text:
Is the correlation between learning a subject and having high grades strong?
I've found myself in a paradoxical situation. I have failed modules over and over, many modules, some modules more than once. One of the failed modules was introduction to computing. After passing it I felt an urge to write lecture notes because I though that the "official" lecture notes made by two teachers of the computer science department were too shallow and unappealing. I took some time to write it and publish in a free webhosting service.
Now I'm feeling like continuing that type of work, expanding it to more modules, such as physics and calculus. It seems that explaning things with plain english, doing comparisons and following a straight path is kinda easy for me. Although I did fail so many modules so many times.
Is the correlation between learning a subject and having high grades strong?
Conversely, is the correlation between not properly learning a subject and having really bad grades strong?

Have the notes you wrote been used in lectures and rigorously assessed? Or, to get more to the nub of it, how do you know that you've learnt any of these subjects?

There's no general answer to the question. It depends on the individual course.

If the course is designed so that grades are earned for demonstrating achievement of a learning outcome, then there will be a strong correlation between having high grades and achieving the learning outcomes of the course.
If the course is designed so that grades are earned for things that don't demonstrate achievement of a learning outcome, or so that students can achieve a learning outcome but not have an opportunity to demonstrate it to earn a grade, then the correlation will be weak.

Also, your general description of "learning a subject" may not necessarily be strongly correlated with the desired learning outcomes of a course. It's possible to earn a poor grade for a well-designed course even after having "learned the subject" if the course has specific learning outcomes (i.e., "Students will know how to solve a certain class of problem," "Students will have learned this particular skill") and what you are learning about the subject happens to be orthogonal to those learning outcomes.

I've heard students criticizing teachers that either repeat the same exam paper every year or make questions that assess memorization, causing a negative correlation. I didn't have classes with one of them though.

@0kelvin I think you mean "no correlation" rather than "negative correlation". Negative correlation between grades and understanding would be funny - in that case, correctly answering the questions would directly show a complete lack of understanding of the material :D

The correlation between learning facts and getting good grades at the postgraduate level isn't particularly strong, no.
At lower levels an appearance of education can be simulated by the rote learning of facts. But that becomes less true as the education level increases. By postgraduate level, although some facts are useful, it's much more about being able to use academic tools, to be familiar with theories and their strengths and weaknesses, and being able to think things through deeply and critically.

I don't see anything about "learning facts" in the original question. Granted, "learning a subject" is so broad it's difficult to say what the OP is referring to.

To give a practical example: in Calculus 1, a student should be able to understand the proofs and do the calculations. But it also means memorizing the rules of calculus to some extent.

No. I can recall many things that I learned in college 45 years ago from classes in which I received poor grades, and I have forgotten things from classes in which I received good grades.

Could you expand on this answer?

Asked and answered.

"Learning a subject" and "remembering a subject 45 years later" are not equivalent. Claiming a weak correlation between grade earned and recall decades later doesn't really answer the question as asked.

I have remembered all along, not just recently, much from classes that I got poor grades in.

A few notes:

Are you actually allowed to post lecture notes online?  Many schools or professors will take exception to this.
I will disagree with some other answers: there isn't a correlation with learning materials and having high grades, but, there is a correlation between knowing enough at a given point in the class and having high grades, if the class is taught well.  That is, if you know what you should know at a given point, your grade is more likely to be higher.  However, just because you are learning a lot doesn't mean your grade is necessarily good.
[Edit: wording improved] You mentioned you're studying computing.  As CS grad student, I can tell you that studying computing is somewhat different from studying other fields: you cannot "learn" computing in the same way you learn other subjects.  Memorizing facts and techniques aren't enough; the largest part of succeeding at computing is understanding at a deep level the implications of the facts.  (This is of course important in other fields too, but you can get away with rote learning for longer.  In CS, though, lack of understanding is an immediate path to failure.)

To prove this, I will mention that I never took notes in my CS classes.  I didn't because while the lecture was proceeding, I was internalizing everything I didn't know already, and then applying it every chance I got.  Guess who did better.
To elaborate, practice and application are literally the most important things to do when studying computing.

I agree with the commenter that you need to ensure that what you think you are learning is actually correct.  For a technical field, it is easy to screw yourself up with mistaken beliefs.  Computing, in particular, is a field where being a smartass is a prerequisite.  You need to be highly attuned to very slight differences in meaning, and if you're going at it alone, you're going to miss things.  Talk with the professor.  Talk to your TA.  We're there to help you understand these finer points and check yourself.

"I can tell you that computing is somewhat different from other fields [...] the largest part of succeeding at computing is understanding at a deep level the implications of the facts.": While in other fields, instead...

You cannot "learn" computing. — Wow. I assume either you are not a native English speaker or your education has been incredibly substandard, because otherwise you would know that "learn" does not mean "memorize". You can learn computing, but (like everything else) only by actually doing it.

@JeffE: Did you actually look it up?  The definition of learn is "to acquire knowledge of or skill in".  This is also the way in which educators use the term.  It is also something you cannot only do to succeed in computing.  Knowledge and skill aren't enough.  You need understanding.  My immediate next sentence made this abundantly clear.

@MassimoOrtolano While in other fields, instead, knowledge of underlying facts plays a larger role, and true, deep understanding can come from later experience.  You can still be pretty successful in most other fields without really living your subject matter.  But, in computing, that's an immediate path to failure.

@GraphicsResearch  I don't need to look it up; it's my job. Yes, this is indeed the way that educators like me use the term "learn".  By your own admission, you are claiming that "You cannot acquire knowledge or skill in computing."  This is laughably wrong.  You can acquire both knowledge and skill in computing.  Understanding is a prerequisite for both knowledge and skill, not something added on afterward.  And no, computer science is absolutely not special in this regard; all disciplines require understanding (or as you put it, "really living your subject matter") to master.

@JeffE that is not what I said.  I said: "[acquiring knowledge or skill] is also something you cannot only do to succeed in computing".  Emphasis original, even.¶  As for the rest, no, understanding is absolutely not a prerequisite for knowledge and skill.  Try memorizing one of the analytic continuations of the Riemann-Zeta function.  That's knowledge.  It doesn't mean you understand what it's doing.  A computer can execute instructions.  That's a skill.  Not understanding.

There is what's approaching a crisis in software engineering of new college graduates with plenty of skill at hacking code, but no understanding of what they're doing.  Ask programmers.stackexchange.¶  And yes technical fields, especially CS (and to a lesser degree mathematics) show this distinction most strongly.  You can memorize facts in history.  You can get lab skills in Biology.  But, you can't just do these things in CS.  It doesn't generalize.  Every original line of code must be generated, not remembered.  Semi-intelligent copy+paste is a skill, but it's no substitute.

Yes, that is precisely what you said.  Quote: "You cannot learn computing".  Quote: "The definition of learn is 'to acquire knowledge of or skill in'."

@GraphicsResearch: You know, those "other fields" are quite a lot to make such a strong claim that you can be successful in every one of them without deep understanding (and is there any where you can be successful with shallow understanding?). I suspect you have quite a distorted view of the other fields, but pay attention that having a distorted view of a whole world can lead to a distorted view of your own world, that is, your field. It's not the first time I hear or read a claim like the one you made, but every time it was related to a different field: so? For the rest, I second JeffE.

@JeffE: Okay, I mean this in the best possible way: you cannot read in context.  The immediate next sentence clarified the first: "Even if you memorize all the facts, the largest part of succeeding at computing is understanding at a deep level the implications of the facts."  I fundamentally fail to understand how you think that meant I don't know that "You can learn computing, but . . . only by actually doing it."  In any case, my comments should have clarified this even further.  Now, I will admit the original wording can be improved, however.  I have edited.

@MassimoOrtolano: I have some experience as an educator in different fields, but it is true I am mainly limited to technical areas.  I predicate my statements on the observation that it was the kids who took diligent notes and studied for tests and read their textbook but never actually wrote much code who did the worst in CS.  This is, in my view, less evident in other fields of study--even technical ones.  Please: I invite you to verify this for yourself.

@GraphicsResearch Well people don't usually need to write code for other subjects. However, I imagine that history students who don't write essays usually do badly, for instance.

@GraphicsResearch: So, let's make an analogy: I invite you to teach, for example, analogue circuits design without letting the students to design many circuits and verify in the lab if they work. How many of them do you think will be successful as circuit designers? None, I tell you... it's 25 odd years that I verify this ;-)

I didn't write it thinking it would be used in class, it was more about typing my notebook so I could have paperless annotations that I could reuse anywhere.
To agree, in some extent, about the difference in learning computing: my grades in the programming assignments were 1st low < 2nd very good < 3rd excellent. But in the two exams were like 1 in a scale from 0 to 10. Because I did took an overextended time to acquire the basic programming skills to program the assignments. Yet, at the same time, I didn't acquire the skills to solve programming exercises with pencil and paper.

@MassimoOrtolano Which will do better, the students who design only the circuits in class, or the students who also apply their knowledge to design their own circuits?  I (hope) the answer is obviously the second.  All I'm saying is CS is like that.¶  To both of you: I've done my best to describe these larger points--and I am dismayed that it has proven ineffective.  Based on experience teaching CS and watching study habits of people across disciplines, I seriously thought they were obvious.  But, from the getgo, it appears the community disagrees.  Since I can do no more, I'm done here.


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Reverse-engineering results in a published research paper
I am trying to implement work in someone else's published IEEE research paper, to verify its results and observe some data. To fully implement what was done, I will need to implement the published algorithm - this will involve some reverse-engineering of what was done in the paper.
Normally, when I face particular programming problems, I might use Stack Overflow or other sites to ask specific questions. Given that doing so it this case would reveal that I was reverse-engineering published work, are there any specific professional or ethical issues around the reverse-engineering aspect of this?

Could you clarify what is meant by "implementing?" Are you writing one? And for point 3, can you also explain a bit more clearly? Do you mean can you cite a paper that is still not finished?

@Penguin_Knight: I just mean implementing an already published research paper just to verify its results and observe some data.

Have you asked the authors of the original paper whether they'd be willing to make their implementation (source code) available for you to work with?

@BrianBorchers: I have not asked them for their implementation. I am not kind of sure whether it is perfectly allowed to ask them for their implementation.

It's perfectly reasonable to ask.  They may or may not be willing to share.

Reimplementing published methods is a perfectly valid and common thing to do. Research papers should describe the utilized methods to enable other people to reperform the experiments and verify the results, so I don't see a reason not to speak publicly about what you're doing.

In fact, this used to be the standard which helped keep science accurate, and it's all too lacking today. "Checking other people's work" is vitally important but doesn't draw funding or reputation.

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Journal allows me to choose whether to transfer copyright – why would I do so?
I am a mathematics undergraduate in the USA. Recently I had a paper accepted to a math journal, and in the final steps of the process I had to fill out a “consent to publish” form, in which I had the choice of whether to transfer the copyright to the journal. My question is: given the option to still have the paper published while retaining the copyright, is there any reason to still transfer the copyright?
In this situation I don’t think it matters much, because regardless of which option you choose you still retain the right to post on ArXiv and your personal website, etc. But I’m curious about what is considered acceptable and/or standard, in case I have to make the decision again.
The specific form I had to fill out is that of the AMS, and choosing not to transfer the copyright has the effect of deleting points 3 and 6.

In the USA at my National Lab, the government retains copyright not the journal.

Hmm. I've only met such a choice with the option to retain copyright coupled to substantial service fees.

@JonCuster technically copyright does not apply to works of the US Government because the works cannot be copyrighted (link here for my agency. Although, some DOE national labs are contract labs (e.g., Sandia), which are slightly different than direct federal employees writing the documents.

@RichardErickson - indeed that is true, which is why the copyright can't be assigned to the journal. I'll also note that all DOE labs (including Sandia) are GOCO - government owned, contractor operated.

@JonCuster To be clear, I agree with your posts (tone is hard online), Also, thanks for sharing about the DOE labs. For some reason, I thought some were non-contractor run.

@RichardErickson Actually, NETL is an exception. It is the only DOE national lab that's both government-owned and operated.

To expand a little on user2768's answer, the text provided by the publisher normally explains the benefits and implications of the different options quite well.

If you choose to retain your copyright, you are only giving the publisher permission to publish and sell your work, but all rights to your work remain with you. You are in principle free to give other publishers permission to print your work, but there still may or may not be a rider about exclusivity (for a specific time or forever) in the copyright agreement even if you choose to retain the rights to your work.

If you choose to transfer your copyright, the publisher becomes the owner of this piece of text, similar to if you had written a book through a contract with them. You cannot simply turn around and sell or give away the same work to another party.

The (theoretical) incentive for you to transfer is that if the copyright is with the publisher, the publisher has the legal opportunities and incentives to protect their intellectual property, for instance by taking legal action against plagiarized versions of your manuscript. If you retain your copyright, the publisher basically can't know whether you have given another publisher permission to reprint your work, and they also don't really care since it's your work, not theirs.
However, in practice a publisher is only willing to protect your work to the extent that they suffer actual financial damages. For instance, if an obscure spam open access publisher publishes a plagiarized version of your article, you may be very annoyed but the publisher is unlikely to take legal action (or at least none that goes beyond sending them an unfriendly email), since the actual financial damage for them is very, very limited. In that light I agree with you that for most people retaining their copyright is probably the more natural choice.

A spam publisher is unlikely to republish just one paper chosen at random, and the damage to the reputation of the original publisher is certainly significant if all their publications are being pirated. (Why would you submit papers to reputable journal A if they are going to appear in spam journal B?) There would be financial damage as well, since people are not going to buy subscriptions to the reputable journal if they can get all the content free from somewhere else.

@alephzero Spam journals don't normally republish anything directly, since they don't make money off of selling papers. However, they don't check nor care if one of their paying authors simply submits your papers with tiny modifications.

(+1) if an obscure spam open access publisher publishes a plagiarized version of your article...the publisher is unlikely to take legal action That depends on the agreement. I have to confess I rarely scrutinise copyright agreements, but I know they can be written such that the publisher has a duty to protect authors' work. I wonder if any publisher includes such a clause... Perhaps doubtful!

@user2768 I don't know, but we tried to make IEEE actually protect their IP as promised in two separate cases, both times without apparent success. Essentially, the thanked us for the info, remarked that they would be unable to further comment on this for legal reasons, and the plagiarized article remained online. We concluded that they decided that this simply wasn't worth going after for them.

Thanks everyone for the answers and comments! I also found the comments of Paul Garrett and Marc Glisse useful: "Do you really want to have to ask permission to reuse your own figures when you later collect your work into a phd thesis, or write a book on the topic, or just write a later article that could use that figure for background?" In my case this is probably the most relevant reason not to transfer the copyright, since reusing some material in future papers is a likely scenario and I want to minimize the chances of that being a problem.

given the option to still have the paper published while retaining the copyright, is there any reason to still transfer the copyright?

There are benefits of a publisher holding the copyright, e.g., they can enforce copyright, whereas you likely cannot.
When royalties are involved this is particularly useful. When they aren't, it can still be useful, e.g., the publisher can handle instances of plagiarism. (Perhaps readers can list other benefits below, or write their own answers.)
I suspect plagiarism is rare, so I see little benefit in giving-up copyright, and I'd personally keep the copyright.

But unless you get royalties, why would you care? - Papers authors are (with very few exceptions) not paid for their publications.

@DetlevCM Why give-up something for nothing? Beyond academic publishing, there's an advantage of giving up copyright: You get royalties and the publisher enforces. For academic publishing, I see no advantage to giving up copyright. (I should make that clearer in my answer.)

I see no advantage to giving up copyright Should be: little advantage

I checked the edit history to make sure I read what I thought I read :D (on the phone the night before commenting on a computer in the morning). - If you are given the choice, of course you can retain it. Though realistically you don't gain a lot by retaining it. Where people mention plots, these can be easily recreated in a slightly different format for example. I guess this can become an eternal debate quite easily about the access to knowledge (especially if it is funded by public research grants...) - I'd rather not go down that route right now...

In and of itself, the only advantage to giving up any part of your copyright would be altruism; virtue signalling, if you must.
Of course it's true that publishers and agents have more resources available for defending copyright and so what?
All decent publishers, agents, etc, will be happy to negotiate terms for using their resources to defend your rights. Who won't, isn't the right publisher, agent, or what.

@paul garrett Sorry you missed both the point of "altruism; virtue signalling, if you must" and the meaning of virtue signalling. Either those, or could you explain in a lot more detail?

... [cont'd], and, often, it's worse than that. So there's no virtue of any sort signalled (to anyone who understands how things work... which is maybe an issue you had in mind?) by giving up copyright... IF, especially, the alternative is that by retaining copyright one makes the thing freely available on the internet, maybe with some free-use requirements/recommendations. I put all my stuff on-line... Made a bad choice c. 2000 and regretted it since... :)

Paul I'm glad you noticed that's not worth discussing and sorry someone thought it was.
I thought it clear, giving up copyright to anyone, it's not at all that the general public benefits by that, in any way we could not have arranged ourselves... [cont'd]
Paul I'm glad you noticed that's not worth discussing and sorry someone thought it was.
I think it's fairly obvious, the only reason for giving up copyright is that developers and Users could benefit from open-access software - which hardly applies to text!
More…

Yes, of course you can make "the products of my labor" available by giving up copyright and that's not what you said, and it's fairly clear the OQ didn't understand that…

@paul garrett That's odd. Which is your world, where "giving up copyright" tends to mean "restricting access", please?

@paulgarrett Thanks and how was that helpful? I truly hope that changed no-one's slant on what I Posted…
If "Giving up copyright" meant anything remotely like "to a/the journal" you would be to explain how that worked.
Why not try that, Paul?

@paulgarrett Sorry no-one told you this and there is a huge difference between "giving up" and "transferring" copyright.
In your world, "giving up copyright" clearly does not mean "giving the copyright to the journal publisher". That would be "transferring…"
In your world, "giving up copyright" clearly does mean "making it universally available…".
Why is any of that difficult?

@paulgarrett Thanks and you might not be intending to be combative but you clearly did wade into something you have never really thought about, as witness  "giving up copyright" means "giving the copyright to the journal publisher"…
Either you do, or you don't recognise the difference between "giving up" and "transferring" copyright - either in law or in simple English.
Which works best for you?

Since my comments did not seem to be helping anything here, I've deleted them.

Well done, Paul Garrett!

Retaining the copyright as an individual is fairly meaningless. First, you can't afford to deal with copyright violations, and second, assigning the copyright to the journal won't prevent you from using the intellectual property of the paper in any way you like.
On the other hand, if you are employed in industry (or a national lab, etc) and the work reported in the paper was done "for hire", the copyright most likely belongs to your employer and not to you personally, so it is not yours go "give away" in any case.

"...assigning the copyright to the journal won't prevent you from using the intellectual property of the paper in any way you like." -- that seems wrong. If you assign copyright, then you would not be able to use the IP however you like since it no longer belongs to you.

@GregSchmit, the IP is not what the copyright refers to, but your objection is still correct, in my opinion, because one cannot re-use the text (which one may have carefully crafted, even optimized...)

As asked in another comment, unless you get royalties, why would you care about "defending copyright". Once you publish a paper as an author you are "done with it" except for follow up work/responding to reader queries. Citation rules equally apply to documents in the public domain or out of copyright, so it doesn't matter there either.
Now a book that pays you as an author royalties would be another matter, however this doesn't apply to papers (in most cases).

Do you really want to have to ask permission to reuse your own figures when you later collect your work into a phd thesis, or write a book on the topic, or just write a later article that could use that figure for background?

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Is getting back to normal life difficult after PhD?
As a PhD student, during the four years of research, you are your own boss. PhD students are not restricted to specific working hours (or place) – as long as they do the work it doesn’t matter when, how, or where they do it.
I spend most of my time working at home or in coffee shops instead of my desk in uni, and I take a day off after long meetings...
I find that this freedom is what enabled me to be creative, come up with new ideas, start collaborations with others in my group, and publish papers.
Now that I am almost done with my PhD, I am worried about life after PhD.
I am wondering if it would be difficult to get back to a normal job working a set amount of hours every day, in the same place.
Is that why most people stay in academia after getting a PhD?

What is your major and which part of world you are living in?Because the freedom of life style as you mentioned is not true in all cases. It depends on your major, country and culture of research group etc.

There was another question (some time ago, I cannot find it now).  This guy was complaining that his wife was getting an academic job, and that she would no longer be able to take a week off in the middle of the year so they could go skiing in the Canadian Rockies, as they had done in the past.  (It seems that if they went during school vacations, the skiing wold be too crowded.)

If you are in a field where you can work remotely, then such freedom of movement/location is quite typical. So this is going to vary hugely by industry and employment type. In some places you clock in and out at set times, only leave your position for 15-30 minutes for breaks 1-2 times a day - but most types of employment leave you somewhere inbetween in terms of freedom of movement.

Did you thing about a career as an uber driver? Just kidding, but being a consultant or an entrepreneur might be for you. Or continue to work in academia in a groups that are compatible with your preferred lifestyle.

To answer your question, we have to clarify some misconceptions it seems to carry. First, a fixed routine is a staple in most jobs you'll come across. You're going to have to accept this. Even at Google, employees are given the freedom to take time off anytime they want -- but this time has limits, and it's on the promise that they'll return to work for a chunk of hours. The vast majority of jobs, no matter how flexible, will not be lax enough to let you work at a coffee shop in the long run.
The same goes for academia. As a professor or academic, you'll be required to teach, do some forms of public service, and, of course, do research. A lot of things from the first two will be fixed beyond your control in terms of task variation and scheduling. As for the rest, there's some freedom to allot time to tasks as you see fit, but given the amount of work you'll have to do, it will come to be structured in some way or another.
Second, it's more accurate to say that a lot of people aren't staying in academia after their PhD. The market today is vastly different than it was twenty years ago. Academic jobs are harder to come by, and tenured positions are an endangered species. Most people will find themselves working as adjuncts or lecturers for a large chunk of their careers. And so PhD grads are now more commonly seeking employment outside academia -- industry, governments, NGOs, etc.
Third, most importantly, no one chooses or should choose a job because of a free schedule. That's far too limiting. Choose a job whose tasks click with your interests, something that motivates you to work. Consider the reverse for your own background: if you hated research, I'm sure that no matter how many hours you were allowed to spend in a coffee shop, you wouldn't have enjoyed yourself or done well.

Fourth, while this schedule seems to have worked for OP, it is by far not a "normal standard PhD" one. I am free to do with my time what I want if I get my work done, but I have loads of meetings to attend, teaching to do, and then squeeze the actual PhD work in. For a lot of people it means to be "free" to work long hours, come in on weekends and sometimes (rarely) use that freedom to get to personal appointments without having to juggle this all with your job.

Strongly disagree with the last part. Prior interests does not correlate with later job satisfaction. Focusing on a career because of the lifestyle it allows it's actually a pretty good way towards a happy life

I am wondering if it would be difficult to get back to a normal job
  working a set amount of hours every day, in the same place. is that
  why most people stay in academia after getting a phd?

Forgive me if I'm wrong, but it looks like the question you're really asking is if you will be able to find a workplace with the same schedule [lack of], or if not, if you'll be able to adjust. The only advice here is: try it. Get a job, in academia or not, and see how you handle it.
From what I've seen, this kind of organization is definitely not the norm even in the academic world, since once you start collaborating with people, they will expect to be able to see you at office hours without having to set a meeting weeks in advance. (For what it's worth, it's not even that common for PhD students in my experience).
However, this does not mean that you will not be able to find a boss who allows you to have your own schedule - though in the "normal life" (amazing choice of words in your title!), working in coffee shops or spontaneously taking a day off because you're tired may be pushing a bit too far. The point is, every workplace is different, every boss is different: some people will trust you and only care about results and allow you to set your own schedule, some will be controlling freaks and check if everyone arrived on time. Depending on the field, some companies have policies for working remotely if the kind of work you do allows it. Don't hesitate to ask about the schedule and flexibility if you're offered a position, it's definitely one of the points to consider - and obviously an important one for you.
Basically, you will have to find a job, either in academia or not, and see if you can handle their rules. If you can't, look for a more flexible one, and repeat the process. If you still really can't handle any of it, you may need a longer job search to find the perfect place where no-one will care. Personally, I noticed that the more interesting the job is, the less I care about having to be there way earlier than I'd chose to. And a lot of places offer flexible time, which is a good compromise even if it still means you have to come five days a week... all in all, you should be okay. Good luck!

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Citation: refer to author or paper?
What is the British English way of referring to a source in-text.
Is it plural because there are two authors, like this:

X and Y (2011) describe ...

Or is it singular because you are referring to a singular source, like this:

X and Y (2011) describes...

So what I am asking is whether you refer to the source or to the authors?

This may depend on the field and the particular journal/publication medium.

In literature I generally see references to people much more than to source. When faced with ambiguity, I prefer choosing what sounds more correct grammatically, even if the difference is slight.
In the example above, it should be 'X and Y (2011) describe', because the verb 'describe' would apply to an animate subject (person) rather than an inanimate subject (source). Similarly, demonstrate, suggest, propose, hypothesise would be apt for people.
The source would be better referred to when using 'inanimate verbs' like contains, comprises, constitutes etc.
Examples:
X and Y (2011) propose that trees be considered sapient.
X and Y (2011) contains compelling evidence for trees to be considered sapient.

Supporting @user153812, I'd write

Marx and Engels (1888) propose sharing property ...

but

The paper (Marx and Engels, 1888) provides the first definition of communism ...

The rule of the thumb is that a citation in parenthesis should not disturb the flow of the sentence. Every time this not happens, I find myself referring to the authors, hence the plural. The only exception is when there is a sole author.

Lenin (1907) provides a crucial extension of the initial suggestion of Marx ...

I had to correct myself, having written it initially in past tense, which sits better with my belly felling, but does not provide a good reference to the genus.
(Note that I did not proof-check the dates, it's just the May spirit.)


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Non-English content in English paper
I want to include an image in my lecture-note paper written in English. The image elements are fully made with non-English language. Below I show a part of the image:
.
I use this image because a reviewer commented:

The authors could have given fig 1 with the actual example of the
  contest data.

And the contest data is Persian, however I want to publish it in prestigious proceedings.
I want to know if it is wrong to exactly use the data or I shall use the translated format?

I suspect the translated format will be more useful to the broader readership of the journal, but you could let the editor make the final decision. I don't know the context of your figure, but it's possible if the symbols don't really have a language meaning that the original version is fine as well (i.e., if they are equivalent to labels like "A, B, C, D" rather than having some phonetic or linguistic meaning). If there is some phonetic meaning that is hard or impossible to translate, that might be even more reason to use the original, and include an explanation of the characters for English-readers.
Provide one version with your revised manuscript, and provide the editor a copy of the other version as well, explain your choice, and see what their opinion is. They might decide the translated version is sufficient (with a note that it is translated from the original), or they might want you to include the untranslated in a supplementary figure, or vice-versa.
Another standard to think about for whether to translate or not is "does this content have the same meaning when translated?" For example, if you had a questionnaire asking basic biographical information, you would expect English and Persian participants to read and participate in the same way and the translation is fine. However, if your content is in reference to phonemes or some other language construct, there might not be any direct equivalent, and information would be lost in the translation.

Thanks. They absolutely have  a language meaning, and translating them would ruin everything. According to your answer, I am going to insert the non-English image and describe the whole process in the body of paper. I just was worried if doing this would be informal.

I think that sounds not at all informal and a good way to go, especially if information would be lost or misconstrued by translation. Good luck! (also, although I have very limited experience, I recall some speech perception papers that were studying, for example, first-English-speakers perceptions of Mandarin speech, which included the characters plus, in parenthesis, the closest Roman-alphabet representation that was possible; some of these might be standard in the field).


text:
What should you do when your supervisor is ill?
While somewhat related to this recent question but this situation is different in that my supervisor has over the recent months had unspecified health issues. It has not overly effected our relationship other than a bit of a delay in some of our emails. Without knowing exactly what is wrong it was conveyed at one of our meeting that it was not overly serious. In the last email I received it was noted by my advisor that their health was poorly over the summer.
As someone who has previously had a prolonged serious bout of Crohn's, I can understand how poor health can impact on someone's life and would like to be able to make our professional relationship work in a mutually beneficial way.
So in a way my question is two-fold.

Is it appropriate for me to sympathize/empathize with my supervisor about their health issue?
Should I ask them how they best wish to proceed when they may be ill in relation to submitting work etc.?

Just to share an experience which may not be so related to your question: In our faculty, there was a very very good professor who was suffering from cancer. I remember when he was alive, he used to advise his students by assistance of another professors. I don't know what was his reason; but I guess he wanted to decrease the impact of his health problems on his students' thesis. Even after he passed away, there were two or three students who were at the end of their thesis period, they continued their work with their assisting advisor and finished their thesis successfully.

Since in a recent email your advisor has told you about the health issue, it is perfectly acceptable for you to sympathize/empathize with them and it would not be out of place to ask if you could do anything regarding your work to accommodate them. That said, if you feel uncomfortable raising the issue, you should be able to depend on your advisor being mature enough to tell you what he/she needs in terms of accommodations.
If your advisor had not mentioned anything to you and you wish to sympathize/empathize with them, then you need to be more delicate.

Depending on how much it slows down your research, how far you are from graduation and how bad the illness is, a common solution is to get a temporary or permanent co-advisor. As StrongBad said, your advisor should be mature enough to tell the students if it is necessary to do so (this actually happened a few weeks ago to a friend of mine), but illness can be treacherous (also happened during this summer...) so more risk-averse people might prefer to start looking for a co-advisor even before they are advised to.


text:
Style guides on structured/ordered bibliography?
Edit: The best guideline I have found so far is the Chicago Manual of Style 16th ed, section 14.58 "DIVIDING A BIBLIOGRAPHY INTO SECTIONS" (I have boldfaced the part which best answers my question):

A bibliography may occasionally be divided into sections--but only if doing so would make the
reader's job significantly easier. Where readers need to refer frequently from notes to bibliography, a
continuous alphabetical list is far preferable, since in a subdivided bibliography the alphabetizing
starts over with each section. Rarely should books be separated from articles, since a book and an
article by the same author are best listed close together. It may be appropriate to subdivide a
bibliography (1) when it includes manuscript sources, archival collections, or other materials that do
not fit into a straight alphabetical list; (2) when readers need to see at a glance the distinction between
different kinds of works--for example, in a study of one writer, between works by the writer and
those about him or her; or (3) when the bibliography is intended primarily as a guide to further
reading (as in this manual). When divisions are necessary, a headnote should appear at the beginning
of the bibliography, and each section should be introduced by an explanatory subhead (see fig. 14.9).
No source should be listed in more than one section. For alphabetizing, see 14.60--62.

I'm trying to find a style guide or similar on how to structure or organise a bibliography or reference section at the end of a book. Perhaps this applies most to a dissertation thesis where there are many different types of references. I am not looking for citation style guides on how to format specific types of references (I can find many such guides), but rather how to order them into groups by type, or even whether to do it in the first place.
For example, in my dissertation, I am currently considering a structure roughly like below (very simplified and inaccurate but only to get my point across). Now suppose I add more sections for journal articles, anthologies, etc... and this bibliography grows quite large, say over 30 pages or so. What is considered good practice here? See the two examples below. I find the first alternative a lot more tidy and easier to read, while the second is cluttered and just doesn't feel right.
I have found some recommendations which contradict each other. https://www.dur.ac.uk/resources/library/teaching/writingyourbibliography.pdf on page 3 says

You should not divide your bibliography into separate sections for different document
types.
References should contain all of the information required for a reader to find a source. Standards
have been set for different document types to ensure that each reference contains the information
necessary to aid retrieval of the source.

But there is no further explanation why there shouldn't be separate sections.
On the other hand, http://www.open.ac.uk/Arts/history/docs/thesis-guide-v51.pdf says on page 15:

The bibliography at the end should be divided into Primary and Secondary Sources.

And http://www.st-andrews.ac.uk/history/infoug/stylesheet.html says:

The bibliography should be divided into manuscript, printed primary, and secondary sources.

I'm writing as a historian/scholar and we tend to work with many different types of sources, so not just books and journals but also manuscripts, letters, promemorias..yes even postcards, maps, brochures, etc.
I'm open to hear what it's like in other fields as well and regardless of national traditions.
The three examples:
(1) Ordering by document type:
(2) Unpublished documents
(3) Archival sources

Letter from Ms. A to Mr. B
Letter from Mr. B to Ms. A
Other unpublished documents
Miss A. Diary notes.
Published sources
Public documents
Parliament records, 1980:CA-2:12231-13.
Parliament records, 1980:CA-2:71236-01.
Literature
Foucault, "The History of Sexuality" 1960.
Latour, Bruno, "Science in action" 1987.
Stevenson, Sue, "This is a book title", 2003.

2) Ordered by alphabet only:

Foucault, "The History of Sexuality" 1960.
Latour, Bruno, "Science in action" 1987.
Letter from Ms. A to Mr. B
Letter from Mr. B to Ms. A
Miss A. Diary notes.
Parliament records, 1980:CA-2:12231-13.
Parliament records, 1980:CA-2:71236-01.
Stevenson, Sue, "This is a book title", 2003.

@Coder Would you please re-examine this edited version. We have "2) Ordered by alphabet only", but where is "1)"? I do not believe the edit is correct. That's why I rejected it.

Comment above CC to @Joe_74

The first person to ask is your advisor and/or committee members for whether dividing the bibliography into types is a good idea, and then if they've seen other examples. Next, check with the graduate school or other group that will be accepting the dissertation for publication. There is likely already a style guide and templates. Third, if there is still no clear guidance, look at previously published dissertations in your field.
Having a bibliography grouped by type could make it difficult to find references from the text. You don't really want to make your advisor or committee members do more work.
There's no reason that you can't keep a working copy of the bibliography sorted by type, just be aware that you'll likely have to convert it into one list at the end.
Personally, I can't recall seeing a bibliography sorted by type. I have seen ones divided by chapters or sections. I find this type of bibliography difficult to work with, as I have to find the chapter's list, then the individual reference.
Note: I have STEM degrees, but attended a liberal arts university as an undergraduate, so I have no graduate level experience in your field.

Those are very good ideas. I've had a look in recent dissertations in my field, especially those published locally, and I can learn a lot from that, and as you mention by talking to colleagues and supervisors. But still, I wish there were some "official" guidelines.

Your "official guideline" that you look for will come from your supervisor : ask them and they will give the "correct" answer they and the committee expect.


text:
What do the abbreviations 2:2, 2:1, or 3:2:3 mean in terms of teaching loads?
I often see people abbreviate faculty teaching loads ("course loads") as 2:2 or 3:2:3 or 2:1.
Sometimes a note such as "3:3 with 2 preps" is added.
What do these abbreviations mean?

Posted as a community question since we occasionally get this.

A complete answer will talk about how classes are counted and what "number of preps" means.

Will this answer help you? And the other answer?

I asked this as we have the "answers" in responses to other questions (and in scattered comments) but we don't have a single question that asks just this question. This will help us in pointing other questioners to this in the future.

@RoboKaren: good idea.

They refer to the number of classes you teach in each semester. ie 2:1 would mean two classes one semester and one the other.
Three numbers (like 3:2:3) refer to the number of classes in each quarter for schools on the quarter system (i.e., three terms per academic year). [Thanks to Mark Meckes]
Not all courses are the same size, although I suspect that the vast majority are the standard "3 credit hour" size. A minority but reasonable number of courses, though, are 4 credit hours (particularly in my area, math). A few courses are even 5 credit hours at some institutions. It depends on the field to a great extent. Nevertheless, the number of courses is still very important. Teaching a four-hour and a five-hour course for a 2-course load is less work, usually, than teaching three different 3-hour courses. [Thanks to Oswald Veblen]

To supplement this answer, three numbers (like 3:2:3) refer to the number of classes in each quarter for schools on the quarter system (i.e., three terms per academic year).

Could you add to the answer the information if the number of hours taught per course is standardized (such as 2 or 4 hours per week per course)? Otherwise, the numbers are not very informative.

So, in the US, all courses are the same size?

No, not all courses are the same size, although I suspect that the vast majority are the standard "3 credit hour" size. A minority but reasonable number of courses, though, are 4 credit hours (particularly in my area, math). A few courses are even 5 credit hours at some institutions.  It depends on the field to a great extent. Nevertheless, the number of courses is still very important. Teaching a four-hour and a five-hour course for a 2-course load is less work, usually, than teaching three different 3-hour courses

@MarkMeckes Three terms per academic year would be trimesters. Quarters would be four terms.

@KRyan: You would think so.  In reality, many American universities use the term "quarter system" but three of them comprise an academic year.  Off the top of my head I don't know of an American university which uses the term "trimester". I suppose there is also a summer quarter...and also a summer semester.

@KRyan: That's what American universities call the quarter system. The fourth quarter is the summer, where most professors don't teach (but some classes are still offered). Stanford, for example, explicitly calls their summer session a "summer quarter".

To answer the part of the question about preps:  It's easier to teach two sections of the same course than it is to teach two entirely different courses.  A 3:3 load with two preps means that you teach 3 sections per semester but two sections are of the same course.  For example, you might teach two sections of Calculus I and one section of ordinary differential equations for a 3 course load with two preps.
In the US, most academic courses are 3 credit hours, nominally meeting for 3 hours per week (often 3 sessions of 50 minutes each on Monday, Wednesday, and Friday, or two sessions of 75 minutes each on Tuesday and Thursday.)  However, you'll find some courses that are two credit hours or four credit hours (or even five credit hours in some science courses with labs.)  In assigning teaching load it's common to just count all of these as one course even though four credit hour courses take more time than 3 credit hour courses.

"In assigning teaching load it's common to just count all of these as one course even though four credit hour courses take more time than 3 credit hour courses." Is it?  In my department, four credit courses count for...4/3 as much as a standard course.  (On the other hand, once I was told that at the end of a given academic year I was ".9 courses behind".  Being a number theorist I wondered what could possibly have resulted in a 5 appearing in the denominator...) I expect that if we didn't count the extra 1/3 then we would have a lot of trouble finding people to teach the 4 credit courses.

I'm sure that practices vary, but in my department (and many others that I've seen), teaching a 4 credit hour calculus section still counts as one course.

Yes but sometimes it's saner to teach two entirely different courses than it it to teach the same course.  After 3-4 semesters of Calculus 1 you might be pretty darn sick of it.


text:
Should I inform about an updated CV post deadline? (CS PhD USA)
Background: CS Undergrad applying to CS PhD Programs, USA.
(Assuming) I have a paper A in review at a Journal B, and I get the acceptance for the same 2 months post the deadline of applying.
Question:

Should I send the places I applied an e-mail saying that the paper which was in review (and mentioned in my SOP/LOR/CV) got accepted?
Does it have any effect on their decision?

If it is April and you are not on a waitlist, at an American university it is probably too late.

@Aymuos Are you waiting for a decision now? Or is this for next cycle?

This is for the next cycle!

Should I send the places I applied an e-mail saying that the paper which was in review (and mentioned in my SOP/LOR/CV) got accepted?

No. Your CV/application is a snapshot in time, institutes likely won't update your CV/application, and they don't need such an additional burden. (Especially after two months, institutes are likely nearing or have made decisions.)

Does it have any effect on their decision?

It would improve your CV/application, equally it may annoy the institutes: It may have a positive or negative impact.

Thank you, this was exactly what i wanted to know!


text:
Colloquial forms (let's...) in articles
I am writing an article for a peer reviewed journal in the field of literature, and I am wondering about the use of colloquial expressions like: "Let's take a step back", or "Let's look at the data", "Let's look at the coxtext" etc.
Would you suggest avoid these forms? Could you maybe suggest me a subsitute formula to express the same idea?

Would "Let us take a step back ...", or "Taking a step back ..." work?

In general I don't think it's a big issue but alternatives may look better, here are a few suggestions:

"Let's take a step back" -> "from a broader perspective"; "in a larger context"
"Let's look at the data" -> you don't need this at all, you can just start talking about the data: "the data shows that...", "in the data we observe that..."
"Let's look at the context" -> you don't need it here either: "the context consists of...", "to put this analysis in context, ...."

It is probably a mistake in extremely formal writing, but many people write as if the paper is a conversation between the author and the readier. If the material is appropriate for that view, then the form is quite appropriate.
How formal the writing should be depends somewhat on where you do it and even more on the audience.
One way to know whether it is appropriate in your own circumstance is to look at how other recent papers in your field are written. It is probably safe to emulate them.
I'll also note that historically we seem to be moving from a more to a less formal presentation style in general, but the rate isn't uniform across fields. We are, in fact, normally writing for our colleagues, so it is fairly normal to consider our writing as a conversation. This is especially true if, in writing, you are mentally focused on the reader him/herself, rather than the material itself. Which view is more or less natural depending on the field.

After posting my answer I noted that it applies to your answer as well: Does the last paragraph starts with "I will" or "I shall"?

@Dirk, I honestly didn't consider it. The colloquial meaning is close enough. But "shall" is becoming a bit archaic, I think. See https://everything2.com/title/will+vs.+shall

Never mind - and thanks for the link! I didn't know that the matter with shall and will is so intricate.

I would avoid contractions and a too chatty manner.  This doesn't mean you have to be stilted either.  You can still use short sentences and short paragraphs and gutty Anglo-Saxon words.  This will be enough to make your articles enjoyable to read--more so than the norm--while still passing the pompous preening set.

I think this is frowned upon in academic writing. Personally, I am happy with abbreviated form like "let's" or "didn't", but since English is not my native language, I always need some time to extract the meaning of something like "that'd" (is it "that would" or "that had" or maybe something else?).
So I would suggest to just the full unabbreviated form: Just write "let us", "did not", "that would",...
It has exactly the same meaning, always sounds as good or better to non-native speakers (which are likely to be the majority of your readers), and is faster to parse for them.


text:
Importance of QUANT score on GRE for math grad school
I am not the best at standardized test taking and scored a very poor score of quant 153 on the GRE. I go to a good undergrad institution with no grade inflation (Purdue university). My grades, especially in upper level math classes, are good (A's in Real Analysis, ODE, Vector Calc, Statistical Analysis, A- in PDE). Though I did get a B- in Linear algebra and a B in Probability. I have a cumulative GPA of 3.72 with a major GPA of 3.6. Would I still be able to get into a Group 2 program with my current marks?
I am registering for the Math Subject, and oddly I feel much more confident with the types of questions asked compared to the regular GRE. Would a strong math subject GRE cover up the blemish of my GRE score?

Is this question USA-specific?

@TommiBrander Yes

I added the corresponding tag.

In the US, at least, no single thing is likely to knock you out of contention. Aim high, but don't put all of your eggs into too few baskets. The competition is fierce, of course, in top level schools, but if you put together a good application that clearly predicts success you should come out well. But, make sure that you have very strong letters of recommendation from people who can speak both of your past success and your likelihood of future "wins". How hard you work, how serious you are, etc.
I suppose there are a few places that might have a cut-off score, but not everywhere you might want to go would do that. It is rather foolish in any case.


text:
What is a good rule of thumb for the cost of a Postdoc, in the US at an R1 university
Suppose I want to pay a postdoc $65K for salary. How much research fund do I need to have to support this postdoc (on average, of course, not exactly)?
Is it only the 65K or are there many other hidden costs?
PS: this is about ballpark, back of the envelope calculations, and to understand the general costs involved in such hires. It is not to get an exact number.

You should ask your department's financial officer. But as a rough rule of thumb in the US you should double the salary to determine the amount of funding you need to find to employ a post doc. And your department or institution may set that salary.

I cleaned up the long thread of comments which was clearly veering toward a polemic. NewAP, please familiarize yourself with the rules of this site having a look at the [Tour] and at the [Help]. And please beware that we expect everyone to keep a professional tone in the comments and to adhere to the Code of Conduct.

@MassimoOrtolano thanks. Can you re-open the question, by the way? A question about ballpark estimates, and understanding hidden cost in general clearly can't be closed due to depending on "individual factors."

Eg: if specific percentage in one institution is 47.5% and in another 37% it doesn't matter that much to the question, so it doesn't make sense to close due to this reason.

@MassimoOrtolano or if you don't want to re-open, can you (or other moderators that cloased it) at least explain how do you want the question to be worded?

@NewAP - Most open/close decisions here are made by community vote, not by moderator fiat. If you edit your question, it will be placed in a queue for a reopening vote. The hard part of question-asking is the amount of detail: it should be specific enough that there is a correct answer rather than an open-ended discussion, but general enough that future readers might find the question useful. In your case, a good starting place would be to specify your country (or part of the world) and field.

There is a meta discussion on the closure of this question here

This differs significantly by country.  In some countries, it will also be different for each university.
In the US, each university shows the government what its additional costs for supporting research are and negotiates percentages with the federal government.  This calculation will apply to all federal government funding but other funders are free to make other demands. You ask your university's grants office for the details that apply to you university.
For my university, the calculations are:
On salary, my university adds 30.70% for fringe benefits, so an additional $20K on top of the $65K.  This pays for things like social security tax (the part paid by employers), health insurance, retirement benefits, and life insurance.
In addition, on the $85K (from $65K+$20K), my university adds 47.50% for indirect costs, which is a little more than $40K.  This pays general university resources that the postdoc will use, like office and lab space, heat and light, library books and subscriptions, the accountants managing the grant, and basic office supplies.  (Any grant project specific supplies, like lab equipment or lab consumables or travel, is budgeted separately in the grant.)
This comes out to roughly $125K total.  Note this doesn't include some items you almost certainly need to have, such as travel funding for the postdoc.

If the postdoc is working online (zoom) can the university still charge these "indirect" costs?

There is a lower rate (26%) for activities that are off-campus.  If the postdoc is permanently working remotely, you might be able to convince your university that this should apply.

I don't see why you care about this.  You just write the larger amount in your grant budget.  The size of the grant has basically zero effect on its likelihood of being approved.  The grant will now look bigger, but that looks better on your CV.  If it's a private funder with limited budget, they can negotiate separately with the university.  The whole thing is just a scheme for the university to get more money from the government (and we can argue about how justified it is somewhere else).

Thanks, I might have funds coming from elsewhere already, and want to know how I can make best use of them.

@NewAP - but other funders are free to make other demands.  I have a small grant from a private foundation which said "We will pay this much for indirect costs.  Take it or leave it."  My university allowed me to apply.


text:
How do I describe my "academic profile" for graduate school application?
I am filling McGill's Area of Research and Applicant Profile Form for admission to the Electrical Engineering M.Eng. program. I'm not sure how I should answer this:
"Academic Profile: Describe your academic profile, highlighting particular achievements and relevant scholarships or awards."
My scholarships and awards take up about 0.15 of the space provided, and I can't think of a particular achievement. Can I use this space to describe the projects I completed, the software I learned and particular skills I learned through coursework and special topics that were covered? I don't get to upload a CV for this application, and I was hoping I could mention these in this space. However I'm not sure if it would be appropriate.

Projects completed are more important than skills learned from coursework. Give preference to what distinguishes you from every other student. If you did an internship, mention that. If you worked on a project at a university department, mention that. If you did a Bachelor's Thesis, write about what you did there.
Saying something like "I learned about LTI systems in course X and I acquired MATLAB programming skills in course Y" will not distinguish you from every other Electrical Engineering student, so those statements should have the last priority.

The thing is I don't know if that's the right place to put those. For example I included my thesis and internship in the first field and TAships in the last one.


text:
What is the relative prestige conferred by an invited review article vs a research article?
What exactly is an "invited review article"?  I have the opportunity to be an author on one of these, but I have no clue how this looks in comparison to research articles.  (I am referring to invited review articles for reputable journals well-known in the field only.)

Related: Survey or original article: Which one is more important to get postdoc or tenure-track position?

What exactly is an "invited review article"?

It is an article that appears in one issue of a journal. The article goal is to review the recent development of a specific topic (sometimes it goes with a special journal issue in that topic).

how this looks in comparison to research articles.

Research articles contain original ideas and contributions to the field done by the authors. In contrast, a review article usually has no absolute originality in a sense that the authors are not coming up with something totally new. They are nicely summarizing what is happening in the field and identifying possible challenges.
The benefits you get out of publishing a review article in your field (specially when you are at an early stage of your research career and with a reputable journal) are numerous
1. You get to know your topic.
This has the advantage of organizing your thoughts and identifying possible contributions into the field.
2. A Good Critical Review = High Citations.
Good review articles tend to have many many citations. This means many people going to know your name (and possibly look for your other publications).

I generally agree, but want to add a cautionary note: "invited review" is also something frequently requested by low-quality publications that spam you and try to play on your vanity.  Make sure the journal is one that is actually credible.

It's a 14.5 impact factor journal.  Would that be credible enough?

@James I think there is no reason to be snarky. Your question is not only read by you, and jakebeal's warning is spot-on - clearly not in your case, but likely for others who find this question later on.

Hi @xLeitix.  There was no intent to be snarky at all!  jakebeal (or seteropere?) originally had a comment on here that said to edit my original post to include that sentence and asked what the IF was.  I'm not sure where that comment went, so now my reply appears oddly out of place...

Hi @jakebeal - That indeed is a very valuable comment. It may be a great idea to expand that into an answer, from the perspective of scammers/spammers. Because, then we will have a variety - a regular answer pertaining to the ideal situation, and a cautionary answer describing how we don't live in an ideal world. One upvote guaranteed if you do it!

Journals accept different types of articles apart from regular articles such as for example, short communications, letter to the Editor, Correspondence etc. The definition of these vary. Journals publishing regular research articles may have guidelines that state that they do not accept review articles. There are also journals that focus on review articles. The reason for not accepting review articles probably vary substantially between journals but clearly review articles are usually very extensive and require much more work from reviewers and editors and so may be disrupting the regular flow of articles.
So, in the cases, I know of, including "my own" journal, Invited reviews is a way for a journal that focuses on publishing regular research articles to put strict limits on what is submitted as a review article. The "Invited" meaning that there is no point in submitting in a review article to the journal in the hope of getting it published. Instead the journal will in some way invite the reviews they will accept for review. By "invite" the journal can consider receiving suggestions for a review by an author or by having editors identify and suggest authors to write a review, I am sure the processes vary. In this way, the review becomes a more exclusive entry in the journal focussing on a topic that is considered of key interest to the journal and its audience. The main difference from reviews in a review article journal is thus the selection method of the manuscripts.
So, for what it is worth, an invited review, given the points provided above, will be slightly more prestigious than an ordinary review article in a review journal. In the end, however, it will be the usefulness of the article that provides the real value of the publication.


text:
How many papers should I be reviewing as a referee?
Like many academics with an active research program, I am asked to review many papers. Borrowing an idea from peer-to-peer file sharing companies, I try to keep a rough sense of my recent "ratio" of reviews I have done on other's papers over reviews my papers have received. I try to make sure I have a ratio that is consistently above 1:1. Since many of my papers (and presumably the papers I review) are co-authored, this seems very generous to me.
How many reviews should I be doing? How many is normal? Is a ratio an effective way to keep track of one's reviews? Is a minimum 1:1 ratio appropriate and defensible?

Related: How much time should I spend on reviewing

I have wondered about the same question.  One thing that I've noticed is that there is an incredible amount of variation in the amount of reviewing done.  I have two good friends who are strong, active mathematicians.  The last time I spoke to them they were each at least six years past their PhD and had never reviewed a single paper.  This seems bad, but it's not their fault: they are not being asked.
I suspect that the lack of coordination among journals in the same field causes the same small number of people to be asked to referee papers over and over again.  I am not a journal editor, but I have begun to wonder how editors choose referees: I am someone who is getting (what I think is!) a large number of referee requests.  I submit maybe 2-4 papers per year.  Not so long ago I used to get that number of referee requests per year, and they were all from people who knew me directly and pertained to topics related to my thesis work or to the areas in which I have written multiple papers.  Now I get at least a dozen referee requests a year, and in addition to the above I get some very strange-looking ones.  Not so long ago I got asked to referee a paper in (what I think is!) control theory.  This was so baffling that I assumed it was some kind of email crossed wires situation and asked the editor about it.  It turned out that the paper on real analytic solutions to Bezout equations had been sent to me because of a question on math.SE that I answered, in which I explained why the ring of analytic functions on the complex plane is a Bezout domain.  This is distressing: I can see why google would make a connection like this, but in the realm of academic experts, is it not obvious that we are on different sides of mathematics?  Experiences like this make me wonder who is refereeing papers.
I'm not sure that counting papers is the right way to gauge whether you are pulling your weight referee-wise.  As I mentioned in a comment to another answer, many -- I think most -- papers are refereed by more than one person, either simultaneously for the same journal or sequentially, as many (most?) papers are submitted to more than one journal before they are accepted.  Here are some things that I have thought about:
1) It cannot be appropriate for everyone to referee the same number of papers.  More experienced people should referee more papers, but also should referee more important / difficult papers.  People who have permanent / senior positions in academia (especially: tenure) should have more obligations than those who are struggling to stay in the profession.
2) Not all papers take the same amount of time to referee: not even close, actually.  I try to make a point of quickly processing especially short and simple papers: I probably do 3-5 of those each year, and I often process them in a week or even a day.  But it would be silly to equate this kind of referee work with the long, difficult papers that you spend weeks or months working on, perhaps having to do considerable outside reading in order to adequately evaluate.  Doing 2-3 substantial papers a year is what really keeps me busy as a referee.  I suppose I try to keep my eye on the total amount of time I've spent refereeing rather than on the number of papers, although I admit that I don't do this in any formalized way.
3) Unless a paper is clearly of the "one day" variety as above, I try not to let my queue exceed 2 papers.  This is also out of respect to the authors: if I have to read two papers before I get to yours, then you'll be waiting for at least six months, probably more.  If at any given time every sufficiently experienced/qualified academic had either 0 or 1 papers to referee and made a point of processing papers faster than they submit them, then things would work relatively smoothly, I suppose.

If you are submitting 4 papers per year and getting at least 2 reviews for each paper, then 12 papers is about the amount that you need to be reviewing to pay back the reviewing and editing time that is being put into your submissions. See My answer below for more on why. As to how editors select reviewers, we look for reviewers who are already in our database and have keyword matches with the submitted paper, or else we look for people who have published on similar topics in recent years. If your reviews are good and timely, you will be asked more often.

I think that point 2 is an excellent one: simply counting the number of papers reviewed is pointless. Measuring the time spent on the reviews is much more meaningful.

Speaking as an editor and conference organizer, good and reliable reviewers are hard to find. For somebody to be a good reviewer, in addition to being in the right discipline, they must be:

A strong enough scientist that I trust their opinion
Capable of expressing their analysis of a paper clearly and constructively
Good enough at time-management to return the review rapidly
Not too overloaded with other responsibilities to accept

Lots of authors fail these tests, especially the first one---anybody who has spent significant time reviewing knows that there are a lot of very bad papers being written.  Moreover, papers that are rejected often get revised and sent elsewhere, so they may require multiple sets of reviewers.  All of this adds up to the following: if you are a good and trusted reviewer in your community, you will be in high demand, and it's reasonable to have a ratio of greater than 1:1.
For example, in the last three years, excluding grant and tenure case reviews, according to my records I have reviewed 31 papers in 2012, 24 papers in 2013, and 30 papers so far in 2014 (with a few more committed to return before the end of the year).  This puts my ratio well above 1:1, with the actual value mainly depending on fluctuations in the denominator.
In sum, I recommend viewing reviewing not in terms of ratios, but in terms of how much time you are comfortable devoting to quality reviews for venues that you wish to support.  Don't accept review requests from journals or conferences that you do not respect: there are many low-quality publications that can waste your time. Also, don't accept more reviewing than you can handle, even if that means your ratio is lower: it's better to give one well-thought review than two hasty and shallow reviews that may miss important points and piss off the authors.  Do respond yes or no to every review request promptly: otherwise, you are making a problem for an editor who doesn't know whether they need to recruit more reviewers or not.

You could count each n-author paper you are on as 1/n of a paper. Thus each time you submit for publication a 2-author paper, a 3-author paper and a 6-author paper, it's time to referee another paper.
If the journal uses more than one referee per paper, adjust up accordingly.
In some sense this must be what most people do, on average.
Edit: One could ask the editors how many referees they use per paper. Better yet, the editors should volunteer that information.

I don't know of any evidence that suggests that this is what people do on average. My sense is that some people review tons of papers and many people (e.g., graduate students) submit papers but are rarely asked to review.

@BenjaminMakoHill: On average, people do exactly as many reviews as they receive (scaled by the number of coauthors). Every review that someone receives comes from someone.

The averages must be exactly the same if we average over all people who have ever submitted or reviewed a paper, but not necessarily over people currently active in the field.  (For example, it's possible that people who leave the field have on average submitted more papers than they have reviewed.)

@JukkaSuomela. If we treat the groups of all authors and reviewers as a single pool to average over, that is correct although I'm not sure that's fair. I only meant to suggest that if we were look at the distribution of reviews over reviewers, I suspect to see a very skewed distribution. In any case, I'm less interested in the mathematical statements about averages than I am in a discussion of what someone should do.

@BenjaminMakoHill: I fail to see how the "recommended" number could be below the average number. Otherwise, if everyone followed the recommendation, the system would collapse.

@JukkaSuomela. Yes, but it could certainly be above.

The fact that many (most?) papers are reviewed by more than one person (either by the same journal or for different journals) does not seem to be taken into account in the analysis of this answer.  This makes a figure of reviewing twice as many papers as you submit look fairer/safer from a "pulling your average weight" perspective.

Added: I missed the sentence "If the journal uses more than one referee per paper, adjust up accordingly." Sorry.  But some journals use only one referee, some use several, and I don't know all the statistics, so it's hard to adjust.  Also: this does not take into account that the same paper may be refereed by several different journals.  If I say that I think on average each paper is refereed by 3 people and you say it's 2, then we're differing significantly in how much work we think any one person should do.  So does everyone just solve the Fermi problem in their own way?

@PeteL.Clark: "…so it's hard to adjust…": Actually, all this is trivial to adjust. You do not need to consider "average papers" or estimate anything. Just consider those papers that you review and those papers that you submit. Everyone knows (at least in principle) how many reviews they have personally written, and everyone knows how many (coauthor-normalised) reviews they have received in total (including everything: re-submissions, multiple reviews per submission, etc.). Just keep track of these two numbers and make sure that in the long run their difference is positive.

(Just to clarify. When you review a paper, the math goes like this: "this counts as 1 review written by me". And when you submit a paper with n coauthors and receive the reports and see that there are k reviews, the math goes like this: "this counts as k/n reviews received by me". You do the same thing regardless of whether your paper was rejected or accepted. There is no need to get any additional information from the editors.)

@Jukka: Just because you see k reports does not mean that only k referees were enlisted to review the paper.  I have had papers both accepted and rejected without receiving any referee reports.  Also, the business about the coauthors and fractions assumes that your coauthors are doing the same amount of refereeing as you are, which if they are much more junior or senior than you may not be the case.  Many of my coauthors are graduate students who do little or no refereeing.

But I agree with the gist of what you're saying: trying to compute the average is needlessly complicated.  You can probably get a pretty good idea of how many referees you "use" per year and make sure that you stay ahead of that.  How far ahead you want to be is still a judgment call, as I talk about in my answer.

@BenjaminMakoHill, just add up the papers submitted and the papers reviewed, the sums must match. Handshaking lemma of graph theory in disguise ;-)

First of all, I totally agree with the answer of Pete L. Clark.
However, I do not agree with the mentality that thinks: "Reviewing a paper is JUST doing a favour to the community". We all read papers to stay on top of our fields, get a better understanding of the world around us and to get new insights. I personally read several papers every month. Nonetheless, every paper that I read, I must maintain my critical view. So, there is no harm in reviewing many papers.
When you receive a paper that seems interesting to you, you can decide to review it (of course there is a burden of writing down your thoughts, which is negligible). If the paper is not interesting, you can just decline the review request and move on.

Four times as many as you submit as corresponding author.
My reasoning is:

Most journals solicit between two and four referee reports for each paper that is sent out for review. Add to this the time of the volunteer editorial board member who is probably handling the manuscript.
Some academics do not do their duty to the community and decline all review requests, so the rest of us have to make up for them.
By my reckoning, this works out to about 4 x the number of papers you submit being a fair load.

"Most journals solicit between two and four referee reports for each paper that is sent out for review." This is highly subject-dependent.  In my field -- mathematics -- the most common number of referees is one.  I have submitted over 30 papers for publication and never gotten more than two.

By the way, if you want to be quantitative about it (which, as I say in my answer, I don't necessarily think is the best way to go), then how is the number of coauthors taken into account in your reckoning?

The number of co-authors is irrelevant if you count only the number of papers that you submit. You, personally, as corresponding author. I'm really surprised to hear that one review is sufficient in some fields. That must speed up the review process a lot, and make responding to review comments much easier (no navigating conflicting reviewer opinions)! The journal for which I am an editor prefers 4 reviews and requires at least 3 for each manuscript.

"That must speed up the review process a lot, and make responding to review comments much easier (no navigating conflicting reviewer opinions)!" Well, one frequently gets referee reports in less than a year, but not always.  I hope, for your sake, that that doesn't sound that fast to you.

I missed the "corresponding author" part of your answer, in part because it didn't appear in your comment.  No one I know would interpret "I submit 2-4 papers per year" as "I submit 2-4 papers per year as corresponding author," since in my field "corresponding author" means precisely "the person who sends the email to the journal / fills out the online form".  I know of no reason not to divide corresponding author duties roughly equally among authors, but on the other hand I have no guarantee of it.  Some people are undoubtedly corresponding authors more or less often than their coauthors.

Should someone who doesn't enjoy filling out online forms and therefore has her coauthors do that really be relieved of all refereeing duties?  Or if e.g. a three author paper needs to be shopped around to three journals before it gets published, probably the same person will be corresponding author all three times.  Shouldn't this count as one referee job per author, not three jobs for the corresponding author? So your reckoning doesn't seem very accurate to me.

Corresponding author has high significance in some fields.

@PeteL.Clark Fair enough. You could use "first author" instead of "corresponding author" if you prefer. Or simply divide the number of papers on which you are an author by the average number of co-authors on those papers. I'm used to the corresponding author being the first author, and the first author being the one who has done most of the work and prompted the submission of the paper, but I agree this isn't always the case.

@Significance: Please remember there are several academic fields -- like mathematics -- in which "first author" means "the author whose last name comes first alphabetically".  This would be a strange way of assigning referee duties.   If you only intend your answer to apply to certain academic fields, that 's fine but please say so.  On the other hand, there is already an answer here (Kjos-Hanssen's) giving a system which works independently of any implicit cultural assumptions about coauthorship.  Why do you need to list one number that is intended to work for everyone but actually doesn't?

@PeteL.Clark the comment to which you are replying already acknowledged this point (that not all fields follow the same practices). Kjos-Hanssen's answer is now generic and sufficient, as it has been edited, but the original version, which was there when I first commented, assumed only one reviewer per paper, which is unlikely in most fields. My answer was intended to make the same point more clearly and simply: i.e. pay back what is done for you.

@Significance: Kjos-Hanssen's answer has not been changed for more than a year before you joined the site.  "Pay back what is done for you" is a good, simple answer but is certainly not equivalent to "Referee four times as many papers as you submit as a corresponding author."

You don't seem to acknowledge that there are entire academic fields in which your answer is a huge overestimate.  For instance, I am supervising a postdoc who in the last year was the "corresponding author" on one paper and the referee for one paper.  Number of referees involved in getting her paper refereed: one.  You are saying that to pull her weight she should be doing four times as much refereeing.  But four times as much refereeing for a careful, junior mathematician would put her out of business.  So my comments are based on imagining someone like her reading your answer.

@PeteL.Clark I acknowledge, and have now acknowledged three times that there are academic fields in which the average number of reviews is lower and/or the corresponding author is not the best way of assigning responsibility. I am certainly not saying that your postdoc is not pulling her weight. I stated the assumptions in my original answer clearly so that it was clear in which circumstances they did not apply. I don't believe that you sincerely think we have a substantive disagreement here, so I will not be drawn further. Yes, you may reply and have the last word.

"I stated the assumptions in my original answer clearly so that it was clear in which circumstances they did not apply." You give a figure unconditionally, not under certain hypotheses. "I don't believe that you sincerely think we have a substantive disagreement here."  I sincerely think we have a substantive disagreement: you are giving advice that would be harmful if followed by some, and I disagree that it will be obvious who should follow your advice (and you certainly have not said).  But I do think that the comments and voting will help readers not be misled, so it is probably okay.


text:
How to determine peer institutions?
Are there standard criteria to determine the peer institutions?
My institution is an american private liberal art university that follows the semester system, for which I can think of the following criteria:

Liberal art university
Private university
Semester-based university
Endowment of the university
Number of faculty in the department
Number of graduates with BS every 3 years say
Number of graduates with MS every 3 years say

Will that be OK? anything else?

Endowments may not be very useful in non-US institutions, which are often publicly funded.

I often hear the phrase "peer institution" used to mean an institution with which mine competes to attract students and faculty.  So it is often a question of the institutions (perceived) quality.

The Carnegie Foundation gives 6 types of criteria:

Undergraduate instructional program
Graduate instructional program
Enrollment profile
Undergraduate profile
Size and setting
Basic classification

There are many factors involved--for instance, geographic region and percent of full time students are factors in 5 and 4.  I don't think semester versus quarter system is too important.  See the link for descriptions of these criteria.
There also seem to be a couple of Chronicle articles about selecting peer institutions:
http://chronicle.com/article/in-selecting-peers/134228/
http://chronicle.com/article/Who-Does-Your-College-Think/134222/
however I can't access the Chronicle website right now, but did find this other article which discusses the first Chronicle article linked:
http://theairspace.net/commentary/u-s-colleges-name-their-own-peer-institutions-rank-themselves/


text:
Accepting European math postdoc offers and leaving after a year
I am a finishing Ph.D student in pure mathematics in the US.
In November, I received a 3 year postdoc offer in Europe on a PI's grant with a December reply deadline and accepted starting in 2015. Recently, I was offered an NSF MSPRF at an American school, starting in 2014. My plan is to use the NSF in 2014-2015 and 2016-2018 and go to Europe for 2015-2016--the NSF and my US host institution are OK with it.
However, when I accepted the European offer I did not specify that I would be staying for only a year (I had no other offers at that point).
A what point am I obligated to tell the European PI that I will stay for only a year? Now, before accepting the NSF? After starting the position in 2015?
More generally, in Europe is it considered normal or unethical/breach of contract to leave multi year (mathematics) postdoc positions after a year?
I know it's considered normal in the US but the postdoc hiring here is done at a departmental rather than individual level...

Going for one year would fulfill your obligations as I understand them, but I can't guarantee the PI will see things the same way.  You should discuss it as soon as possible, to settle the issue and so the PI can at least make realistic plans.  (I'd be a little offended if I discovered that someone visiting to work with me had dramatically changed their plans without telling me until much later, even if I thought the change was otherwise reasonable.)
There are several plausible outcomes:

The PI might insist that you have made a commitment to stay for more than a year.  I don't think this is reasonable or likely, but it's better to find out now than later, so you can figure out what to do about it.
The PI might be fine with one year.  Then you won't have to worry about this issue any further.
The PI might accept one year but seem unhappy about it.  In that case, you could explain that you would really like to come for a year if possible, but you would be willing to withdraw if the PI would prefer to hire someone else for the full three years.

I think this depends a lot on the hiring practices from country to country and from university to university. For instance, if you're offered a multiyear position on what amounts to a renewable annual contract, then there's much less of a problem leaving after one year than if it's a single multiyear appointment.
However, essential communication with everyone involved is required before you start the positions. If people are not aware of what you want to do, and you spring it upon them as a surprise after you sign the hiring paperwork, you're setting yourself up for much bigger problems than if you talk to them and make sure everybody's OK with your plans in advance.


text:
Confidentiality of thesis data: PhD with industrial partner
In the field of Mechanical Engineering, when doing a PhD in a University but in partnership with a company, at some universities, an agreement is signed between the company and the university (or Laboratory) in which the company remains the owner of all files provided (e.g. geometries, meshes) as well as the results produced, but allows for publication of most of the results. The line drawn between what its supposed to be published and what remains strictly confidential is hard to draw and often depends on the company as well as the topic.
Usually, in order to preserve this confidentiality, researchers scale the figures to unknown values and do not provide geometries or mesh/material properties for example. I was wondering if this common practice in scientific publication can be applied when writing a PhD Thesis. Basically, are all results presented in a thesis supposed to be public and more importantly, is an independent/external researcher supposed to be able to reproduce all of the results ?

"generally, an agreement is signed between the company and the university in which the company remains the owner of all files provided (e.g. geometries, meshes) as well as the results produced, but allows for publication of most of the results" - maybe that is "generally" so at your university, but some other universities also "generally" refuse to sign any such 360° gagging agreements before any results have even been created. Therefore, maybe "generally" should be replaced with "at some universities" in this question.

@O.R.Mapper Thank you for your comment. I edited the question accordingly.

The standard for a Ph.D. thesis is simple and universal: it must make a contribution to the sum of human knowledge.
As such, all results in a thesis should be public and presented in enough details to allow another researcher with sufficient background to reproduce them.
It's fine for some of the work that you are doing to not be public, just so long as enough of the material is public to make up a Ph.D. thesis.  For example, if you have figures scaled to unknown values or missing geometry information, then you need to ask: is there significant scientific value even without this information?  For example, if the proprietary figure is an example of how a method was applied, that's probably OK as long as there are other forms of verification elsewhere.  If the proprietary figure is the verification, however, and it's missing critical information, then that is not OK.

Some schools (e.g., Prudue) allow for a renewable 2-year embargo to be placed on theses while other schools (e.g., Colorado School of Mines) only allow a non-renewable 1 year embargo.

@StrongBad I am aware of this type of mesure is available but actually does not answer my question, it just puts the Thesis on hold for a while before it goes to the public domain. My question is, should the published results be "reproducible" by others ?

@jakebeal i couldn't add a comment to your answer and so, i had to add a answer. Is it the case for a master thesis also?

@Askingquestion No, it is not.  A Masters thesis needs to demonstrate that you have attained a certain level of skill and completed a significant project.  What exactly that means and how it is tested varies from institution to institution.

The answer to this question is going to vary from university to university. At our university thesis can be placed on a restricted access list, and examiners made to sign confidentiality agreements. Agreements I have signed to specify a time limit on how long the thesis must be kept confidential, but do say that the commercial partner will indicate when they no longer need access to the thesis to be restricted.
Once the thesis is published, it is entirely possible that materials that cannot be disclosed may have been used in the thesis. For example, one would not include code for proprietary routines, but would rather say "the XXX function from the library provide by Blogs Ltd". I guess it would then be up to the examiner to judge if enough information had been provided that they could judge the value of the work. It may be that, since the examiner has signed a confidentiality agreement they can be made privileged to information that other readers cannot. In my experience these issues are sorted out on a case by case discussion between the IP holder, the university and the examiner.