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Non-citation of basic knowledge
We all know how important proper attribution of ideas is. At the same time, certain things have become basic enough that citing the paper where they were first discussed is overkill: to give an extreme example, if you need to do some differentiation in your math/physics paper, you don't need to go and cite Newton and Leibniz. Now, on occasion students ask me how one can determine if a piece of knowledge is common enough that they can forgo a citation. The rule of thumb I give them is:

If it is something that is explained in a standard first-year undergrad textbook, then anybody who is going to read your papers knows about it and you don't need to provide a citation.

[Here I want to emphasize that I give this to them as a rule of thumb, and I always tell them to ignore it and provide the relevant citation if they think it is necessary to do so in a specific case]
Are there better or alternative ways of drawing the line?

It probably depends on your audience. Do they "know about it" or would they find a reference useful?

Very closely related question :Almost everything we know is taken from someone else, so what do I cite in a paper?. I am almost for certain it's a duplicate. Please take a look at it.

I frequently see references to textbooks in articles, they are less "overkill" than the original paper and they usually include remarks about history, similar results (which you don't necessarily learn of when you are first shown the result). Plus, one good textbook line in the bibliography can cover many "common knowledge" references throughout the text.

@scaaahu The linked question is not asking for advice for academic publications, but for a student paper which will consist (almost) only of bibliographic references. But the answer does seem applicable to this question too.

I find Latour and Woolgar's spectrum of "facticity" a useful tool for thinking about these questions (a nice summary can be found at this link).  It breaks scientific statements into five rough categories by level of certainty in the assertion:

Speculations - don't have to be backed by anything
Descriptions - not established, so need to be directly backed by evidence
Tentatively established - need to be backed by citations
Well accepted - should be stated, but don't need evidence or citations
Tacit - should not even be stated

Where exactly a fact lies on this spectrum depends on the community and state in discussion.  In general, the broader the audience, the less well accepted facts should be assumed to be.  I think the notion "Should everybody reading this have been taught in a class?" is a good one, though undergraduate is not necessarily the stopping point.  For a machine learning audience, for example, you should assume everybody has had graduate level machine learning courses, while for a biology audience you should not assume they have even had undergraduate computer science.

Since the OP mentioned an example from math, I must say that I don't understand where mathematical theorems fit into this system. The numbered list seems to contrast "well accepted" with tentative or speculative; in that case, proven theorems are definitely "well accepted". On the other hand, the paragraph seems to conflate "well accepted" with "widely known". But there are plenty of specialised theorems that are familiar to an extremely small group!

@ArtiePrendergast-Smith I think the notion of "proven" is less absolute than it appears at first glance.  "Proven" means that a mathematical argument has been found convincing (and therefore accepted) by some community of reference. Consider that there are plenty of people who assert that a paper they have written contains a proof resolving the P=NP question.  You probably don't consider P=NP to be "proven," though, because neither you nor people whose opinions you trust have read and been convinced by their proofs.  Acceptance, I would claim, is just as valid a concept in math as in medicine.

There's something in what you say, but I think it's not realistic to claim that there's no distinction between, say, math and medicine in this respect. However, this is beside the point of my original comment: what I am saying is that your spectrum implies that anything that requires a reference is tentative or speculative, which is not the case.

Let me quote Kate Williams and Jude Carroll (2009, pp. 26–27) with a good overview on this topic:
"You need to reference when you:

use facts, figures or specific details you pick from somewhere to support a point you’re making – you report
use a framework or model another author has devised. Let’s say you ‘acknowledge’
use the exact words of your source – you quote
restate in your own words a specific point, finding or argument an author has made – you paraphrase
sum up in a phrase or a few sentences a whole article or chapter, a key finding/conclusion, or a section – you summarise.

You don’t need to reference if you:

believe that what you are writing is widely known and accepted by all as ‘fact’. This is usually called ‘common knowledge’
can honestly say, ‘I didn’t have to research anything to know that!’.

But
If finding it out did take effort, show the reader the research you did by referencing it."

Williams, K. & Carroll, J. (2009). Referencing & Understanding Plagiarism. Basingstoke:Palgrave Macmillian.


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What do conference organizers expect from an invited speaker?
I am asking this because I am going to be a plenary speaker in a couple of months (this is not going to be my first invited/keynote/plenary talk, but for some reason I never stopped to think about this issue before). I've spent  10 minutes thinking of plenary/keynote speakers I've seen in past conferences, and they roughly divide into two classes: (i) a majority who give a talk that, other than being longer, is pretty much indistinguishable from the talks of speakers that get in through peer-review ("here is a very well-delimited problem, which I propose to solve as follows"); (ii) a minority that attempt to give a loftier, programmatic talk ("recent developments have this overarching theme, which is pointing the field into this direction; here are some remarks on what this means for us all and a sketch of some neat things we can do if we take things seriously").
The organizers of this particular conference don't really have a preference either way, but I am wondering if audiences at large do. Personally, I prefer (i), but that is just because I'm more of a problem-solver than a theory-builder.

Who are your audience? Problem-solvers? Theory-builders? Or combined?

Combined, but I'd say with a somewhat higher proportion of problem-solvers.

If you personally prefer (i), that is what you should do. There is nothing more useless than listening to somebody give a talk about something they did not want to give a talk. On the other hand, even if I am normally uninterested in the topic, a well-spirited speaker might catch my curiosity if  they seem to really stand behind what they are saying.

The title of the question doesn't match with the text, which in some sense has no question.  I'm worried that the question which isn't there is basically asking for a poll.  Can you make this into a more proper question?

@Kimball: Indeed, in this case it seems that it's already known what the conference organizers expect: "do whatever you want".

Here's my take: as a plenary speaker, you will have an audience that is broader than those who may come to a minisymposium or parallel session, and consequently also have a less deep understanding of technical details of your particular field of work. They may also lack an understanding of the motivation for what you are doing: For things in my particular field, I know why people want to do them, but for other areas I often would like to know "why should I care" before I want to hear the details.
Consequently, the talks that I have often found to be a bit boring are those that really are just longer minisymposium talks. The ones I find interesting are those that explain to me the bigger context of a problem: where does it come from, what are the historical connections, were there dead ends in developing solutions, etc. Then show me how you approach the problem and where this leads. I also find it interesting to hear about open problems and ideas for future research -- an invited talk should not just be about the great results of the speaker, but also inspire others to work in this field.

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What does "NN" mean (submitting a proposal to a publisher)?
I recently heard about the possibility of submitting a proposal for a book to the publisher as "NN". I assume it has something to do with the fact that a couple of possible contributors have not yet confirmed their contribution but the editors want to go ahead anyway and submit the proposal already.
Am I right with my assumption? If so, what does "NN" stand for?

May be this: https://en.wikipedia.org/wiki/Nomen_nescio

Nomen nominandum, "a name to be named" - if you don't know the person's name yet, this indicates that you will supply the name later.
Which sounds a bit more reassuring than a simple nomen nescio, "I don't know the name".

I had only ever heard the second (in the plural - nomen nescimus) as the meaning of the abbreviation.

I think "Nomen Nescio" is the correct expansion of NN.
My source:
Introduction to Scientific Publishing: Backgrounds, Concepts, Strategies By Andreas Öchsner;
Page 77, table 7.3: "Some standard abbreviations from Latin language":

N.N.  -- Uknown name, used as a placeholder for unknown names, (from Latin 'Nomen Nescio')

Google books link.

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How to address the issue of the widespread use of protected material in informal publications?
One thing that always bothered me is the liberal use of protected material in informal academic publications (for example Powerpoint presentations, handouts and internal reports rather than published papers).
It seems that the "everything on the Internet is free" attitude is also widespread in the academic world. And while I regularly spend a considerable amount of time either creating the graphic material I need or search for it on the Internet, nearly everybody else is not even thinking about it. Need a nice picture of a sunset or a little fish to include in your graphic? Just google and use the first one, without thinking twice!
This does not happen on single occasions only, I've made that experience in several countries, working in different environments.
Sometimes, among co-workers and friends I raise this issue and am usually met with understanding. Most of them see the problem with the additional time they need to spend to search for relevant material or the creation of an appropriate space to include copyright notes or references to graphic material. Some also mention that it would be considered unprofessional including a user name on the Internet as the source for their imagery.
My questions therefore is, how do I sensibly raise this issue among supervisors (which may consider this a waste of time) or an unknown crowd, especially considering above-mentioned criteria?

To quote section 107 of the US Copyright act: "[t]he fair use of a copyrighted work, including such use by reproduction in copies or phonorecords or by any other means specified by that section, for purposes such as criticism, comment, news reporting, teaching (including multiple copies for classroom use), scholarship, or research, is not an infringement of copyright."  So at least in the US, it looks like you're trying to solve a problem that doesn't exist.

As JeffE points out, what you're describing is protected fair use in the US, and indeed, in many if not most Berne convention signatories, so it's not clear why this bothers you or what "the issue" actually is.  As such, I'm not sure the question is answerable.

I don't understand the downvotes and close votes.

@JeffE, it being legal in the US due to Fair Use doesn't prevent someone from suing you. That could be quite costly to defend, and it's not guaranteed to get thrown out automatically. You, or your expensive lawyer, actually need to make an argument against the copyright holder's team of lawyers in briefs or maybe actually in person to a judge in a courtroom. Those costs can add up. The odds of suit from a presentation with a stolen pic are low, IMO, but they are not zero.

...doesn't prevent someone from suing you — Okay, sure.  But why is that your problem?

@BillBarth the odds of being struck by lightning while walking down the street on a cloudy day are also low but not zero. It seems like a strange principle by which to live your life that we should be afraid of doing things even when we are confident that they are ethical and legal just because of some hypothetical fear of a lawsuit by some malevolent person. Is a copyright lawsuit for using an image from Google Images in a presentation really the biggest thing you have to worry about in your life? If so, I envy you.

@JeffE, it's not Bill Barth's problem, but it might be OP's or anyone else in OP's position. If you use copyright protected material without license, you may be subject to an expensive lawsuit, DMCA takedown request, or have to deal with a cease and desist letter. All of which is annoying, two of which may remove your material from world view, and one of which is, perhaps, ignored at your peril. It's one thing to tell others that it's normal to be cavalier about these risks, and it's entirely another to be cavalier yourself. Personally, I never want to have to defend a copyright lawsuit.

@DanRomik, same to you as to JeffE, but also, there's a difference between malevolence and corporate policy. Several of the big publishers are on lookout for misuse of their IP. They might choose to deal with you (a malevolent misuser of their property in their opinion) in a way that is perfectly legal, moral, and right from their perspective. Telling OP to not worry about the chance of lawsuit , DMCA take down, or C&D is pretty cavalier in my opinion. People lose Fair Use defenses all the time, though I don't know of an academic/research case where they have. It all still costs money.

@FranckDernoncourt: I thought I made clear why I voted to close (I didn't downvote, incidentally): the question "this thing bothers me...how do I raise this issue?" is unanswerable unless OP feels like telling us why this bothers them and what purpose they have in raising the issue.  Without that, it invites answers - like yours - discussing whether or not this should bother OP, rather than answers to the stated question.

From an ethical point of view, I think most people can still sleep well despite taking the first fish from Google from time to time.
From a legal perspective, it depends on your jurisdiction and the license of the image. As Jeff points out, it's often fine in many places.
You should define your goals (ethics vs. legal), and act accordingly (which is my case would be do nothing).


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What could be incentives for publishers to waive fees for reusing figures?
I'm in charge to obtain permissions to reuse figures from previous publications for our future work. Our publisher is a STM-signatory so for most journals there is little problem as their publisher are also STM-signatories and therefore allow to reuse up to three figures free of charge.
Other publishers request substantial fees which are sometimes waived when our head editor gets involved and states that the purpose of our publication is purely academic (though it is published for a profit by our publisher).
Sometimes even that fails and there seems to be no other way than paying the fee or not using the figure. We don't have a budget for this though.
My question is, are there any other non-monetary incentives for publishers to allow the reuse of a figure? I'm thinking of appealing to their "academic consciousness" to help to contribute to scientific advancement or possibly include a line in the figure caption: "With very kind permission from PublisherX" (is latter a common approach or desirable for a publisher)?

I've never had a problem getting permission to use a figure with proper citation – ideally such a usage drives traffic back to the original article / source too.  So that's one incentive right there.  Be sure to let them know you will send traffic / credit back and ask how they want to be cited and / or linked.
But authors ordinarily do not really expect to lose control over their IP, so authors would probably avoid such publishers if they found out that a journal "jailed" their figures. This is obviously a stick not a carrot, maybe saying something like "I think the authors would be very disappointed to find out if they have been disadvantaged by publishing with you, it might discourage them working with you in the future."


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When does "distributing the submissions" process usually start for conferences?
For a conference, when do the chairs distribute the papers to referees for review?
I have submitted a paper and discovered an error in the paper. Now, I want to withdraw before the submission deadline. Is this something advised against?

I doubt that the distribution time is important for your actual concern. It probably wouldn't be prior to the deadline, but might be. There are too many conferences with too many policies to be definite.
But you can withdraw your paper and it is unlikely that it would be a problem even after the deadline. But if you want to replace it with a newer version, rather than just withdraw it, you should probably contact the program (or conference) chair and ask for advice.
Many conferences give you a chance to provide a new version after review in any case. If the error isn't such that it would result in rejection, you might be able to just provide the corrections as part of the regular process. But for a serious flaw, contact the chair.

Unfortunately, the error is not very easily correctable and I want to prepare a better version for a conference whose deadline is one month after this one's. Even if I have the correct result, I highly doubt that they will accept any changes after one month.

You can still ask, of course. But it may be best to just withdraw. It should certainly be possible at just about any time.

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References in supplemental material - include in main reference section?
I have some supplemental material that condenses results from a couple of studies in a table (Supplemental Table 1). In the manuscript I refer to my supplemental table. My question is: where should I include the references from Supplemental Table 1? I cannot include them in the main manuscript (right?) as I do not cite these studies in the text and any journal would just list them as references that have not been cited before. I would tend to just list them right under Supplemental Table 1. Is there any correct practise?

Which journal is it?

It's common practice, however, these might differ between journals.
Likely, when you include them in the main references, they will be flagged as not being mentioned in the manuscript and removed. Unless otherwise instructed in the author guidelines of your journal of choice, simply add them to the supplementary material and see what happens.

Then again, if not being cited in the manuscript they might not be indexed by databases.

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Uploading supplementary material to figshare. How to refer to it before making it visible to the public?
My problem is the following: We want to upload supplementary material for bookchapters I'm editing. We have decided to use figshare.com for this. One advantage is that they supply all material with a DOI. But (as far as I understand) they do only so when material is made available for the public, not for private data.
Now, it would be a little strange to make supplementary material available a long time before publication (possibly more than a year).
How may I obtain a permanent reference (doi, link, etc) to the supplementary material which I can add to the respective bookchapter already without making said supplements visible to the public?
And if this is not possible, what would be a workaround? Make it public just shortly before handing in the edited volume to our publisher (this would still be months before the publication date)? Just refer to the account (not a single file) on figshare the material will be hosted on? Include a placeholder DOI within the chapter and include it after we received page proofs from the publisher? Just publish the supplementary material already because nobody cares?

At the bottom of the Edit Item screen is an option to create a private link. There's more info about private links on their blog.
For peer review, the private link feature has the added advantage that it hides the author information.


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How to deal with leftover work after changing employer?
In the academic world, how is work generally handled that has not been finished when an official contract ends? This is, I imagine, more the rule than the exception, for example when papers were submitted shortly before the end of the contract.
Is it common practice to "bill" (i.e. work within the work hours of) the new employer? That seemed ridiculous to me until I thought that the same situation of unfinished work will likely arise with the current employer also. Quite a number of academics, including me, are on short term contracts (< 1 year). Recently I had to sink about 1 week of work time into such a former unfinished work which of course delays my current project.
Is it expected that I work on it in my free time as a commitment to my former employer and see it as a personal mission to finish this work? Should I request a compensation for it?

How do you decide whether work for a given paper is "work for your previous employer" and not "work for your new employer"? What about requests by readers related to papers you wrote a few years ago, while still working elsewhere?

@O.R.Mapper Well, if the new contract is paid from the budget of a specific project which should be completed within a well-specified deadline, I think that the distinction is pretty clear, and in this case I'd expect the new hire to work full time on the new task.

@MassimoOrtolano: Working "full time" on one thing sounds like quite an unrealistic expectation in any academic context to me. At least, the boundary to what belongs to a given project and what doesn't can often be very blurry.

Perhaps you can clarify the nature of the work (research, teaching, service, ???), and the nature of your job (faculty, postdoc, staff scientist, ???).  A common case is that the "work" is an academic research project and that your job duties include pursuing your own self-directed research program - in that case, you simply continue working on the project as you see fit, considering it to be included in your research program and hence part of your duties.

This is maybe handled differently in different fields, but in any case you should inform you new advisor that you have to finish work from your previous position and discuss how this should be handled. Here are some models that I know:

Often it is expected, that postdoc do some independent work, so using this time to finish work with another workgroup is totally fine is this case.
In case your new position does not allocate time to do such work, you should inform your previous advisor. You may offer to work in your free (i.e. "non-work") time and ask for compensation (e.g. using a special contract - in German this could be a "Werkvertrag" but I don't know an English translation).
Your new advisor may get "on board" of your started project, so that your work on the project also falls under your new contract.

In my field, new institutes are typically quite happy if e.g. half-written publications are finished in their work-time, seing that your affiliation/contact is the new institute. Such papers are often "double-counted": the old institute counts them as beloning to the old project (as specified in the acknowledgements) and the new institute counts them as they are the affiliation ;-)

Upvoted especially for the first item. At least the way I observed things, being funded from/assigned to one project has nothing to do with working only for that project. It means that you are responsible for getting the contractually agreed upon tasks done for the project, but beyond that, no-one can or should restrict what you do with the remaining time research-wise. But maybe that is something more prevalent in highly collaborative fields where everyone co-authors something with everyone at some point, thereby kind-of bridging (read: ignoring ;) ) any project boundaries.


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First time opportunity to give a seminar
Recently I had a talk about the topic of my master thesis with the professor I currently work for (he wasn't involved in the thesis). I mentioned that there are interesting results and that I would like to present them, if he'd agree. He proposed to not only give a presentation but a seminar.
I've just graduated from my Master's and never given any lecture, course or seminar before. I would be happy to take this opportunity as I enjoy teaching and I expect a good experience.
If I'm willing to do it the professor expects a scheme of the seminar and that's the point where I am stuck. For how long of a seminar time should I aim for? Introductory or deep into the matter? What exactly is the difference between a seminar and merely presenting my thesis again? In my understanding seminars include practical approaches. Should I focus more on practical issues or my own work?
The subject is quite technical in detail but this is not very obvious from the topic alone. I expect students to may have heard of the methodology but never employed it themselves.
I'm quite lost on how to tackle this task though excited to have this opportunity. I realise that my question isn't really well fleshed out but I'm happy to hear opinions nevertheless.

I'm not sure what the difference is between a "seminar" and a "presentation" unless by "seminar" you imply a semester-long series of lectures.

If you have presented your thesis before, the seminar could be something similar to it. However, a seminar is usually given to a wider range of audience, and thus you need to make it more accessible for someone in the audience who may not be familiar with the subject. Aim for an accessible introduction, and save the technical details to the second half of the talk.
As for how long the seminar should be, you need to ask the professor how much time you have to talk, and how much time you have for questions and answers.


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On discrimination in retake exams
I'm experiencing a practice at my university where the overall number of students who would pass the exam is adjusted based on how many students passed the first exam, so the retake exam contains questions which are beyond the lectures if previously the percentage of students who passed the exam is very high. Another question is that in first exam questions are repated from the previous years. The student might be absent in the first exam due to the illness, etc, so I consider it as discriminative practice and I need some ethics based formulations, codes, laws etc. that will help me to prove this discrimination. Thanks.

I'm not sure I understand.  You're saying that when students miss an exam because of illness, the retake exam they are given is one that is intentionally designed to be more difficult?

Yes, when the student lodge an objection the argument is that it ivery high the percentage of the student who passed the exam, but this is in the first exam not the retake, so overall they consider the percentage of both although in the retake practically nobody passed, The main motive is that having more than 90 percentage of the students that would pass the exam is in contradiction of the characteristics of the subject considered as difficult and therefore more respected by the other professors.

Not everything that isn't fair is also "discrimination". According to Wikipedia, discrimination is when students are disadvantaged due to being in a specific "group, class, or category", where groups, classes, or categories are individual traits of the student (gender, nationality, religion, etc.). Arguably, "students that take the retake exam" doesn't qualify as an individual trait.

I would also suggest you to make clearer what exactly you are looking for. At least I don't really understand your last sentence "I need some ethics based formulations, codes, laws etc. that will help me to prove this discrimination".

Related: Are identical make-up exams fair?

On what basis do you allege this system is discriminatory?  Without this information, I had to vote to close the question as being unclear.

@299792458 thanks for the link XD

I'm afraid that quoting external regulations and grading guidelines here won't do you any good. The question is what are your university's internal grading policies. Do they have a recommended grade distribution? Are there rules governing repeat examinations for students who had to miss the first one? Are there policies on what is allowed to be covered on such examinations?
Whether good or bad (and it's a bit of both), grading standards differ between institutions, and even within different departments at the same school, and sometimes even course to course. That means you can't rely on what others do to help, and you can't really claim "discrimination" here, either. Such policies are clearly unfair and unethical—it's not right to force a fixed percentage of students to fail, regardless of their actual performance. However, unless your university's regulations specifically forbid such behavior, there's not much you can do to fix this.

I can imagine one scenario in which this might conceivably be discriminatory -- if a student misses the first exam due to a disability (e.g. chronic migraines), is not permitted to make up the first exam, and is assigned a grade based on poor performance in the killer second exam.  I admit this is quite a long shot interpretation of the question, though.


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Saying "After doing this work we learned..." in a paper
I have seen several math papers which end with a statement like "After completing the research in this paper, we learned that all the results are already known."  I wonder what are the situations in which such a comment is appropriate.
Such statements usually sound lazy to me, as though the author opted not to do a literature search at the outset, and after learning of previous work the author opted not to edit the paper (or withdraw it from submission for publication) beyond adding one sentence.  Putting the comment at the end of the paper seems especially questionable, in that the beginning of the paper gives the reader the impression that the results are new.  But I realize that mine is an extreme perspective which does not apply to all situations, and I would be interested to hear other perspectives.

Did you see those papers in reputable journals or  low quality ones?

Reputable journals.  Not in the top 10 in pure math, but certainly in the top 50.

I usually see such comments in the introduction and they mostly refer to work that was completed either simultaneously or very recently.

I agree that such comments occur also in cases of simultaneous discovery of the same results.  In those cases they are completely reasonable, so much so that it slipped my mind that such comments occur in that case.  What I had in mind is the situation where the result was published at least 20 years previously.

In part, I agree with you: if one finds out the result one has proven is in fact "trivial" (for various definitions of trivial), the "right" thing to do is to not bother submitting it for publication. (Though leaving it up on arXiv, for example, may be useful.)
But, here are some possible defenses:

In mathematics it is not always the result that matters: the journey getting you there is a big part of it. This sentiment is very well-expressed by Thurston in his essay "On Proof and Progress". Just because one has re-proven a well-known result doesn't necessarily mean that the paper is trivial! If the approach is new this can lead to better understanding. But in this case I, at least, would advertise this fact in the introduction beyond a single sentence.
As indicated in the comments, most of the time when I saw such a sentence it refers to fairly recent (perhaps even simultaneous) publications. Given that sometimes mathematics research takes time to complete, it is not entirely impossible that the authors genuinely started working on an open problem only to have the result solved in the mean time. And if the problem is somewhat obscure, I think the authors can be forgiven for only doing a detailed literature search before they start their research and not repeatedly doing it once every few months. In this case the language you quoted seems rather appropriate.
It could honestly be a case of ignorance! Suppose the same essential problem manifests in two distinct field of mathematics which have their own lingo. Then it is quite possible that even most experts in either field would not have recognized easily that the two results are the same. (The "two-way" relation above can also be a "one-way" relation, where researchers in field A generally don't know about result B in field C, while for researchers in field C the applicability of result B to problem D seems obvious.) In this case having the duplicate paper published will (a) help raise awareness that the problem has been solved and (b) perhaps even help the two fields become aware of each others' results.
Similarly, one may have discovered a simplified proof for a special case of a very powerful general result. While the result may be well-known, having this simplified proof in the special case maybe worthwhile, if only for pedagogy.
In the modern day of electronic communications this should happen less, but one should remember that in the history of mathematics there are many results which have been discovered, forgotten, and then rediscovered. And even with the advent of MathSciNet, sometimes very technical results are hard to search for: you have to know exactly the right string of keywords to discover it in the literature.

Thanks very much for your wise and well-thought-out answer!  That's very helpful.  Now that I think about it, what strikes me as somehow wrong is to wait until the end of the paper to acknowledge that the results were previously known, since that makes it too easy for readers to come away believing that the results are new.

My 2 ct about ignorance and language: I've been in in a situation where I have been able to describe the problem I needed to solve in the vocabulary of my field, but couldn't find literature about solutions anywhere (including askig around at conferences). After solving the problem, the solution allowed/suggested different search terms, and it turned out that a different field indeed had some work on that. In another case, I learned much later that other fields use different vocabulary, unfortunately terms which already have a (different) meaning in my field... I don't think it is that seldom.

@MichaelZieve: on that I agree with you wholeheartedly. I can understand that the authors want to talk about their own contributions first and foremost, but anywhere later than the end of the introduction section/paragraph would be too late in my opinion to acknowledge those other works.

In life sciences this is quite common, although the cause may be different. Authors will typically use this sentence if after their paper was reviewed/accepted but before publication, a relevant paper was published. This can happen because many groups often work on similar subjects ("competing"). A lot of times it can be something that the reviewer/editor asks the authors to add.
In this scenario I think it is more justified, because the authors really could not have known about the other paper since it was not published yet. Also, revising the whole paper after it has gone through review may be a problem.


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Am I obliged to share my most promising data?
I have just started a PhD along with another candidate. We are each looking at different aspects of the same subject. His data provide context for mine, while my data simply add value to his. As I will be asking him for some of his data, he has decided that he wants some of my data.  However, he is interested in using a particular part of my data which I think will be the most fruitful part of my PhD.
His data are quicker to prepare than mine, and he will undoubtedly write up his chapters/ publications before I get a chance.  I am worried that this will have a negative impact on my ability to publish my papers.
Do I have to give him my most promising data?  Is there any way around doing this? I would prefer to rely on older data from Honours students looking at this subject and not ask for his data, if this allows me to keep my own data.

You can give him your data and maybe put your name on his paper as last author, since you will have an important contribution to his research?

Yes, if and only if you are also obliged to share your least promising data.

What does your supervisor say about this?
I've seen situations where someone not sharing data not only prevented papers being written, but completely obliterated the collaboration.
One possibility is handing the data over, but helping with its analysis and the subsequent writing of the paper (with co-authorship). You could offer the same to the other candidate.
In any case, as you have only just started, I wouldn't worry about the negative impact. There's plenty of time to build.

Am I obliged to share my most promising data?
From my personal experience, it depends on the way your advisor runs the group. For example, if you are in a group where co-authorship with other students is encouraged, then opening up your data vault to other students (and them doing likewise) can benefit everyone involved. I've seen other groups at my university (and other schools I've attended) run this way and it seems to work well for all parties involved.
However, if your group is not such as that described above, you need to be very clear (to your advisor and collaborators) what you expect to gain out of the collaboration/data sharing. In this case, don't assume that someone will look out for you and give you the credit you feel you deserve.
I encountered a situation early on in my studies where I shared data with a fellow student. Everything they did with my data was kept secret from me, i.e. it was obvious to everyone that this student had no intention to include me in any of their scholarly works (yes, I did deserve co-authorship). It was only due to the fact that they couldn't get anything to work that their chances of getting anything published fell to zero, and I wasn't screwed over.

If both of you are working in similar fields, you should likely co-author papers (and share results).  Very rarely have I run into profs that didn't encourage (or almost mandate) cross collaboration among their students, and the profs I did run into like this were nearly impossible to work with.
A couple of tips
1) Be sure to make it clear you want co-authored papers - you did some of the work, you deserve some of the credit.  Also figure out who will be first author BEFORE you go any further.
2) With the other student, discuss your paper ideas, and see if you can carve out a piece of research that will be mainly yours, and another piece that is mainly his.  Make him a co-author if appropriate.
3) Try to work out an understanding without involving your prof first.  Go to him/her after you've made a good effort come to a mutual agreement and failed.
3) Remember that your graduate program is a small group of people who all know each other.  This situation sounds like it could blow back on you (for not sharing all the data), or the other guy (for not giving credit where its due) in a big way.  If you've promised him data, give it to him.  If he decides to be a jerk and bogart his research, then don't work with him again.  You have other great research projects you can keep for yourself.

Why this urge of researchers to keep things secret...
Why don't you talk to your college about this and see if he is open to having you as a coauthor (you write the section on the data for instance) = double win. Or could you publish your draft as a report from your university that he could cite? Or another option...
It will depend on your supervisor in the end, but you can subtly make him aware of the problem.


text:
Collaborative paper-writing with non-LaTeX-using colleagues
Background: I work in a field where the use of LaTeX is common but still far from universal. So far I have been lucky in that all my coauthors in the past have been fellow LaTeX users, so collaboration boiled down to creating a shared Dropbox folder with the .tex and .bib files we were working on. Now I'm starting a collaboration with two colleagues who use Word, so they have proposed to collaborate with Google Docs. There are various reasons why this is a bad idea, the main one being that writing this paper is going to require doing things that are easy in LaTeX but difficult and time-consuming in Google Docs (or in a standard word processor, for that matter) ---e.g., Greek letters for variables, assorted math/logic symbols, trees (in the graph-theoretic sense), or frequent crossreferencing in the running text of numbered examples.
Conflict: One of my colleagues has already said he has no interest in learning LaTeX. On the other hand, I don't want to go hunting through the Google Docs character map every time I need to insert a non-Latin character.
Question: Is there any collaborative writing software that allows including LaTeX tags and environments in a Word-like document? For example, when I'm writing semi-informal things like lecture notes, I can get by with markdown and then generate a pdf with pandoc. I don't know of any online services with similar functionality.

What do you mean by "collaborative"? Would LyX in Dropbox be an option?

It will take your colleagues longer to learn LaTeX than it will take you to stumble through a standard word processor. Welcome to collaboration - I think you just need to suck it up.

Writing math without LaTeX is like a one-legged kicker trying to kick a field goal. Silly.

One of the least-bad options may actually be MS Word, if everybody has access to it. Recent versions have a new maths system that allows much LaTeX syntax.

@SimonW: unfortunately, all my computers run Linux, so I'm stuck with LibreOffice. It pains me to say this because I really want to like it, but LibreOffice ss bs compared to even much older versions of MS Word.

@user31013: I disagree. The colleagues do not need to learn all of LaTeX. I am pretty sure Koldito can use his LaTeX experience to write up the preamble, plus any macros that might become necessary. At that point, using LaTeX for the body of the document is about as simple as any other markup language.

http://tex.stackexchange.com/q/20859/39306 is relevant, also http://tex.stackexchange.com/q/61967/39306.

@Koldito, sure. MS Word was utter crap. My daughter wrote her thesis (a bit of math included) in Word (way bac in the .doc days). It crashed, had weird bugs when equations came to be at page top, froze when editing mildly complex equations, and produced awful looking output. It has features for full-length texts, but nobody I know even suspects they exist ("memo editor" is the principal use), so I'm sure they are riddled with bugs.

@DevSolar, just have them write plain text, and perhaps add handwritten equations as images (or teach them a bit of LaTeX syntax for that). Have OP take over the integrating and polishing. I know that would be faster for me than struggling with the likes of Word.

Excluding LaTeX-focused online collaboration services, such as ShareLaTeX, due to your new collaborators' preferences, I think that you have pretty much two major options, as follows:

Overleaf (formerly WriteLaTeX)
Authorea

Both online academic collaboration services support simultaneous use of LaTeX and WYSIWYG rich text mode, Authorea also supports some other formats, such as Markdown and HTML. Both services (to various extent) offer other nice collaborative features, such as data sharing, version control, revision notes and much more. Due to multi-format support, I would prefer Authorea to Overleaf, however, the final decision should be made upon a comprehensive comparison of both services across all available features and your detailed requirements as well as some testing.
P.S. Just for completeness, I will mention two other options. The first is to use blog engines that support both WYSIWYG and LaTeX (most of the major ones do: from WordPress to Jekyll). It's a decent option, but I would prefer one of the above-mentioned dedicated services, for multiple reasons. The second option is to self-host RStudio Server (or maybe a custom Shiny application), which would allow academic collaborative writing, using RMarkdown, but IMHO this is the worst solution possible, as trying to implement various needed features and solve issues, such as version control integration, would bring you and your collaborators a lot of headaches.

With a non-LaTeX collaborator, we just decided to give markdown (not much greek or maths anticipated) + git a try. Our institue policy prefers to keep the evolving documents completely in house, so we use our own git server and cloud services are typically not an option (would need formal approval wrt. data security/privacy - which is burocratic nightmare - and e.g. US based services are unlikely to get approval).

@cbeleites: Thank you for your comment. Yes, Markdown + git seems to me like a sensible solution. BTW, Markdown supports math, etc. via extensions and/or external tools. The most popular one is likely pandoc (of the latter), which I'm sure you're aware of. Many other options are listed on this page.

If you're willing to drop "online service" requirement you might consider showing them LyX, which is a WYSWIM/WYSWIG editor that:

Compiles to latex
Allows one to add basic formatting as in word
Allows one to add figures, tables, citations as in word.
Allows one to add raw LaTeX code
Has super-usable equation editor that compiles code to latex, but you can insert equations without writing latex (you can write it if you want).

Lyx is not so good at sharing --- but I've collaboratively worked on Lyx files using Git repository (you might use any other versioned service), and it was a very good experience.
There is a slight problem --- if your colleagures don't use any version control system (or don't know what it is), in this case it is possible to:

On windows: use some Git Gui (Tortoise Git). I've seen non-technical people use Tortoise SVN to share documents.
On Linux: add some scripts that perform VCS operations.
In comments using Dropbox was suggested --- but Git is obviously better choice in terms of feature-set and stability, Dropbox may be easier to learn.

Git beats Dropbox even blindfolded on a unicycle, in terms of solidity and capabilities. I suggested Dropbox only because it is easier to use for non-techies. If someone isn't willing to learn LaTeX, I imagine they don't want git either.

I strongly support that git is better than Dropbox for sharing, as Dropbox easily becomes a nightmare of there are conflicting files.

I worked with someone who didn't use LaTeX, and by the last paper we worked on together, we figured out something that worked for us:

I wrote it in word, peppered with things like\cite{CiteKey}, \caption{\label{fig_some_figure}This is the figure caption} and \ref{fig_some_figure} (i.e. all the crossreferencing stuff).
The equations (only a handful) were pasted as images from a compiled LaTeX .pdf.
The figures were converted to .bmp (word doesn't handle any sensible vector graphics formats, or at least didn't in the version I couldn't be bothered to upgrade from).
The contents of the relevant .bib file was at the end.

The figures needed commenting on and only the text needed editing so it worked out for us.  We used word's "track changes" tools for the text edits. At the end I just pasted the text into a text editor, added about 3 \emph{}s and compiled.  It's a complete hack of a way of working but the extra effort was minimal and all on my side, so a saving of effort compared to writing a paper in word, which realistically was the alternative.

To address the non-latin character problem you mentioned in the "conflict" paragraph, you should use AutoHotKey (Windows) or AutoKey (Linux) to insert the characters for you when you type in specific sequences of keystrokes. The gif explains what I mean. You type /delta and it automatically gets converted to δ (regardless of application).

Instructions are given here

Why is that a forward slash and not a backslash? Is it because of Windows' 'reverse all slashes' policy? ;-)

It's intentionally the opposite slash so as to not obstruct standard LaTeX commands. I wouldn't want to be writing LaTeX files and have \delta change to a δ

Makes sense, and I take back my sarcastic remark.


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how to avoid to being blamed of self-plagiarism in this case?
We have the following "weird" situation in the institution that I am currently working on. We have a master´s degree in CS that requires that the students present a thesis or a research article so that ourinstitution could grant them their MSc title. The background of the situation is the following:
a) Some students had published an article or had an acceptance letter, from a conference or journal, related to their MSc research. This situation has occurred, in some cases, just when they had finished the compulsory courses.
b) It is required from our institution that all the master´s students must present a public dissertation of their research work, this is commendatory to do it for grant them the MSc title. After this dissertation, the student should submit their research work, article o thesis, to be stored in the public repository of our institution.
The problem that we are facing now is how to avoid that one student who had his research work, accepted or published, before it has been put on our institutional repository or vice versa to be blamed of self-plagiarism. For example:
A student X has decided to submit its research work when he is about or just finished his master´s courses. The publication get accepted so it appears in the web page of the conference or journal in which he has submitted his work. This student X need to make the public dissertation and put his paper on our institutional repository, in this part we see two probable outcomes:
a) Somebody could blame the student that he has put, in our repository, a research work that has already been submitted; so it is a case of self-plagiarism.
b) Let´s suppose that the journal or the conference proceedings suffer from a delay, which usually happens when the proceedings are published by a third party, so this student X makes his public dissertation and his research work is put on our public repository. Then one person from the conference or journal could say that this person has made self-plagiarism because the work has already been published in another repository.
How to deal with this situation?
Thanks

Is the work identical in all "published" venues?

Having work shared between a thesis (masters or PhD) and a research paper is completely standard, so why should it be a problem here?

@Buffy, it should be, but the public dissertation is not necessary peer-reviewed.

(b) is usually not a problem (to my best knowledge and experience), as university repositories don't count as "published" in the sense that conferences and journals see publications

There are two issues here. One is self plagiarism as the term is commonly used and there is what a University will accept for any course or degree work. The latter can be stricter than the usual rules because the goals are more nuanced, involving the student's education, not just the validity of the work.
I doubt that this can be considered self plagiarism, provided that what was submitted to both places is the same. Keep in mind that the purpose of self plagiarism is that a reader needs to be able to see the entire context of a work in order to judge it and to extend it. If people just copy without citation from their own work it breaks the chain of reference that scholars require. But publishing the same work in different venues doesn't do that. Each work is complete. And when copying does occur, citation avoids any claim of self plagiarism, since the thread of context is maintained.
But, given that, the student may still not be meeting university requirements, in particular if there is a rule that submitted work not be previously published. If this is the real nature of the problem, then you need to find a local solution, since we can't advise on rules we haven't seen and have no ability to enforce or not.

Multiple publication of the same work might run afoul of copyright rules, but I don't see a hint of that in this case. And multiple publication does occur as when old papers are put into collections. This can be valid or not. But it isn't plagiarism or self plagiarism.

It is extremely common for a dissertation to overlap substantially with one or more seperate published papers.  In practice, the dissertation often has an initial section in the front stating the papers submitted/published from the material, and copies of those papers should be submitted to the referees along with the dissertation.
To counter any accusation of self-plagiarism, while avoiding annoying repetitive citations, this is a situation where a "blanket citation" is warranted.  This should generally be inserted as a footnote at the start of any chapter that draws on material in the papers ---e.g., something like the following:

This chapter has been adapted from the paper Smith et al (2018), and overlaps substantially with that paper; some sections of the text are identical to parts of that paper, and some other sections are substantively the same as parts of that paper, but in different words.  To avoid excessive citation, we offer this note as blanket citation, and we give no further citation to this paper in the body of the chapter.  For readers who wish to cite material shown in both pieces of work, we prefer citation to the published paper.


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how one is not accused of plagiarism when including an article in a MSc thesis?
Let us suppose that I am following my MSc studies. At the end of my compulsory courses I have an accepted article for being presented in a conference with my advisor. For graduating, I need to prepare a thesis, and I want to include this article as the main part of my thesis (80% of the thesis). So I have the following questions (I believe it is not necessary to open another thread for this):
a) How should I do this thesis? Should it be an extended version of the article that is about to be published?
b) How should I cite the article that will be published in my thesis if most of it is based on my article? I believe it would be somewhat troublesome to cite one's work at every moment in the thesis?
c) What would happen if, after the article is published and my thesis is in the digital library of my university, somebody passes a plagiarism checker (like Turnitin) to it? It would detect my thesis in the university repository. I could be blamed for self-plagiarism or even plagiarism (because my supervisor's name would not appear like an author in the thesis document, but as a supervisor).
Any help would be much appreciated.
Thank you very much.

https://academia.stackexchange.com/questions/45888/can-one-include-already-published-papers-in-a-monograph-thesis

Talk to your advisor / program director. They will instruct you what they want you to do.

Many journals have specific policies that allow the submission of material that has previously appeared in an MS or Ph.D. thesis.  This is an exception to the general rule that submitted manuscripts must consist of new, not previously published, research.
Similarly, many academic institutions have policies that allow for the inclusion of text from published papers in MS and Ph.D. theses if the journal publisher also allows this.
Assuming that both your institution and the journal that you're publishing in have such policies, then you can reuse a journal article in your thesis.  This is really quite common in many STEM fields. When you do submit your paper, you should make it clear that some or all of the paper has previously appeared in your thesis and refer to the publisher's guidelines on this.

I don't follow your opening sentence: new, not previously published, research includes technical reports, which is what a thesis essentially is.

many academic institutions have policies that allow for the inclusion of text from published papers in MS and Ph.D. these: Are you aware of any exceptions to this?

You could include the article verbatim and not be accused of plagiarising. (Self-plagiarism isn't relevant here.) But, a thesis has different demands to a journal, so changes will be required.
Explain that your thesis is based upon a published journal article (or published articles), you can include the explanation in the introduction, a single citation (to each article) will suffice. There's no need to distinguish material that hasn't been published (or has been published elsewhere).
In cases when a journal article appears after a thesis, include a mention, e.g., a preliminary version of this article appeared in X's thesis [cite].


text:
Tips for publishing a summary of an article to be published
I want to write a short article about a paper that has been accepted for publication in an upcoming conference. This short article summarizes the accepted one and will end up in my workplace's digital library. The reason mainly is to make the article to be more accessible and understandable to undergraduate students.
In this summary, I should cite the upcoming article to be published. However, I doubt where I can put that citation of the upcoming article to avoid putting it everywhere in my short article. For example, in the methodology, experimentation and results I will present a summary of the original article. However, I do not think it will look nice if I should put something like this in every paragraph: "According to Layla[2020]...", "the Experiments made by Layla[2020]," and so on. What can I do with this sort of "self-citation".
I have been trying to find examples on the web about this situation, but I could not find anything. Any help would be useful.

You don't cite it here and there. You make clear that any reader understand that s/he is reading the summary of an article. This can be done in the intro section, or by "TITLE*".... *this is a summary of xxxyyyzzz, Layla, 2020... Etc etc.

Alchimista's comment is good. Moreover, you should look at the many summaries of articles that exist -- Science and Nature have short articles that comment and summarize research articles in each week's issue, and they don't require convoluted or repeated references since it's clear from the start what paper is being referred to. There are lots of informal summaries as well, e.g. mine: https://eighteenthelephant.com/2020/04/10/putting-the-brakes-on-gut-bacteria/


text:
would it sound weird to ask for a professor to be as a permanent reviewer of a journal or conference?
In my current work, we organize a CS conference every year, and we also have a journal in the CS field. However, we are currently facing a problem with some reviewers. On few occasions, we have a couple of reviewers who rejected the sent paper, saying they have not been appointed for the current year. However, they have acted as reviewers in previous versions of our conference. The question would be if it would be sound weird to ask a reviewer if he would like to form part as a permanent reviewer of the conference or journal. Are there any suggestions about how to deal with this?
Thanks

There are long-term editors in journals. Long-term reviewers is not something I heard of in many journals, although Frontiers seems to have some kind of model like that.

It doesn't seem odd at all. You can simply ask a "good" reviewer if they are willing to review again in the future. I suspect many will say yes and some will fail to respond.
When you ask, you can also ask for subjects/topics that most interest them. This would ease the work of the program committee in the future, as they would be a bit less likely to send requests that are unlikely to be fulfilled.
Another approach, used by some CS folks is to put up a page with received papers, perhaps just titles, and send out a broad appeal to previous reviewers (and others, perhaps) asking if they are interested in any of the papers.


text:
publishing a poster in a conference and then an extended version in another conference, is that possible?
I was planning to submit a couple of posters to a Computer Science conference because there are some final experiments that I should perform with the data we have at hand. I wondered if there would be an issue if I submit the complete work to another conference and citing the first conference in which I present the work as a poster, would there be some issues regarding the level of novelty required for a conference. Any thoughts?
Thanks

As long as you cite the earlier work, you can submit it without issue. But it is up to the conference committee to decide if the "complete work" is sufficiently novel, given that the earlier version already exists. For many such things it would be fine, but no one but the committee can say anything about acceptance.
But, with proper citation, there are no ethical issues such as self plagiarism.
But you should also consider copyright if you have given it up. If so, this limits how extensively you can copy from the earlier work into the new and you may be restricted to quoting (literally) brief passages or paraphrasing (with citation).
The more extensive the changes are, the more likely that you will have success. Just make sure it ins't perceived as "old news".

Note that there may be overlap in the conference committees.

In the field of natural language processing (NLP), the main conferences explicitly state the maximum overlap requirements between the paper submissions and past published work, e.g. (mirror):

In addition, we will not consider any paper that overlaps significantly in content or results with papers that will be (or have been) published elsewhere. Authors submitting more than one paper to ACL-IJCNLP 2021 must ensure that submissions do not overlap significantly (>25%) with each other in content or results.


text:
how do you write a State of the Art section in this particular case?
How can I write an adequate State of the Art section in the following case for the field of CS? Let´s suppose that I am writing an article that solely relies on using classic Machine Learning techniques to detect spam. However, nowadays, the research has pointed out the use of advanced Deep Learning methods such as transformers, but I will not like to point my research toward that path. In this case, what would be the recommended way to sketch my State of the Art? I have been thinking of two possible ways:

To briefly mention the studies that relate to Deep Learning at the beginning of my State of the Art section and then narrow the description of these studies and focus more on those that used classical ML techniques. These articles, of course, would be outdated compared to the DL ones, but I am trying to avoid a critique of my work that would point out why I have not used DL techniques if I mention them in the State of the Art.

To not describe these DL works and only focus on those related to ML techniques.

Which one could be a feasible option in this case?
Thanks

Let me suggest a third way, a variation on your first option. Explain that you are extending classical ML techniques in this paper (and why) and give the state of the art on that. At the end, mention that current research has been exploring a different path, DL... Give a few sentences about where that is currently.
Say the things most important to your paper first, not last.
It would probably be a mistake to ignore Deep Learning.
For a thesis, rather than a paper, you have a lot more space, probably, to be fairly complete on both.

Generally speaking, you can not omit the current state-of-the-art solutions from the comparison entirely. The elephant is in the room.
The main question, of course, is why are you using something else in the first place. Yes, there are very good reasons for opting out of "black box" modern machine learning techniques, but you have to make a convincing argument here. What is desirable, but not achievable by those deep learning models?
And then there is a problem of implementation. It is hard to keep up with the AI/ML field if you do not collaborate with a lab doing specifically that, and as a result, articles with poorly implemented and/or woefully outdated models are all too common. This consideration should go in the planning phase of your research: do you have resources to properly reproduce the current state-of-the-art? If no, how can you compare your results to it? Should you be using some well-known public dataset? If your work is contingent on collecting your own data, maybe opt for an indirect comparison based on the existing research to make statements about that data.
I have now spent a few years preaching that the research dealing with machine learning must either improve on SOTA or be still valuable in some other way in several years when the performance goalposts move a lot. Coming from that perspective, it is perfectly valid to not pursue the "hot" topic as long as you could still provide the sufficient research motivation. Publishing papers just to heat up the interest for ML in your field of study seems superfluous at this point.


text:
change of study plans within ABET accreditation
Currently, I am working in a CS program that has decided to follow the ABET accreditation. The problem is that we are about to implement a new study plan for the next year, which is more suited to the outcomes that ABET asks for an accreditation in CS, because the current one has some drawbacks. The question that I have is which study plan should we present to ABET, the current one and state that the new one should be enclosed into our continuous improvement plan? What about the graduates that we have with the old study plan, should we assess them or wait until we have graduates with the new study plan?
Any help?

You should be honest. Present both plans, old and new. Better yet, why not ask ABET?

@JeffE we strive for honesty, the problem is that ABET asks for outcomes related to graduate students, I know a university that was dealing with the same problem and they present both plans, but they do not want to disclosure the details

The best answer that can be given here, as JeffE suggests, is to ask ABET. I have had good a good experience with getting clarity regarding questions that are specific to my program's situation.

Following the comment in the OP's question, this answer provide a reasonable course of action.


text:
How do I ask for an extension to revise a manuscript submitted to an Elsevier journal?
I have submitted an article to an Elsevier journal and received the manuscript with reviewer comments and a "revision response due date" within the Elsevier evise system.
I am unable to meet that deadline and I need to ask for an extension. I assume it would be the most usual way to ask the editor, and I have done so about a week ago and not received an answer yet.
Now I wonder if there is any way to do this within evise. But if I click on "Agree to Revise" from what I understand I'm asked to submit the actual revised version already (see screenshot). I don't really dare to click the "Confirm" button to advance but may that be the way to ask for an extension also?
What would be the usual way to ask for an extension?

Send an email outside of the system

As an aside, in my experience, even if you don't resubmit by the deadline, there is no harm done.   I had a manuscript which I did not want to resubmit.   Elsevier continued to chase me long after the stipulated deadline.

Write to the editor. This can be either via the system (see if they have a "send email" function) or simply reply to the decision letter email. It's likely the editor will say yes so you don't have to wait for a response to start revising your paper.
About the "agree to revise" button, clicking it tells the editor that you will be revising your paper after all. Some authors abandon their papers after a revise decision - I don't think they abandon the paper entirely, but they stop caring about the submission to this journal. It's good practice to remove these dormant papers from the system; otherwise it'll get cluttered. If you do not agree to revise, then after a reasonable length of time (several months, say) the desk editor might remove your submission. Since it's only been a week, you don't have to worry yet. There's no need to agree to revise for now: in the unlikely event the editor does not approve an extension, it's a (minor) administrative hassle to change the article's status again.


text:
Copyright-related advice for graphic designer creating content for academic publications
I'm in the following situation: I'm a researcher and hold a degree in life sciences. I also like graphic design and occasionally doodle up a figure to include in a report or such. I'm not a professional graphic designer and not being paid for that specifically (though see it as part of my academic obligation). Now my supervising professor noted this and now starts to ask me to create figures for other academic publications I haven't worked on personally. This happened twice so far. Some figures I just modified from existing sources but others are my very own work based on, and tailored to, the academic publication in question. There are a couple of questions arising from this situation but I'm most concerned about the copyright aspect.
I'm a firm believer in the benefits of open access and creative commons and have no problem with anyone reusing and modifying my work for noncommercial purposes. I do have a problem however with academic content being locked away behind a paywall, possibly along with my images. I do not have any influence on which academic publisher is chosen for the articles I design the figures for.
My questions are,

Are my designs still mine after being published? This may depend a lot on the publisher in question but can it be generalized? Any experience?
Do I have a choice of the copyright licence to be applied to the figures?
Can I use my graphics afterwards in any way I like and apply any copyright licence I wish, possibly mentioning “also used in Academic publication x”? For example, could I put them on Wikipedia?

In general, I want to avoid a situation in which I can be hold legally responsible for using my work as I please.

If the authors of a paper do not specify otherwise, when they transfer copyright of a paper to a publisher, that includes its images. That's what most people do.
But, during the copyright transfer process, an author can specify

if there are original images of independent value that they'd like to retain copyright to, or
if there are images whose copyright is held by a third party, which they have a license to reuse.

See for example this ACM copyright transfer form.
If you are creating images for papers on which you are not an author, you can retain copyright of your images and just give a license to use in the paper. The authors will have to specify on submission that they are using third party images, and show that they have permission from you to use them.
If you are creating images for your own paper, you may be able to claim them as an "artistic" image and retain the copyright, depending on the publisher.


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Unable to grade student assignment in blackboard
I created an assignment for students using blackboard. This assignment is something that is completed externally. When going into the grading center I am unable to assign grades unless the students have submitted something. How can I grade this without requiring them to submit anything? I've already tried setting the column as external the the category to no with worked for a different assignment.

I'm voting to close this question as off-topic because this is about the features of a particular piece of software, not about academia as described in the help center.

@JeffE Which site would you suggest for this question?

Maybe http://discussions.blackboard.com/ ?  Or your local IT people?

I believe the "Grade Center Assignments" page is only for assignments that students will submit through Blackboard.  For other graded items, go to "Full Grade Center" and click "Create Column".  You can then make a column into which you can type arbitrary grades.

I found a cleaner solution. If you click on the column and click "View Grade Details" you have the option to override grades.


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Alternatives to paper handouts in conferences
So, last month I travelled to one of the big conferences in my field. The copies of my own handout weighted about 5 pounds; on the way back, I took another 5 pounds worth of other people's handouts. This was the case for pretty much everybody else. This seems kind of wasteful for a couple of reasons.

When I got back home, I ran the handouts I had collected  through the scanner, backed up the files in Dropbox, and put the handouts in the recycling bin.
The conference organizers offered the possibility of making handout pdfs downloadable from the conference site prior to the start of the conference.

In fact, a couple of people (including one of the keynote speakers) told me over a coffee break that, if it was up to them, they would forgo paper handouts altogether and just provide a pdf that people can download and look at during talks. This is something I agree with, if only because it makes post-conference storage and retrieval way easier (also, pdf handouts are awesome when you are sitting in a talk by a 23-year-old grad student who is under the delusion that older people can read 10 pt text comfortably).
Question: is there any reason, other than force of habit, to keep on distributing paper handouts? Technology is not an obstacle, I think, given how these days everybody brings a laptop or a tablet to conferences.

Well, I have been attending conferences from several fields and some interdisciplinary ones and I have never seen a single handout. Just being curious: What’s your field?

I've noticed trend towards fewer printed proceedings; from 4 computer science conferences I attended this year, just one had printed proceedings given out, the others handed just had USB flash sticks.

@Wrzlprmft: theoretical linguistics, which admittedly lags behind other fields in the adoption of certain types of technology.

There is almost no reason to give out paper handouts any more.
Almost none of the conferences that I attend hand out anything paper other than an updated program, if that.  Instead, everything is either in a USB stick or simply online at the conference web site.  Conferences with full papers tend to give out a USB stick; conferences with abstracts tend to place them online.
And here is where I see the only reason one might still want to bring a piece of paper: if the conference is handing out USBs stick or some other form of program that must be produced many weeks in advance, then if you want to give your audience some piece of information to look at that was not available then, you might bring paper.  To me, however, that sounds like a relatively rare case and not something that needs preserving as a typical custom.

Jake, I edited "now something that needs preserving" to "not something that needs preserving".  If I guess wrong at what you meant, please roll it back.


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University metalshop / makerlab - metric or imperial?
I'm applying for some funds to set up a small makerlab-type metalshop in my department (American research university, although I should note that I'm in the social sciences). My plan is to get a CNC mill and lathe along with some 3D printers for rapid prototyping of equipment.
My question is whether to get metric or imperial CNCs. Yes, it's easy to flip the display controllers between metric and imperial, but the gearing of the mill itself is usually based on a metric or imperial leadscrew, so that 1 turn of the handwheel turns a certain metric/imperial based distance.
I checked the other metalshops at my university and they are use imperial-unit Bridgeport mills and lathes. I myself grew up in a metric country (i.e., somewhere other than the US, Liberia, and Burma) and so find this incredibly backwards.
Is there any good reason to go with imperial-based lathes and mills -- except for the cost of finding a good metric one?
Note 1: For lathes, it is relatively easy to change the gearing for metric, so this is not as much of an issue as it is for mills where the X, Y, and Z leadscrews and indicators  would need to be swapped out. Not to mention the difficulty in sourcing metric borers and bits...

We really need a Mech E stack exchange, or a maker see.

This seems to be a question about metalworking, rather than a question about academia.

There's no mech e SE and I'm curious whether metalshops at other universities in the USA also only use imperial or if we're an anomaly.

A private metal shop can do what the heck it likes, but a university is supposed to promote knowledge and engage in best standards.

The funding agency may have an opinion. Beyond that there is no "right" answer. You could ask the people in charge of the other shops on campus what their reasons were.

It's internal funds. I did ask the other shops and they didn't think it strange to operate on imperial and that I was an oddball for thinking metric. Then again, my university is better known for its humanities than its sciences. Was curious if other American universities were this way.

@RoboKaren There is Mechanical Engineering website on Area51 on Stack Exchange. Area51 is a website in which new site ideas are discussed and proposed.

The decision will be decided based on where, or in what, you think the resulting parts will be used. Since you are in the US, going for the imperial would make most sense.If you start machining metric based parts you will soon find that you may have problems adding off the shelf parts. I think the sound way forward is to figure out if you will depend on parts from elsewhere and to what extent these will likely be metric or imperial. Being able to switch will solve some issues but as you state, if there are mechanical differences in the machinery, you may end up with less accurate parts when switching to whatever system the machinery was not made for.


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Is it ethical for a part-time professor to use his position for other interests?
There is a professor who works part-time at a university as a moderator of one of their student groups. He does not teach any actual classes but spends a hugely considerable amount of time with the members of the group outside of class hours.
Is it ethical that he uses his position to scout between those members for a company in which he is either a founder or a senior-level position (currently cannot recall which). He does not offer them jobs but instead constantly pushes and offers them to become "interns" with no pay, bad hours, and extremely heavy workload.
I'm not very well versed in business ethics but this sounds very wrong to me, and something of a conflict of interest.
Would the university have grounds to officially respond to this such as sanctioning him? I know that this professor was previously warned to stop doing so but nothing official/major was ever done despite him continuing to do so behind the administration's back.

offers them to become "interns" with no pay — Unpaid internships are illegal in the US except under very specific circumstances.  The employer benefiting from the activities of the intern is not one of those circumstances.

As you remark, it is probably not okay, although it is always a fine line to draw: it's ethical (and highly encouraged) for a professor to help students procure good jobs and/or rewarding experiences outside the university (where “rewarding” covers not only monetary gains, but also experience learnt, etc.). He can do that through his network, and first and foremost in that network is the company he knows best. However, it is not ethical for him to abuse his position at the university and the student–professor interactions to the good of his own company.
Now, how active are universities in taking action against such behavior? It probably depends on the field, the country, the local situation and power of the professor, but in most cases I would say they will be willing to close their eyes, and it would really take a lot of evidence and someöne pushing them very strongly before they take disciplinary measures.
If you want to do something about it, discuss it very openly, and very calmly, with the director of your program, the students' representatives, the dean or departmental chair, etc. And document everything in detail.


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Is there a standard dictionary for referencing English words?
I am working on a paper in which we need to reference the meaning of english words as foundation for the analysis in the paper (we are categorizing situations using these words, and there is no method of categorizing these items, so no precedent).
Before internet, using the encyclopedia Britannica or merriam-webster dictionary was easy for referencing the book itself.  These days, words and meanings change and are sometimes updated.  Even more, looking online for a dictionary for finding a word returns many results.
When searching for oxford dictionary there are three results
http://www.oxforddictionaries.com/
http://www.oed.com/
http://oaadonline.oxfordlearnersdictionaries.com/
Merriam webster:
http://www.merriam-webster.com/
Cambridge:
http://dictionary.cambridge.org/
The online dictionary:
http://www.thefreedictionary.com/
And of course wikipedia usually has some definition.
For example, if we categorize something as 'multi-' , In this dictionary: http://oaadonline.oxfordlearnersdictionaries.com/dictionary/multi multi is "More than one".  However, in this http://www.merriam-webster.com/dictionary/multi , multi is "More than two".  That is a huge difference in terminology.
Is there an academic standard for the age of online dictionaries?  Have words just begun to mean different things and its futile to use dictionaries in this way?

The OED is unquestionably the "gold standard" in English-language dictionaries. Everything else pretty much pales in comparison.

Words have ALWAYS had somewhat fuzzy meanings. Local usage, jargon usage, usage change over time, and so on. I would assume that anything called a "learner's dictionary" is likely to be oversimplified, but beyond that I think you're going to simply have to accept that this is a fuzzy-logic problem. Natural language analysis is an EXTREMELY hard problem; it's a minor miracle that supercomputer systems such as IBM's Watson are finally making some progress in that area.

If anything, the availability of on-line dictionaries has simply made apparent the fact that there never was such a thing as an "objective" or "true" dictionary definition.  Choose a dictionary of high repute -- the OED seems like a good choice, but you could have factors which nudge you in a different direction, or force you to use more than one -- and stick to it.

@CharlesMorisset: There most definitely isn't.

www.oed.com is the online version of the full, official Oxford English Dictionary. Requires a subscription (institutional or personal) to access. This is the site you should use whenever possible.
http://www.oxforddictionaries.com is an ad-supported version with some features cut. Avoid if you have subscription access to the full site (as any university should).
http://oaadonline.oxfordlearnersdictionaries.com/ is, clearly, for learners of the English language. Use it as a guide for learning, sure - but not as a guide for writing papers.

The OED is the English dictionary to use. Other dictionaries are probably fine in all but the weirdest corner cases, but it helps to have some standardization.
Your journal probably specifies its own preferences in this regard. Every publisher's "guide for authors" that I have seen tells you to defer to the OED. Sometimes you'll see specific instructions to use either British or American spellings, and you may specifically be told how to spell words that don't have a British or American "standard" spelling, such as parametrize.

But when the topic of research is word meanings, simply going by the OED alone may be inadequate.

onelook.com is a nice resource; it links to several online dictionaries from one convenient place. (Although it does not link to the OED, and I agree that the OED is both authoritative and reputable – more on that in a bit.)
Still, words often have fuzzy meanings, and it's often good to cite a couple of reputable sources when establishing definitions.
Your multi- example is a good one. When you find dictionaries have conflicting meanings of a word, it might be best to provide multiple definitions, and then declare which meaning you intend to use throughout your paper or thesis.
Collins has an interesting listing for multi-, in that it lists both of the meanings you allude to:

multi-
  1 many or much   ⇒ multiflorous, multimillion
  2 more than one   ⇒ multiparous, multistorey

It's also important to know what kind of dictionary you are citing, and what that dictionary's goal is. For example, some dictionaries list what they deem as primary meanings first, while others order a word's definitions based on how the word evolved.  Others, like Cambridge Dictionary Online, are designed to be a learner's dictionary; CDO's definitions are relatively basic, and geared more toward those who are learning English as a second language. Some online dictionaries are wikis, like Wiktionary, which might be good for finding the most up-to-date slang usages, but are probably not the best sources to cite in scholarly works.
The goal of the OED is a comprehensive, exhaustive list of usages, starting from the very early usages, and going to more contemporary. For example, looking up multi- in the OED yields 10 results; one of them begins with:

Forming parasynthetic adjectives, with the sense ‘more than one, several, many’. From the adjectives are formed adverbs (e.g. multiserially) and nouns (e.g. multicellularity). Some formations of this kind acquire a noun sense, as multicore, multiengine.

It then goes on to list dozens of examples, many of them rare or obsolete, along with references that stretch back as far as the 1700s, such as:

multinodal adj. having many nodes.
  1839   J. Lindley Introd. Bot. (ed. 3) i. ii. 160   The multinodal cyme offers no fixed rule in the spirals of its nodes.
  1902   Biometrika 1 264   These maxima must arise from the mortality curve itself being multinodal.
  1979   Cell & Tissue Res. 199 225   Probit frequency analysis, a graphic method for determining whether a population is normally distributed, skewed, or multinodal.
multinodate adj. rare = multinodal adj.
  1840   B. H. Smart Walker's Crit. Pronouncing Dict.,   Multinodate, or Multinodous, many-knotted.
  1979   Proc. Linn. Soc. New S. Wales 102 194   Most often, on multinodate axes and particularly in large inflorescences, reduction in degree of branching does not occur alone.
multinodous adj.  [ < classical Latin multinōdus ( < multi-  multi- comb. form   + nōdus   knot: see node n.) + -ous suffix] Obs. rare—0 = multinodal adj.
  1727   N. Bailey Universal Etymol. Eng. Dict. II.,   Multinodous, full of Knots.
  1840   B. H. Smart Walker's Crit. Pronouncing Dict.,   Multinodate, or Multinodous, many-knotted.
multinodular adj. Med. characterized by or composed of a number of nodules.
  1900   W. A. N. Dorland Illustr. Med. Dict. 399/2   Multinodular, composed of many nodules.
  1924   F. de Quervain Goitre 33   The fourth type is represented by the multinodular goitre with large nodules.

In other words, it's one thing to say that the OED is the "best" dictionary to use, but it may be overkill in some instances.
I'm active in some of the SE's English forums; I've found Macmillan and Collins to be reputable, and I would trust them for scholarly work. Miriam-Webster is often regarded as reputable, too, but I tend to avoid their online edition, owing to the number of ads they splash on a screen (my computer often starts running slower as soon as I go to one of their pages).


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Is it appropriate to ask professors to give you a mock interview?
Suppose that an undergraduate student is preparing for interviews for Ph.D. positions in natural sciences. Is it common/acceptable to ask a professor with relevant expertise and familiarity with the student's educational background and research ability to conduct a mock interview with the student as a way to ascertain problems in the student's preparation? Or will such requests be viewed as unnecessary or "asking for too much"?
I'm primarily interested in the acceptability of such requests in US colleges.

It depends on the professor. If it's someone who knows you well and has the time, then they would probably be happy to help. Most of the professors I came across during my undergrad were more than happy to help preparing me for grad school interviews. Just make sure you ask well in advance, so they have time find an appropriate time, and don't take it personally if they say no: professors are really busy.
EDIT: Make sure you ask professors that have been through the graduate application process in the same country you are applying, if possible. Ones who received their PhD elsewhere, or say 50 years ago, will probably turn you down simply because they don't feel familiar enough with the process (unless they are directly involved in admissions for your school's graduate program).

Yes! We welcome such invitations. It's good for the entire department -- for both younger students to look at, as well as your peers so make it a big event.
Not all faculty can go but the good thing is that these tend to be self-selecting -- that the faculty who are the most helpful are the ones who come.


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Effect on image of a vanity award on CV/Profile
I could not find any previous questions on the effect of vanity awards compared to vanity publishers.  I recently noticed a CV on a university website with a few awards of International Scientist of the Year, or something as such.  I found the giver of this award as IBC https://en.wikipedia.org/wiki/International_Biographical_Centre .  It seems from the page to be criticism on the organization.
I am curious, how do these types of awards being listed effect the image of the Professor?
If it is bad for the image, is it worse than vanity press, since it requires no work at all (compared to having to write a manuscript, even if it is bad).  Or is it not as bad because it doesn't look like passing off published work?
I am looking to know these answers to conclude if putting this type of award on a CV is beneficial, detrimental, or neutral in the general/international community.
For context, I know the Professor is in Asia, in which there is probably a good amount of pressure to come up with activities or awards for their career.  For diplomatic reasons, we can assume someone nominated them for the award and they are unaware of the feedback on Wikipedia.

Utterly worthless and a negative impact, plain and simple.

If I saw a vanity award of this type on somebody's CV, I would have a hard time ever taking that person seriously.
At least with predatory publishers, there is often a reasonable excuse: it's easy for people early in their career or at smaller institutions to get tricked by the slicker operations.  Indeed, sometimes the line between low-tier venue and vanity publisher is quite unclear.  As a result, real, sincere scientific work can end up getting sent to a horrible venue. It's unlikely to be very good work (just by correlation, since poorly connected researchers are less likely to be producing good work), but any shame associated with such a publication can be readily diluted by publishing good publications in good venues.
A vanity award of the sort you describe, however, I can see no such mitigating circumstances. When random people you've never heard of before ask you for money to call you "Scientist of the Year," you can only accept if you are very gullible or very vain.  Moreover, unlike a publication in a bad venue, there is no reason to keep such a terrible award on one's CV unless you still believe it is somehow valid.
In short: I would consider a vanity award on a CV to be quite ridiculous, and a good reason to have a high degree of suspicion of a person's work unless given strong evidence to the contrary.


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Are comments considered publications
The journal Science has two sections for submission, Research articles and Commentary.
http://www.sciencemag.org/site/feature/contribinfo/prep/gen_info.xhtml
Under commentary, there is a section for 'Policy Forum'.  Unlike 'Education Forum' there is nothing explicit about research related to Policy.  If one submits (not invited) a manuscript to Policy Forum, is this considered peer reviewed publication? Is there a difference in citation both in format of a citation and if it is common to cite a manuscript published in Commentary?

The general discussion for the Commentary section mentions this:

Commentary material may be peer-reviewed at the Editors' discretion.

If you look up a sample Policy Forum paper online, you can download the citation information. For example,
NUCLEAR WASTE
Yucca Mountain
Rodney C. Ewing and Allison Macfarlane
Science 26 April 2002:  296 (5568), 659-660. [DOI:10.1126/science.1071886]

and then in various formats. Here's the BibTeX entry:
@article{Ewing26042002,
author = {Ewing, Rodney C. and Macfarlane, Allison},
title = {Yucca Mountain},
volume = {296},
number = {5568},
pages = {659-660},
year = {2002},
doi = {10.1126/science.1071886},
URL = {http://www.sciencemag.org/content/296/5568/659.short},
eprint = {http://www.sciencemag.org/content/296/5568/659.full.pdf},
journal = {Science}
}

In general, a "Comment" is always a publication. However, your question is whether it should be listed in someone's publication list, presumably along side peer-reviewed articles. I believe the relevant criterion, as mkennedy suggests, is if the comment has itself been peer-reviewed. When yes, it can go in the regular list; if not, then it should presumably be relegated to a "additional publications" list or something of that type.