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What is proper author order when you write paper based on colleague's work?
My colleague has developed a software framework. I have not contributed towards software development but I have been asked by my advisor to write a paper describing the software since my colleague is not experienced in writing.
In this situation, what is the proper order of authors ?

In this particular case

Author of the framework
you
your advisor

but that is strongly dependent on your local and institutions' customs and practices. Ask your advisor informally. When still in doubt, always add yourself second to the first draft. If appropriate, your advisor will suggest moving you to first position, which is a lot less embarrasing than the other way around (your advisor suggesting you should take your name down a notch)


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Is it ok to mention assistance in grant writing on your CV?
On behalf of my advisor, I recently wrote a grant to obtain some specialized and expensive hardware. Is it ok to mention this on my CV, even though the grant is in my advisor's name and if yes, what would be a good way to word it ?

You can list on your CV whatever you think is useful information for the reader. In your case, whether something is useful depends on what your position in life is. If you're a full professor with a long history of funded research, what you describe is likely not useful to list on a CV. If you're a graduate student with an otherwise relatively short CV, then that's a different story. I would suggest wording such as

Co-authored the proposal for grant XY-1234-5678 (PI: Professor Z).

Now, whether an entry such as this has any impact is a different issue, but it is certainly not going to hurt.

I would list all relevant grant activity on your CV. Grant activity is something that many departments consider when considered people for academic appointments and it's often missing or hard to see.
It is completely normal for graduate students to apply for grants with their advisors listed as PIs. Be honest about your role and about your advisors leadership role (I like Wolfgan Bangerth's suggestion for wording) but do go ahead and include it.
Bangerth is right that this kind of thing will be less useful for individuals further on in their career but I think it should still be included because it is relevant and it makes your CV a more complete record of your academic activity.

I wouldn't put this on a CV, but it is something that you should bring up during an interview as an example of your experience with the grant writing process.
To elaborate on this:
An individual is either a PI/Co-PI on a grant or they aren't.  Some readers might read your CV and think that you're claiming undue credit.
In recent months I've interviewed many candidates for a faculty position.  Some of them had helped to write grant proposals in this way (and we would discuss this in an interview), but they didn't put those grants on their CV.   Other candidates had submitted proposals as a PI/Co-PI, and they appropriately included this information on their CV's along with whether or not the grant was pending or had actually been funded.  Listing proposals that were not funded is not something that I've seen on CV's that I've reviewed.

Why do you think so?

I would disagree with this answer. Just demonstrating that you have a basic to good understanding of grant writing and/or experience in grant writing will be helpful, both for academic appointments, and if you decide to go into industry but remain in research (such as not-for-profit or government work)

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Does mathematical sophistication play a role during paper review?
I am currently in the process of writing a paper for an international conference in image-processing area. One thing that bothers me somewhat is that the mathematical formulation I use is simple(specifically, I quantify a measure as a simple ratio). I happen to have just 2 equations in my paper. The formulation is sound,though, and is a natural outcome of the framework I have developed.
Ideally, simplicity or sophistication of equations occurring in a paper are not a measure of its worth, but I wonder openly -- what role does "density" and sophistication of mathematics used in the paper play in impressing the reviewers ?
Just for clarification, I am not saying it should or should not. I would like to get a candid view of reviewer experiences and inclinations.

This is highly dependent on your target audience. In some computer science conferences, complex mathematical derivations are almost required (even when they are unnecessary); in others, they are essentially forbidden (even when they are necessary).  Without specific knowledge about the community you're submitting to, there's really no way to answer this question.

@JeffE As I mentioned in my question, the field is image-processing.

The answer may still depend on the specific conference.  But in any case, you should first write the paper with whatever mathematical sophistication that your results require, and then send it to an appropriate venue, rather than artificially inflating/deflating the math in your paper to fit some target venue.

Mathematical sophistication is surely not a requirement for the key equations of a paper, but an outcome that appears natural to you might not appear as natural to a reviewer, who, in turn, might ask you to add a mathematical proof of the fact that the simple parameter you are introducing is a good measure.

Mathematical sophistication and mathematical density are often confused for one another, and this confusion often extends to reviewers and the "customs" of scientific communities.  To my mind, the best mathematical presentation is the most lucid and simple, and it is certainly the case that important consequences often come from rather simple equations.  The simpler your equations, however, the more that the contribution of the paper will depend on your exploration of those consequences (theoretically or empirically), rather than the mathematics per se.
It can be very tempting to "puff up" the perceived complexity of your mathematics by adding notational complexity or other baroquery.  It may even work well when dealing with some communities (I know of some rather cynical and unfortunately successful experiments performed by certain colleagues of mine).  I would strongly advise, however, against doing so.  Write the paper as clearly and simply as possible, given the true nature of the mathematics within.  Doing so may incur negative judgement from those who confuse "simple" and "trivial," but to do otherwise is scientifically dishonest. Moreover, if your work has value, it will show in the consequences of the mathematics rather than its nature, and writing it more accessibly is likely, in the long run, to increase its impact.
Finally, note that this dictum goes the other way as well: when you are presenting a complex mathematical result to an audience that does not appreciate mathematical complexity, do not attempt to pretend the mathematics is not complex.  In this case, however, appendices and supplementary information is the way to go: keep only as much of key elements in the main text as is appropriate for the audience, and put the rest where those who are interested can readily find it without interrupting the flow of the main text.

Keep also in mind that Terence Tao, who does know one thing or two about mathematics, is a strong advocate of using plain English whenever mathematical notation is not strictly required (http://terrytao.wordpress.com/advice-on-writing-papers/take-advantage-of-the-english-language/)

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Cultural Differences in the Hard Sciences
I saw this question, and I got interested.
Besides a culture or country having a lower level of technology or research ability due to wealth, access, etc, is there any difference in how cultures study and research hard sciences (think physics, chemistry, etc) differently from one another? E.g. does an Eastern European scientist think about or conduct scientific research differently than a scientist from the United States, Australia, Africa, or any other country or culture? I don't need an exhaustive list, if there are strong differences, but some examples would help in my investigation. I am trying to decide if I want to pursue a graduate program in physics/materials science abroad, or just stick to my own culture, for now, since it is what I am used to.

There absolutely is a social/geographical component in choice of textbooks, curriculum design, exposure to ideas where they're popular, etc. Presumably this shapes thinking to some extent. For example, in physics there is a common impression that Russians are more terse in their writing than West Europeans and Americans, and guaranteed to be comfortable with the use of special functions.

Having several years spent Western, Eastern Europe, USA and Japan, my opinion is yes, academic culture can be very different country by country. However you should formulate more specific questions if you want to compare them. Teaching, research, life, writing style etc can all be different, so you should focus on one topic in your question.

Greg? You there, bro?

It's not impossible that there is some effect, but figuring it out would be a complex task. A researcher would also need to guard against making value judgements that would, in the end, be treated as racist.
However, if you look at other fields, you see some differences, but I would attribute a lot of it to language more than culture, and some to history. In literature, the South Americans in general have produced some amazing stuff in Spanish and Portuguese that is quite different from literature elsewhere yet shares some characteistics. Art is another field in which different cultures have produced qualitatively different things, say China and Europe.
As humans we use language to express ourselves and the language both captures and guides thought patterns. If your language structure helps you think in a certain way that may effect how you think about, for example, mathematical problems and what insights you have naturally.
Likewise history (and the accidents of history) play a role. If one region of the world generally does something different than others, it may just be the accident that some person started a line of thought in a place and it was picked up by others.
On the other hand, the academic community is pretty much a world-wide phenomenon now, with a long history of students and teachers moving about. The effect you suggest is likely dampened, if it exists at all, by this world wide exchange of ideas and the consequent sharing of thought patterns.

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Letter of Recommendation from Instructor
I am a graduate student pursuing my masters in physics, with the intention of eventually getting my PhD (just not from my current institution). This past summer, I taught a physics course, and several of my students asked me to write letters of recommendation for them, and I offered to write letters for others, too. The students who asked did very well in the course, and I am happy to write letters for them. Most of these letters are for employers or graduate/medical schools. Would it be in their best interest for me to write them, since I am not an established/tenured faculty, and, in fact, have not even received my masters? I don't want to write them letters which will be disregarded by their employers/institutions because I am not a faculty, but was just the instructor of record.
Cheers

This depends a lot on what the student is applying to. Being an instructor means you're qualified to assess the students' ability to do well in your class (and some related things like study skills and desire to learn), but not a lot else. For e.g. Ph.D. admissions, they really want someone to speak to the student's potential to do research, which you probably won't be seen as qualified to do. Thus is for two reasons - first, being somewhat early in your career yourself, you haven't established a ton of credibility by your own research career; second, you only know the student from class, not a research-related activity. Whether fair or not, I think in reality a well-known professor's recommendation will be taken much more seriously than yours, even if you know the student better. If you were a postdoc or other junior/non-permanent faculty the balances would tip a bit, but not having a graduate degree yourself is likely to make the reader be skeptical of your recommendation.
On the other hand, if the student is applying to a summer program or a job that isn't directly related to physics research, writing that they're a strong student who did well in your class and asked good questions and came to office hours or whatever is perfectly good. I have no idea how professional schools (med school etc) work but my guess is you'd be taken more seriously - it seems to me that their admissions process puts more emphasis on grades/class performance, which of course you're qualified to speak to!
I'm a PhD student and have been asked to write recommendations once or twice for students I've been the TA for (at my university, TA's are typically the only people interacting directly with the students in the larger classes). I have warned the students that I'm likely not the best person to ask and asked if they have even a tenuous connection to someone more senior, and helped them out if they can convince me I'm actually the best person for them.

There shouldn't be any issue about this as long as you clearly state who you are and what your position is. If your institution trusts you to teach students the receiver of such a recommendation should also trust it, though weigh it against your experience in these things. But if your position is Lecturer or Instructor, or some such, it should be clear enough.
I would, however, also advise the students for whom you write these letters that they should also seek other letters from professors with a more established reputation. But it may also be true that you know them better than the professors if you are in a place where they have mostly big classes with the big names.

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Chances of Being Accepted for a Book Author as a Graduate Student
I recently identified a textbook which is currently looking for authors of chapters. It states "For selected and invited authors" on the website, so I am wondering, if I submit a chapter proposal, if it has any chance of being accepted having myself being the only author, and not having graduated with any graduate degree yet. I also have no publications, but several are in the process.
I asked my PI if he would coauthor it, and he responded stating that he gets several requests to write book chapters per year and does not do any of them because he does not have time.
My question to the more experienced: if a chapter proposal has content which is completely golden and is well-written, does it have a chance of being accepted to be included in the book? Are book authors generally desperate to find authors for currently-researched topics, or is it generally competitive? Would they even consider a graduate student author? If it matters, the field is physics/nanomaterials.

Not a full answer, but in general you will find a huge variance in how competitive and/or prestigious and/or picky editors are for any given book or collection. It ranges from somewhere to "anyone with a pulse and a decent grasp of language" to "only names we already recognize as at the top of their field" - and there is no real way of knowing unless you apply and see what happens. You should just make sure it is actually worth your time and effort before you apply.

This is good feedback. I've kept my feelers out and found the editor of the book on research gate. Even there, he pretty much asked his community if there is anyone with interest and expertise, but then again, his community might be full of big shots.

Be careful and avoid predatory book publishers - there are many out there!

If there is a listed article processing charge (APC), does that necessarily mean it is predatory?

@RJP For a book or book chapter? It definitely sounds shady to me.

Me too, but it could make sense because it's open access, right?

@RJP I don't think there is a big open access culture among traditional, well-reputed book publishers either. This does not sound like an opportunity I would be excited about.

I don't know about physics, but in Computer Science book chapters tend to be the lowest class of peer-reviewed publication. Most book editors are struggling to get any good contributions, and the only chapter-books (as opposed to text books with a single, or few, dedicated authors) I really see succeed nowadays are written by a closed group of people for a specific purpose. For instance, I know that some Dagstuhl seminars collectively decide to write a book - every participant writes one or two chapters, often together with (a subset of) members of their research group.
For books with an open call, you can in my field basically never be too inexperienced to write a chapter, as long as your English is good. That said, I generally advise my students against writing one anyway. Chapters are fairly long, so they may take an inexperienced writer substantial time to write, and the reputation and scientific impact of having a chapter in a book that is virtually never read is so negligible that the same effort is better directed to writing a different kind of paper.
Finally, the reaction of your advisor may also be a hint that they don't value book chapters either. Even if you can get your chapter accepted, is it a good use of time to work on something that your advisor appears to not put much stock in?

Certainly, a good paper would be valued more highly than a book chapter also in physics.

I don't know that publishers are desperate, but they are on the lookout for people who can write intelligently on subjects of interest to them. I think you have about as good a chance as anyone in this if your writing is good.
Publishing in books is a bit different from scholarly papers and you will likely get more feedback on your submission than you are used to. It will probably be reviewed by a subject expert, but the writing itself will also be guided by an editor whose main function is to deal with language, not content. The editor may also try to make the overall writing consistent across chapters when they are submitted by different people. I often found this to be very helpful.
Don't worry about the "invited" part. They can't invite you if they don't know about you. Perhaps your advisor can write a letter of introduction to the editor on your behalf as well.
It is possible, of course, that they are looking for the big names as authors, but as your advisor points out, such folks may be too busy to write.

Strongly related: Is it OK to publish a book as an undergraduate?
It's an unfortunate fact of life that books don't sell well unless the author is well-known and has the authority to write it. Publishers may love books, but there's still no point in getting a book proposal if the book doesn't sell. I realize it's just a chapter proposal, but a chapter written by you still means they can't claim the chapters were written by leading experts in the blurb / promotional materials.
You can ask, but your chances of succeeding are poor unless you can persuade your PI to add his name to the chapter.

I guess I disagree. They will claim expert authorship even if some chapters are written by less well known people. There are books and there are books, also. If a book appeals only to the already deeply knowledgeable in a field I don't think they will mind a chapter or two by an "up and coming" academic. If it appeals to a more popular audience, instead, then the readers will be less knowledgeable about who is hot and who is merely toasty. But the big names will dominate any marketing materials, of course. And it is good to get your name associated with theirs. Worth the effort, I think.

In the Humanities and Social Sciences it depends on the book’s purpose.
For many HASS fields the primary or most esteemed output is the scholarly publisher monographic book, not the chapter in an edited collection.
Edited collections are often the result of significant small topic conferences, if you missed the conference then your chances are lower. This kind of book is valuable due to the restricted domain and small number of active researchers. It puts your work at the head of the queue, and the introduction hopefully notes it’s field relevance.
Predatory solicitations tend to be with low quality publishers or no quality publishers. Also known is the rat bag editor. For example, The Black Book of Communism’s editor didn’t inform the contributor of the Soviet chapter on the editors “unique” thesis of causation which the editor pushed to great length in the introduction and conclusion. Younger researchers may also be prey to this kind of deceptive intellectual project.
If you have to submit, it is a good sign, especially if revisions are required. If you are solicited, and you don’t know the crew, display caution.
HASS edited collections will judge based off quality and fit (constrained problems or topics in original research).  You are as competitive as others working to your standard in that problem or research programme.
That 5000 words of research output might always be placeable somewhere else. And writing 5000 wd of new content based on primary research you were planning to use elsewhere may not be in your queue.
Generally: DOIs and open access are lagging behind the sciences here. But HASS works are usually cheaper than STEM works, and Interlibrary loan usually works, as long as your national level library system has a deal where someone buys at least one.


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Letter of Recommendation Coordination?
I am currently applying for a research/study grant, and need three letters of reference. Would it be out of line to ask the recommenders to coordinate with one another so that they don't say anything conflicting, and don't double up on the same exact content? Not sure what the norms are.

Seems like a bad idea.

It's also worth noting that all three already know one another, at least tangentially

Still, sounds like a bad idea. Perhaps they will do so naturally. You could inform each of the identity of other two, but I'd let it go at that.

It's certainly a good thought to make sure your letter writers don't double up on information to the detriment of their unique perspectives.
However, it certainly sends an odd vibe to ask that they three communicate with each other to do this ... They are doing you a favor writing the letter in the first place, but adding to that to try and make them coordinate with two other professors is a huge load, and plus, if you want three professors to work together, you might get your letters in a year, if they aren't too busy.
That said, it's absolutely normal to talk to one professor and ask her to write about your programming abilities in particular, and to ask a second to talk about how you are a quick study, etc., so that the letters are complementary.

It's certainly a good thought to make sure your letter writers don't double up on information — It is?  Why?

@JeffE I updated that sentence to explain my thinking.

I'd think do not ask them to coordinate. Not that it's such a terrible idea, but that writing letters of recommendation, while arguably part of one's professional responsibilities, is not quite obligatory, so has a component of "doing a favor". In that context, to ask for coordination would be adding (possibly considerable) work, since academics are not known for their cooperation. E.g., I myself will invariably write letters, but if I were obliged to cooperate with colleagues not of my own choosing, I might balk...
Anyway, "doubling up" on content is confirmation.
If there is "conflict", well, why would there be? As a long-time reader of recommendation letters, it does not surprise me when people have different opinions, or even different recollections of fact.
So, also, I think don't worry about those issues.
EDIT: To be clear, it's not that I imagine myself to be uncooperative (probably no one does!), but that my experiences with colleagues have made me dread most "cooperative" work. That is, I'd rather do twice (or more) the work than have to "coooperate" with randomly-chosen people. Certainly other people may feel otherwise, but asking for cooperation is asking for more, and perhaps quite a lot more work than you'd anticipated. Thus, since I think there's little if any to be gained... just let it go.

I agree with your advice, but have reservations about some of the reasons you give for it.


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How and when do departments decide who is teaching which course?
How and when do departments decide who is teaching which course?
I am a graduate student at a state school in the U.S. The process has never seemed clear to me, as it seems that when none of the faculty particularly want to teach a course, sometimes graduate students are asked if they want to teach them.
I ask because I really like to teach courses, and want to ask if I can teach a 300-level undergraduate course, but I want to know the best time to do it.

I don't think there's any standard answer.  I could tell you how my department does it, but would have no reason to think your department would be similar.  But in any case, the best time to ask is "now" - let the appropriate people know you're interested, and that you'd like to be kept in mind if there is an opening.

You would hope some months in advance, but some places manage to ask people just days before the start date of the course...

The department head/chair is the go-to person for such requests. Sometimes there is a curriculum committee that may or may not have some responsibility for seeing that courses are covered.
When you ask, it would be useful if you go with a plan and some evidence that you are or will be prepared for it.
You might also talk to someone who has taught it recently.
Don't wait to make your request. It may take a while if it is unusual for grad students to teach at that level where you are.
If the faculty is unionized you might run in to a problem. I've been places where the union for adjunct professors might want to complain even though the regular faculty wasn't unionized.

I'd probably start with the person who leads the graduate program (graduate director / vice-chair / whatever) instead of the department chair.  But in either case, if they're not the right person, they can tell you who is.

@NateEldredge, the lead for grad studies probably doesn't have anything to do with undergrad courses, but, yes, can point you in the right direction. If there is an undergrad dean (for the department) then that might work. I'm assuming 300 level is UG.

Well, in my experience, the graduate director is often responsible for the teaching assignments of graduate students, and so such a request would go through them (though the department chair and others might eventually have to sign off).

@NateEldredge: In my experience, the graduate director is also often not responsible for the teaching assignments of graduate students.  As you said above, there's no standard answer here.  In any case, either the department chair or the graduate director would be a good person to ask, since either could point the student in the right direction.


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How much preperation is required for GRE
I am a student going into my 4th year at a Canadian university.
I am pursuing a degree in electrical engineering, although in the last 6 months I have taken up programming and have been working this summer as a C++ developer. I will also be working as a C++ developer part time during the school year.
My grades are good (slightly above A average. 9.3/10 on CGPA scale).
I do not know if I am going to pursue a post-grad, but I definitely will if the company I work for offers to pay for it.
From your knowledge and experience, how much preperation is needed for a problem-solving/mathematically inclined person to do well on the GRE?
By well I mean qualifying for top-ish schools in the states.
I'm trying to collect information to decide whether I should just wing it or prepare extensively after I graduate.
ps. Don't crucify me for a subjective question please

Probably too many variables to make any firm suggestions. It depends on how well you retain what you have learned for quick recall and how well you do on tests of that kind. As a minimum you should practice a bit on each of the kinds of questions asked and be certain of the grading rules on the test. Know how "guessing" answers can be good or bad. If you do practice tests, do them under testing conditions.

The ETS (makers of the GRE) offer two free practice tests as part of what they call their POWERPREP offering. You can simulate authentic test conditions on your own, and they'll even give you an estimated score that I personally found to be within 5-10 percentile points of the real test I took later the same week.
So there is really no need to go into the process blind. Spend a few hours going over their practice questions to understand the types of questions they'll present you and how to answer them, and take the practice test to get an estimate of where you are now (takes about an afternoon of your time).
However, no one can give you any meaningful guess on your score based on self-descriptions, nor is there any guideline on how long to prep. The main thing to know is that, beyond perhaps a week of study to get comfortable with testing methods and types of questions, the GRE is quite resilient against short-term efforts massively changing the score on a retest. If you want to change the score you get by more than 10 percentile points, you'll need to put in a lot of work over a significant period of time to do so, because the ETS is quite good about making tests for which there is no easy way to 'cram' or make large leaps quickly.
As a rough guideline, if you are below the 50th percentile on a portion of the test and you want to get over the 80th percentile, I have not heard of any reliable way of doing so without a month+ of sustained, full-time effort, and even then there is no guarantee whatsoever. Some people train for the GRE for 1+ year and still don't do very well, while some only spend a few hours to prepare and find it reasonable easy to do 90%+ on at least 1 part of the test.
Regardless, the GRE is only one part of the process of applying to graduate school in the US, and every program (and individual involved) puts their own value on what it means. No one gets accepted to a top program just because of a great GRE (not even with a perfect score), but a very low score is a disadvantage.
My advise is to take the free test after a few hours of getting to know the types of questions, and then you'll know just what kind of situation you are in and can plan ahead.


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Copyright issues of using free clipart
I'm a master student in psychology. A year ago, I downloaded a lot of free clipart online to create my study stimuli. For example, some clipart are from this website: http://clipart-library.com.
I basically created my study stimuli using clipart from multiple sources. I finished writing up my thesis and plan to publish it soon. However, it occurs to me that if I publish my study with a few figures of experimental stimuli, it may incur copy right issues. I'm wondering what would be the best option for me at this moment? Should I not include any figures in my publications?

There are different meanings of the word "free". See https://www.howtogeek.com/howto/31717/what-do-the-phrases-free-speech-vs.-free-beer-really-mean/, for example.

The terms of use page of the site in your link says "All images on our site are for Non-Commercial Use," which should include academic use.  If you include any of their figures, give appropriate credit.  For material from other sites, read their terms of service and give the required credit.
In any case, be sparing in using clip-art in a thesis.

Thank you very much for your response! I used clipart to create my experimental stimuli that I showed to my participants. In the manuscript I'm preparing to submit for publication, I want to include one or two stimuli images as figures, but I won't show all the stimuli. I know think I should just not include any figures to avoid copyright issues. Or I can ask someone to draw these figures, so I will own the copyright.

@user96976 If you publish some figures, they'd better be the exact ones used in the experiments, not redrawn versions.

Thank you! I decided not to include any figures in my manuscript to play it safe.

I'm not a lawyer but the terms of use say:

All images on our site are for Non-Commercial Use.

So, as long your thesis has no commercial implications, you should be fine. You may want to add somewhere a reference to the website or to the individual images, like:

Adapted from [1]

or

(image source [1])

where [1] is a permanent link to the image in the repository.

Thank you very much for your response. I quickly checked license of other images, some websites state "Image License
Personal Use Only". Does personal use only refer to non-commercial use?

@user96976 What do you mean by other websites? You should check the license terms of the websites from which you took the images. In my answer, I assume that you downloaded images only from Clipart Library as mentioned in your question. In any case, no, personal use does not mean non-commercial use.

Thank you. I meant that I selected cliparts from different sources. Some have a different type of license.

No, "personal use" likely does  not include academic use. It is for web cards to your mom, and such. But if you are in doubt, you can normally ask the creator/rights holder for permission, explaining what you want to do.

@user96976 In this case, there cannot be a general answer valid for all sources.

Carefully distinguish between "using" an image, and republishing it. If you analyze tens of thousands of images but don't republish any of them then you are fine as long as you obtained them legally.
Copyright doesn't apply to "using" something. It applies to republishing it.
Another issue would be in play if you went around paywalls to get access. Now you are in the area of theft, not copyright.
But you can look at anything and you can think about anything and generally speaking you can write about anything. Just don't steal it and just don't republish it without permission of some kind.
As an example, if, in those tens of thousands of images you find 600 that depict Minnie Mouse, you can say so without violating any of Disney's copyrights. You can even say that in 300 of those she was dressed in red and in 200, in blue. Not a problem. Just don't include any of the images without permission.
For purposes of your thesis, just include images that you are sure are free to use for the purpose as stated by the copyright holder. As others have stated "Non Commercial" should be fine, but "Personal Use Only" maybe not.

I’m not a lawyer, but I’m pretty sure that it’s not theft to circumvent paywalls, just copyright violation, since you’re copying something that they said that you couldn’t; you aren’t depriving them of their copy. It might also run afoul of computer crime (hacking) laws if you do so by obtaining unauthorised access to their computer equipment.

@nick012000, my usage was colloquial, not legal.


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I'm frustrated with college because I feel like I'm never given the opportunity to explore the material
I'm a freshman at a private polytechnic institute, and I'm very disillusioned with the whole idea of college. I feel incredibly pressured with the work here and often find myself depressed. Oftentimes I have to find supplementary material online to cover the gaps in the material, since I can't always understand the teaching styles of the professors or the textbooks. I always feel like I'm required to know the information, but never have time to understand it. I want to study theoretical physics, and couldn't care less about going into industry. During high school, I was able to breeze through the required courses, and spent my extra time going above and beyond. Instead of filling my spare time playing games and hanging out with friends, I spent it reading, learning about modern physics theories and the upper limits of human knowledge pertaining to the universe. Here, I have no time to explore, no time to understand, and no time to think. I only have the time to study what I need to know and regurgitate it on tests. I can't remember most of physics 1 because I felt so rushed by work.
I feel that I might be able to do better studying independently over the next three years, learning physics from its foundations to current theories, beyond what they teach at college. I don't care about the "college experience", I came to understand physics. I don't feel like that's happening, even with the material already covered. I'm considering dropping out or transferring to an easy state school back home, so I can breeze through the work and focus on understanding and learning again. What should I do?

I'm sorry you're having such a hard time at college, and I hope things improve for you soon. However, this question is about the high school-to-undergraduate transition, which is a fundamentally undergraduate experience, and this site is about graduate-level education and beyond (as per the [help/on-topic]). (The answer to this question would be very different for a grad student, so this isn't a question that can be generalized to grad study in order to remain in scope.)


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"Awaiting EO Processing" for 2 weeks after submission. Should I contact?
I recently submitted an article to a relatively well-known academic journal in information system.
The journal uses ScholarOne.
After the initial submission, the status of my article has been shown as "Awaiting EO Processing" for more than 2 weeks.
Should I contact the journal at this moment?

I'm aware of many posts on "when to ask the status" for journal submissions. But most of them are issues during/after review process. So I would like to ask this.

It might just be that the editor cannot find reviewers who are willing to read your manuscript. I would give it a month in total and then ask politely.

@George I think it is the editorial office searching for an editor.

Depending on the journal, two weeks isn't really a long time for editor assignment. Your manuscript might be at the end of a pretty long queue that might take time. Moreover, getting the right editor for your topic is also sometimes an issue.
Another point to note is that ScholarOne is not always up-to-date with the process of the publisher. This may also depend on the frequency of updates sent from the publisher's editorial office to ScholarOne.
In my experience with ScholarOne, I had "Editor now searching and inviting referees" for about a month before I received the review result, "Resubmit [with minor edit]". There was no "under review" status in between. Hence, there was nothing to worry about.
If this is prolonged over a month, you may send a polite request for the current status of your manuscript through ScholarOne helpdesk. They are very helpful in this regard and usually reply within a day or two.

As you suggested, my submission moved in "Under review" after 25 days of "Awaitng EO Processing" Thanks!

@Pengin Hi. The same happened to me as well. From "EO Processing" to "Under Review". Can u let me know what exactly "Under Review" meant in your case? Was it the case of editorial review or the case of external peer review? Would be helpful if u let me know.


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What is the difference between Elsevier's 'waterfall system' and 'cascading peer review'?
A lot of people are grumbling about USPTO 9,430,468, "Online peer review system and method", which describes (if I'm reading it right) Elsevier's system of reallocating papers rejected from Journal A to a potentially more suitable Journal B. Parts of the patent describe the general process of peer review and (partly because of this) some of the criticisms currently circulating seem to think that this is a patent on the process of online peer review itself, which would clearly be ridiculous. However, the Electronic Frontier Foundation has picked this as its 'stupid patent of the month' for August, pointing out various examples of a similar process called cascading peer review dating back to at least 2009 (example 1; example 2). Eff clearly has concerns about the novelty of this patent.
My question: what, if any, are the differences between Elsevier's now-patented 'waterfall system' and 'cascading peer review'?
(I'm not sure if this would be a better fit for Law.SE, but thought the audience here would be more familiar with the important areas of the peer review process)

Patents, as legal documents, should not be interpreted by mere mortals (such as myself). Many of the words don't mean what you think they mean, because they have specific legal definitions. Therefore, any lay interpretation of 'differences' laid out in the patent are highly suspect. Generally, that means that we can wildly speculate, but a patent lawyer is the right place to go. (Now, the EFF has/is lawyers, so I'd lean towards their conclusion.)

I'm voting to close this question as off-topic because it's either a matter of opinion or a question for patent attorneys.

@CapeCode I'm not really expecting legally watertight advice here, just an attempt to break down the two processes in plain English and highlight any obvious differences between them. If I wanted a legal viewpoint I'd have gone for Law.SE.

I've asked for clarification from Elsevier's head of corporate relations (https://twitter.com/arboviral/status/773971629198151680) so fingers crossed.

It's unclear that you are actually looking for any kind of advice, legal or not. What exactly is your issue and how do you believe can the users of this site be of any help?

As I said in the question: "what, if any, are the differences between Elsevier's now-patented 'waterfall system' and 'cascading peer review'"? Like (I assume) most of the members of this site, I regularly peer-review papers and grants. I do not review many for Elsevier (I'm not boycotting them, I just don't get invited to do many) so am not familar with their system, and I hadn't come across the concept of cascading peer review before reading the EFF article. I'd like someone familar with both to comment on the difference.

I'm more mystified at the idea of patenting a method of peer review than anything else, as I had not heard about it until now.

I managed to get some more information on this from William Gunn (@mrgunn), Director of Scholarly Communications at Elsevier. So not an official legal statement from a patent lawyer, as he notes himself, but a plain-English explanation from someone familiar with publishing and who has had a chance to ask the people involved, which is pretty much everything I could have wanted. Short Twitter-transcript follows (stripping out Twitter tags; otherwise as written); I'll probably try to come up with a better way to format this later.

@MrGunn: "The Elsevier legal team says this just covers our
implementation & is defensive."
(https://twitter.com/mrgunn/status/777989863748448256)
@MrGunn: "IOW [in other words], not to be used to sue anyone else, just to prevent us
from getting ripped off"
(https://twitter.com/mrgunn/status/777990251667087360)
Me: "Thanks, that's helpful. So what makes system distinct? How do
you tell if ripped off?"
(https://twitter.com/arboviral/status/778146459044745217)
@MrGunn: "(making room) It's common for software companies to patent
their implementations of a more general process. That's all this is."
(https://twitter.com/mrgunn/status/778269748236685312)
Me: "thanks - that helps. So it would only be enforced if someone
literally copied the Elsevier code and tried to pass it off as
theirs?" (https://twitter.com/arboviral/status/778497951232618496)
Me: "Well, not necessarily line-for-line, but if you had reasonable
suspicion that they'd used the Elsevier system as a starting point?"
(https://twitter.com/arboviral/status/778498336156418048)
@MrGunn: "Enforceability of software patents is not a subject I know
very much about, but I would guess so."
(https://twitter.com/mrgunn/status/778606526160175104)

So it's not intended to cover the general process of cascade reviewing, but only the specific implementation used by Elsevier.

I feel genuiunely bad about accepting my own answer, but I can't really imagine getting anything closer to a plain English explanation from an authority close to the relevant information.

This answer is purely speculation.
Looking the file over, there does not seem to be much difference between the Elsevier system and other peer reviewing systems that have already been in operation.  It doesn't look to me like there is enough innovation there for patent protection to be warranted, but I am not a lawyer, so I may be misunderstanding the technical language and/or the standards for patentability.
However, the fact that the Elsevier system is named "waterfall" suggests to me that it was originally developed without any expectation that it would be patent worthy.  Indeed, I suspect that the name was chosen specifically to point out that the "waterfall" package was Elsevier's in-house implementation of cascading peer review.  "Cascade" and "waterfall" are synonyms, although "cascade" is more general and has a standard metaphorical usage that fits well with the description of how "cascading peer review" works.  I find it difficult to envision how somebody could come to the name "waterfall" for the process unless they already had the "cascade" terminology in mind.  (Of course, the people designing the system were likely fluent but non-native English speakers, so they may have seen the "waterfall" analogy as more apt than I do.)
Eventually, people higher up noticed the well-implemented peer review system and, in consultation with Elsevier's legal team, decided to try to patent it.  I suspect that these people were largely unaware of the extent of prior art in this area; in particular, they did not recognize that "waterfall" was an implicit reference to the existing "cascade" framework.  Or if they did, they thought that cascading peer review was too obscure for the similarities to be noticed; and they were right insofar as the patent was granted.

Cascading Peer-Review is the result for focusing on reducing costs and improving efficiency (specially time and improvements on network of journals), many publishers have implemented services to redirect rejected manuscripts to related journals within their field.
It seems the “Waterfall Process” is the same with Cascading Review in the first glance. However we are not lawyers to judge this matter. It can be fully determined by professional review of the claimed patent. But it seems in overall, as EFF states: "The waterfall idea was not new in 2012. The process had been written about since at least 2009 and is often referred to as cascading review."


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How do I check whether I retained copyright for a figure in a paper from ten years ago?
I have been contacted by a student who wants to reproduce a figure from a paper of mine in Phil Trans R Soc B (this one, in case it's pertinent) in their thesis. The paper itself is apparently not under a CCAL (I normally choose this option if it is available, but it looks like it wasn't for this one), and I can't find any record of the copyright agreement at the time - the manuscript was submitted about ten years ago.
The journal has a link to the Copyright Clearance Centre for requesting permission for reuse; I ran the form myself and it seems that the student can pay a fee to get permission from the journal to reproduce my figure. That is not my question.
My question is, how to I check whether I transferred copyright for the figure at the time? If I didn't I can presumably just send him the submission version of the figure.
I tried searching the Royal Soc website but it seems surprisingly difficult to find this (which I have noticed before with Elsevier; I think they'd rather we assume they always get the copyright).
Related: How to legally re-use images in paper and still continue to use and distribute them in slides? (but this is about a situation where the copyright transfer status is known).

Unless the paper is open access, the publisher usually holds the copyright. This can be seen in the imprint on the first page of the paper. If it says "(c) the publisher" then the publisher holds the copyright, while if it says "(c) the authors" then it's the authors who do.
In the case of your paper though, the Royal Society's plagiarism, copyright and intellectual property page says

Authors of non open-access papers retain the copyright, but grant the Royal Society the exclusive right to edit, adapt, translate, publish, reproduce, distribute and display the article in printed, electronic or any other medium and format.

I'm no lawyer, but I take this to mean that while you cannot distribute the paper in its final form, you can distribute a single figure.

I thought normally the journal only held the copyright to the presentation of the content, not the content itself? Hence you're allowed to host preprints on your personal websites, etc, but not the published version. I'm just not sure how that applies to figures, even if it's true.

Usually a figure is a sufficiently substantial piece of an article to be copyrighted together with the article. So you may only distribute it with the consent of the entity that holds the right to distribute, even if it's separate from the article.

@arboviral policies vary from publisher to publisher, but yes, my educated guess is that you're correct. You can use the figure that you have (i.e. before the publisher did anything to it), but not the figure that's in the article directly.

@arboviral Presentation vs content means something like this: if you published a graph or table of some data you collected, the publisher cannot use their copyright to prevent you from sharing the data itself. The data are the content, the graph/table is the presentation. Similarly, copyright cannot prevent you from telling other people about the conclusions of your research. However, I doubt that logic applies to sharing a preprint of a published article, nor to sharing a figure taken from it. The relationship there is more likely one of "derivative works", not content vs presentation.

I'm also suspicious of the argument in this answer that distributing a single figure is okay. I could easily see that qualifying as editing or adapting the paper, followed by distributing it, so it'd be illegal on two counts. I think it'd be better to clear this with a lawyer first.


text:
When should service providers (core or external) expect authorship?
There are a number of areas of biology research where specialist knowledge requirements or expensive equipment mean that it's more efficient to outsource work to core or external facilities. This seems particularly common for next-generation sequencing (here and here), transcriptomics and proteomics, but Science Exchange is based around this concept and I'm aware of proposals for similar models in other areas, e.g. for work with pathogens that require high containment. The Diamond Light Source offers something similar, too.
On the whole this seems like a good thing; it has the potential to reduce duplication of investment in infrastructure, increase use of nationally-funded resources and facilitate multidisciplinary and interdisciplinary research. However, I've recently heard a few people assume that a commercial service provider is ineligible for authorship, even in situations where I strongly suspect they would normally include someone as an author if they were doing the work for free. I'm also aware of situations where collaborations have faltered due to differences of opinion over this.
Personally, if someone has made a substantial and unique contribution to designing the experiment, running the experiment and analysing the results, I think I'd be uncomfortable not adding them as an author. Not to mention that such a paper could easily end up including experiments that none of the authors knew how to design or conduct. I'm pretty sure there are a lot of papers out there now reporting NGS which none of the authors could actually have generated without help.
How should commercial service providers be acknowledged in papers reporting work they assisted with, and does the fact that a service is paid for change the criteria for authorship? Is this affected by whether the PI pays for the access, or if the access is paid for from a central budget?
Good-subjective answers only, please. I'm particularly keen to hear personal experiences or evidence from the biological sciences (hence the biology tag), but would welcome answers that compare and contrast this to other fields.

In materials science, there are many companies that will provide a service for payment. Examples include places such as the Evans Analytical group (once Charles Evans) for materials analysis of many types. You send them a sample, they send you results from generally standard analytical techniques. It is a purely transactional relationship - they get paid, you get the data. You generally would indicate in a paper that the analysis was performed by them, but they do not get authorship. The same goes for various other things, like ion implant houses - you send a sample, they implant with the ion species and dose. You are getting a standard service performed, not intellectual effort.
There are other situations where you need to interact with the external entity to develop a new technique, or new twist on the technique. This is no longer purely transactional, and may result in authorship. Clearly the reverse can also happen - if you are a beta site for a new instrument and are working closely with the company to test it and expand the capabilities, you would get on any papers written by the company as well.
My analysis: if you and anybody else can walk up and pay for the service, they are not co-authors. If you have a joint project, with dollars and intellectual effort from both sides, they are. And then there is a broad grey middle ground...


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Life sciences publishers that support/encourage collaborative manuscript review?
Full disclosure: I'm asking this as a displacement activity while I should be reviewing a paper.
Given how well journal clubs etc work, it has occurred to me a few times that reviewing a manuscript as a group would probably result in faster turnaround and more detailed comments. However, typically journals approach individual reviewers and place confidentiality restrictions on the reviewer so this mechanism wouldn't work. Does anyone know of any journals, ideally in the life sciences, which support or even encourage collaborative peer review of manuscripts?

Your idea makes perfect sense to me. If it takes a group of authors to write a paper, why can't another group of people review it?

Most of the European Geosciences Union (EGU)/Copernicus journals do something sort of like this - they've been doing it for some years and it mostly works out well. The journals are fairly reputable in their fields and from what I can see authors seem to like them.
EGU describe them as "two-stage journals with public peer-review and interactive public discussions".
Unhelpfully for you, though, these are all geosciences. (List)
The process is:

article submitted
posted as discussion paper after initial approval by an editor
reviews & responses posted publicly, with third parties able to post uninvited reviews

The system still works on individual not collective reviews, but the fact that they're public potentially allows them to build on issues raised by each other, and I can't see an obvious reason they wouldn't accept a review contributed by a group.

Elife is a relatively new, high-impact (8-9 Impact Factor if that's important for you) life science journal that does something along these lines:

Reviewers get together online to discuss their recommendations, refining their feedback, and striving to provide clear and concise guidance. If the work needs essential revisions before it can be published, the Reviewing editor incorporates those requirements into a single set of instructions.

I have heard from authors/reviewers that this review procedure often works well (but it is not perfect and has its own disadvantages). Elife also has other interesting features, I recommend looking in their website.

Many thanks for this - I had heard of eLife but didn't know any of these details.


text:
Correctly licensing someone else's photo for publication in open-access journal
When articles are accepted by open-access journals such as PLoS journals, the editors sometimes ask for a 'striking image' to attract attention to the paper on the contents page (see examples here; every paper has an accompanying image). When in this situation in the past we have used images which I or my institute own, but I know a couple of very good commercial photographers and can easily see situations where their images would be more suitable. What sort of license would I need to buy the photos under in order to have the authority to give the journal permission to publish them under a CC-BY-3.0 license?

Buy the work under a contract that gives you exclusive license or copyright transfer under which you can sub-license or transfer to the journal publisher.


text:
Email sample for requesting a dataset for a joint paper
Im interested in collaborating with a researcher and he is willing to collaborate and share his data with me for the joint paper but I need to send him a formal email and ask if I can look at the data and use it for the paper? Does someone have a sample email?
Many thanks

Roland: Make it an answer.

As you say that he is willing to collaborate, that means that you already talked to him about it and the formal email is just a prerequisite for his institute/university. Thus, it is most likely different from others and unique to this case, so it would be best to just ask him directly about the format he needs.

Thank you for your response. Where can I find a sample of a formal email for a general request? it could be for any institute or university, I just need to take a look at a sample before. Thanks

Oh my gosh. As mentioned above, they agreed already, thus the mail is a formality. Now, just be formal.

Dear Prof. Tihiy,
Would it be possible for me to access the raw data from your recent work "Sepulki and Sepulation"? I am planning research on the forms of sepulation in vaccum and your data would be of immense importance to me.
Of course, should my research be fruitful, a <meaningful outcome, such as a joint paper> would arise.
Best regards,
John Doe

When you write an e-mail to a professor, do you not capitalize the first word of the first sentence? Bad example.

Notice the comma instead of full stop after the name.

Why, after the salutation and name of addressee, followed by a comma, is the following word capitalized?

Oh, oka-aaay. It's different then in English than in my native language.


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why do some research articles not have issue number?
How can I get the information for issue number for this article?
I am trying to cite this article
https://www.sciencedirect.com/science/article/pii/S004060901300117X?via%3Dihub
doi: https://doi.org/10.1016/j.tsf.2013.01.016
this is what I got from doi2bib.org:
@article{Taylor2013,
  doi = {10.1016/j.tsf.2013.01.016},
  url = {https://doi.org/10.1016/j.tsf.2013.01.016},
  year = {2013},
  month = mar,
  publisher = {Elsevier {BV}},
  volume = {531},
  pages = {354--361},
  author = {A.A. Taylor and M.J. Cordill and L. Bowles and J. Schalko and G. Dehm},
  title = {An elevated temperature study of a Ti adhesion layer on polyimide},
  journal = {Thin Solid Films}
}

Clicking on the volume number for this paper at the web page you gave for the paper itself, I was led to this, which strongly suggests to me that for this journal (and at this time; may have been different 10 or 20 years ago) a volume is not separated into different issues.

do you have any idea about suppl/C in the link?
https://www.sciencedirect.com/journal/thin-solid-films/vol/531/suppl/C.
for now, I put supplement C in issue field.

I get what looks like the same content when I remove /suppl/C from the URL, so I have not idea what "suppl/C" is. However, I don't think "suppl/C" should be used for an issue designation. If you go here and click on "1981 --- Volumes 75-86", you'll see that, in the earlier years of this journal, issue numbers were used, but it appears they were phased out sometime in the early to mid 2000s.

yes, there are some variations even after 2000s.
so, should I write --, or leave it empty, or any other idea?

Maybe just ask the journal when you submit your article? All my references were just typed directly in, and I simply followed the style of the journal (italicize paper titles or italicize journal titles?, etc.), but I haven't submitted anything in the past decade or so. In fact, my present style (for informal posting on the internet) has evolved into giving full names, full journal titles, volume/issue and date as precise as I can determine, etc. as in these examples, but I don't know whether you have this freedom.

@DaveLRenfro is correct - for Thin Solid Films each issue is its own separate volume. TSF isn't the only journal that does that these days either.


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Was I wrong to rebutt unjustified rewiewer comments in the review?
Recently submitted a manuscript which got a decision of Reject & Resubmit, i.e. the editor invited a resubmission provided we can address the reviewer's comments. In my previous experience, all my manuscripts were always accepted after a resubmission was invited, so I thought the editors basically use this type of decision to give themselves a little more leverage.
One reviewer's comments were very negative, but unjustifiably so. For example, he/she stated that the "experimental treatments" weren't independent, while our study was purely observational and didn't include any experimental manipulation. The comments looked like they were made by someone who didn't bother to put any thought into the review and had a poor understanding of statistics (our study is loosely in the field of ecology/conservation).
We rebutted these comments firmly, but politely. The other comments, including those made by the second reviewers, were minor and were addressed by revising or clarifying the text in certain places.
We also explicitly drew attention to the issue with one reviewer's comments in the cover letter accompanying the resubmission. We stated that we carefully considered these comments, but they were unjustified, and again explained why.
This resubmission was rejected outright very quickly, within a week. The editor acknowledged the revision did improve the manuscript, but still rejected citing the standard "our acceptance threshold is very high" etc.
It is the first time my invited resubmission was rejected, and I can't help wondering whether the firm response to the reviewer's comments was the cause.

It's fine to push back against reviewer comments, but it can be a bit of a delicate dance to do so.
First, I would suggest you take reviewer comments that are unjustified to mean that you didn't do a good enough job explaining what you did. Although it's possible the reviewer was simply sloppy in reading your paper, a lot of people are going to sloppily read your paper: give them as few ways to get it wrong as possible by being extremely clear. Communication is between the reader and the writer: it isn't only the reader's fault if the reader gets it wrong. You can apologize for your role in the miscommunication and do better in the revision.
Second, I would suggest whenever you plan to push back against large parts of an individual review, rather than just a modest misconception or two, have a less-involved person that you trust to give honest feedback review your remarks. Sometimes a coauthor with a smaller contribution is sufficient (i.e., not the primary or senior author, who may feel most personally involved in the work), other times it may be helpful to reach out to someone else outside the authorship group. Ask them explicitly whether they think your response is sufficiently polite. Ask them to play the role of that reviewer or the editor. Additionally, give yourself a bit of time to sleep on both the reviewer comments and your response, at least a day or two and maybe a week or two. Personally, I sometimes write my angry/snarky response in a private document for myself to "get it all out", spend a couple hours complaining to people close to me about how worthless peer review is, and then come back to the original comments later and start working on real responses to what turns out to be helpful criticism. You can skip the first two parts of that if you want, but the last part is crucial.
Third, make sure you aren't really missing something in the comments you think are unjustified. Your question here is vague, so I am only guessing, but you say:

he/she stated that the "experimental treatments" weren't independent, while our study was purely observational and didn't include any experimental manipulation

If you responded to the first part of that comment and say "this comment doesn't apply because our study was purely observational" I would, as the editor, probably reject your paper. The real, important comment there is the lack of independence, which is often a critical weakness in an observational study. It may be that you interpreted your data in a way that implies an experiment has taken place, when it hasn't, and that makes the reviewer's comment very very relevant, even if they misused the word "experiment." Be careful that you haven't used causal language, that you have done field-appropriate comparisons between any groupings you made in your observations, etc.
Finally, it's quite possible for you to do everything "right" and still be rejected. For a more selective journal, especially, an editor may reject if there is insufficient support from the reviewers, even if you are able to refute some of the criticisms. They are looking for papers that the reviewers agree are excellent, and it's possible that observational work is simply not a good fit for this journal.

+1 for "I would suggest you take reviewer comments that are unjustified to mean that you didn't do a good enough job explaining what you did." and the rest of this excellent answer. There are usually very few truly unjustified comments in peer review. Additionally it is important to obtain some emotional distance to the reviewer comments (sleep one night). Then it is easier to spot the helpful parts in the more difficult comments, and to improve the manuscript accordingly.

@Alexander Agreed, though I might suggest a week or two rather than one night. :) I had that in mind when writing my answer but didn't include it, I'll add it now.

Having been in the OP’s shoes, I’ll note that even a week may not be enough distance.  It took me and my co-authors a complete rewrite over the course of several months, a one-on-one analysis of the rewritten paper between one of the co-authors and a friend in the field who was not involved in the research, and then two more complete rewrites before we got our paper accepted.  In all of that work, not once did we do what the original reviewer suggested, it was all about changing the framing of the paper so subsequent readers wouldn’t make the same mistake.

Whenever you get a negative reviewer comment that misunderstands an issue in your paper, or is otherwise unjustified, you should take that as a signal that you have not explained the relevant issue sufficiently clearly.  The response should therefore usually entail a substantive change to the paper (to add a clearer explanation) accompanied by a response to the referee comment that identifies the additional explanation, perhaps with some additional discussion justifying your change.
Aside from improving your paper, one advantage of this approach is that it gives the referee a response that shows that you do not think he/she is stupid or misguided.  By putting the blame on yourself, you avoid a negative reaction from the referee (or editor), and by making a substantive change to the paper as a result, you show that you have improved the explanation so that others will not misinterpret the paper in the same manner as occurred in the referee comment.  Also, this kind of change usually does entail an actual improvement to the paper, since it prevents other readers from making the same mistake as the referee.  Here is an example of what this would look like.

Referee: The experimental treatments in the study are not independent.
Response - Revised: On review of the paper, we can see that we failed to adequately explain the experimental setup.  Our study is actually an observational study, which did not entail any controlled treatment variables (i.e., the explanatory variables were observed without intervention).  There is indeed multicollinearity between some of the explanatory variables, and we had not addressed this sufficiently in our previous draft.  We have now made a number of changes to the paper to clarify the experimental setup, and to discuss the effect of multicollinearity between the explanatory variables.
We have now added an additional sentence in the methods section (p. 3, line 8) to note explicitly that this is an observational study, and to stipulate that we have not "controlled" the explanatory variables of interest.  We have repeated this in the results section, in our remarks on the difficulties of making causal inferences from the data (p. 12, lines 14-16).  We have also added an additional paragraph to the results section (p. 11, para 2) discussing the multicollinearity in the explanatory variables, and its effect on our inferences.  For the reasons set out there, we are satisfied that multicollinearity does not invalidate our statistical inferences or conclusions in the paper.

Unless your literature uses a different terminology, a reject and resubmit is not a review and resubmit. The editor will have told you what you have to do, before submitting again (from fresh). Typically this means a larger revision of what you have done. Therefore, it's a rejection: to let you know that the hurdle of acceptance is higher, and there is much more work than usual required. With that information, you may simply want to submit elsewhere instead.
However, a new submission also means that the editor is free to change the reviewer if they want to. A Reject+Resubmit is often a nice way to get rid of a reviewer that the editor regrets having assigned to a paper.
For this very reason, if indeed you have a reject+resubmit and not a review+resubmit, do not dwell on the reviewers' comments, but focus on what the editor wanted. Did you really manage to address everything you were asked?

Yes, there is nothing wrong with writing a rebuttal whenever necessary.
However, carefully ensure the response to the reviewer's comment is not directed personally at the reviewer (this should be observable from your tone of response and choice of words), rather it is directed at the comment.
Also, try to remind yourself (or pretend if that be the case) that the comments are not directed at you but the content of the paper. This implies that while responding, ensure that you emphasize that the content of the paper (or the revised paper) has answers to the reviewer's comment.

If they were indeed unjustified, it is certainly good to correct them.  But you must think, "Am I right?" or is the other person right? (in this case the reviewer).  Being right is not a shield, however, for the necessity to be polite at all times, and treat the comments with respect. Often adding clarification (such as which of some instance of something you are using) can make it more understandable.  So, respond would be a better usage than 'rebut'.  The latter implies a possibly negative response.  (NOTE: in my post, I originally had 'rebuke' here incorrectly, and that would be very negative).  However, according to dictionary.com 'rebut' does have negative as a related word:
https://www.dictionary.com/browse/rebut?s=t


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Should I recommend rejection for a paper I referee if the authors don't make changes that they could have made?
Earlier this year, I received a paper to referee for the top journal in my field of research.  I know both of the authors.  The first recently completed a Ph.D. working with a friend of mine.  My faculty friend is the best-known person working in our area; he is an extremely careful and conscientious researcher, and working under him, the student produced some very good work. The other author of the manuscript I'm refereeing is the new post-doctoral supervisor of that recent Ph.D. grad.  He is a very senior but not terribly distinguished scientist, and I think that some of his work is rather slipshod.
The first manuscript draft I got from this pair of authors had a glaring problem.  There may have been a fundamental error in how they interpreted their results.  There are two different ways that the system they are studying could behave, and they assume that it goes one way, apparently without even noticing the other.  They might well be right about how the system behaves, but I sent back a report saying that the work would be publishable if they either explained why they only considered one of the two possibilities or expanded their analysis to cover both.  The final conclusion is likely to unchanged whichever way the system behaves, but it is important to verify this; moreover, it is interesting in its own right to know which way things go.
After a rather brief period, I got a revised manuscript back from the journal.  The authors had made a number of other minor corrections that I asked for, but they basically ignored my main point.  At this point, I'm not sure what to do.  I still feel like the paper contains a significant amount of interesting material, and it could be fixed without that much effort.  However, I am upset that the authors made not effort to fix the actual problem I pointed out.  They don't even really acknowledge the problem in their resubmission letter.
I was the only referee who turned in a report on the first draft, so what I say will almost certainly determine whether the paper is published.  Should I send it back one more time, insisting that the changes I called for actually be made this time?  Or should I recommend rejection, since the authors are apparently unwilling to make reasonable adjustments.

Is it well known that there are two possible ways in which the system could behave? Have you backed up your claim with references? Was your remark sufficiently strong to convey its importance?

I spend about two thirds of the report discussing the matter, so the authors must have willfully avoided responding.  I suspect that the authors had not realized that different behaviors were possible when they wrote the paper.  They made an assumption, based on how similar systems behave; however, the very features that made the more complicated system they decided to consider interesting also make it possible that it could behave differently.  That might not have been obvious when they were thinking about the problem, but it occurred to me as an obvious question when I read the manuscript.

@Ben Crowell:  The paper could still be a worthwhile contribution if they actually made the changes, which makes me hesitant to reject it out of hand.

It's totally reasonable to be upset that the authors ignored your comments, but for the purposes of reviewing the paper, I think you should set that aside.  I would let the editor make the decision as to whether the authors are "unwilling to make reasonable adjustments".  Send him/her a note saying something like:

I mentioned in my initial report that it was essential for the revisions to address the issue of XXXX, but this has not been done, nor mentioned in the authors' comments.  This paper has many good qualities, but I do not think the paper is suitable for publication if this issue is not addressed.  If you feel it is worth the time to ask the authors for a further revision addressing this issue, I would be happy to read it and give my opinion.

I think it's up to the editor to judge between "this is a paper I really want in my journal, so I'm willing to put up with a little bit of crap" or "the authors are wasting our time, to hell with them".

@nateeldregdge: As an editor, I rather have reviewers come to the point than be circumspect. "This paper has many good qualities, but..." and "If you weel it is worth the time..." really don't adequately communicate what you think. Be blunt: "I believe that it is important that the authors address the issues raised in the first review, but they have failed to do so." It's the editors job to make a decision, your review does not need to point this out.

I find the response clear. It makes the expertise statement and makes clear that it is ultimately an editorial decision.

If it is indeed the case that:

The potential flaw really could fundamentally change the conclusion of the paper, and
The authors didn't even address your issue at all even in their response letter

then I would recommend rejection.
When doing a major revision, it is imperative that the authors at least speak to every point raised by the reviewers in the response letter, even if it is just to say: "No, we will not do this."
If an author blatantly fails to address a critical issue, then I feel that it is reasonable to conclude that they are avoiding the issue and recommend rejection.  If the issue is important but not critical, or if you disagree with how the authors address it, then I think it is better instead to recommend major revision.
Even though you recommend rejection, if the editor wants to give them another chance, they can certainly do so.  Similarly, even if they are rejected, they can amend their ways (or not) and go to another lower-level journal.  So: vote your scientific conscience.

Should I send it back one more time, insisting that the changes I called for actually be made this time? Or should I recommend rejection, since the authors are apparently unwilling to make reasonable adjustments.

As long as they don't even react to the remark, the polite move would be to assume a good faith communication problem, especially given the amount of involved people. So I'd just ask for another revision and point out the remark was not addressed anyhow.
Personally, I'd avoid being subtle once they missed the point, so I'd just spell out that the authors should address the remark (in the paper), convince you they shouldn't in the resubmission letter, or you will recommend rejection. To avoid being too negative or aggressive, I'd also put in positive comments — say, you expect the point to be easily addressed.

I was already very explicit about what they ought to change.  The only possibly conclusion is that the authors willfully ignored the main point of the review.

@Buzz: or they didn't communicate well with each other on who should address the issue. Or the two "good authors" trusted the author you don't like to deal with it and he didn't. I've seen from close much more complicated screwups, so I won't try to cover all possibilities.

There were only two authors on this paper, the recent graduate and his new postdoctoral supervisor.  I don't think poor communication between the two of them is likely, although extreme incompetence could always be an explanation.

You should encourage the editor to get a second opinion. If you feel strongly, you should reject the paper again citing or repeating your comment about the alternate explanation. Based on what you've said here, it seems likely to be important.

I'd add an option of contacting them directly - if this has not yet been done. Seeing as both authors are apparently well known to the OP this might facilitate things.

@Nox: Assuming the journal uses anonymous refereeing, many people would consider it to be inappropriate for the OP to contact the authors directly (thus revealing his/her identity).  See http://academia.stackexchange.com/questions/9523/is-it-acceptable-as-referee-to-contact-an-author-on-a-paper-you-review

It seems to me that you should write a brief review which starts by saying something like "I recommend rejecting the submission X, on the grounds that the paper fails to even consider a plausible alternative interpretation of the experimental results, and thus the theoretical significance of the paper is indeterminate". In my review, I would reiterate the essential points about the alternative made in the earlier review, and I would also state this as an "I already mentioned this" summary. It is scientifically not acceptable to claim or imply that a specific conclusion has been established based on some evidence, when in fact multiple conclusions are consistent with that evidence.
It is not clear whether your previous recommendation was "revise and resubmit" or "reject" -- I assume it was "revise and resubmit", otherwise it would be strange for the paper to have been revised and resubmitted. I think therefore that it would be useful to explain to the authors and the editor the rationale for a more strongly negative recommendation, when the paper has not (apparently) gotten worse. A number of journals use the "one round of revision" standard, where you judge that after one revision, the paper is likely to be acceptable. Under that standard, if you judge that a paper is likely to be acceptable after one revision, it should be rejected. A corollary is that if a paper turns out to not be acceptable after a single revision, it should be rejected. Now, I do know of journals where 4 rounds of revisions are tolerated, so you may not be able to contextualize the "reject" decision based on announced journal policy, but you can certainly adopt such a standard, implicitly or explicitly, as your own quality standard for acceptance.

My first review was not a rejection, but it called for a major revision.  The journal guidelines set a goal of determining publishability with at most two revisions.  That gives time for major revisions, if necessary, then minor revisions that can be identified on a second round of reviewing.  However, the review process can, at the editor's discretion, go on quite a bit longer.


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Can a professor do an internship?
Can a professor (let's say a math professor) do something like an internship at a tech company during the summer as a way to keep their industry skills sharp / relevant? Does anyone ever do this?
Perhaps the word "internship" is not quite right, but the idea would be to show up, be useful for 6 weeks or so, then go back to the university and teach students relevant real-world skills they'll need in industry.

I think that unpaid internships would be rare and there would be legal difficulties in some cases. But short term subsidized employment works. There are also nondisclosure agreements to contend with. These two things are related, actually. How can a company require your silence on things you learn about if it gives you nothing in return?

They often do sabbaticals e.g. http://muratbuffalo.blogspot.com/2018/08/azure-cosmos-db.html

Feynman did it (at least) once - http://longnow.org/essays/richard-feynman-connection-machine/ - it was a typical internship too: he got the result they asked for and they ignored it.

Anecdote: I worked at a data sciencey startup. We had a professor come work with us for a few weeks, do some work. We enjoyed it, he seemed to enjoy it, it all seemed very normal.

No...Nobody is really useful in 6 weeks time. You are learning new the business language, processes, the nature of the products and services...etc. What a professor should do is take a sabatical to start a company with several other people. And then after 6 - 12 months, go back to teaching, while providing a few hours a week of guidance for the business (Attend meetings, meet with clients, etc)

Yes, but they are usually called "visiting researchers" or, in some cases, "residents", rather than "interns". See for example Facebook, Microsoft, or Google.

I've spent quite a bit of time during summers as a visiting researcher at Microsoft. Although the official title is different, visiting researchers are classified as "interns" for many administrative purposes.

@AndreasBlass I can see that, given that it's basically the same thing on a different career stage. I guess as a professor it's easier to sell to your university administration that you are spending your sabbatical as a "visiting researcher" rather than an "intern".

I think the reason for lumping "visiting researchers" together with "interns" is that both are temporary employees, appointed for a pre-determined and rather short interval of time (usually a two or three months). My official appointment letters never contained the word "intern", and the job description was, of course, quite different.

I know a full professor at Stanford who spent a semester at Google; his official job title was "intern".

Yes, absolutely. I am not able to answer for every discipline and country, but this is common in many places. There are company schemes, government schemes, charitable schemes and university funded schemes to support such arrangements.
For a specific example, in the UK the Royal Academy of Engineering provides Industrial Fellowships to support such activities.

+1 for this existing in the UK. There's several emails in my inbox about this right now. It's a boon to the Unis as they not only get you fresh for teaching, but they hope research collaborations and partnerships (and ££) will come from it.

Mathematics professor Robert Talbert, in a 2018 article titled "What I Learned On My 'Secret Sabbatical' As a Scholar-in-Residence at a Private Company", described how he was an intern for a year at the furniture company Steelcase:

Last fall I started my first day on the job as an embedded faculty
  member with a corporation—as a scholar-in-residence at Steelcase
  Education. But don’t be too impressed by the title; according to the
  employee system, I was just an intern.
Actually intern is probably the best lens through which to look at
  what I’ve been doing at Steelcase for the last eight months. I was
  nobody special: Just a guy, at the bottom of the org chart, working
  with and around a lot of people smarter and more talented than I am in
  any number of ways, and tasked with making their work and the
  collective work of the organization better. It’s kept me a little bit
  humbler than I would have been otherwise.

He also wrote about this experience in this answer to his own question on Academia.SE.

The short answer is of course.  But it isn't necessarily going to be easy to get your foot in the door for a short time.  You would almost be better off applying for jobs and then giving your notice before returning to teach.
There are two issues at play here.

The company the professor would intern at would not want to sink cost into temporary training.
The company would not want to expose private data.  Especially to a mathematician that would usually mean working with customer data or insights, or company revenue etc.  Companies usually don't want to expose themselves or their clients data to what would be a temporary hire that isn't getting vital work done.

Basically, a company tends not to want to hire or give space to someone who isn't going to produce some results or profit for them.  If a mathematics professor genuinely expressed interest in helping the company in exchange for learning about the industry along the way (to benefit students as well) I do believe that it would just be a matter of communicating with enough companies.
Heck, it would probably benefit the professor to say that they will recommend future graduates to that company if they allow them to learn about the industry.

Just take a Sabbatical, which lets you take time off to work in-industry. Some universities require you to take a sabbatical of a certain length at fixed times. It's odd that you haven't run into this, unless you are relatively new.
The problem for you is that it won't be 6 weeks, it will be closer to 6 months. Nobody can be useful in 6 weeks, so you can't get cutesy over-the-summer work, especially not unpaid.


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Salutation for a letter of recommendation to be uploaded to mathjobs
What is a standard opening salutation for a letter of recommendation to be posted on mathjobs?
One possibility might be, "Dear hiring committee", or "Dear search committee".

I always start my reference letters with “Dear committee members”.

Most of my math recommendation letters do not have an opening salutation.  They have the date at the top right, and the first sentence orients the reader with something like "I write to recommend Dr. X to you for..." If I recall correctly, this is fairly typical for such letters.  I am more confident in saying it doesn't matter: in general, the format for these letters is all over the place, and no one cares.

I agree that it doesn't matter. I usually use "Dear Colleagues" but I've also used other salutations without feeling any need to worry about them.

There is the widely used

To whom it may concern:

and also

Dear Sir/Madam:

+1 "To Whom It May Concern" still works. Some people might think it is too old fashioned but I have been using it everywhere with no problems.


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Reverse engineering the acceptance rate?
Assume that we have an educational instance X which requires a certain prerequisites (mininum TOEFL, GRE score, etc.). In total 100 applications have been received and 50 students have failed to score above the minimum threshold while the remaining 50 have scored above it. The acceptance rate is given to be 10%.
Is it calculated basing on all applications or only the applications that have passed some certain criteria?
In this case,

if taking into account all applications => 10 students accepted
if taking into account only those who meet criteria => 5 students accepted

I would suspect that the acceptance rate is calculated against the total number of applicants (so 10 acceptances). But, unless you read the number in some official document that also precisely specifies how exactly this number is to be computed, I don't think you can (i) say for sure what it means, (ii) assume that the number is accurately computed against any particular approach you know, or the person who computed the number knows. For example, if you get the percentages of acceptances from a department web site for the previous 10 years, you have to expect that these ten numbers will have been computed by different people and with different definitions.

Is it so? So a new technique every year? Sounds a bit weird to me...

Why not? Likely the newest admin person gets the assignment, with no requirement for being statistically accurate. The number is not a high confidence data point.

Like @JonCuster said. If I were the new graduate director and had to provide the number to someone or to the website, I'd skip the step of asking the old graduate director how they calculated it. That's not worth my or her five minutes.


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Applied vs academic future goals
The universities and programmes I am going to apply emphasizes their research, hands-on experience, startup environment, etc as well as strong academia.
Is it fine to state in the Statement of Purpose that after graduating I would like to apply the knowledge to non-academical area?

As opposed to lying?

Is thin an undergrad or grad-level application?

Considering that the alternative would be to either write nothing about your future plans or to lie about them, it seems clear that sticking to the truth is the best option. I myself find it convincing and a good motivation if somebody says the she wants higher education to use it for some practical purposes afterwards.

If that's your plan, I don't see why you can't say that. I think that you institutions know that not everyone who does a thesis has to work in Academia!
If you are worried that mentioning that would hurt your chances of being accepted/getting funded, then I can see that some schools/faculty might shy away from your application (although in theory, they shouldn't! [depending on the institution]).
Remember, people change their opinions with time! Maybe after a while you want to work in Academia! Maybe someone who stated that they wanna work in academia in their SOP, decides to not do that few years in their program. This is why I'm saying it shouldn't matter that much ch.
Once you get your degree, you can anything you want!


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Is it acceptable for university to ask for detailed financial report?
I'm applying for a university in the USA and one of the section requires to enter up to five previous employees, their contacts, start/end dates, hours per week, and salary. I mean, that some of the previous aspects are considered personal in Europe.
Is it acceptable for university to ask for financial data and should one provide full, candid answers?

"Up to five" would include the option of zero.

Are you applying for admission to a graduate program or for a job (e.g. a post-doc, visiting professor, or tenure track position?)

@BrianBorchers no, for graduate degree studies.

Outside of business schools, this is very unusual in my experience.

@BrianBorchers yes, the school I'm applying to offers technical education only.

As far as I know this is quite normal, also in Europe.

I'd say those details are a bit too detailed for comfort, especially for a graduate admission programme. However, the technical rationale behind could be that they might have some consideration for scholarships based on the financial details you provide. In the end, it is your decision.
If you are still concerned about the necessity of those details, you may request the respective department of the University for a clarification of the reason behind them.


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Subjective grading scale: US vs Europe
I currently hold a Bachelor's degree in Pure Mathematics and my plan is to pursue a Master's degree in the USA. However, I'm a bit worried about the possible non-injective grading scale transition that exists between the USA and European universities.
What I mean here is - majority of the sites out there postulate that ultra-high GPA of 4.1+ is required to get admitted into top USA universities. I've also read about the scaled GPA where the topmost grade is 4, so this might be the case of my university.
Another issue was that getting a good grade, for example 8,9,10 (almost impossible) out of 10 points, was really, really hard. Moreover, I remember myself happy getting 4 out of 10 points in a specific subject. On the other hand, I know some friends of mine who study Humanitarian Sciences and get top grades all the time... So is there some difference when comparing the fields of study?

What exactly is your question?

A common way of translating grades is with percentiles.


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Why some universities don't require GRE AWA section?
I've been rereading the admission requirements of the universities I've chosen and stumbled upon the fact that only Verbal Section and Quantitative section have certain threshold that has to be reached, however, nothing is said about the Analytical Writing Assessment, also known as AWA.
Is the AWA score is merged with the Verbal score or is it irrelevant to some universities (since nothing is said about that particular section)?

It's only a guess but as an admission committee member I have weighted AWA lower than the other two as well for the following reasons:

The range of the score is pretty narrow (0 to 6 with 0.5 increment) and according to the guideline, it appears a good tool to find out who can't write, but not who can write well. Anything about 4 is kind of hard to tell.
Verbal and Quantitative have algorithm that is carried out by machine. AWA is graded by hand, thus can make admission committee feeling doubtful about the objectiveness or specificity to their program ("GRE's thoughtfulness is not our kind of thoughtfulness!!"). And I'm not to say algorithm is perfect, but it may still beat grading by hand (for instance, you can get locked into a low-score path just because you got the first question wrong, making the first few questions more determining than the rest.)
Most of the writing skill and thought process can be gleaned from the personal statement. (Of course, conspiracists can also argue that the statement may be written by someone else. But they should also know that all GRE writing topics are publicly available (1, 2). Two of them will be randomly selected and presented in the test. In a way, the students could have also gotten external help on this part prior to the test as well.)

So basically, any person who has the score above 4.0 threshold can be considered valid for the admission?

"So basically, any person who has the score above 4.0 threshold can be considered valid for the admission?" No, for me, anything lower than 4 may indicate problem. Anything higher than 4 is vague. I usually also refer to the statement and related grades/projects/papers, etc. Most admission committee members don't make or break an application based on just one number, bur rather validate the decision with a more all-rounded consideration. Also, institute by institute there can be differences in practices as well.