, Bentham Open journals publish articles that no legitimate peer-review journal would accept

Now, the initial question is: how bad can it be? Well, it can be bad. As a researcher (or wannabe researcher), your publications list is like an artist's portfolio. When you look for a job, apply for a grant or try to recruit new team members, this is what they will judge you on.

Now, for a young student (say undergrad or MSc level), one weird paper would not completely freak me out. It would mostly speak to me about the quality of the tutor/advisor/program director: a newbie can sure get a wrong idea at some point, but how come noöne was there to tell him it was a wrong idea? On the other hand, if he was told and did not listen, it might speak to his character!


Which Universities admit CS graduates for their theoretical physics course?

I can't speak for the UK, which has a different educational system altogether, but in the US, most programs would find a CS graduate "acceptable" for a physics doctorate. This assumes a good record overall, of course, and probably a few physics courses in which you did well. In the US, a CS student probably has a few such courses, though not advanced ones.

But to actually be admitted you have to be better than "acceptable".

In the US, the graduate program has quite a few courses available, primarily to prepare the student for comprehensive exams. But the normal path would be into a doctoral program, perhaps with an MS along the way.

I would guess that in the UK the university would expect an applicant to be further along in the major subject, but others would need to verify.


Grants.gov v NIH ASSIST for grant submission

Functionally, you can use whichever system you prefer; there is no inherent advantage in submitting via either system, since both are approved methods for submitting proposals.

The decision on which system to use basically boils down to which system you feel is easier, and which one your university's grants and contracts administrators are more comfortable using. (The easier it is for them to use the system, the easier it will be for you to submit your proposals according to the rules and deadlines!)


When to start contacting possible PhD supervisors (Europe)?

Can't give you a generic answer, but here is my particular situation: I am an assistant professor in the Netherlands. Contacting me to pursue a PhD is futile, since I have no funding at the moment to host PhDs. If such funding would become available (which can happen at any time; there is no rhythm to this), positions will appear on my university's vancancies page. You are most welcome to apply to any such positions, but contacting me beforehand is not necessary.
In all of the Netherlands, PhD students are viewed as university employees. Therefore, a PhD vacancy is not a matter of student admission, but a matter of employee hiring. As a consequence, the human resources department will manage the bulk of the procedure; although professors definitely get to choose people that would be a good topical match, the hiring process is much more centralized than in some other countries. In Germany, situations vary: at some universities and in some groups, PhD positions are 100% paid as jobs, while at other universities and in other groups, PhD positions are 50% employee, 50% student. I cannot vouch for the situation in Belgium and/or France.


No reply from PhD supervisor after meeting

Given the initial enthusiasm of the supervisor and the silence since she took my draft should I accept my proposal must be horribly wrong and must be binned.

No, that's not a reasonable inference.  Students often seem to think that professors use silence as a form of implicit rejection, but I've never actually seen this, and it would be unprofessional in this context.

It's vastly more probable that she has just been too busy to reply, especially if she had planned to write something relatively complex, or hasn't been able to finish reading your proposal.  (And honestly, your initial response about throwing it all out may have complicated it more, since now she probably wants to write something that will not only express her opinion but also reassure you.)  She may also be ill, out of the office, on vacation, traveling to a conference, etc.  July is a major travel period for many professors.

I would suggest that you try to set up a meeting in person, if possible.  It should be much faster for her to reply to that message, since she only needs to check her calendar, rather than trying to articulate in words her response to your proposal.  And having a meeting scheduled will create a deadline for her to have her response ready.  It's best if you suggest a few times when you are available, to minimize the number of back-and-forth emails needed to agree on a time.


Google Scholar gets the information (title, authors, journal name, date,...) directly from google scholar indexed journals. It produces the different styles from that information. Usually this works quite well, however, sometimes things go wrong so it's always good to check if everything is correct.

I also recommend using a citation manager like endnote or mendeley, that way you can download citation styles directly from the source/journals, manipulate them, easily change styles and correct errors.


How to react to strongly erroneous and irrelevant citation of my article?

Begin by trying to speak to the author and see what he says.  Then:

Speak to the editor of the journal, unless the author is willing to submit a correction instead.  If the problem is big enough that it:

a) Misrepresents your work to the degree that someone would think, from this article's citation alone, that you did or did not do something critical, or

b) Invalidates the results of the paper in which the citation is published, or

c) Undermines those results by providing a false citation to make it look like a claim is better supported than it is

then it is important that the editor be involved and the article be corrected.

If it's a small problem, then speaking to the editor may not do much.  As an example, a paper of mine was cited incorrectly once.  It was actually a small and irrelevant mistake, and the authors probably meant to cite something else.  It was along the lines of: "Other techniques to solve this problem include Y, which was explored in [1][2][3], but we are approaching it differently" and that was it.  In this case, embarrassing the author was not something I felt like doing so I let it go.


Follow up email if you have not heard back after tenure track facutly interview

Ideally, towards the end of your visit in January the search chair would have let you know the projected timeline. Unfortunately that doesn't always happen.

In any case, I don't think it's unreasonable to drop them a quick email to ask if there are any updates. Before you do, however, be aware that you are likely to get an evasive answer or a non-answer. There are three likely reasons that you haven't heard anything:

They don't want to hire you, but they forgot to tell you.
They have offered the job to someone else, but are keeping you around as a backup in case the first person turns them down. They may be currently negotiating with the first person.
They are still interviewing candidates, and won't decide for a while.

In case 1, you'll get a definite response. In cases 2 and 3, you won't learn anything, although they might be able to give you a rough estimate of when to expect to hear from them.

NB: If you have been offered a job at another institution, but you are still interested in this position, do definitely tell them. They may be able to speed up the process on their end to give you some more information.


PhD in a science with a professional MS degree

The way you word your question "hinder me from one day" makes it sound like you're going to apply later in the future. I have known people who have a BS in Theater and a MFA and was accepted to a PhD program in business after spending years in the business world. So it definitely is possible - just depends on your experience and the candidates that you're competing against. There is no "yes" or "no" to your question unfortunately.


Are references from an employer in an unrelated field useful when applying for graduate school?

You need a recommendation that will convince a committee that you will be able to rise to the occasion (i.e. be successful in your coursework, exams, research, thesis and thesis defense) if they admit you to graduate study in their department.  Choose letters that will have as close an effect to that as possible.

You haven't given us enough information about your employment to enable us to provide an opinion about that potential letter.

Note that if someone asks for one reference, and you have two references which, combined, give the desired picture of you, then the thing to do is submit both letters.

Also note that there are threads here that provide advice to those who don't currently have any suitable references (e.g. take another class, do an internship -- something to garner a new reference).

After you've read some of the related Q&A threads, feel free to edit your question, giving additional information about your situation, and pointing out how yours is different from the others you read about.


Professor says he won't report my cheating if I admit it in writing. Is it a trap?

You betrayed your professor with this cheating behavior and lost his trust. But trust from others is the most important value in academia and in science. It is a necessary, but not sufficient, condition for any kind of research in any scientific domain. It is necessary for any homework (the goal of any homework is just transmission of skills and of knowledge, nothing else; correcting and grading home-works is the worst part of any teaching job). And when you read any research paper, you have to trust its author. If you cannot, the author committed academic dishonesty. Unethical behavior is the number-one enemy of science.

Your professor is responding by asking you some email (that is some formal confession). He is likely to not use it now but could use that later.

I would have behaved as he did. He is giving you a last chance. Be grateful to him!

We all make mistakes, but you should try hard to avoid repeating yours. Errare humanum est

Your past behavior (described in your question) was unethical, not an adult one and incompatible with any PhD studies.

Most of us cheated at least once in our studies. My best teachers in French high school (collège) told me: "don't try to cheat, at your age, I cheated more than you can now". And I'll be 60 years old in August 2019.

  I am thinking about just withdraw my PhD right know before his complain gets to the dean.

Doing a PhD is hard work, and you'll make a lot of mistakes. They are part of the job (and that is why I like so much the "Philosophical degree" in US academia: in France I am just a "Doctor" of computer science, but the only thing I really know is that I know almost nothing; read more on the etymology of the Doctor word).

NB: I am not a native English speaker, since I am French. During my own PhD I did pay for professional help from a psychotherapist, and as a human being (probably as old as your own father), I believe you should do likewise, at least to increase your soft skills and probably to be able to achieve your PhD. It is a really hard journey.

I welcome any private email about this question (cited by its URL) and my answer above if it is written in French by a non-French native speaker.


Does the person who downloaded the data deserve to be a co-author?

The proper answer here is clearly that this person does not deserve to be an author.  Downloading a bunch of data files is not any kind of intellectual contribution to the research.  It may have been a necessary task, which was required to get the project operational, but the same could be said about administering your institution's e-mail server or keeping the HVAC system you use operational.  Workers that do not contribute intellectually to a project do not merit authorship on papers, although they could be thanked in the acknowledgements, if they put in a large amount of time in support of the project.

You seem to be concerned that your funding agency may not want to see people paid to work on a project who are not authors on the resulting publications.  While some agencies may have concerns about this, what they are ultimately worried about is whether their money is being spent on the research it was intended to fund; they do not want the funds redirected to other projects.  They must also understand that some money is going to go to people who do not end up making intellectual contributions to any papers.  Some people just end up doing scut work; some people quit before they make any progress; some research projects unfortunately never produce anything publishable.  All these situations will be familiar to the funders; they may not be thrilled about any of them, but they know that they do happen.


Why there is "Dr." before name of PhD degree holder?

Yes, this is the right practice.

A PhD degree is a "Doctor of Philosophy", and the appropriate formal title for that is "Doctor". That there are other professions that can be called "Doctor", for example holders of an MD degree, is simply because there are multiple fields one could be a Doctor of.


Applying for jobs without significant publications: is it worth the pain and what to highlight?

Disclaimer: this question is seriously underspecified. For a reasonable answer we would probably need at least the city you are looking for, your field, your qualifications beside publications, etc.

That being said, I feel that the Assistant Professor market in Europe is insanely dry in most fields, and, honestly, getting an Assistant Professor position directly after your PhD graduation is very unlikely even with an extremely good CV. If your CV is not absolutely top-notch for your field, I am afraid applying is largely a waste of your time. On the other hand, at least in my field, getting a PostDoc is often comparatively easy and uncomplicated, and reasonably payed in many places. A PostDoc is also a really good time to write up a backlog of publications and improve one's CV, so maybe this is what you should be shooting for.


How can I proceed if my email is not working, and I am in the middle of creating proofs for my new accepted paper

Many journals have an online system where you can log in and change the e-mail information. If not, just contact the responsible person (by using another e-mail account).


Community College or extension programs as a way of preparing for a Masters in Mathematics

I fear that not so many community colleges would offer the upper-division courses a math-major sort of person would want, especially to aim toward graduate school in mathematics. Further, you'd be needing letters of recommendation for grad school, and community colleges would not generate letters that would help you, since the letter writers (by far most often) would not be familiar with grad school from the side of mentoring and supervising grad students (even if they themselves did have a Ph.D.).

It is true that community colleges are usually much cheaper than "universities", but the coursework, context for coursework, and outlook of faculty teaching the upper-division courses you need, and their letters on your behalf, are things that you can't avoid but need.