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Indicate Journal name for "under review" and "accepted/in press" publications on CV
there are similar questions on how to list on CV publications that have not passed the accepted or in press stage when applying to junior research positions ( PhD/postdoc).
I am not clear if such publications should include the journal name or not, and what would be the reason for either choice.

Everyone I know feels that "accepted / in press" is just as good as appeared: the delay between acceptance and publication has nothing (or anyway, too little) to do with you.  You should certainly list them on your CV, no matter who you are.  I don't even list these as in a different category as the ones which have already been published: the only difference is that (roughly speaking; electronic publication and DOIs complicates this somewhat) I can't tell you the bibliographic information if it hasn't appeared.  I think it is very important not to list a paper as accepted without listing the journal, because therein lies the route to verifiability that your paper has been accepted.
In my opinion, you should list submitted articles on your CV no matter who you are.  (I would be interested to hear why @aeismail feels differently about this.)  This advice comes from someone who works in a field (mathematics) for which recently submitted articles ought to be freely available: if you want to get credit for having submitted an article, then whoever you are trying to get credit from ought to be able to see the article.  Ideally they don't have to ask for it specifically (because maybe they won't), so you should include a weblink to submitted papers on your CV.  (This last part is more for people who are in a potential-hire situation...which is not restricted to grad students and postdocs.  Nowadays, lots of academics are in a potential-hire situation or would like to be.)
In mathematics, each paper takes a long time: the period between when you say "Aha, I can prove the theorem" -- and e.g. start to give talks about it -- and the period which it gets accepted is probably over a year in many cases, and closer to two for serious, important work in many cases.  Who is reading this part of your CV and isn't  interested in what you've been working hard on for the last year or two?!?
Whether to list the journal submitted to is a well known question mark.  I do not put this information on "external" documents -- i.e., the CV and the publication list which are on my professional website.  I do usually list it on "internal" documents -- annual reviews, grant applications, job applications (well, it's been a little while).  There are a lot of nuances here: one is that it is really hard to know how much credit to give someone for submitting a paper to journal X.  After all, anyone can submit a paper to the most prestigious journal in their discipline, and in many cases they will spend a nontrivial amount of time before rejecting you.  So you want to be careful about this.  Nevertheless, where you submitted a paper is an important piece of information about how you feel about the paper, which is worth including in various cases (e.g. grant applications, where the panel will be suitably skeptical).  Another issue is that one commonly submits to more than one journal (not at the same time, but in sequence) so the information about where you submitted a paper is likely go out of date, so is less suitable for a sporadically updated CV and more suitable for a CV guaranteed to be complete up to such-and-such a date.
Note also that in my discipline, many people -- especially young people but not always -- also include papers which are "in preparation" on their CVs.  This is, frankly, a little shaky: I have papers on my own CV which have been "in preparation" for getting on a decade.  But the above philosophy still applies: if you've been working on something for five years and you're 75% done, then shouldn't you say something about it?
One last piece of advice: it behooves you to make absolutely clear the distinction between all these categories.  I get annoyed as a hirer when people use categories that don't fit easily into any of these boxes: e.g. some job candidates list papers as provisionally accepted, conditionally accepted, or accepted pending revision.  What a hiring committee litmus test that becomes: their proponents will insist that these be counted as actual publications, their detractors will insist that they don't count as any more than submitted, and people in between will get a headache.
(I don't mean to imply that it's necessarily the candidate's fault.  Sometimes the journal tells me that my paper has been provisionally accepted, and when I need to create a CV for a grant application that gives me the very same headache: please give me a paper status that has a clear, unambiguous meaning!  They do enjoy their little games, the journals...)

I would definitely include publication titles for "in press" articles, since they've already been accepted (and you could provide the confirmation email if asked to do so!).
As for "under review" articles, I would only list them in the CV at all:

If I were a graduate student or postdoc
If I needed to demonstrate that the articles were under review (internal performance reviews, etc.)

In both instances, I would also include the journal name.

A related question: http://academia.stackexchange.com/questions/57839/what-are-the-drawbacks-of-making-public-which-journal-a-manuscript-is-submitted Thanks Sir!

An accepted article is as good as a published article and you should include it in your CV / Resume. As pagination - issues etc are not yet final, including a DOI with the details of the articles is good practice. You should also try to publish pre-print versions of these articles if your publisher allows that to get some further exposure.
In my area (Electrical Engineering), a submitted article does not mean much. It takes almost no effort to prepare a couple of articles and submit them to even the highest ranking journals for review, only to have them rejected a few months later. In many cases, it is seen as an effort to fluff publication records. If the manuscript has been through the first or second stage of reviews and you need to show some more publications (and honestly who doesn't?) then you can include them but the distinction that the paper has been through some stages of review, together with the name of the journal, should be clear.

How soon is a DOI assigned after paper has been accepted?

This depends a lot on the publisher. In the outlets where I usually publish, it is assigned almost immediately after the editor has been fully accepted or during the typesetting stage.


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PhD application asking what other insitution I am applying to, how to answer?
I understand that schools are trying to gauge the chances of an offer being accepted by a potential candidate. Similarly to what has been described for job applications and other questions that a lower ranked program might not offer admission to someone who applied to just top schools.
How much should a candidate divulge about the other schools he/she is applying to? If applying to a top school will it decrease your chances if you are stating you are applying to another top school?
I find this kind of questions a bit intrusive and that might even compromise to some degree my application. Perhaps some people that have been in admission commitees can shed some light on the dynamics related to applicants that applied to several schools.

Related: http://academia.stackexchange.com/questions/782/should-i-be-truthful-about-graduate-school-rejections

Are you asking whether or not you should lie (by omission) on your application form?

I'm applying now, and I find most of such questions optional. Since it is optional, I opt not to tell.

Sometimes they ask for N other schools. So there is value in knowing which N to divulge.

If the question does not require a response, meaning the electronic system allows to submit without answering, simply don't answer (obviously, not answering is not lying). Also, I believe providing an incomplete list is not lying either, unless the question specifically asks for a complete list of schools (by using the word "all" or similar). Just my opinion @EnergyNumbers

There is no really good reason for schools to ask what other schools a student is applying to. I personally make it a point as much as possible never to ask people who I'm interviewing or whose applications I'm reviewing what other programs they're considering. I do ask, however, if they are actively considering other options, this is something that can affect our internal decision-making process, so I ask if students are entertaining offers, but not where.
Schools are likely to be using this answer to gauge what schools you're applying to, with a view towards planning whom to admit. But again, I do agree that this question is invasive, and isn't really necessary. In addition, schools shouldn't be checking up with other graduate schools about their admissions, so I would answer in whatever way you feel comfortable.
Moreover, you can always claim that your answer was accurate at the time, but changed following the point at which you submitted the application.

They probably aren't comparing notes with other programs. Many programs only get to make a certain number of offers, so they're trying to determine which choices are most likely to fill out the class and not result in a bunch of rejections.

Repeat after me:
“I'd rather not tell you.”

I think it matters that you'd tell them. So that they won't have to waste their admit on you, if you were set on going elsewhere, possibly due to a better fit for your work.
It makes admissions easier for them as well as for you. I'd rather have that a student gets into one of the programs at his top programs of choice and rejected at others, as compared to a few students getting 7+ admits while the rest don't even have a chance.

But the point is that nothing is guaranteed, so if you list 5/6 institutions, then one likes your application but doesn't make an offer because they think you will not accept, and then you don't get any other offers, at this point it would have been better not to list anything and at least you would have got one offer. It sounds like this is only unethical if the student doesn't say but it's ok for the university. That's what waiting lists are for, they just should be made more efficient. It seems the admission commitee is just speculating on where you might be admitted.

You should not typically apply to 6+ universities without having a safety. So the rare case which you are worried about is well covered. In addition, waiting lists have been found to be very unwieldy especially for international students. I know of cases where an international student got an admit from waitlist a week before his course started.

It may be in the admissions committee's best interest, but it is definitely not in your best interest to suggest to any admissions committee that you'd rather go elsewhere.  Be selfish!

No need to be flat-out adversarial about it.  The same end is accomplished by simply leaving it blank.

It looks as it is a practice out of the work environment, here in Japan usually they'll ask you which companies are you applying to, and in UK I got to see similar practices.
I do not think you'll get down points for not putting anything, I do not really think Admissions Officials are really accepting or rejecting people on the basis of to which Universities are they applying.

I never seen a question like Are you applying to other schools when applied to different universities.
I do not think you are required to expose such information. The committee should evaluate your application regardless of your status in other schools.

The current UMich application asks the same question. The UNC, Chapel Hill Application asks this question as well. Its something which has started recently.

cannot find any reason to ask such questions. You suppose to either accept or reject based on his/her documents/application..

I think it matters that you'd tell them. So that they won't have to waste their admit on you, if you were set on going elsewhere, possibly due to a better fit for your work. It makes admissions easier for them as well as for you. I'd rather have that a student gets into one of the programs at his top programs of choice and rejected at others, as compared to a few students getting 7+ admits while the rest don't even have a chance.

But most of the PhD students are aware of accepting/rejecting their offers once they have them. No one wants to occupy two places where there are tens in the waiting list.

Perhaps. However, that does not hold true for a Masters Application. Phd students contrary to what you said, hold their offers till the last. Especially because of funding issues. X University may grant funding while Y university may not grant funding.
X university granted a TA while Y university has given a fellowship based on profile.

Many universities ask such question. Berkeley, U Washington, Stanford. Why do these top schools even care, since I find it unlikely that someone might turn down an offer from them.

@user4050: a lot of excellent students get admits at all of the above universities. What if you got an admit at stanford, uwash and berkeley?

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What is the purpose of an article repository
I was asked by a publisher to choose a repository where the article to be published will be uploaded to. What's the point of this if the article is already available on the journal website?
Can someone please explain what is the purpose of a journal repository such as PubMed, Europe PMC, PMC?
What are the pros and cons of uploading an article on a repository? Is it desirable to use more than one?

I was asked by a publisher to choose a repository where the article to be published will be uploaded to.

I've never heard of that before. Publishers usually want exclusive distribution rights.

What's the point of this if the article is already available on the
  journal website?

You can update the repository version to make corrections, should they be necessary.

Can someone please explain what is the purpose of a journal repository such as PubMed, Europe PMC, PMC?

To disseminate research.

Is it desirable to use more than one?

One suffices. Increasingly it seems that repositories don't want you to upload elsewhere.

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Submit to journal when another paper already in review
This question is about broad-topic and highly cited journals such as Nature or Science in which papers submitted from different subsets of authors could cover slightly overlapping subjects.
Would a paper under review in one of these journals interfere with the submission of another paper to the same journal? Or maybe the other way around that the new submission could interfere with the editorial decisions for the paper under review? The first author would be the same in both papers but the other authors would be different and the subject of both papers would overlap slightly.
A senior colleague with extensive experience in publishing in these journals suggested that the new submission "may interfere with the paper under review" and suggested to submit to a different journal.
In theory I don't see how one submission could interfere with another given that they would have very likely different handling editors. But obviously editors communicate among each other and might think that we are "spamming" the journal. We don't submit to these journals regularly.

In my experience, people with extensive experience in publishing have a variety of superstitions about publishing.

I would guess that the circumstance in which one such paper might interfere with the handling of the other is when the subject matter and results are very closely aligned.
The second paper might be considered not novel enough if the first paper is published. Or an editor (or a couple of them) think the two papers should be combined into one.
But, I doubt that if the new paper is sufficiently novel in light of the existing literature and the new paper it would have any effect.
In particular, if the new paper is independent of the first (field, topic, results, methodology (perhaps)...) then most editors would treat them individually. But, of course, we can't predict the decisions of all editors, since we don't know them.

Thanks for the answer. The results and methodology of these two papers are not connected at all. But I was wondering if journals might have other concerns such as publishing the same author/s over a few months.

They should not, but who can say. They should be concerned with the content of the paper, not the authors. Their job isn't to manage reputation, but to publish the best research advances. I think you can proceed with confidence.


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Use 1st or 3rd person for university webpage description?
I am in the process of updating my teaching and research descriptions the main website of my university. It seems many of the best descriptions are written in the 3rd person, but as far as I am aware, they were all written by the individual being described. Presumably those willing to talk about themselves in the 3rd person also put in the effort to have a good web presence. It seems disingenuous to write about myself in the 3rd person. My university has no guidance or policy on this issue (it must be an oversight given how much they love to manage everything). Is there a preferred style for official descriptions on the web? The webpage is dynamically from a CMS system so it is possible that some pages (either now or in the future) would present the content in a way that it is not obviously linked to an individual.

Personal pages, it is fine to use first person. Department pages, like faculty listings, I generally see these as 3rd person. Alternatively, are you talking about yourself, or as if the department is talking about you?

@Compass I feel like if the department was talking about me the format would be more structured then it is, but the text is presented as part of a faculty listing.

I don't think there's anything wrong with first person with faculty listings, I just see more of them in 3rd person, like Dr. Potato has been cultivating at University of Tuber for the past decade.

I think that it depends on whether the web site is written from a personal or an institutional perspective.

Personal perspective: On my own web page, I use first person because I have formatted it as a web page about me personally and about my personal work.
Institutional perspective: A close colleague of mine has formatted their page as "Name Laboratory", and it includes description of both themselves and of all of the students and postdocs in their group.  Their web page is written in the third person, including their self-description, because it is from outside perspective of the group as a collective, rather than their own perspective.

Just as in most questions of writing and tense, either can be correct, and I think the question is really about which you feel most comfortable doing.

I've seen both 3rd and 1st being used. Though I mostly see 1st person used. I'd opt for 1st person to properly propel your voice.
Many of the 3rd person ones that I have seen are non-personal and feel awkward as I can't get a sense of the voice of the author.

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Is it plagiarism to paraphrase multiple sections?
I sit on my department's academic misconduct committee. Today we had one of those cases where it wasn't clear what the right answer was. The assignment was for the students to design an experiment based on a previous experiment of their choosing and to write it up like a research proposal. The student took large blocks of text from the article describing the original experiment and tweaked each sentence to fit with the new experiment. After every sentence the student fastidiously added a reference to the original article. Has the student committed an academic offence?

The committee decided that it was not an academic offence and that the work should not be penalized for plagiarism, but that it would likely receive a very low grade due to a complete lack of originality and a failure to show any understanding of the key concepts.

I feel like this is more a case of extreme laziness than actively trying to deceive. If he wanted to plagiarize, he certainly didn't have to write and cite anything. A poor grade is punishment enough, IMO.

I don't think this is plagiarism as the student claimed none of the paraphrased content as their own. Instead, it should simply get a low grade for lacking originality.

Why on earth should an experiment description have to be re-written, assuming the original was clear and the experiment isn't changed?  This is not laziness, it is common sense avoidance of redundant work, and has the benefit of making it obvious that you are checking or extending the previous work.   If it's properly cited and still considered plagiarism, then there's something badly wrong with the academic definition.  (Though I do think citing every sentence verges on sarcasm :-))

@jamesqf would you elaborate that in an answer? Seems quite interesting…

It is often remarkable to me just how much work a person will put in just to avoid doing a different piece of work.  In this case, it sounds to me like the committee made exactly the right call: it sounds like rubbish work deserving a terrible grade, but certainly not plagiarism.

The inverse: Once I submitted a paper I wrote for class A to class B's grader by accident (even wrote class A in the header and didn't notice till I got it back). Got a B+ on the assignment for class B. Now that was a dilemma.

This happened to me with one of my students, who wrote a research paper that was just basically, the exact same as an article I had published (and had been included in the list of recommended readings for that research topic).
While they had cited everything it was not considered plagiarism, it was still an issue. I spoke with the program convener who reviewed the essay, agreed that it was just a copy of the article I had published, and we marked the paper down accordingly. They were a good student, and I don't think it was a case of malicious intent or laziness. Rather, I think the student just used too much material from the one article as opposed to formulating their own original insight.
The committee is correct in that yes, it is not a case of plagiarism because the student has cited everything. But they are also correct in marking down the student for lack of originality/direct copying of someone else's work.  It is not really an academic offense under most university faculty policies and procedures because they cited the work, but it is perhaps a rising practice that might need addressing, especially if students are not entirely aware that what they are doing is considered bad form.

While I agree that this is not the right thing to do, this is clearly not a case of misconduct. I also feel that the reason behind copying large parts could be attributed to lack of confidence rather than laziness. Sometimes, young researchers are unsure of what they write and resort to copying or closely paraphrasing parts from trusted sources as they are afraid of making mistakes. Possibly, the student in this case does not have a clear understanding of the concept or has a difficulty with expression. This is especially true of non-native speakers of English for whom expressing themselves in English is a problem. I agree with the committee's decision that this is not a case of plagiarism as the student has cited everything. Of course the student deserves low grades, but could possibly be encouraged to be more confident and not be afraid of making mistakes.


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What documents need to be shredded?
I prefer paper documents when reviewing manuscripts and grants. While these are confidential documents and generally sent to me electronically, they generally do not come with any instructions not to print them. Am I required to shred them or can I throw them out in my office or put them in the communal recycling bin?

If it is confidential, I always shred. Anyways, in regards to documents, I always err on the side of caution, even if it's not marked confidential. Worst case scenario is a few extra minutes at most. Worst case scenario in not shredding is a lawsuit.

When if comes to reviewing grants and publications, from an ethical perspective, my understanding is that you have three duties:

To not compromise the authors' priority in their investigation of their ideas and their ability to capitalize on investments in preliminary work.
To not compromise any intellectual property claims through premature release of information.
To not expose the authors to potential embarrassment due to the harsh and mocking comments scrawled all over the place in red pen.

If you personally are behaving ethically, then it really comes down to how much you trust your recycling waste stream.  Is there any likelihood of a student, colleague, or other malicious agent going through the bin and pulling out the information, either intentionally or just in a search for scrap paper?  Shredding is definitely safe, but a low-priority piece of information in a big communal recycling bin with a latch is also certainly exercising a reasonable standard of caution unless you have reason to believe that you or your institution are being targeted for industrial espionage (yes, it happens).
Honestly, though, in most cases the information just isn't important enough to worry about.  An incremental paper presenting the next step of a well-established program, a badly written manuscript on its way to a well-deserved reject, a grant proposal filled with "you should totally fund us to keep doing what we're doing"---these sorts of things just aren't of much interest to anybody except the authors and their close colleagues in any case, and are probably perfectly safe in the recycling bin.  It's not ideal, but it's also very low risk.
Beyond ethics, I believe that there are also sometimes legal requirements, particularly when it comes to being an external reviewed of grant applications for government agencies.  In that case, the best thing to do is to ask the program manager involved.

If it is a bulky document I have just shredded the first few pages and recycled the rest.
Anything with any confidential information I shred or avoid printing off, especially student data.


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Following up on a postdoc application at an academic conference in person
I will graduate with my PhD in a few months and I have starting applying for postdoc positions at national research labs and universities. Our field is relatively small (a few hundred people) and most of us know each other and the rest we know by name or by face. My question is that, after I apply for a postdoc position, I then meet the hiring scientist at a conference, then how appropriate is it ask them about my application? If it is appropriate, then what is the best way to do so? In person? In email, this week? In email, after we return? Or something else?
This is in the field of hard sciences in the USA. One potential employer is a friend I have known since my beginning graduate school. Another potential employer, I just know her by name and never had any contact of any kind besides my application. Should I ask/say anything? I am obviously curious how's the process going and if I am high on the list. But what would I say? Or is it better to just be friendly but professional and pretend like I didn't apply and not mention anything at all? I can only imagine a useless "we are still looking and evaluating applications". Is any other response even possible if I ask the right questions in the right way?
It has been about a month since I applied. And yes I asked my advisor but he wasn't helpful. Both solicitations were clear that they wanted the postdoc to start as soon as possible (three months) so a month seems like a fair amount of time to follow-up. And after the application acknowledgement I haven't heard anything from either scientist.

You could try to reach out by email and tell them that you've applied for a postdoc position in their lab, and that you are going to be at the conference where you'd love a chance to discuss your research contributions and qualifications as well as the opportunities that they may have. If they have an interest and tell you as much, by the time you two meet you both know why you're talking to each other.

They already know I applied because I exchanged emails with them. And currently we are already at the conference. The question is, is it appropriate right now at the conference to bring something up face-to-face.

It should be ok, I would think. You could say that you wanted to take the opportunity to tell them personally that you're very interested in the position, you could ask about the process/timeline, etc. I think based on their reaction you will learn pretty quickly whether to chat more about it or drop the subject.


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Who can peer-review articles?
I was unable to find any information online about this. I asked a colleague who told me that there are no restrictions on who may review an article, although he thought it was very unlikely that an un-published person may be asked to review. I would like a general answer to this question; nevertheless, the specific context is in the following paragraph.
I am submitting an engineering research paper in the near future and the submission process requires that I suggest at least three reviewers. One of the reviewers I would like to suggest has not yet completed their PhD, although they have three publications that are closely related to mine. I know that it will be up to the editor to decide whether to contact this person, but it made me wonder if there are any specific criteria that reviewers have to meet.

Though I have seen it in the past, I find the idea of authors directly suggesting reviewers to be strange. In any case, perhaps you could suggest the supervisor of the PhD student you have in mind? The supervisor will have a more senior name and (s)he would likely have the expertise to review the paper (or otherwise delegate/oversee the review from the student). In terms of an answer to who can peer-review articles?, the answer is generally anyone who is good enough to be asked in the first place.

@badroit I could suggest the supervisor. There is a text field where I am required to state the reason for suggesting the particular reviewer - maybe I could mention that the work done by the PhD student is most relevant.

Yes, I think that sounds like a good solution.

@badroit make it an answer ?

@Suresh badriot's comment makes some sense, although I would hope the actual answer includes some reference to online documentation and/or personal experiences.

Yup, I tried extending it and turning it into an answer. I also tried to give a bit more depth on the general question in the title. @NauticalMile, it may or may not be the authoritative answer you're looking for, but I think it'll be difficult to find anything more concrete. Let's see. :)

speaking more generally youve run into a soft spot verging on Achilles heel of the scientific process, which is currently somewhat opaque but increasing in visibility/transparency with open science. there is no formal criteria. conventions vary between fields & publications. the process is in the midst of/undergoing potentially large shifts related to internet mechanisms/publishing etc... currently its an informal, behind-the-scenes social network...

An anecdote: When I was an unpublished graduate student, my advisor was given a paper to review. He passed it to me for comments, and after I had found a serious problem (the observed "effect" had the wrong sign but the right magnitude, and only appeared as a squared term so "agreed" with theory), he wrapped the review in his own words, sent off the rejection. I don't believe he would have taken the time to do the detailed analysis required to find the problem I spotted. So while he was, on paper, the "qualified" reviewer, I was, on that day, for that paper, the better person to do the review.

Who can peer-review articles?

Anyone competent enough to be asked in the first place.
For conferences (e.g., in engineering or computer science), peer-review is conducted by a Programme Committee. To be invited to be part of a Programme Committee (typically done by Chairs or Senior Programme Committee in larger conferences), you need to have a reasonable track record of research and a solid reputation in the area in question. I have seen PCs of reputable conferences in CS with many senior PhDs (I was in PCs myself as a PhD student).
For journals, you are invited to review by a member of the Editorial Board. They would weigh your experience and track-record accordingly. Again, you may get asked to review journal papers as a PhD student (I was also asked to review various journal papers as a PhD student).
Last but not least, you may be delegated a peer-review by someone who was asked to do a review (where that person was asked by the EB of a journal or as part of a PC for a conference). In that case, however, the responsibility for the quality of the review lies squarely with the delegator. In this case, a junior PhD student might be given a peer-review but with the idea that the delegator will check over it and discuss before submitting. (This is a good way to learn the process of peer-reviewing.)

I was unable to find any information online about this. I asked a colleague who told me that there are no restrictions on who may review an article, although he thought it was very unlikely that an un-published person may be asked to review.

I agree with your colleague. The delegation of peer-review is left to the judgement of the EB/PC/Chairs. They will take into account seniority and research track record in their judgement. Formal restrictions would only serve to rule out qualified reviewers from an often already too narrow field.

I am submitting an engineering research paper in the near future and the submission process requires that I suggest at least three reviewers. One of the reviewers I would like to suggest has not yet completed their PhD, although they have three publications that are closely related to mine. I know that it will be up to the editor to decide whether to contact this person, but it made me wonder if there are any specific criteria that reviewers have to meet.

I suggest submitting the name of the supervisor of the PhD student you think would be a good reviewer. The supervisor offers the editor a more senior name, should be knowledgeable in the area and if not, can solicit the advice of the PhD student in question or delegate the review entirely if appropriate.

As per my comment (and as a side note since it is not directly asked about) I find the practice of suggesting reviewers for your own paper a little strange (though I have seen it before on occasion). First there's the obvious possibility of selecting one's friends or of prior deal-making (assuming the suggestions were taken into account ... otherwise why would they ask?). Aside from that, if I'm submitting to a journal in my area, I expect the editorial board to have some members that would be sufficiently knowledgeable about my topic to get the paper in good hands. Having to suggest reviewers calls into question (slightly) the competence of the EB and/or the relevance of the journal. In any case, if the journal is otherwise reputable, this should not hold you back from submitting.

+1 nice and thorough. I didn't think about the fact that mandatory reviewer credentials would limit the reviewer pool too significantly in some fields.

Most engineering journals require you to suggest reviewers. It is a bit odd, and the editors don't inform you if they picked your choices or not. But on the positive side, it does give you an opportunity to put your work on the radar of the big names in the field if the editor does select them to review it.

There are also at least some editors out there who abuse the list of suggested reviewers as a blacklist (for the mentioned reasons).

To add one small thing to @badroit's answer, there are two very common ways to get asked to be a reviewer for a journal or conference:

know the editor or someone on the program committee
submit an article yourself for review

I've gotten more requests to review from my PhD supervisor who edited a journal and from journals and conferences I've submitted to. Journals are particularly prone to this in my experience--I've had review requests come in within a few days of my submission of my own article. Conferences tend to be delayed by a year such that submissions to the prior year's conference can generate invitations to review in the current year. This seems to be especially true if you've had a paper accepted.
So, that being said, eligible reviewers tend to be eligible submitters.

If you submit you will be in the journal specific database. This makes it easy to find you and ask you to review. Otherwise the editor will have to find you outside of the pool and create an account for you (much more work - esp. if it is less likely that you will accept)


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Using grants while on unpaid leave
When a professor goes on unpaid leave from her university, can she normally continue to use her grants to fund graduate students and postdocs?  Or, do all grants "freeze" until the professor returns?

I don't see any reason that a professor wouldn't be able to continue to use grants while on leave.  In fact, I'm on unpaid leave from my home institution right now, and have been able to use my grants (for travel support for myself), so that's one data point.

I'll add another "yes" data point. Unless the leave is disciplinary, I've never known an institute to freeze grants. And, often the leave is granted to give time specifically to work on projects supported by grants.

Thank you for the answers. Would this still be true even if the professor was on unpaid leave because she was planning to leave her university?

@anonymous555 Why not?  I think they still need to have an official appointment, but I think even 0% appointment (one with no pay) suffices.  It's possible that if the university really wanted to, maybe they could find some way to do this, but why on earth would they?  The PI would just transfer the grants and they wouldn't get the overhead.

The answer is "yes".  For instance, I was on unpaid leave this academic year, and used my grant to support a graduate student.

It depends on the breakdown of the grant. If there are students or staff who were hired to do the proposed work then I don't see any reason why they wouldn't continue being paid if they are continuing to work. The same goes for research related services and products. Sometimes sabbaticals are unpaid, but that doesn't mean that the work stops. Most grants are on a schedule, so PIs need to be making some form of progress on the project (whether or not they are getting paid from it).


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How to correct the missing citation counts/citing References in the adsabs.harvard?
How could we correct the missing citation counts and the missing citing References in the adsabs.harvard?
For example, I find that other resources such as https://inspirehep.net/ that have much precise and better citation counts, while both the Google Scholar and adsabs.harvard misses some citation counts/missing citing References.

These three resources have their own advantages and disadvantages:
1) Google Scholar: Google scholar miss citations from arXiv (sometimes but not always).
2) adsabs.harvard: In principle, it counts everything in arXiv, but even if so, the bib format citations may be missing -- perhaps it is the LaTex generating issue.
3) https://inspirehep.net, it only counts articles that are relevant to particle physics, high-energy theory, quantum field and string theory. It misses other disciplines such as Atomic-Molecule Optics or Condensed Matter physics.

I am happy to receive comments from experts working in all disciplines.

For NASA's ADS at least, there's a "submit missing references" form available here.
(note that this link is dysfunctional if one doesn't allow the site to set browser cookies)


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Is it possible to attend grad school in cognitive sciences without a medical degree?
I'm currently a first year undergraduate student in pure math but recently I've become interested in neuroscience and related fields. Is it possible to pursue neuroscience and cognitive sciences without a medical degree?
If yes, do you know any universities in North America or Europe that accepts people with pure math degrees in programs that are related to neuroscience and bio-mathematics?
Sorry if my question is too naive, I don't have much information about academic stuff yet.

Wouldn't your question be "can someone with a math degree pursue graduate study in cognitive science?" Medical or not has nothing to do with the situation.

Most of the people doing research in cognitive sciences do not have a medical degree. Most are biologists, psychologists, physicists and computer scientists.

At least in the US, a neuroscience or cognitive science PhD program generally admits people with undergrad or masters degrees, which generally can't be medical degrees since many US schools do not offer medical degrees at those levels.
So the answer to your first question is yes.
As for the specifically a math background, I expect that most schools would consider such an application. Even in fields that have corresponding undergrad majors, it's not uncommon for people to enter PhD programs from very different undergrad studies. An application would have to address the question of having an adequate background and understanding of what the field is like.

In one word: absolutely!
For Psychology the top rated public university in the US (UW Madison) states absolutely no specificity for an undergraduate degree for consideration, and in fact no psychology department I could find in my short searching stated any such requirement. Even most engineering schools, for example, don't require an undergraduate degree in engineering for consideration (though they often state a preference) - and this includes what in the US we refer to as "Industrial Engineering", which includes a variety of fields that do work in the cognitive sciences.
For neurology, the picture is a bit different, but the answer is still "yes". For neurology there is "clinical neurology", which are usually programs geared towards medical students (those seeking a medical degree - not necessarily who already have one). However, for pure "neurology" degrees the fact is the same - they don't universally require a similar undergraduate degree.
However, on the other side a word of caution - some degree programs state a preference for a related undergraduate degree. The University of Pittsburgh Neurology department states:

"In general, successful applicants have a BS degree in neuroscience,
  biology, chemistry, or psychology with a cumulative grade point
  average of at least 3.4 (on a 4.0 scale), and a cumulative Graduate
  Record Examination score of at least 160 verbal, 150 quantitative and
  a 4.5 in analytical writing."

Every department sets its own requirements, and just because one says "in general..." doesn't mean they don't admit people who don't fit their exact stated mold - just that your chances will be higher.
Being an international candidate (I assume), you'll probably have to apply to more programs as the chance for admittance is generally small per application to US schools (it's not uncommon for schools to accept 50% of domestic applications, and but only 1-10% of international applicants), but again - this is not all that uncommon.
If you had the opportunity, it wouldn't hurt to try to direct some independent study or work towards even a single mathematical problem that relates to something like decision or control problems or statistics - which you could then provide as an example of proof that you are interested in cognitive sciences, etc - but you don't have to.
Bottom-line, you will have to figure out what angle of attack you'll want to have on the cognitive sciences. It is a very big field, and you can technically do cognitive science in the field of Business (especially Behavioral Economics), Psychology (where most undergraduates are required to take a course in cognition), Engineering, Multidisciplinary design/art programs (like Human Computer Interaction), Computer Science (especially in Artificial Intelligence), Neuroscience/Neurology, Linguistics, and even Philosophy. None of these require medical degrees, either.
On the downside, if you don't also acquire a medical degree they generally won't let you cut people open and play with their brains or run them through radioactive/high-magnetic machinery by yourself (but you can collaborate with people who can!). If that's OK with you, no medical training is required.

Allow me add to this answer: For an unofficial list of schools, check wikipedia. Some of them, like MIT, actually encourage candidates with mathematics background to apply.


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Exam exceptions for student with disabilities
I am registered as a psychologically disabled student with my University, and (for disability reasons) have asked my professor to allow me to take the exam at a date later than the ordinarily scheduled time.  I have not received a response from my professor yet; my guess is that she is hesitant to agree to this exception for several reasons. One, is the notion that I might have some kind of advantage over the rest of the class. Second, should my professor make modifications to the exam (e.g. change problems, make it harder) for my exam, then she may argue that the other students' exams will have to be graded differently from mine, and that's unfair. Third, the exam is scheduled at the normal class time, 10:00 AM - 10:50 AM, so it can be argued that if a student attends class regularly at those times, then there is no reason why the student should need to take the exam at a different time.
My professor hasn't said any of the above (yet) and I don't read minds; this is just my best guess of what she will think of my request. University policy leaves the decision on such an exception entirely up to the professor. (No department in the University has authority to influence her decision. Not even the office of disability services can influence her decision in this case.)
From your experiences at universities, how do most professors typically respond to such exceptions? For you professors, does the exception I'm requesting appear reasonable to you? Are there any other reasons you can think of for why the professor would/should not grant me an exception for the exam?

I reposted this under a new name to protect my identity.

What is your justification for taking the exam at a later date? You need more time to prepare than others? In some tests (SAT, I believe) students with challenges like yours are simply given extra time. However, the question I would ask any of my students is "Why should you get a different test as opposed to simply getting more time to take the same test as everyone else?"

Is your disability accommodation covered by the ADA in the US? If so, does your accomodation specify that you are allowed to reschedule an exam at your convenience? If not, why exactly do you think you are entitled to such an accommodation?

@earthling I am not asking for a different test, necessarily, unless the professor wants to give a different one. I just expect she would, because of the possibility that students will talk about the exam.

Exceptions can always be made under certain circumstances. Interestingly in your long and detailed question, there is no trace of a reason for requesting a delay other than your general condition, which I cannot see as a reason by itself. The university/department probably has some rules or policies for such cases. There are usually ways for people with different disabilities to take an exam in parallel with the scheduled exam in a a separate room, sometimes with specific tools and help. I can for example see that hospitalization and family funeral can be clear cases for such exceptions.
So if an exception is made, what would you have to expect? To provide exactly the same exam twice seems extremely unlikely for the reasons you provide. So from the teacher perspective, making a new exam is not something to take lightly, it requires a lot of work (if done seriously). In other words, you would get a different exam designed to be of equal difficulty. From a student perspective a new exam can always appear either easier or more difficult based on what and how well you have studied but in general, the exam would not intentionally be made more difficult.

no trace of a reason for requesting a delay — Nor should there be!  The request was apparently channeled through the OP's university's disability office, who is charged with determining whether accommodations are appropriate.  The specific condition that justifies the accommodations is none of the instructor's damn business (or ours).  That said, I agree with @earthling's comment on the original post — requests for extra exam time and a less distracting exam environment are fairly standard; requests for extra preparation time are not.

Where in "... and (for disability reasons) have asked my professor to allow me to take the exam at a date later than the ordinarily scheduled time" do you read "channeled through the OP's univesity diability office"?

"Not even the office of disability services can influence her decision in this case."

@JeffE I agree with Peter Jansson. If a student in the US is entitled to an accommodation under the ADA then the instructor must provide that accommodation. Since the OP said it is at the instructor's discretion I am assuming that this is not part of an ADA accommodation. The instructor is well within their rights to ignore such a request, particularly without justification. Providing accommodations beyond ADA requirements is not fair to other students.

@JoeHass: I agree!!  US professors are required to provide accommodation under ADA (given appropriate documentation from people who are actually qualified to judge the need for such accommodation), but we have wide discretion in exactly how we provide that accommodation.  It looks like the OP is trying a little too hard to exploit that discretion.

@JeffE, to your first comment, you're correct about most, standard requests being under the authority of the Disabilities Office. In my case, however, the request is non-standard. The University policy on accommodations for students with disabilities, most certainly has ADA at its foundation, but has added additional provisions. So just because something is not in ADA does not mean it's not in my University's policy for disabled students. I disagree about "trying too hard to exploit that discretion". The word exploit has negative connotations. I don't see how I am "trying too hard".

@PeterJansson, there is only so much detail I am willing to volunteer. (You read my comment under my question?). But even without the details, you've given a very helpful response. What specifics would you have wanted to know?

@Necron It is not details about your condition that matters but rather what conditions the university provide to you that interests me. If they provide possibility to take exams late is quite different from you requesting a late exam for other reasons. So it is not the detail of the reason but whether or not it is part of your plan with the U. that makes a difference to how to relate to the problem o the exam.

In my case, however, the request is non-standard. — Ah. In that case, you should realistically expect your request to be refused, unless you can convince the Disability Office (that is, turn it into a standard request).

@PeterJansson: at my University, the (Disabilities Support Services) DSS Office handles issues of this sort. There are many possible accommodations that DSS can make. and I quicklu reviewed the policy with an avvisor. The Policy essentially categorizes the rules into 2 groups:

@PeterJansson: 1.  Standard accommodations for students, e.g. 1.5 time on exams. extended due dates, test in parallel, and on. DSS students may also register to take the exam at the normal class time, or should the professor agree,, on a different date (it is highly encouraged to take the exam on the same date as the rest of the class.

@JeffE 2. Then the University policy allows DSS students, like any student, to make an informal aragreement to take the exam at a different date, under extenuating circumstances. Of course, the professor is free to accept or reject. I have seen professors make exceptions for non-disabled students. If you knew the full nature of the disability (which is beyond what I will disclose here), then this exception; my request to take the exam at a later date may (but may not) appear more reasonable.


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How to format a citation in the abstract
This is a follow on to Are citations in abstracts considered bad style? It is unclear to me how to format the citation. Are citations in the abstract covered by any style guide (APA, MLA, Chicago, AMS, etc) and how do they depend on if a numeric system is being used versus an author-year type system?

I was not able to find any mention of references in the abstracts in APA, MLA, Chicago, ASA (both statistics and sociology). There is no indication of if they are allowed and if so, if new formatting is required. I have found a few style guides that do describe references in the abstract.
APS style says:

References cited in the abstract must also be found in the Reference List, where the complete information for the reference is provided. However, in the abstract, these references are not cited by their reference number alone. Instead, the following form of citation is used: the entire author list with initials (in roman); the journal name (in italics); and the volume, page numbers, and year (in roman). The article title is omitted for the sake of brevity.

which is pretty thin in regards to a citation style
IEEE style says:

Numbered reference citations are not allowed.

which might imply full text citations are allowed like APS, but it goes on to say

The abstract must be self-contained, without abbreviations, footnotes, or references. It should be a microcosm of the full article.

AMS style seems to be the most complete:

The abstract needs to be edited to
  remove
  or
  rewrite
  reference citations.
  Rewrite reference citations by placing the following information within
  brackets at the callout point. For journal article references, insert (in
  all lightface roman text) the journal abbreviation, volume, year, and
  page numbers, but not the article title. For book references, insert the
  title, publisher, location of publisher, and year. Only
  book titles
  appear
  in italics

it then gives three examples (article, book, and what looks like a book chapter).

The URL for the AMS style guide is broken. These are valid URLs: https://www.ams.org/publications/authors/AMS-StyleGuide-online.pdf, http://www.ams.org/arc/styleguide/AMSstyleguide.pdf, https://web.archive.org/web/20170611022112/http://www.ams.org/publications/authors/AMS-StyleGuide-print.pdf (or the generic one: http://www.ams.org/arc/styleguide/index.html).

I checked my copy of the Chicago Manual of Style, 16th edition, but I couldn't find any reference to this problem (I might overlooked it, though).
We had once to cite a paper in an abstract, because the results given there were central for our paper. The publisher put the reference inline, within parentheses, with the same format of the other references. That particular journal has a particularly short form for the references, and the inline citation read as:

(Author A, J. Abbrv., Vol. (Year) Start page)


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University advocates for students facing academic misconduct charges
I sit on my department's academic misconduct committee. When students are suspected of academic misconduct they are invited to a meeting with the academic misconduct committee. The university polices are pretty clear that students not only can, but should, have an advocate attend the meeting. The policy also states that the advocate cannot be a lawyer providing legal representation, but can be a friend/family member who happens to be a lawyer. The university student services provides an advocates if students request it. At our last meeting we had a case of suspect collusion by two students. Both students had been assigned the same university advocate.
These collusion type meetings tend to be messy and involve bringing one student in and hearing that side of the story, sending that student out and bringing the other student in and hearing the other side of the story, and then often iterating a number of times. We attempt to keep the students isolated so they do not hear each other's side of the story. In the case of the same advocate representing both students there is obviously a confidentiality issue.
Based on the evidence we had it was clear student A had copied/worked with student B and produced a "joint work product" and turned it as her own. This expressly prohibited and constitutes academic misconduct. We did not have evidence that student B had knowingly colluded with student A and therefore were going to let student B off.
We called student B and the advocate in for a final meeting and began explaining to the student that they had not done anything wrong and no penalty would be applied, when the advocate proverbially threw student B under the bus and said that student B had colluded with student A. The end result was that both student A and student B were penalized. It is not clear if we applied a lighter penalty to student A because of admission of wrong doing by student B. I walked away from the incident feeling dirty.
We have not referred the case to the central university committee because of "procedural irregularities" because the central committee is consistently harsher than us and we are confident the central committee would have penalized both students (even without the admission of student B) harsher than we did. Should that matter or should we just report it to the central committee?
This incident has raised a number of related questions for me. Should the advocate be reported? Do we need to convince the university to change its advocacy policies for claims of joint work? Is there a fundamental conflict of interest of the university advocate and should students be encouraged to get their own independent advocate?

It seems to be that the overall process is working well. The problem is that Student B was denied the opportunity to have an advocate truly being a proper advocate.
In absence of any university regulations which require you to bump it up higher, I would recommend handling it locally if you can. There seems not benefit to engage higher ups if not needed.
I would, however, have someone examine the entire advocacy system used. The fact that two students were given the same advocate on a case where they are basically claimant and defendant comes off as wildly unfair. Of course, the advocate is not a lawyer but still, the system simply should never allow that to happen. When you saw it happened, it would have been better (if it is allowed) to stop the proceeding immediately and sort out the advocacy issue.
In short, the problem is with the advocacy system, perhaps not with the advocate. Someone should dig into and fix that so that such problems never happen in the future.
As for the current two students, if Student B (not the advocate) did admit, then it seems clear that blame should be shared (it was not theft but rather collusion).

This may be a bit over the top, but I think it's pretty unethical to have one advocate represent two students who may be in opposition to each other. US states, at the very least, have ethical rules for attorneys that are designed to prevent this sort of thing and are taken pretty seriously. The fact that your University has its own procedures for dealing with academic misconduct that attempt to mimic the legal system (a "trial", "advocates", etc) without some of those ethical safeguards is troubling.
Without discussing the case at hand, I would recommend raising the issue up through the chain of command or committees that sets the rules for these proceedings. The process clearly needs to change. If your school is a state entity in the US, it has left itself open to lawsuits claiming lack of due process. If it is a private school in the US, it may also open itself to legal claims of another nature.

Indeed, the only way forward I can see that doesn't have significant legal implications would be be retract all decisions made by the first committee and rerun it with all new staff.

If I was on the panel I would want to refuse to make an binding judgement and request that the whole matter be heard by a fresh panel. I would also be questioning the ethical standards of the advocate working for both students


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Attending job talks when you are leaving the department
I am leaving my current department in the next few weeks. We are currently in the mist of our hiring season and have 12 job talks and campus visits schedule before I leave. None of the positions we are currently trying to fill are explicitly the replacement position to mine and the areas of expertise of the candidates are pretty far removed from mine. We are a large enough department, that there will still be a reasonable sized audience and enough people for the candidates to talk to. Is it inappropriate to skip the job talks and not meet the candidates, unless they specifically ask to meet with me?

Among other things, I think it depends on why you're leaving. This depends on your department's culture of course, but if were mine: If you're leaving for a department which is obviously much stronger, or to be closer to family, or to solve a two-body problem (or any other reason which does not reflect badly on your current position), I'd be inclined to introduce yourself and freely answer any questions; if you don't much care for your department or the town in which you live, it might be good manners to absent yourself.

You do not need to attend all 12!  If anyone questions your absences -- which I doubt they will (people may well not even notice) -- you can say you are up against some deadlines, and also mention needing time for packing and such.
Perhaps you could pick out a small handful of talks that you are sincerely interested in attending.

Impossible to answer well without knowing more and I don't think it is appropirate to post more on a public forum!
I think it really depends on your relationships with your colleagues who you are leaving behind. In some situations it is better to absent yourself from situations where people are looking forward to the future of your old department. In other situations your experience may be helpful and it may be supportive to your colleagues who you will leave, but I guess who you want to stay on good terms with and continue to support. (I have not exactly been in this situation before, but similarish ones)


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How does PLOS ONE maintain its impact factor?
The PLOS ONE journal has an impact factor over 3. The specialist journals in my field top out with impact factors of about 3. As impact factor is in essence a measure of citations per article, it seems surprising that a journal like PLOS ONE that prides itself on not making subjective judgments on things like "importance" can maintain a higher impact factor than journals that prioritize "importance".
I have only cited handful of articles published in PLOS ONE and looking at what has been published in PLOS ONE in my field, the majority of things look "unimportant." It seems like in my specialty that PLOS ONE publishes a higher percentage of "unimportant" work than the specialist journals. This of course could be due to sample size and my own bias.
I am curious about what drives the impact factor of PLOS ONE. Are there specialties for which the PLOS ONE impact factor is low compared to specialist journals? Are editors and reviewers of specialist journals particularly bad at identifying "importance"? Is there something else?

I do not know about PLOS ONE specifically, but I guess part of the answer will be that impact factor is quite field-dependent.  For that matter, other interdisciplinary journals manage to achieve much higher impact factors.

While I am comparing PLOS ONE to Nature, I should note that the size of the journal is also critical.  The journals with very high impact factors achieve them largely by publishing only those papers which are likely to get a large number of citations.  There is an interesting editorial in PRL from a few years ago about this effect.

Slightly more meaningfully (being based on a credible and public scoring system), the Eigenfactor of PLOS ONE is now 1.533 compared to Nature's 1.499, so overall it can be said to be more impactful, but the Article Impact is massively lower.  This seems to indicate it publishes an enormous number of papers of which most only receive a few citations, whereas Nature publishes fewer papers which almost all are highly cited.

There are, I think, two distinct factors at work that may help explain some of your puzzlement:

Your field's impact factor is not academia's impact factor. For example, society journals in my field have an impact factor of ~ 5, and some of the big names for very splashy studies have impact factors ranging from 20 to 56. Depending on the balance of fields submitting to PLOS ONE, their impact factor may be coming from more cited fields.
Long-tailed citation papers. Impact factors, like many averages, are susceptible to long-tail effects. PLOS ONE is an open-access journal, and a highly visible one. It's possible that the occasional highly accessible generalist paper makes it there, and yields a large number of citations as a result, pulling up the overall impact factor.

Both of these are helped, in my opinion, by the lack of review for "importance" - beyond your suggestion that this does result in less important papers ending up in  PLOS ONE, it's also a benefit to papers that don't quite "fit" in highly specialized journals, but may still be impactful.

I agree with both these points, and I think they lead towards an unstated #3 - a nonselective megajournal like PLOS One may well tend towards an impact factor broadly representative of the scientific literature. Is the overall citation rate of all published papers on the order of 3 citations over two years? Someone must have studied this...

Quick check on WoS: papers published in 2012 across all subjects were cited 3.8 times in 2014 for authors called 'White' (7k papers), 6.03 for authors called 'Black' (1.5k), 3.48 for authors called 'Green' (5k), 3.03 for authors called 'Clark' (6k); weighted average 3.83. So it's plausible. Hmmm. More work needed :-)

The average number of citations received within two years is roughly equal to the average number of citation given to articles from the last two years by a random paper. This is very field-dependent, but 3 looks like a good ballpark estimate.

@Andrew I was thinking they should be less than average since they are non selective.

@StrongBad But a slightly above average impact factor might be explained by an uneven distribution of what fields the papers are from, which might be skewed towards those with higher averages (certainly math has a quite low average, and I have so far not heard of anyone publishing their math papers in PLOS One).

@StrongBad I'd expect it to be a bit under (because the top material in all fields certainly does preferentially go to other journals) but not dramatically so. Regarding your original query, it might be very interesting to "subdivide" PLOS One (eg 'all paleontology papers') and see how that subset compares to other topical journals... but a bit more work.

I've just come across this study which seems somewhat relevant - http://leo.cineca.it/index.php/jlis/article/view/11257/10621 - about half the JCR categories have an OA title in the top quartile, and the highest-IF journal is OA in eight of them. However, none of these are PLOS One style megajournals.

I think that PLOS ONE is gambling on two key hypotheses:

People are very bad at judging future importance --- thus, no "significance" filtering.
Search engines and social networks are now much better at delivering articles than subscriptions --- thus, open access.

This certainly conforms with my experience: at present I have two PLOS ONE articles, each published about 5 years ago, one with 80 citations and the other with 9 citations as of this writing.  Both are quite specialized and likely would have had a hard time getting published in "selective" journals, yet have found some sort of audience.  I'm thus not surprised that they seem to be able to maintain a reasonable impact factor.

I don't think PLOS is interested in "maintaining" the journal impact factor of PLOS ONE. Many people involved with PLOS view journal impact factor metrics as actively harmful to science and scientific publishing.

@MichaelHoffman are you kidding? It's their product: no editorial rejection and an IF that approximates the one of good journals in many fields. How else would they generate so much revenue and pay their CEO half a million a year?

No, I am not kidding.

Many people involved with PLOS view journal impact factor metrics as actively harmful to science and scientific publishing. – I've seen this opinion also in no relation ton Open Access and PLOS. But, as far as I can tell, this opinion has not reached your typical tenure and search committees. Yet not?

Note this answer is anecdotal, but since I have heard this stated by 3 high volume publishing professors now, I believe that it may be a factor. These 3 professors claimed to rank journals as follows (approximately)

nature and science
PNAS and the top specialized (but still fairly broad) Journal in their field
All other journals including PLOS one

One philosophy for academic success is that once you have many publications in reasonably good journals, the marginal benefit of one more isn't that great. However, the marginal benefit of one more Science or Nature paper is quite big. Therefore, since PLOS one is often less of a hassle to submit to, if a paper is rejected from Science or Nature or PNAS the next stop for these high impact professors is often PLOS one. It just isn't worth it for these busy professors to trudge through multiple submissions down the journal food chain because they want to focus on their next Science/Nature submission or Grant proposal which could lead to such a paper. This means PLOS one gets a lot of papers that are written by pretty famous professors that just weren't jazzy enough for Nature and Science. Of course, PLOS one also gets a bunch of unimportant papers (by famous and non-famous authors) but I suspect some of the heavy tail papers that @fomite suggested are from academics with this philosophy.
I again stress that this is anecdotal and that I have no data to confirm this hypothesis.

I think this is quite possible.

While PlosOne ostensibly publishes papers from all fields of science, it is heavily weighted towards biology and medicine. Journals in these fields have higher impact factors because (a) they have more references per paper (I'd hypothesise that this might also be related to the use of numeric citations rather than apa/harvard style), and (b) they have shorter reference half-lives (i.e., papers accrue a greater proportion of their total references in the two to three years post-publication period that is used to calculate impact factor).
These are purely idiosyncratic factors that influence the average impact factor of journals in a particular field.

If you come from a field in biology or medicine, you might see an impact factor of 3 as perhaps average or a bit above average.
In psychology where I come from, some of the best journals in a given subdiscipline have impact factors in the 3 to 6 range.
In other fields like mathematics or the humanities, an impact factor of 3.0 would be perceived to be even greater.

The main point is that impact factors are more highly correlated with subjective evaluations of quality and importance when such comparisons are performed for journals within a discipline.
In addition, even relative to fields like medicine and biology, the impact factor for PlosOne is respectable. Articles are clearly being cited quite a bit in these areas. You can see more information by going to scimago or Web of Science Citation Reports.
If you want to compare journals in a more discipline-neutral way, you might want to look at the SJR. It uses an iterative weighting procedure which I believe weights references coming from more prestigious journals more highly and allows each article to only give away a finite amount of prestige. So for example, an article with many citations can only give fractional prestige. This allows disciplines with more references per paper to count a little less.
For example, on that metric, PlosOne has an SJR of 1.3.
In contrast, a psychology journal I know which has a similar impact factor to PlosOne had an SJR or 1.8, presumably adjusting for the different citation practices and relative prestige of source publications. You might want to look up the SJR of journals in your field to compare.
As an aside, metrics of impact at plosone have declined substantially in recent years (compare 2010 to 2016); albeit, it is still a first quartile ranked journal.
Two possible explanations: (1) as a multidisciplinary journal, the mix of articles the proportion of articles coming from disciplines with high numbers of citations has declined, or (2) the average quality/impact of the research has declined.

https://www.scimagojr.com/journalsearch.php?q=10600153309&tip=sid&clean=0

The answer to this question is given by the Central Limit Theorem. Basically PLoS ONE is so large that is samples the population of all papers out there, which together (if published in a single, catch-all journal) have an IF=3. In statistics this is called "regression to the mean."
For more info, please see my paper "Impact Factors and the Central Limit Theorem: Why citation averages are scale dependent" in the Journal of Informetrics.

The key selling point of a top-tier journal is not that the content is more important, rather, their standards for publishing in general are much higher. Of course one criteria is impact, but arguably the most important criteria is the level at which the peer review is done. I've seen papers requiring 3 or 4 new experiments to please reviewers in Cell/Nature.
What difference does going-the-extra-mile in due diligence have on a paper's citation rate? I doubt little if any. People cite publications relevant to their work, regardless of how many replicates that cited paper used or how many supplementary figures there are. Of course, high-impact journals have other criteria that does push up the citation rate, such as impact, but my point is that it's a false assumption to assume the only thing going for top-tier journals is their impact requirements.

A reviewer asking for replication is not uncommon in any journal. Plos one is pretty rigorous about the quality of the science (arguably just as much as nature, although likely more variable given the number of papers handled). I don't buy this explanation.

@WetLabStudent pretty rigorous about the quality of the science indeed.

@CapeCode I knew someone was going to bring this up. Considering plos one publishes 85 papers a day, about 50 times more frequent than even the most prolific journals (e.g. Nature), if Nature and Plos one were equal quality you'd expect Plos one to have about 50 times more ridiculously bad publications that slipped through the crack than nature. I know of many papers that have been rejected by plos one and then successfully published in reasonably good (Q1) non-open access journals.

To be fair to my initial argument, ridiculous papers aren't really the issue. Both PLOS and Nature will slip up, at a roughly similar rate assuming the rate of reviewers who dont give a **** exist at the same frequency. My argument was that Nature et al, under positive reviewing circumstances, are more through. This is what I look for in a paper, and it why I read Nature/Cell -- however it doesn't improve the impact factor directly.

@WetLabStudent thanks for bringing up the staggering volume figures, one more factor of course is that PLOS makes money every time it accepts a paper. A strong incentive to accept more papers.

That adds up to 46 million $/year in revenue, no wonder they advocate the obsolescence of editorial rejection.

@CapeCode Your point about revenue is well taken. However, what do you mean by "no wonder they advocate the obsolescence of editorial rejection"? They've argued for not rejecting papers based on "importance" but they have strongly argued for rejecting papers that are incorrect. Of course mistakes happen due to lazy reviewers and even worse lazy associate editors. Many quality papers have been rejected by PLOS one, see

The large number of papers published by PLoS ONE may increase the likelihood of some being very highly cited. This may drive up the Impact Factor.
I agree it may also reflect the average (geometric or arithmetic) across all journals. Because PLoS ONE publishes a lot of biology, especialy biomed papers, these tend to be more cited because it is a larger field (e.g. compared to geology or statistics).

One thing that seems to have been left out of this thread is the volume of articles published by PLOS ONE. Approximate 85 per day according to their wikipedia page. It seems that that would argue against a long tail effect.

Why do you think that would argue against a long tail effect?  it seems to me that the high number of samples would actually make it easier for the long tail to occur.


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Should departments have a policy regarding updating online resources?
My department has gone paperless and uses Moodle to provide all information to students in an electronic format. With a paper based syllabus the expectations were cast in stone (okay ink on paper). Now that we are on Moodle, we can change the syllabus whenever we want. Today, we had a staff member change the word count on an essay, that is due in two days, from a 1500 word maximum with a 10% allowance, whatever that means, to a strict 1500 word maximum. The students are confused and screaming about it. What type of departmental policy should be in place to prevent changes.

I have a view of policies that probably does not reflect that of the majority of academics here, but I think that policies should be put in place to address very serious problems (e.g. security issues), not the lack of common sense from staff members ;-)

Fundamentally, I don't think this problem has to do with the shift to a paperless format. Even with a syllabus on paper, my experience has been that a professor may well change it, often for good reason (e.g., shifting to make room for an excellent guest speaker, extending a deadline on a lab that many people are having problems with).
I think that the real problem here is that the faculty member has made a last-minute change that makes life harder for the students.  Student who thought they were done with the assignment have just discovered that they have more work to do, it may be interfering with their other plans, class or non-class, and it just plain doesn't feel fair.  Perhaps a good policy for that would be that no assignment can be made more restrictive once it has "started"?
There is also a place where the electronic aspect can enflame or mitigate the issue, and that may also address your original question.  Online documents offer the potential for making a "sneaky" change that is not announced directly to the students.  That seems to me to be something that should definitely be prohibited, and might be handled automatically by having the system send an announcement to all of the students whenever a course document changes.  I don't know Moodle, so I don't know how hard or easy it would be to set up automatic notification; even without automation, however, you could certainly regulate that all non-trivial changes must have a notification sent to students.

I agree, at least the students are aware in this case and  may complain if necessary. You'll have bigger issues if the students are not made aware.

+1 for no assignment can be made more restrictive once it has started. This should be true regardless of the medium.

I agree with jakebeal that "online resources" is a red herring.  The issue is simply that the instructor has made a last-minute change to the expectations for an assignment.
I think it's a pretty basic principle of teaching that expectations for assignments need to be provided to students in plenty of time for them to create the assignment.  If expectations are to be changed after they are communicated to students:

There should be a compelling reason for the change.  (I can't imagine a compelling reason for 1650 words to suddenly be unacceptable.)
Students should have a reasonable amount of time to take the changes into account.
Changes that may invalidate work that students are likely to have already done should be avoided if at all possible.
Students should be notified by some "push" method (email, announcement in class, etc).

However, I don't think that you need to turn this into a departmental policy.  It sounds to me like you have one person who needs to be counseled about their teaching practices - take the matter up with that person.  Imposing a department-wide policy for something that should be common sense is passive-agressive, wastes the time of those developing the policy, and places an unnecessary burden on everyone else who now has to check whether they are complying.
(I made the same point here.)


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What are the drawbacks of HTML5 presentation software?
I use pdf files, generated with Beamer/LaTeX, and whatever pdf viewer is available on the computer I am presenting on. While I like the Beamer/LaTeX/PDF combination better than PowerPoint type applications I am not particularly happy with its ability to embed media (sounds and videos). Further, common PDF viewers (e.g., Acrobat, Evince, and Okular) do not provide any type of "presenter" view with a clock and notes on one screen and the slides on a projector. The presenter view in advanced viewers like impressive are pretty limited. I am thinking of switching to an HTML5 based system (possibly reveal.js), but wanted to know what the drawbacks of HTML5 based presentations are.

It is not clear for me what problems you would like to solve, and how reveal.js would help in it. Can you give some details?

@Greg I am not sure I have problems I want to solve. What I want to know is if HTML5 based presentation software has any serious drawbacks.

Not really an answer but I have made the switch and have not had serious issues — I encourage you to try it out! I wrote about my experience here.

isn't this question suitable to Software Recommendation more than Academia?

@seteropere I thought about whether it was on topic or just a big list question. I am not asking about which software to use, but rather the drawbacks of HTML5 based "software". Further, I think the way academics do presentations is very different from industry presentations.

@StrongBad "but wanted to know what the drawbacks of HTML5 based presentations are" seems to me a technical question not related to academics. I believe technical people (tex.SE or softwarerec.SE) are the ones who are able to answer such question.

This question appears to be off-topic because it is about drawbacks of HTML5 for presentations.

As currently written, this question doesn't indicate why considerations related to HTML5 presentations could be expected to be different for academics vs. everyone else (and consequently, why it should belong on Academia). Please [edit] this information into your question.

Possible to add from a student's perspective as most students know what a .pdf is or a .ppt is, but mention JavaScript and HTML5 and I'm sure people in non-CS place may be convinced that sorcery is about.

From a web developer perspective, the only issue I can see is compatibility. If the provided computer does not provide an HTML5-ready browser, the presentation may not work. Unfortunately, having been in labs and lectures with institution-provided computers, there is no guarantee that an IT department has provided the newest browser. While I'd like to think that people, especially at institutions, are keeping their machines up to date, we have to assume that some machines have been forgotten or have not been maintained.
This HTML5 readiness graph demonstrates that IE8, which still has a huge market share, is woefully prepared for any HTML5 feature. IE9 has some functionality over IE8 and appears to cover the audio/video portions you require, but only IE10 appears to be HTML5-ready as of last year.
I tried the reveal.js demo on IE8 just now. The rotating transitions don't work at all (it acts like Powerpoint basically), but it was usable. Since there are no videos or audio, I can't test those, but a standard presentation would at least be doable even in that browser.
It is unlikely that any IE9- browsers will ever reach full HTML5 support due to the security risks and time drain required, so any attempt to present on an IE8 browser is likely to be bare-bones and equivalent to viewing a PowerPoint.
However, this can be largely mitigated with the use of a PortableApp web browser such as Portable Google Chrome. A small footprint that can be carried around in a flash drive with the presentation.
From a student perspective, reveal.js might appear to be more confusing if you share the files, as it probably isn't just a foo.ppt file, but a source document, the JS, and so on. You will probably need to provide a read-me for being able to view the presentation. I'm sure everyone here knows how to open and view a PowerPoint, but some of us might stumble a bit with a more complex solution that may depend on multiple files and folders. That, and the student would need an HTML5 browser to get all the features working.
You probably will also need to direct PDF copy of the slides because I didn't see any noticeable way to print the presentation unless the stylesheet natively does that from the print menu.

It can do pdf export.

@StrongBad and apparently it falls back gracefully. As long as you don't find a mythical IE7 browser, of course.

If you have to use a provided computer to show your presentation by inserting a USB stick, you could put Portable Firefox on your USB stick and run it to show the web page.

@BrenBarn As long as the computer is compatible with whatever you have. There's at least 3-4 incompatible systems widely used in academia.

Overall HTML5 Presentations are great, but that's not to say that they'll be better than the alternatives in every respect, or that you'll never have a bad time.
One challenge I've experienced is when I need to collaborate with colleagues on the presentation -- many lay people are intimidated by HTML or Markdown-based tools. There aren't a lot of cloud collaboration apps that will let you upload plain HTML/Markdown and then let your friends add, edit, or comment on your work. You may end up having to do a lot of converting back and forth between HTML and Office formats if you work with non-techie collaborators.
Similarly, people are often confused about how to open an HTML presentation when you send them an index.html file and a folder full of assets. You can remedy this by hosting things yourself in a Dropbox folder, but that isn't always awesome.
I use Reveal.js often, but I think it's fair to say that I spend more time developing an HTML presentation than I would in Apple Keynote. I usually write out my ideas in Markdown first, then convert that to HTML and edit it further within the Reveal.js codeset (from my code editor).
If your presentations are mostly made up of text and un-altered images, Markdown/HTML can be very fast. If you like to futz with the colors, fonts, and modify your images, that's faster in a presentation software like Keynote. Even simple things like cropping images, writing over images, etc. would require you to do them in an external graphics editor before incorporating them into your HTML presentation.
So basically the biggest problems with HTML presentations are working with other people and focusing too much on the visuals. Other than that, it's great.


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Should I assume that attendees have read my papers when I give a talk?
On occasion during talks, presenters will say, "as you know from reading my papers" or during a Q&A someone will say "you should know from my papers".
The above clearly seems inappropriate for most settings outside of a group meeting. However, to what extent should I expect my audience to know what I am talking about vs. completely assuming that my audience know nothing?

As a basic talk-giving etiquette: it is much better to say "I dealt with that problem separately in my paper X" as opposed to "as you know from reading my papers" or "you should know from my papers".

The Law of the Ignorant Audience states: "There is always someone important in the audience who doesn't know a vital piece of information, even if you take into account the Law of the Ignorant Audience.". I first read it in the Latex Beamer user's guide.

This really depends on your audience.

At a department colloquium, I assume very little background, probably an undergrad degree in math, but not even an undergrad class in my research area. Here the audience will often be smart, but ignorant of the relevant background.
At a research seminar with lots of undergrad and/or masters students, I still don't assume much background, maybe an undergrad class in the area, but even then I "remind" the audience of important information they "should" know.
At a research seminar with mainly PhD students and active researchers I assume more, but even here I usually don't assume that they're familiar with the problem or the relevant literature or techniques.
A conference special session (or minisymposium) is similar to a research seminar with mainly PhD students and active researchers.  Here I often expect that much of the audience is familiar with the background and the techniques, but I still usually review them at least briefly.  I've never gotten complaints about giving too much background and context.

I never assume the audience has read any of my papers.
I typically view my talks (at least in part) as advertisements for my papers.  The audience will never want to read my paper if they don't see why it's important (so that's my job during the talk).  For those few that already want to read the paper, I hope they leave my talk with an outline of the paper, which will make it easier to read.  Any time you're talking to an audience with varied background, it's good to briefly describe the key definitions.  If you can do this quickly, perhaps only verbally, you don't bore those who already know, and you give the rest a fighting chance to keep up.

I agree 100% The only time when assuming the audience has read the papers is justifiable is (a) when presenting for a journal club/group meeting  or (b) presenting at a workshop where participants are specifically requested to read certain papers. And even in the case of (b) an actual expectation that they've read the papers in question is often naive.

In general, when giving a talk, my only assumption about the audience is that they found the title (or me) compelling enough that they decided they didn't have anything better to do with that hour (or 15 minutes).
Or at a conference, that they can't be bothered to get up and leave before the session ends, and decided to stay.
While I will give references to papers I've written, it's always a "For more information..." rather than a "As you all know..."

I think the causality is probably reversed: a talk at any level is a chance to "advertise" or "promote" ideas (whether "your own" or due to a larger enterprise) far more dynamically than in a paper. Thus, a good talk will motivate people to read your (or others') papers. Papers and talks are not in the same currency.
Further, if you have any reason to believe that most people in the audience have read your paper that you intend to talk about... you'll surely be boring them, and making them sorry they attended, no? Certainly if the talk is just an abbreviated form of a formal paper.

I guess that this would strongly depend on the culture within your scientific domain. In my case (software engineering) making this assumption would be inappropriate. You can suggest to read your paper if, e.g., there are some technical details you are not going to present since they might not be of general interest, but you cannot assume that this already happened.

In general, the broader the audience, the less you're able to assume about the audience's knowledge of your work. For example, at a general meeting for your profession or a department-wide seminar, you'd have to be more careful to provide background and context than at a smaller, more specialized event like a Gordon Research Conference.
However, time limitations will also be a major consideration—and in some cases, can outweigh the specialization issue. If you only have ten or twelve minutes to give your talk, then you don't have time for more than a minute or two of background information, regardless of how complex or novel your topic may be.

You left out the two most important words:  If you only have ten or twelve minutes to give your talk, then you don't have time for more than a minute or two of anything except background information...