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When does it make sense to send more inquiries asking about review progress to PLoS ONE?
My paper has been under review for 2.5 months now at PLoS ONE. I am still waiting for the first review result.
I have sent three inquiries to ask about the progress, and all the responses were telling me that the paper is out for review and PLoS ONE is doing their best to process my paper efficiently.
In the title of the PLoS ONE website, it writes "accelerating the publication of peer-reviewed science". I am really disappointed. PLoS ONE is the slowest among all the journals to which I have submitted.
My question is, does it still make sense to send additional inquires about the progress to the journal? If it does, what should I write in the inquiry?
===update===
Three months now from the submission, I still have not got the first decision. My case is an example showing Plos One is very slow. If you want to publish something quickly, Plos One is the wrong choice! Indeed, it is the slowest among all the journals I have submitted to.
===update===
Just got the first decision a few days ago. i.e. The first decision is made around 3 months after submission. The review results are very simple and positive actually, simply asking to cite more references and add some discussions. Still can not understand though why so simple and straightforward review comments need 3 months to conceive!

Two and a half months is slow for journal publication?

It is maybe only my personal experience. After 2.5 months,  I have not got the first decision yet. I have submitted to journals including Plos computational biology, Journal of royal society interface, Scientific Reports, IEEE communications letters, Plos One, etc. For me, Plos One is the slowest....

I have never received an initial decision within 6 months of submission.

My research only includes some classic math (Differential equations etc.), and is relative easy to understand. So, that might be why I normally receive the first decision in no more than 2 months. I know mathematic studies need lots of time to review. Our fields are different. @MarcClaesen

three years is my record!

@Leo Sorry, that's probably only your impression. In almost all of math, waiting for less than half a year is a miracle.

@yo' My research field is not Math. The paper I submitted to Plos One includes calculation on a data set and some simulation results. There is no hard math.

@MarcClaesen this is highly field-dependent. In life sciences 2.5 months is slowish, especially for something like PLoS ONE (but not unheard of).

@ChangwangZhang Very interesting topic. One reason why I recently have been considering PeerJ and PeerJ Computer Science for submission is that they claim they take only 1 month for the revision. I suggest you to do the same.

PLOS One are pretty good at hassling editors to get a move on (I know, I am one) and if an editor doesn't move on a paper, they will reassign it to a new editor. So I don't think asking what's happening will help.
The usual reason for delays is reviewers. You ask someone to review. They don't reply. They are reminded. After two weeks, you give up and try to find a new reviewer. You invite them to review. After one week they agree. Two weeks later  a reminder is sent. A week after that another reminder is sent. A week after that you give up and invite a new reviewer. We are at two months, and we don't have a reviewer yet.
The one thing that you might do to help is suggest reviewers. You might be aware of people who are working in the area that the editor may not know about (for example, because you have seen them present at a conference).

If I'm ever sent a reminder after only 2 weeks, the immediate response will be probably a decline of reviewing the paper. I know other people who feel it similar. Do you really annoy your reviewers with spam so early?

@yo' - I've clarified, the system is automatic. I don't send anything. :)  When an editor invites someone, there is a box to say when the review is due. The PLoS one default is 10 days, and after that the reviewer will get a reminder saying that the review is late. I always change it to something more reasonable.

@yo' I would assume that the reminder is simply to check if the reviewer wants to agree to do the review not to get the actual review itself. Maybe it's a matter of different standards but I'd probably consider a contact useless if they can't even reply to an e-mail within a few days to a week at most.

@Lilienthal Ah it seems I'm dyslexic, I misread the bit. My apologies.

@JeremyMiles Thanks for the explanation. A simple thing you can do is to reassign the paper to another reviewer after just few days, instead of waiting for 2 weeks.

@DavideChicco.it - I think you'd burn through reviewers much too fast. Many people say yes, after a few days and a nudge or two. You can spend a long time trying to find another appropriate reviewer. (But I"m no longer an editor. :) ).

Chasing the journal again doesn't seem like a good idea - you'll almost certainly get the same email back. Most PLOS papers are still out for review at this stage, so annoying though it is for you, it's not unusual for them!
As of mid-2013, the mean time to publication acceptance in PLOS One was 134 days (~4.5 months) with a median time of 100 days (~3.5 months). Anecdotally I don't believe it's got much longer or shorter since then, so 2.5 months seems entirely normal.

I am not sure about PLOS One, but time to publication/acceptance is generally very different from time to getting the first reviews back since usually you will need to make revisions and have the paper reviewed again,

Good point. (This was acceptance, I've corrected my error). PLOS One claim a time-to-first-decision of around 30-35 days per http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115451 (see table S1), which is low but by no means remarkable, and will of course include any papers immediately rejected. This one presumably survived that first pass...

I don't know about your field, but 2 1/2 months doesn't strike me as particularly long. I realize that in part you feel that their reference to being speedier than others seems now like false advertising; still.
I would not push more too soon, but if and when you do, I wouldn't ask "Is it ready?", but something like "I realize that the paper is out for review, and so out of your (=editor's) hands. I don't mean to keep stepping on your feet, but is there any way in which I could help speed turnaround up; and if not, do you have any idea when the reviews might be in, based on your experience with the referees?"

I think PLoS ONE's "accelerating" tagline has more to do with their open-access philosophy than the time to publication.  My two experiences publishing there took 5 months and 8 months from submission to acceptance---that's still pretty fast compared to many journals, but nothing remarkable.  Just leave it be for a little while and don't worry unless you go 4 months without receiving reviews.

Is it 2.5 months under review or 2.5 months since submission? If the latter, how long did it take to get an editor assigned (i.e. to change to 'With Editor') and when did it go out for review (i.e. status changed to 'Under Review')? In my experience (not with PLOS ONE but with other PLOS journals), it can take a while to get an editor assigned, which can increase time to first decision. While 2.5 months is fairly slow (life sciences at least), it's not uncommon. There is a big difference between 2.5 months under review and 1.5 months assigning an editor and 1 month under review, so that information would be helpful.
A couple of notes about time to first decision stats.
First is in regards to the answer by @Andrew. A first decision of 30 -35 days at PLOS ONE should not include any desk rejected papers because PLOS ONE's mantra is that importance/impact/sexiness does not matter - all that matters is whether or not the methodology is sound. I've never submitted a paper to PLOS ONE but I presume they send out any legitimate manuscript for review.
Second, time to first decision is usually given as a median not a mean. In effect, a median time to first decision tells you nothing about those papers that take a really long time to review. So a journal could still have a low median time to first decision if it 1. it desk rejects a high proportion of manuscripts, 2. returns some of the manuscripts sent out for review in a reasonable time (unless it rejects a very high proportion), 3. takes absolutely ages for the rest of the manuscripts.
Third, some publishers don't issue major revisions in an attempt to lower their time to acceptance stat. Instead they go with the 'reject with option to resubmit', which allows them to assign a new submission date for your heavily revised manuscript, thereby artificially reducing the time to acceptance.
So I'd take the time to decision stats with a grain of salt.

While PLOS presumably don't reject immediately for "this is unexciting", it appears they do reject at least some papers before review, and that proportion is increasing - see eg/ http://blog.scienceopen.com/2014/07/article-vs-journal-impact/ - "Most notably we have seen an increase in the rejection rate ... We put all our papers through rigorous checks at submission, including ethical oversight, data availability, adherence to reporting guidelines, and so more papers are rejected before being sent for review." [Damian Pattinson]

It is the review process that is very slow. Plos One actually was pretty quick to sent my paper to review (state changes to under review) in a few days.

You have already written to the journal thrice within a span of two and half months, which I think could be bothersome to many journals. Two and a half months is really not too long for the review process to get completed. In fact, it might take the journal that much time just to get reviewers. Yet, the journal has responded politely and positively each time. I think you should not write again, but just wait patiently for the decision.

Usually three months are needed to wait for any inquiry form any journal about status of paper, but it is common, journals take more than 3 months of reviewing a paper. This is due to duration, which usually reviewers keep paper for reviewing .


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How to write a follow up paper describing a different solution to a similar problem
I presented a paper last month in an IEEE conference and now I am writing another paper on the same topic but the method is different. While writing the Introduction and Related Works part of the paper, I have noticed that I am unintentionally repeating my words or sentences. I have no intention to copy the same lines from these sections from my previous paper, but by chance if it comes out to similar, is it considered as self plagiarism?

There are two basic approaches to the potential issues of self-plagiarism in such a case:

First write the paper, then ensure there is no significant re-use of text by going through and paraphrasing.
Embrace the reuse and explicitly declare (with citation) which elements are adapted from the previous publication.

You will clearly need to reference and compare with the prior publication in any case, as this is obviously a closely related work.  As such, your text must be different in many ways reflecting the different context created by the first publication.  Personally, however, I would prefer to use the second strategy and perform a declared reuse of text rather than attempt to arbitrarily paraphrase just for the sake of being different.

When reading a series of papers, I strongly prefer the ones that follow the second strategy. If the wording is different there is no way to tell whether it is just for the sake of difference or because of some subtle change in meaning.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


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Writing a paper on a smartphone implementation of previous work
Three months ago, I submitted a paper in an IEEE conference. The paper described a method to detect 'X' in images and a method to recover detected 'X' areas.
Now we want to show the performance and results of such an application on an android smartphone. For this, we have implemented the same detection method that we proposed earlier, however, we have also borrowed ideas from some other papers for a different recovery method (the recovery method proposed earlier was computationally expensive).
To summarise, the present work differs from our previous work in following aspects:

First work to demonstrate detection and recovery of 'X' in an
android smartphone.
A new recovery method, but which it is inspired from other's work.

Does it make a good paper for publishing in a conference like: ICPR?

I'm voting to close this question as off-topic because it is a topic-specific question and not related to academia in general.

@CaptainEmacs: How can I improve it? Basically, I want to know if the new paper is good for publishing.

Your question does not generalise to a question on academia in general. So, there is nothing one can learn if one does not happen to be in precisely your area of work, which is the purpose of this site. Either you formulate it in such a way that, say, a biologist could profit from the response, or you would have to put the question to some other suitable site (or ask your adviser, which is, in any case, a better route).

Stepping away from the details of your particular study, what you are more generally asking about is the distinction between studies of theory and of practice.
The first paper you speak of introduces a method and demonstrates that it can work, but does not characterize its performance.  The second paper would then be characterizing its performance in a particular environment of interest.  From a scientific perspective, that is certainly a contribution of new knowledge (even if incremental).
To determine whether it is of sufficient interest to be published, you need to focus on the question of motivation: who will want to know about the performance and why?  What else will they need to know, such that you can create a complete and informative study.  The answers to these questions will depend critically on the precise details of your work and its context.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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ACM CCS concepts
I want to generate the ACM Computing Classification System (CCS) concepts code in latex. My topic comes under the title Biometrics. But I could not find the broad category where in I could place Biometrics. So, how do I select the category for ACM CCS concepts?

I disagree with the close votes: coping with ACM CCS is a frequent frustration faced by a large fraction of the computer science community.

Perhaps this question can be edited to be a bit more general.

Navigating the ACM CCS tree from the top can be really frustrating, often leaving you lost in a twisty maze of categories apparently all alike.  However, the ACM also provides access to the whole classification system directly as a single flat webpage.  You can then search for words related to what you're looking for in that single page, often finding them at some low level of the tree.
In your particular case, for example, "biometrics" appears in two locations:

Security and privacy -> Security services -> Authentication -> Biometrics
Computing methodologies -> Artificial intelligence -> Computer vision -> Computer vision tasks -> Biometrics

Personally, however, I recommend not stressing over classification much. So far as I can tell, this system is largely obsolete, given modern search technology, and I have never personally used, nor heard of anyone else using, these categories for anything other than fulfilling requirements from the ACM.

... not to mention the confusion between version 1998 and 2012 of CCS...


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Ethics of "saving a publication for later" through anonymous submission?
This is more of a thought experiment than a problem. I just want to know how ethical is it.
Suppose a student discovered a very cool theorem/result that would yield a very good academic paper in a very good journal. But the student know that the admission to the graduate program in his country is based only on a written test (which they are expected to ace), so publishing now will not be beneficial. So, is it ethical for him to save the paper for the rainy day in the future by publishing it under a pseudonym (hence the world will not miss out on the knowledge)?
A generalized version of this problem would if you are overproductive in a certain year, then is it ethical to anonymize the production above the bare minimum and use it in the future when you are going through a lean phase?

Publishing under an anonymous name is appalling ethics. Imagine if that was possible. It is bad enough the fakenews sites. The amount of anonymous submissions would be appalling.

We already have a question on the ethics of pseudonyms in general, see https://academia.stackexchange.com/questions/5408/is-pseudonymous-publication-ethical.  @Poidah, I guess I would say that not everyone agrees with you.

In mathematics where there can be minimal or little consequences of the discovery can be is very different from cancer research or research into health, where lives can be at stake. Saving it for a lean phase seems silly especially when theorems are unlikely to have any discernable impact. Publish it later runs the risk of the theorem being published by others rather than world "missing out on the knowledge".

Pseudonymous publication, while unusual, is not particularly problematic from an ethical perspective.  A famous example is Nicolas Bourbaki, a highly influential mathematician who never existed.  Anonymous publication is more problematic, because then there is nobody taking responsibility for a work.
The practical value of your proposal, however, seems dubious at best.  You cannot time-shift a publication by claiming it later: all that you would be doing is adding the publication to your past.

Actually, Bourbaki is a group, not an individual.

@Buffy Of course: and because the group assumed a single pseudonymous identity, that's consistent with what I have written.

There are more pseudonym examples at https://mathoverflow.net/questions/45185/pseudonyms-of-famous-mathematicians.  It's a long and distinguished list.

I see no ethical issues here, you can do what you like when you like with your ideas.
The only issues are practical. No "very good journal" would publish an anonymous or pseudonymous paper such as this. They require a real corresponding author who literally puts their name to the work and who can answer comments, criticisms, etc. Also, I don't see how publishing it without your name will bring you any future benefits.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Who does the pre-copy-edited version of a paper belong to?
I am aware that the copyright of the pre-peer review version of a paper belongs to the author. Does the post-peer review but pre-copy-edited version still belong to the author? I thought it may do because at this point the manuscript can still be rejected.
As I understand it, post copy-edits the manuscript belongs to the journal.

The key here is not actually the history of the manuscript but the submission of a copyright transfer that moves the rights in the manuscript from the author to the journal.
If you sign a copyright transfer form (or a co-author does on your behalf), then all of the versions of the manuscript transfer in ownership to the journal. Author-friendly journals will then typically grant back a wide variety of rights, including the right to distribute preprints, and there are interesting interactions with preprint servers, academic networking sites, etc. The fact of ownership, however, is changed, and that typically applies to previous versions of the work as well.
Because of this, it is also true that the journal might publish your work but never actually own it!  For instance, the ACM now allows authors to choose between transferring copyright and retaining it but giving the ACM a license to publish.  There are pluses and minuses to both approaches, and it is still very much a question of evolving practice.


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Uploading papers on sites such as Academia.edu - copyright issues/author copy
I'm in the process of setting up an account on Academia.edu and as you may know there is an area that allows you to add publications. My question is how does this work with a copyright agreement (Springer International Publishing) that I have signed?
For anyone that may have also signed this agreement: going by Section 3 it looks like I can upload a non-Springer formatted copy as long as I cite the Springer link as the final version?
I have heard people mention author copies before, but I'm not sure if this is a real thing or just a myth that's been circulated down the line (where you can host your papers as long as you make a slight change from the published copy).
The form if anyone is interested (direct download): Springer Copyright Form

The only thing that matters is the agreement you signed. You should compare what it allows you to do with what you are trying to do and see if they conflict. If you have lingering concerns, you should consult an attorney in your jurisdiction.

The second paragraph of section 3 is relevant. Academia.edu is not specifically mentioned. If your funder requests that you deposit it on Academia.edu, you can do that. It is not your own website nor that of your department or faculty. The matter reduces to the meaning of "on his/her own website". From the perspective of Academia.edu, you are a user or member (not an owner). You do not have the ownership right of withholding access to the stuff that you have uploaded. They say that they may allow members to post their "content". I suspect, then, if you were to pay a copyright attorney to advise you, that you would be told that it is not "your own website". There's one way to find out (and many ways to find out how unanimous their opinions would be).
Also, romeo is useful but not decisive, and in case romeo is wrong, the language of the agreement is what would be enforced (as I know from experience).
[Addendum]
OTOH Springer has a totally different copyright transfer here. Note that this is for informational purposes only; it does say "any repository (after 12 months)". The message is rather mixed, and presumably has to do with the specific series.

Thanks for an informative reply, as for your addendum the case in question is regarding the Lecture Notes in Computer Science series in case anyone views this in the future.

You can check here what you are allowed to do; http://www.sherpa.ac.uk/romeo/
Some springer journals are Romeo Green, and allow you to upload the author post review final draft to an open Access repository 12 months after publication.
With Open Access publications you can do that straight away

The general Springer policy as listed on Romeo is that one can post a pre-review version to the arXiv but one must wait a year after publication before posting an post-review update to the arXiv. This is insane, because it means that if you actually obey the policy, you must leave any mistakes uncovered during the review process on the arXiv for well over a year. That's bad scholarship at best. I don't see how anyone could comply with this policy in good faith, nor why one should review for free for a journal that won't let the author share the results of your review with the community.

I do agree this is not the optimum choice, however we are not here to discus the content of the policy, but merely to explain how it works. If this is a great concern of yours, I would suggest publishing Open Access, as this will free you from the restrictions of copyright transfer.

For what it is worth, I do publish open access whenever possible, with non-profit societies otherwise, and with for-profit publishers only as a very last resort (or if the journal is named Nature -- we all have our price). I serve as an editor only for open access journals and do not review for commercial publishers. That said, there are other ways around copyright transfer restrictions, even legal ones. In my experience one can simply cross out the offending clauses of the transfer agreement, sign, and return. I've yet to have a publisher object.


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If the name I used on the publication is different from my legal name, which one should I use in the copyright form?
If the name I used on the publication is different from my legal name, which one should I use in the copyright form?  Let's say the names are Joseph (legal name) and Joe (name in the paper), or even different last names.

I am no legal expert, but at least in Europe I heard that many people keep their maiden names as official pseudonyms (which are stated on their id and passport as such), to be able to keep publishing under this name. In this case, you are able (to some extend at least) to sign legal documents with your pseudonym, which is especially thought for copyright issues. If it is not a legal pseudonym it might be more complicated.

Between name changes, use names, transliteration, etc., this is a rather common situation, and copyright forms are generally well designed to allow graceful handling of it. Most copyright forms that I have encountered include two separate places where you put a name:

A list of the authors, in which you should write all of the names exactly as they appear on the paper.
A signature line, in which an authorized signer (in this case, yourself) should place their usual signature, in the same form that you use it for other legal documents.

There is no actual requirement that these names be identical, just that the authorized signer take legal responsibility for the assertions of the document, including asserting that the list of author names is appropriate.  In fact, for some authors, their organization may not allow the author to be the person who signs the document!
Thus, if you write your name on the paper as "author" and you write your legal name for signature, this should be fine and appropriate. If, somehow, you encounter a form that does not make the distinction between the two names, then I would say it is highly likely that the organization issuing the form must be rather sloppy with regards to handling copyright in any case, and you should not worry about it.

Indeed, at least in the US, there is no legal requirement that your signature resemble your name at all. You can use a little cartoon drawing of a dog as your signature if you like, provided that you always use approximately the same little cartoon drawing of a dog.


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Are distance degrees from US universities worth anything?
I'm hoping some kind people could help me from making (more) big mistakes.  I've spent several years at a Canadian university, and I've gotten a good number of science and math courses under my belt.  Unfortunately, I hit a rut and made a mess of my third year, and haven't been back to finish my degree.
That was ten years ago, and just now I'm quite taken with the idea of returning to finish my computer science degree.  The problem I'm facing (and am hoping for help with) is that my life isn't compatible with the university experience.  I have a house, two toddlers, a full time job and I don't live near a university (I live in rural Canada, for reference).
Still, I'm doing my best to correct past mistakes and get back to the career path I wanted.  It turns out, undergrad degrees are not exactly flexible.  I'm not sure how long it would take me to complete the degree with full time schooling, but I've been exploring distance courses and part time, first.  Canadian universities do not like to teach computer science over the internet, it seems.
Quite a few universities from the USA are quite willing, however (see, for example Oregon State's online degree program).  I am quite uninformed about the validity of a distance degree, particularly in the computer science field.  I'm hoping someone with some experience in this area could share their thoughts on if this (distance educated computer science from a US university) is a worthwhile endeavour or if I'd best look elsewhere if I want a degree that can be taken seriously.
Any thoughts at all would be awesome, even if it's just pointing out a resource I could use to figure some of this stuff out on my own.  I'm feeling pretty overwhelmed and lost, I don't want to do this wrong a second time.

Hi, and welcome to Academia.SE!  As originally formulated, your question was too much a "shopping question" and likely to be closed, so I've edited it to focus on what seemed to be the key point: whether online degrees from legitimate universities are considered valid.  I also removed the side-question of state vs. private universities, which is answered elsewhere on this site (e.g. this question). Please feel free to adjust if I've misinterpreted things.

Thanks Jakebeal, I think I see how it was problematic before.  I'll be more careful.

Whether an online degree program can give you what you need depends strongly on how you want to use it.  A university degree can typically provide three key assets:

Skills: the technical foundations for professional success, particularly in STEM fields like computer science.
Network: connections with fellow students in your cohort are an excellent way to bootstrap one's professional network.
Prestige: the reputation of a school for achievements in its graduates, typically closely tied to skills and network.

An good online degree program can provide you with valuable skills, but is unlikely to give you much network and is definitely lower in prestige, even for the best programs (though these are slowly gaining in respectability).  If that is enough for your goals, then an online degree program can definitely provide it---and the better US distance learning programs are often explicitly intended to serve people in situations like yours.
It is important, however, to make certain that you pick a good, accredited program, or else your degree certainly will be worthless.  Many rather nasty for-profit organizations have gotten into online education and are essentially ripping off their students.  There are some good guides online to help you figure out the difference, however, such as this one.

Thanks for the information.  Primarily the skills and knowledge gained are of performance, I guess it's the importance of prestige that I'm unsure of, having never held a degree previously.  I'm not in a position to be picky, I'm trying to make the most of what choices I do have.

@Kad More prestige will make it easier to land starting positions at competitive job openings, though is by no means a guarantee.  If your options are limited, then choosing among the best accredited programs you can (whether you should pick the very best you can get into is a different question; some say you get more benefit from being a big fish in a small pond than from being a small fish in a big pond) and then working hard may let you climb up to increasingly better paying jobs.

That gives me a lot to think about, Timmy.  I think I have a pretty good idea what I need to pay attention to with all of this stuff, thanks for the information.

I am not sure you want to open the can of worms, but some comments about what makes a "good online degree program" would be very helpful.

@StrongBad I'll just stick with the link I gave, I think...


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Are there universities where authors can/must transfer their copyright to the university for negotiations with publishers?
Say you are a researcher employed by a university and publishing your work in a closed-access journal, which asks you to sign a copyright transfer agreement. To simplify, let's say you are the only author. In most cases I am aware of, the researcher owns the copyright to the article, and so end up signing the copyright transfer agreement with the publisher themself.
However, in a sense this is curious: publishing your research is part of your job, your employer may want to have a say in what you sign, and they could also provide legal assistance to understand the implications of what you are signing. Indeed, publisher agreements often contain pretty wide-sweeping language (e.g., taking responsibility for errors in the work and subsequent damages), and it's weird that researchers would sign them, especially when they are not lawyers.
So I was thinking that it could be a useful service if a university had an office for this kind of legal matters, providing standard paperwork for their researchers to transfer their copyright to the university, which would then deal directly with the publisher. It could even make sense for the university to require its researchers to only perform copyright transfers via them and never directly, so that they can keep an eye on what the agreements are about, negotiate standard conditions for the publication of their research, and maybe use them as some kind of argument, e.g., when negotiating transformative publishing agreements.
Are there universities that provide such a service, or have such a policy?
The closest thing I can think of is how some researchers, e.g., federal employees in the US, have a different publication copyright process because their work is ineligible to copyright; but this is a somewhat different situation. Another related situation is the University of California requesting permission from their researchers to archive their works, but it does not look like they are involved in the copyright transfer agreement with publishers (except to notify their policy to them).

The topline question is quite different from the body of this. Especially the bolded question in the body. Can you unify them for clarity?

@Buffy, thanks, I have tried to rephrase the topline. Is it better now?

Not really helpful. Compare that question with the bolded one. There may actually be too many questions here. Note, prior to any answers, that copyright law is highly variable around the world. Are you after a US perspective primarily?

I don't think the question really makes any sense. There is absolutely no reason that transferring copyright to the university at any stage of the process would make any difference or be necessary for a university to negotiate on a researchers' behalf.

@Buffy: Sorry, I don't see the difference between the bolded question and topline. The bolded question is about whether there are universities providing a service, or requiring use of the service. The topline is the same question, spelling out what the question is. About the copyright perspective: publisher agreements are the same no matter the country of the paper authors, so I'm interested in a worldwide perspective.

@BryanKrause: Thanks for your feedback, but could you elaborate? The copyright transfer forms of publishers must be signed by the copyright holder to the work, so to me it seems obvious that it makes a difference if the copyright stays with the researcher, or is transferred to the researcher's employer.

Doesn't matter. University could negotiate everything, including terms of copyright transfer and have the researcher approve at that point. Transferring to the university is just an extra unneeded step.

@BryanKrause: I still think there's a difference. To me as a researcher, it is simpler to redirect all copyright inquiries to the university to deal with them on my behalf. So the system I'm asking about could make sense, just in terms of being simpler for the researchers.

So I was thinking that it could be a useful service if a university had an office for this kind of legal matters, providing standard paperwork for their researchers to transfer their copyright to the university, which would then deal directly with the publisher.

I think the approach you describe would be rare. There are certainly institutions providing some phrasing to enforce their copyright/open access policies to the author, and some that have a copyright office that can take a look at a given copyright agreement and OK/veto it. I'm not aware of a place that would directly deal with the publisher. Indeed, given the typical journal system with a single corresponding author it is much simpler to give the author permission to sign it.

It could even make sense for the university to require its researchers to only perform copyright transfers via them and never directly, so that they can keep an eye on what the agreements are about, negotiate standard conditions for the publication of their research, and maybe use them as some kind of argument, e.g., when negotiating transformative publishing agreements.

These goals can be achieved without having the university deal directly with publishers, by instituting a policy and providing guidance.

Are there universities that provide such a service, or have such a policy?
The closest thing I can think of is how some researchers, e.g., federal employees in the US, have a different publication copyright process because their work is ineligible to copyright; but this is a somewhat different situation. Another related situation is the University of California requesting permission from their researchers to archive their works, but it does not look like they are involved in the copyright transfer agreement with publishers (except to notify their policy to them).

As I suggested above, it'd be rare for an institution to be directly involved and to require intermediate copyright transfer to them. However, there's an increasing number of institutions with open access policies, which require a non-exclusive license, and then copyright agreements with publishers to respect said license. (Waivers may be issued for some exceptions.) The policy of University of California appears to be of this type:

The UC open access (OA) policies reserve rights for UC faculty and other employees to make their articles freely available to the public in an open access repository. They do this by automatically granting a non-exclusive copyright license to the University prior to  any later agreements authors may make with publishers. UC retains those rights regardless of what rights authors may subsequently transfer to publishers.The OA policies don’t say where UC authors should publish or require them to pay open access fees to publishers in order to comply.

They direct questions about copyright or the policy to Office of Scholarly Communications, and provide an addendum that can be used to inform publishers about the policy.  Princeton similarly has a Copyright consultation service, and a similar open access policy:

On September 19, 2011, the Faculty approved an “open-access” policy that is intended to make the faculty’s scholarly articles, published in journals and conference proceedings, available to a wider public. Under this policy, faculty members grant to the Trustees of Princeton University a nonexclusive, irrevocable, worldwide license to exercise any and all copyrights in their scholarly articles published in any medium, whether now known or later invented, provided the articles are not sold by the University for a profit, and to authorize others to do the same. This grant applies to all scholarly articles that any person authors or co-authors while appointed as a member of the Faculty, except for any such articles authored or co-authored before the adoption of this policy or subject to a conflicting agreement formed before the adoption of this policy.
To avoid a conflicting transfer of copyright to the publisher and to protect yourself from breach of contract, you can attach an author addendum to your agreement with a publisher. The addendum is specifically designed to deal with the prior license granted to the University.

As a final example, National Laboratories under US Department of Energy have to follow a similar open access policy from DOE. Note that researchers at such institutions are often employees of a federal contractor, not of the federal government directly, so they can create copyrighted works. I know that at least Oak Ridge requires authors to put a "Notice of Copyright" on each manuscript sent to a journal to  inform them about the policy, and that they have a copyright office that will OK/veto signing a given copyright agreement with a journal.

Thanks for these pointers to OA policies, but I disagree about your answer for the part: "These goals can be achieved without having the university deal directly with publishers, by instituting a policy and providing guidance.". Even with all the guidance if the world, if I personally sign a copyright transfer agreement, I am personally liable for what's in there. I would far better prefer to have such a standardized agreement with my university, which I trust, as part of my job duties; and leave to the university the responsibility of the agreements that they sign with publishers.

@a3nm Oh, but "these goals" are from the university's perspective, not the individual researcher's, and specifically refer to the goals mentioned in the immediately preceding quote. Maybe I misunderstood your intent, but that quoted sentence seems unrelated to individual liability.

Ah sorry, I now see how you had structured the answer, so yes my comment was misguided. Thanks.

By the way, your list of universities with a nonexclusive licensing requirement from their researchers could include MIT: https://libraries.mit.edu/scholarly/mit-open-access/open-access-policy/

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
What to do when a professor does not provide an explanation for grades and does not respond to emails?
I am currently a fourth-year undergraduate at a prestigious university (top 10) and am finding myself in a difficult situation with a professor and do not know how to proceed.
For context, I was unable to complete two of a professor's courses because of health issues related to my documented disability. On both occasions, the professor allowed me to submit my assignments at a later date. I took these courses in Spring 2022 and Winter 2023 and received grades of a B+ and A-, respectively.
However, the professor submitted these grades only this month without providing any feedback. Moreover, he took a year to grade my performance in one of his courses.
I found the B+ grade anomalous since I dedicated a whole summer writing the papers for the course, and received a third of a letter grade lower than I did for his most recent one. In my opinion and the opinion of others (peers, family, etc.), those papers were some of the best I have ever produced, and I intended to use one of them as a writing sample for future job prospects. Lastly, I have never received a grade lower than A- in my entire college career, and I plan to apply to law schools.
I sent a grade appeal letter to the professor asking him to review the papers to determine whether they merit a few additional points or, at the least, provide feedback so I can understand some of the papers' serious flaws.
He has not responded to my appeal letter after a week and a half. I sent him a follow-up email with the same result.
At this point, I do not know how to proceed and would appreciate some advice.
P.S.: I cannot meet with my professor in person because I am currently at home since I have completed all the courses necessary to graduate. I also acknowledge that a B+ is an excellent grade, but please understand that grade appeals are a part of the learning process.

"grade appeals are a part of the learning process" -- that's a new one.

It seems like you are imagining that there is a meaningful, objective difference between work that merits an A- and work that merits a B+. In reality, there isn't. I do agree that you are owed at least some response from professor. On the other hand, taking a while to get back to you sounds par for the course to me if he's a busy professor. I recommend patience. Note also that your classmates presumably did not have the opportunity to spend several months writing their assignments, so it's a bit strange when you use this to argue that you might deserve a better grade.

To add to @AdamPřenosil comment, I frequently hear of professors taking a month to respond to things. My own perspective to add, that isn't full enough for an answer, is that there is a chance that since you had months to prepare this, the professor may have gone more strict on some aspects of grading. Mistakes like spelling, grammar, or ambiguous language may have been graded by the book for a paper having such a long preparation time. How long is the standard time given for that paper? How much longer were you given?

You know that thing you do as a student, in which you have a lot of assignments to do and exams to study for, and triage which ones to do first? You get the easy stuff out of the way, the stuff with short deadlines, etc., then slowly go down the list until you get to the really hard stuff that you don't even know how to get started on? Well, professors are also people, and they do the same thing. Your situation is a sticky one from the perspective of the professor: mandated extensions because of documented disabilities involve the university disabilities office and a bunch of ambiguous regulations (lots of use of the word "reasonable", which could mean anything), grading essays (grammar issues aside, a subjective task), and lack of clear deadlines. Once the semester is over, your professor is very likely to be trying to catch up with all of the stuff they could not get done during the semester. So they might want to get to your email, it's just that the email is going to the bottom of the pile.
Professors have broad discretion on how to assign grades, and nobody of authority is going to read your written submissions and argue with a professor over a B+ vs. an A-. One thing would be a multiple-choice exam with clear answers where the correct answer was marked wrong. Another thing are essays. The fact that your friend and family think it's good work says nothing about the actual quality of the work. The fact that they say it's "some of the best I have ever produced" is just an annoying, meaningless statement. You and your family don't get to assign a grade, the professor does. Not to say that grades are not assigned on your personal improvement.
Another thing most students don't realize is that it takes a lot of time to provide detailed feedback, and that sometimes it feels that we are spending more time on feedback than the student spent writing the thing in the first place. Moreover, giving feedback is good practice, but is not required. If I suspect that the student is the litigious kind, I just don't give feedback to the student but keep notes about the reason for the grade on my files, in the unlikely case I have to explain the grade later, which never happens anyway (we are talking about end of semester projects here, I always give feedback on midterm projects, to help the student improve on following assignments.)
None of this is to say that we get to assign grades in a capricious way, or that we don't care about student learning. Many (most?) of us took teaching jobs because we love teaching, seeing our students grow, and we love talking about the details of our academic disciplines. We know how important grades are to our students, and it's one of the most difficult parts of the job, that of judging other's work and knowing that whatever we do will affect their future.

Thank you for your response! This gave me some perspective. Sometimes it's difficult for students, such as myself, to understand what it's like on the professor's end. I'll definitely be more patient.


text:
Contradictory references from my two PhD supervisors
I got interviewed for a research position in statistical epidemiology in a London uni last month. It went well and I got the conditional offer at the end of the interview. I got in touch with my PhD supervisor and secondary advisor. Both of them said they were more than happy to provide references and congratulated me on my new job.
I started my new job today. When chatting with my boss, he mentioned that my supervisor wrote a glowing letter for me. However, my secondary advisor was critical of me not meeting the deadlines and lack of diligence. This temporarily happened during my second year when I got Covid complications and had to take a 3-month leave in the end. But my medical circumstance wasn’t mentioned in his letter. My new boss sort of joked about it and asked if my secondary advisor and I had some personality clashes. However, I cannot remember any clash between us. I didn’t see him as frequently as I met my main supervisor. He were polite to me all the time. My new boss then went on saying it was a bit funny that these two references contradicted each other in this way. One saying I took initiatives and met the deadlines and the other saying I didn’t. Fortunately, my main supervisor was a much more prestigious professor and has known me much longer. So they believed her words.
I was reflecting on my previous behaviour and research and wondering what I have done (except having Covid complications and more or less unable to work for 3 months) to make my secondary supervisor critical of me. I was a member of UCU and went on strike a couple of times during my PhD years over pay and working conditions for teaching and research assistants. My secondary advisor did ask me about this and told me he wasn’t in the union. Could it be a possible reason? In the meantime I wonder if it is normal that your current boss leaks your reference details to you.

Yes, the second advisor seems to think you are unreliable because you are politically involved.
It is a behavior much more frequent than expected. Unfortunately.

I've learned that references had said something not to someone's liking, but not as detailed.

@EarlGrey while possible, that seems to be a leap of logic. Why encourage such wild hypothesising instead of checking with the primary source if the answer is important to you?

@FerventHippo A leap of logic? OP tells us that 2nd advisor explicitly asked about going on strike "did ask me about this and told me he wasn’t in the union.". What else do you need?

@EarlGrey I agree with OP that it is possible but I think it is hyperbolic to assume, as you do in your comment, that the political involvement is the sole/main cause of the comments of the second advisor.

@EarlGrey It is a leap of logic. OP has had a multi-year relationship with this secondary supervisor, and has provided us with only two pieces of information (COVID complications and UCU membership) that might explain the supervisor's opinion. How many other conversations/interactions did they have over the years they have known each other that might explain it? We can't read the supervisors mind or know their decision making, and it's a huge leap to focus on union membership over other potential factors. Perhaps the second supervisor genuinely believes that OP is sub-par?

@academiaTA Put yourself in the mind of the 2nd advisor. Would you say you are happy with giving a reference to the PhD student and then would you go on writing such a bad reference ("lack of diligence" is especially offensive)? Only an idiot would do that. And since 2nd referee is an idiot, they would think that everyone else is an idiot, especially this PhD student involved in politics.
If you do not put yourself in the mind of the 2nd advisor you will not understand them,  if you think mine is a leap of logic, how do you explain their behavior?

@EarlGrey Hypothetical: Adam ate expired meat yesterday and died today. It would be a leap of logic to say that the expired meat caused his death because many other things could have caused his death. Perhaps Adam died in an unrelated car accident. One does not need to provide an alternative explanation to assert that your explanation is a leap of logic. The second advisor being anti-union is a nice theory, but asserting it is anything more than a theory is foolish.

@SamSpade Condolences to Adams' friends.

Also: if you every have any "hiccups" even if uncontrolled/medical-related/etc. talk to you letter writers frankly about it and ask how it affects their perception of you. Some might not like honesty and frankness though, so step into that discussion carefully. Even very smart people can be blinded by their own biases and not introspective about their own psychology. Your 2nd reference seems to be on that category. Try to assess this behavior in potential letter writers moving forward.

Who knows why your secondary supervisor was so critical. Presumably, from their perspective, what they wrote was true. It isn't uncommon for people in those positions to be nonconfrontational about references/letters of recommendation, even if they don't think they can write a good one. Maybe you overestimated their enthusiasm and they felt obligated to write something. Also, in my experience, many people are not great letter writers. Often what is perceived as a "balanced" or "unbiased" assessment is read as very critical. There can definitely be a "secret language" to recommendations and if someone isn't careful a "good" (but not "great") recommendation can come off as lukewarm or even negative.
In any case, I would bet that your new boss was trying to tactfully say "don't use this person as a reference in the future". They may also have been giving you the opportunity to explain, but since you were already hired, I think it was more a courtesy heads-up. I wouldn't think about it too much since it seems like that letter was not reflective of your work and personality (based on the glowing review from your direct supervisor).

This is exactly what I would have written. Some people spend their whole lives trying to parse tea leaves (=the second hand knowledge you have about parts of a letter you've never seen, including opinions you have no knowledge of). Don't be that person. Don't spend energy on trying to figure out what it might all have meant -- you got the job, that's all that matters. Move on and just don't use that person as a letter writer again.

Also important to keep cultural differences in mind. What is a glowing letter of recommendation by German standards could be perceived as lukewarm in the US, and a glowing letter from the US could be taken as weirdly overenthusiastic in Germany.

In economics, many departments have a Placement Director: someone in charge of knowing where PhD candidates get a job, among other duties. One of their duties is to collect reference letters from all writers for each candidate before they're sent out to academic employers. If the director detected glaring discrepancies (such as in OP's case), the director would privately inform letter writers and warmly encourage (but not force) each of them to agree on the bottom line message. I don't know if this is standard across fields or universities, but I feel like it should be.

You cannot know why your secondary supervisor was critical, and quite frankly, it is not useful to speculate.
However, the fact that your new boss shared this with you is very beneficial as it means you can avoid using the secondary supervisor as a reference ever again. It's clear regardless of what they wrote or why, it hasn't been received positively.
Focus instead on maintaining a collegial relationship with your primary supervisor so that they will feel comfortable providing another glowing reference in future (should you ever need one again).

Exactly. This is the actionable point.

This is a great way to go, but it is not an answer to OP question. (Could it be a possible reason?)

Without asking your second supervisor, you will never know why they wrote you a less than glowing review.  Without asking your new boss, you will never know why they chose to share this information with you.
But if I were in your position, I would infer that your new boss has done you the kindness of quietly letting you know which former supervisor you can count on for good reviews and which you can't.  Even if that wasn't the intent, that is definitely they effect.
I would also infer that your suddenly asking your second supervisor what you did to cause this would alert them to the fact that your new boss has had this conversation with you.  And to be absolutely clear on this:  This is one reason not to ask your old supervisor.  It's your decision, of course, but I would nod solemnly to your new boss, thank them for the information, keep it always in mind, and move on.

In the meantime I wonder if it is normal that your current boss leaks
your reference details to you.

I don't know if this is "normal", but this does not look ethical. I would think a person providing a reference expects their reference to be treated as confidential.

I was a member of UCU and went on strike a couple of times during my
PhD years over pay and working conditions for teaching and research
assistants. My secondary advisor did ask me about this and told me he
wasn’t in the union.

Which is an information you did not ask him. As you wrote in the answer, he was a polite person. So instead of telling you are an unreliable idiot for taking part in political activities, he simply told you that second part ("I am not an unreliable idiot and therefore I am not in any union").
He then went on expressing his deep displeasure in a "polite" way in the reference letter.
Please note that I do not share the view of the reference letter, quite on the contrary, I have been judged being an unreliable idiot for my political involvement during my career (sometimes in a subtle way like OP has been, sometimes with much less hypocrisy).
The human mind is a big mistery, always capable of surprising you in the worst possible sense.

this is certainly a take lol

I have a feeling that the downvoters misread this answer. It doesn't say OP was an unreliable idiot; but it says the author of the poor reference may felt so. Which seems plausible. (I don't think it's productive to speculate though.)

@Neinstein thanks. As I said, the human mind is a mistery. I will add a disclaimer.

@overfullhbox would you mind expanding a bit?


text:
(Computer science/Machine Learning) Is it better to take lots of math classes or AI/ML courses the first year of a PhD?
I just finished up my undergrad and am starting a PhD in comp vision/machine learning this fall. I don't have as much math maturity as I'd like.
Do you recommend taking math classes early on or classes such as computer vision/nlp/robotics early on to get a better idea for my research focus?

Can you contact the instructors for the CS classes you want to take? If so,  you could ask about math classes that will actually help you in the CS classes.

Based on vague phrases such as "[not] as much math maturity as I'd like", you may get a spectrum of advice on this site. You should ask people who know you and your background and an adviser in the PhD program.
Presumably, if your background (in math or other subject matter) is lacking, your new adviser will have noticed and will have recommendations how to remedy that.
Issues to consider:
(1) There are probably some CS and ML courses you will need
to take at the beginning in order to be on track to finish your degree during the time the department is prepared to support you. My guess is that these
will not have heavy math requirements.
(2) You will not know everything you need to know even when you finish your PhD, much less at the start.
Learning much of what you need to know is a lifelong adventure.
(3) Your primary objective should be to find an interesting and do-able
thesis topic as soon as possible, to finish a high quality thesis on
schedule, and to get your degree.
(4) A thesis requires original research. If you know exactly what you're
doing, how long it will take, or how much support you will need, then
the project is not research. So you need to anticipate uncertainty and
delay. Accordingly, you should not build any avoidable delays into your program.
(5) All other things being equal (which they never are), you might
consider looking for a thesis adviser who is in the middle of his or her
career, and heavily engaged in pathrbeadking work. Assistant professors may be so frantic trying to do their own
research to get tenure that they have little time to worry about yours. Some senior
professors are not entirely up to date, and may suggest topics that would
have been more appropriate five or ten years ago. A really promising
adviser may have great advice what courses to take early in the PhD program
(6) Most people who get into PhD programs are from the top of their
undergraduate classes. They cannot all be at the top of their PhD class.
There may even be some areas in which you are near the bottom of your
PhD class and you can hope for some in which you are near the top. You
may have as much to learn from some of your classmates as from some
of your professors.
(7) Soon there may be other Answers disagreeing with everything I have
said. Maybe they will be right. But these are some issues worth considering.


text:
How to approach a researcher regarding his latest publication?
There is a group that I've been interested in for a while because we share some of the research interests and because of the very ingenious approach used by its PI. Lately, they published a paper in exactly the same field I work in (but with different models objects).
I feel really eager to react, and I have some considerations about their results, parallels with our work, ideas for future research etc. However, I'm not actively applying for a post-doc, nor do I have any specific (that is, supported by funding) propositions for collaboration. However, I would like to get the conversation started, ideally leading to some kind of common project. It's not a typical cold-call, since

the paper in question cites my group's work,
I've met the PI at a conference and had a brief talk, and
I studied alongside two of his postdocs at a practical course.

We are separated by the ocean, so the communication will have to be via e-mails of some such.
So, how should I approach? E-mail, commenting on ResearchGate, writing to those postdocs first (even though they weren't involved in this particular peace of research)? Specifically, how can I formulate the concluding, "so what" part of the letter?

I think email is always the right way to start a scientific conversation if you have something to say.

I think you are greatly over thinking this exchange. Conversations don't start unless someone speaks, so a simple, "I have read your most recent research/paper/chapter with interest and..." would do for a simple opener. I would go with a direct email as with a good email signature on the bottom of the mail, they will then have all your contact details should they want to get back to you.
You say have some past contact with this person - so also mention that in the email to try to jog their memory of you. If as you say you met at a conference, they may have met many people in a short time, so try to be specific. I would go direct to them and not the other post-docs. The PI is the person you want to work with presumably, and they are simply another human being - not some ethereal creature that cannot be spoken to by mere mortals!
I would not immediately hand out all your best ideas in the email, but you should allude to the fact that you have some interesting findings/alternative considerations etc. that could be the start of some future work that could build upon their recent successes. By doing this, you are encouraging them to respond to find out what you are thinking, and you are indicating that you are interested in completing some future work with them.
Either way, I suggest that the only way forward is to just start the conversation! They will not know of your interests in future work and collaboration if you don't let them know.
Sending an email is direct, but not exactly uncommon nowadays so is considered an acceptable form of cold or in your case, 'lukewarm' calling.
Best of luck.

I have some considerations about their results, parallels with our work, ideas for future research etc.

So use this as a starter. Write/ask about their paper and get a discussion going. In my experience this will very often automatically lead to a collaboration of some kind, like a follow up paper or a whole joint project.
As an alternative I would recommend that you talk to your supervisor, what he thinks about the group and if he would think starting a collaboration would be worth a try. Maybe he will then start to initialise the communication.


text:
What is the exact meaning of an "Abstract Submission Deadline"?
I don't know exactly the meaning of "Abstract Submission Deadline". Is this time only for an abstract, or must I send my whole paper at that time?

Where is this deadline stated?  It certainly sounds like a deadline for submitting an abstract, not a whole paper.  However, some CS conferences have "extended abstracts" which might be the length of a short paper.  I don't think there's any way to say more without knowing the context (preferably which conference you are talking about, but at least the general field).

thank you so much for your answer and help. actually i see that in many conferences such as this site :   http://cpmt.ieee.org/conferences.html     that has a tab with " Abstract Submission Date ".

Please state the field you are in. There are some fields where there is no "whole paper" to follow an abstract submission for a conference.

It is only for an abstract. Usually, there is another one for the whole paper, clearly said.

thank you so much for your help. do you know about those sites that only hint the abstract submission date but not the submission date for whole paper? maybe after i submitted my paper they say me about the exact day of deadline?

There are no particular sites. It depends on each and every conference and the comitee behind it.


text:
Masters Degree vs Masters Certificate / Diploma in Canada
I've seen prominent Canadian Universities (York and University of Toronto, for example) offer a Masters Certificate and Masters Diploma respectively in the subject of financial engineering. How do these differ from a masters degree (in the scope of Canada)?

Does nobody know?

I hope this is helpful this late.

Master's Certificates and Diplomas are typically offered from programs that aren't accredited yet. This does not mean that the institution isnt accredited, just not that particular degree. They also typically take less time than a Master's Degree.

So the word masters doesn't really mean much in the context?

No, Masters just simply suggests it is work done at a graduate level, but not an actual degree.


text:
Is it OK to submit a poster version of an already accepted full paper to the same conference?
My advisor has suggested that I should send a poster version of an already accepted full paper to the same conference.  He suggests that I should do this because he thinks this will trigger more discussions about this work and make it known by more people. The intention is good, but I have a concern since it is a poster version of the same paper in the same conference. I feel weird.
Can anybody give me more suggestions? Should I do this?

From the conferences that I have attended, it is very common to do this.

Some conferences explicitly encourage (or even require) poster presentation of papers.  In this case, there is typically an option to simply request that your existing paper also be given a poster slot.  Thus, it may in fact be quite reasonable to seek to present in both ways, if the conference supports this.
It would not, however, be appropriate to submit a separate poster paper that pretends to be different than the accepted paper.  That would be self-plagiarism, and the conference organizers might look very badly upon you for doing that.
I would thus recommend getting in touch with the poster chair and asking if they allow accepted full papers to have an accompanying poster as well.  If so, that's great, and you probably don't need to submit anything more than a formality at most.  If not, then accept that there will be no poster and don't submit anything!

I just wanted to add that "some conferences" is actually "most conferences" in fields like chemistry and biology.

@VonBeche Not in the parts of biology that I deal with, where there's no such thing as a full conference paper.

I missed that it was based on a conference paper, I just assumed it was a paper published somewhere else. To be clear: most of the posters I see are based on publications (or publications-to-be), and conference papers are not common.

The answer to this hinges on what is meant by "the same". If the gist of the poster is the same as that of the full conference paper, this would be some kind of double submission, which is usually not acceptable.
Posters can, however, be, and at least in my CS subfield, routinely are, complementing the paper by focusing on aspects of the same research endeavour that are more suited for a poster, such as:

a test prototype, which is only a side-note in the main paper, can be in the focus of the poster
the generic methodology used for an evaluation; while the paper might be describing the concrete case in order to focus on the problem, the proposed solution, and the results, the poster can be used to document details about the evaluation of the solution and instruct others how to use the same method for other, similar problems (usually too far out of scope to fit in the main paper, and too "thin" to warrant a regular paper of its own)
possible future work building upon your paper, in order to incite a discussion during the poster session, gather new ideas, and taking advantage of the circumstance that poster sessions often explicitly invite work in progress

In any case, you should reference the poster from the paper and vice-versa, both in the papers and during the conference, to avoid allegations of self-plagiarism, and even more importantly, because you want to make sure people who are interested in your research are aware of both published facets thereof.
If you have an opportunity to inform the conference chairs about the way in which your submissions are linked, it cannot hurt to do so, but this is not always possible or even customary in some fields.

Would the downvoter mind to explain what is wrong with this answer, please?


text:
Should I cite a statement as coming from in journal article or from the related PhD thesis?
I frequently come across PhD dissertations that have spawned multiple journal papers, either while the author was working towards their Ph.D. or after completion. My field is not one with "stapler" dissertations that merely collate a number of papers, so there are often differences between the details of the paper and those of the dissertation.
However, often there are claims/statements/arguments that are present in both sources, so which should I prefer to reference? Should I cite the earlier reference? The later one? Or are there other issues I should consider?

Personally, I tend to prefer to cite the most recent work, as it is likely to be the most updated and correct.  There is also a good argument to be made for citing the peer-reviewed version (as long as it isn't too much older).
In general, however, if the two sources are very similar it doesn't matter much which one you cite. There is also no particular need to cite more than one, and I tend to feel it's better to cite only one when the material is basically the same, so that it doesn't look like you're claiming more support than actually exists.

I wouldn't assume that the thesis is correct if it's been updated from the paper - the approach may have been extended in a way which isn't quite as applicable as it seems.

@ChrisH You also shouldn't assume the published paper is correct, just because it's been peer-reviewed.  You should evaluate either in much the same fashion.

I don't. But it's passed through another level of scrutiny (assuming the supervisor did their job properly in both cases). This is particularly helpful when the work is at the edge of your skill set and you have to take some elements a bit more on trust than you'd like. Coauthors' input is particularly good at catching the crucial typos that change the meaning,and these are lacking in theses

There are a few reasons to cite the published paper (assuming you're writing a paper and not a thesis yourself):

Citing peer-reviewed work may carry more weight (especilly true if it's a masters thesis.
The citation trail is maintained (most journals online now link the citations making them clickable, this doesn't work so well for theses)
Thesis availability online is patchy - if you're citing a thesis from someone you know, that thesis may not yet be online meaning your citation can't include a link.
Theses don't generally have a DOI (mine can be downloaded from a  national online database but they don't appear to assign DOIs themselves).

The main reason I can see to cite a thesis is that often more detail is given on the actual implementation.  So you may actually want to cite both in some cases.


text:
Copyright regulations for and sharing implementations of previously published computer code
For my research I programmed several optimization algorithms as close as possible to their original implementation/explanation when they were published. The original codes were some times described listing the required mathematical opperations or some times with examples in different programming languages (Fortran, C, pascal, or even pseudo code). I was thinking about sharing the MATLAB implementations of those programs, because they are not available yet, and I think it could be useful for a lot of people.
Of course I would refer in each program to the original papers, or code implementation. But could I have any legal problems for sharing such code because it somehow violates copyright regulations?
If the original code already specified some sort of licensing terms, I can read there what the rules are. But the source of most of these codes were printed in books or papers, where no licensing terms were mentioned except for copyright.
An example:
A Simple Genetic Algorithm - SGA - vl.O
(c) David Edward Goldberg 1986
All Rights Reserved

What does that mean?
Do I need to ask permission of the author? The journal or book publisher?
Or can I share my port/implementation how I like?

Related: Code in journal papers

No conclusive answers so far, is this question more suitable for stack exchange? I asked it here because in my opinion it is more about using text from scientific literature (books, and papers) then about porting code that was already licensed in a particular way.

I suspect it's an issue that everyone silently ignores, because the intent of the authors was clearly for others to use their code. You could also try programmers, they have a bunch of questions on licensing.

Related se.se question What does it mean for a software to be copyrighted, but the source is also offered? specifically discusses "All Rights Reserved."

When you create code based on an existing implementation, this is referred to as porting, and the code is considered a derivative work covered by the "derivative works" clause in the software license of the original.  For the code written in an executable language, that is generally the copyright you need worry about, not the copyright of the publication (which is also "borrowing" the code from its original source).  If the code has not been published elsewhere, such that there is no stated code license, then it's probably a short and algorithmic enough segment to think about it like pseudocode.
Pseudocode is a more iffy subject, where people disagree about whether it is copyrightable or not, since mathematical equations and recipes cannot generally be copyrighted but software can be.  Personally, I would take the position that pseudocode used to express an algorithm in a scientific paper should be considered non-copyrighted, since the communication is explicitly intended to enable reproduction of the scientific results.

Thanks for the commend the term porting was indeed appropriate to find more information on this. My problem is that the most of the original code's do not mention any modern licence terms. They were included in book chapters, papers, or source files with commends referring to the paper.  Some times the method is also just explained in successive mathematical operations, without even pseudo code. I will try to clarify that in my question.


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I've been offered a major fellowship in my field, but I've been seriously considering mastering out and don't know what to do
I'm a Ph. D. student just entering my third year. Last winter, I submitted a proposal for a major fellowship/grant in my field, and last Friday my advisor told me that I had been offered funding. However, for quite a long while, I've been debating with myself about mastering out, and haven't yet brought it up with my advisor.
I have until this Thursday (and preferably sooner) to accept or decline the funding.
The grant is extremely competitive - only about 10% of proposals are accepted. It would be three years worth of funding guaranteed, and (if things go according to plan), I would get three papers out of it - enough for most or all of my dissertation. My advisor has never even heard of someone turning it down. However, there are several concerns making it a very difficult decision.
First, I based the proposal in part on experience I planned to gain from the project I was working on at the time - what was originally intended to be my candidacy project. (Candidacy at my school is basically "Write a paper, submit it to a journal, and give a talk on your research to your committee.") However, I was struggling with the project, priorities changed, and that project was moved to the back burner while a different one, intended to get me to a paper and candidacy much faster, became my primary focus. The feedback on the proposal is only available to the PI currently, so my advisor can see it but I can't, and according to her the proposal was accepted in part because of this experience that I fully intended to have, but now still don't. (I was completely transparent that the work was still very much in progress, but still...) So I'd essentially have to start off delayed and make up for lost time.
Second, my advisor has concerns about my productivity and ability to stay on schedule, and If I'm being honest, her concerns are entirely justified. Ideally, I would already have scheduled or even finished my candidacy exam by now. However, due to schedule slip on my part, that hasn't happened yet. My advisor wants a first draft of my paper by mid-August, a deadline I'm worried I can't make, and has set a hard deadline for the exam of December this year. (To further complicate things, my department's grad student handbook says the candidacy exam can happen any time in the first three years, but my advisor claims that the handbook is incorrect - the deadline is two and a half years unless extenuating circumstances justify an extension.)
I've really been struggling to make progress on my work - I have to struggle against some kind of mental barrier to even start working, have a hard time staying focused, and when I do manage to get work done, I tunnel-vision on certain tasks while neglecting others. I've been going to the university counseling center, but it hasn't helped much, and if anything I've been getting worse recently. So if I don't find a way to improve, there's a real risk that I miss the candidacy deadline, or make that deadline but run out of time for the Ph. D. If that happens, the grant money would basically end up wasted when it could have gone to someone else.
Furthermore, I honestly don't even really like my proposal in the first place. It was a rewrite and improvement of a proposal I submitted elsewhere, and while it's a big improvement over that version, I really only wrote and submitted it because I couldn't think of a better idea to propose instead, and my advisor wanted me to submit something. A part of me was honestly hoping for it to be rejected.
In large part because of these issues, I've been thinking for a while about mastering out. (I'm not sure how long, really, but at least 6 months). However, I don't have any sort of plan B (I often feel like I never even had a plan A) and don't know if there are any careers in my field that aren't either research or teaching. I also worry I won't really be able to transfer my skills to another field - I'm not a good programmer, just a barely adequate one, and my field is pretty much pure research. Since the work on my candidacy project would probably become a large part of my master's degree anyway, I've been trying to focus on getting the work done while I learn enough to make a decision - but declining the fellowship while staying in the Ph. D. program would be pure insanity.
In short, I now have to make a decision I haven't felt comfortable even discussing with my advisor by this Thursday. I have no idea what to do; please give me advice.

What prevents you from leaving later if you accept the fellowship and then decide you don't want to continue?

FWIW, you're making EXACTLY the same decision that you were before being awarded the support.  Your timetable for making this decision has shrank a bit, unless you're willing to accept the position knowing you may resign later.

What worries me is that, based on what you wrote, you don't seem particularly interested in the proposed project anymore, and you are lacking some technical skills/knowledge to successfully carry it out. You seem to be struggling a lot with your current workload (and I'm not blaming you, graduate school is draining and though. One needs to have the right mindset, enough motivation and a lot of endurance to go through it) and, based on what you describe about having mental barriers and problems focusing, probably you've reached a "burnout state". Accepting being paid for working in a project you don't slightly like anymore and for which you are not prepared enough is, in my opinion, a bad idea. My honest advice would be not pursuing a major project you don't like, taking it just because you have the chance to do so. You will be wasting your time and money (as well as other people's time and money). If you are seriously thinking about accepting the grant, write down the positive aspects it would have in your life; maybe you are indeed interested in the topic, just tired because of all the work you've had? Do you think you will have time enough to learn what you were supposed to learn during this time?
I would also recommend you to try to calm down (even if you don't have enough time to think about the situation with the deepness and thoughtfulness it deserves), and to talk about it with your advisor. She has way more experience than you in the field, more details about your situation and she can give you honest feedback about the matter. Anyway, you need to talk with her about your plans of leaving your PhD program with a master's degree. Indeed, I'm surprised you haven't talked about this plan with her sooner. She can give you important advice not only for finishing your degree, but also for figuring out possible jobs for you out there.
Lastly, I would like to address this:

I really only wrote and submitted it because I couldn't think of a better idea to propose instead, and my advisor wanted me to submit something. A part of me was honestly hoping for it to be rejected.

Never apply for important things (like major fellowships or job posts) without having a clear idea on why are you doing it or why you want it. Be kind to yourself and don't put yourself in a situation like this anymore. I know it's easier said than done, and that we indeed make a lot of important choices based on what others want or expect from us, but remember that, if you get the opportunity you are asking for, you are the one that needs to do the hard job. And it is something you can do only if you have the motivation and inner convictions to do so.
Best of luck.

It sounds like you've been really brave to express all of these thoughts here, and you should be proud of yourself for that. I'll slip into therapist mode for a while, if that's okay; what I am about to say may be right on target or completely off. Only you can say.
It sounds like you have a lot of anxiety that, to you, is tied to external decisions you have to make about your future (PhDing on vs mastering out; accepting vs declining the fellowship). However, these anxieties often have their roots in internal uncertainty about who we are and what our story is.
Narrative psychology describes people as always reaching for "the story of my life" to imbue their decisions, big and small, with meaning, and hence to decide which way to go. But learning what life story we are comfortable with takes conscious time and effort that we often neglect, partly because that work draws out negative feelings that we want to avoid (and partly because capitalism wants us busy doing economic activity without being sure just why we're doing it).
When we come to a major decision without deeply grasping our personal story, therefore, we find ourselves deeply anxious and unsure which choice feels more coherent with who we think we are, and then anxiety overwhelms is.
(Stop here. Take a breath. If what I'm writing makes no sense to you, that's perfectly okay; go take a walk or do something you enjoy doing and don't waste any more time reading this stuff. :) )

You can't rewire your internal story in a week, but please reflect deeply on this: you will still be who you are whether you stay in the PhD or master out, and whether you take the grant or not.
Academia, in particular, is extremely toxic about wrapping our identity around our job title, our papers and our grants. We feel like we will be happy if only that paper gets accepted or that grant gets funded. We don't acknowledge narratives like yours, where you applied for a major grant feeling full well that you weren't quite up to it (although you might be; anxiety has a way of devaluing our capabilities).
And yet we are more than our papers or grants. We are also our hobbies, our families, our culture, our neighbourhood, our holidays, our fundamental beliefs, our bodies, our souls. Against all that, decisions about grants or career should feel -- not small, but not seismic; decisions we can make trying to reach a future that best expresses who we are, while making peace with any consequences that are beyond our control or prediction.
So, you absolutely need to talk to your supervisor about this. She will have concrete and objective knowledge about you and your competencies that you don't. But you need to talk to yourself about what you're going through. These difficulties you're facing aren't going to go away if you take up the grant, but they also aren't going to go away if you master out. You owe yourself every chance to face your problems head on, and you should absolutely find better help than your university counsellor.
But I just have a hunch that, ultimately, you need to learn who you are and accept it. I can't tell you how exactly to do that, but if you know that's what you have to do, then that's a start.
All the best!

It sounds like there are a lot of things that you need to make your mind up about and for many of them you need more information before you can even take a decision one way or another.
First of all, can you take a couple of days of to collect your thoughts?
Do you have trusted friends or family or a trusted advisor you can reach out to even if it is not your PhD advisor? I would recommend expressing your doubts at some point, since they cannot help or advise you if they don't know, but I can also see that you may not want to start there.
As for options after 'mastering out': can you contact the career center at your university/institute or alumni from the lab?
This would be the time to take some of those get to know yourself or career tests to see what comes out. Plenty of books out there that might be helpful too, like what color is my parachute. None of those are compatible with rush decisions, though.
Good luck!

So there are two things I see from this question, the first is are you still interested in doing a PhD, the second is do you have any neuroatypicalities that explain your behaviour.
The first thing is asking yourself if you are still interested in doing the PhD, given what you've described it sound like you may also be suffering burnout (essentially your brain has been run ragged and you need to slow it down). Try taking some time off for the next couple of days, focus on thinking what you want to do long term if there are any alternatives to what you are currently doing (and make sure not to knee jerk reaction and say there are no alternatives). Work out if you are still wanting to do a PhD/get into academia and have just not been taking care of yourself, or if you have realised academia is not where you truly want to be.
The second is to try to work out if you are neuro-atypical in any way. My first thought is that you have ADHD/ADD, lack of focus/periods of hyper focus are standard (I have it as well). If you don't have support it often feels like you are incompetent since you can't finish things (particularly papers or last bits of research). Excluding medication one way of avoiding the hyperfocusing stopping you from realising there are smarter ways to work is to schedule in 30 minutes a day for a walk or a run or some other kind of light workout that makes you lightly sweat, and make sure to treat it as part of your work, otherwise it will be put to the side. For starting focus regularly engaging in heavier exercise and listening to music helps significantly. Exercise that forces you to focus or hurt yourself/others (e.g. martial arts/climbing/parkour) can help you train yourself to focus.


text:
Is a second PhD a good way to change research direction as I approach finishing my PhD?
I am sorry here but I am very anxious about my future. The conditions are as follows:

There is only one year left before I get my PhD in physics major. I need to finish my dissertation in 6 months.
Although I have published some papers that enable me to apply for the degree, I am not a competitive candidate for a post-doctoral position.
I am not very interested in the research direction I was studying, nor was I in the mood to continue the subject.
I am still impassioned by the idea of researching but have no idea of new directions.

I'm now wondering if it would be a good idea to change direction by pursuing a second PhD, since I don't think that I can find a post-doctoral position in the new direction.
Therefore, I hope to get your advice to help me through this difficult time in life. Thanks in advance!

Use a post-doc to change direction. Other answers cover this topic on this site.

See also: (How) can I switch from field X to field Y after getting a PhD?

You do not need to "tell your story". In fact, if the long tale of your story is vital to your question, then it is almost inevitable that your question will be closed as being too dependent on your individual circumstances and hence, insufficiently relevant to any other reader. Edit your question. Chop most of your "story", and try and condense your question to something succinct.

Thank you for your suggestions! It seems that my ability to search literature is also very poor. I didn't find two similar problems before. The problem "Transition from PhD to postdoc with an intent to change field" in 2013, in particular, was exactly what I thought.  The answer to this question " (How) can I switch from field X to field Y after getting a PhD?" is also brutal and realistic.I will try to find a postdoc position. Thank you all agian!

I'm sorry you're facing such difficulties. It's crucial to have open discussions about your feelings with your friends or colleagues and support networks, as they may provide valuable advice or solutions. Taking time to reconsider what draws you to physics and research might help you identify new paths you'd be more passionate about.
Pivoting to related fields could be beneficial. With your physics background, computational roles, data analysis, or machine learning could be suitable. If you're thinking about a second PhD, weigh the benefits and drawbacks carefully. Consider non-academic careers too, as many sectors value the skills gained from a physics PhD.
Lastly, don't neglect your mental well-being. It's perfectly fine to seek support when feeling overwhelmed. Remember, it's your journey and it's okay to change direction if it leads to a more fulfilling path.
Good luck!


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What's the proper name for the section of a research paper introduction where you propose a method? Not to be confused with actual Methods section
I realize there are many ways to structure an introduction. This research paper's introduction has 3 sections: Background and Significance, Relevant Literature, and a third section where I actually propose the method to be explored later in the paper. What is the proper name for that last section of the introduction? Please note, there will be a Methods section next but I still need to introduce an overview of the method in the introduction.

Perhaps "Contributions": at least this term, as a paragraph title, is common in my area for what you seem to be referring to.

Yes, the same in my field too. But also we have papers without an exclusive section title.

Similarly, "[Our] [main/primary/proposed] contributions:".

If you use structured titles and well labeled references there is no room for confusing the reader.
Section 1: Introduction
Blahing a blah...
1.4 Proposed method
Introductory summary of the method you propose.
Section X: Methods
X.1 Method #1
Description of Method #1...
Then you can use references like "...as mentioned in 1.4...", "...because of limitations in Method #1, following conditions must be met, see X.1..."
If the core purpose of the article is the Method proposal, then the Method should be described appropriately in all following sections:

Abstract - Very brief summary of why you have developped it and what it returns. (Motivate the plausible readers to read introduction and conclusions)
Introduction - Not that brief summary of why and what from you have developped it, and briefly how it works. (Assure possible readers they want to read the Conclusions)
Method proposal - Describe in detail how the method works, what are the inputs and what it returns.
Discussion - Dicsuss all the upsids and downsides of the method.
Conclusion - describe briefly how it works and sum up the dicsussion.

Title:
Proposed Method(s):
Results:
Conclusion: