text:
What if you used an older paper and based your model on it, but authors published a newer paper with modifications you neglected?
Is it ok to form a model based on several papers and omit something from newer papers? Of course, not that someone else proved what you're researching, just that authors said that something was important for one segment and you investigated another segment and neglected that. Later, the author published something and considered the thing you neglected. For the scope of research you couldn't include that and you based your argument on research context, scope and author's first publication.
What do you think? Is this a problem? Does it happen that authors omit some information because it doesn't help them? Please share your thoughts with me. Thanks.
Furthermore, is it ok to make changes in your argument after peer reviews even if reviewers didn't notice and didn't consider it a mistake.
Since I'm new in this research field, I have so many questions. I hope you understand.

When did the "newer" papers get published? Before or after you set your research goals? Since you finished your paper? Long enough ago that you should have seen them?

It was published long enough ago. It's just that the step that they added was too much for the scope of reaearch. Can I change my argument after I get reviewers comments, even if they  didn't comment on that. Just to put that I neglected that not because of previous research, bit because of scope and research context?

It depends on the purpose of your research. As G. Box said "all models are wrong, but some are useful"; wikipedia entry. For example, suppose you are modelling a biological phenomenon. Then, you'd use the simplest model that suits the desired complexity and precision (see also Occam's razor and  bias-variance trade-off). If you aim to model every tiny effect, then you'd need a large, all-encompassing model; if you're focusing on the main effects, then a simpler model -- often a subset of the former -- would suffice.
So, the earlier model published may be a useful subset of the authors' later model and might suffice for your research purpose and empirical data. What is a no-no, however, is to cherry-pick data to fit your model and discard counter-evidence without a good explanation. Another possibility is that you are writing a methodology paper, to extend the model itself. If this gives an original and useful extension, then why not use only the earlier models, if they are enough? There could be details:  for example, if the earlier models have shortcomings, you'd need to address these.
(Note: There appears a separate question in the penultimate paragraph of the  original post; this is addressed in @EarlGrey's answer.)

Furthermore, is it ok to make changes in your argument after peer
reviews even if reviewers didn't notice and didn't consider it a
mistake.

No, absolutely not.
Unless you mean change your argument and then submit for peer review again.
In that case the answer would be ... still "No".
It is not okay. It is a waste of time: you are your first peer reviewer, do at least a good job that you and yourself are agreeing with your arguments, before sending it to other reviewers.


text:
Regarding Publication Authorship
I worked with this teammate on a 4-people class group project. We did research, conceived ideas and prototyped the concept together. I just found out that he is publishing this research work with himself as the first author and another guy who was not in our group as the second author. He may write the entire paper, but the implementation of the research and the majority of the published results come from the team effort. He did not even notify us that he planned to publish it. It seemed like he consolidated the research work and did all the writing with the other author behind our back without notifying us. I am wondering what should I do with this situation?
We are all graduate students enrolled in a master's program. Both he and I are applying for the same Ph.D. program this year. He has a few publications before coming to this graduate program. I am totally new to the academic publication and just started collaborating with a professor this summer on a project which could lead to publication. I am not sure whether this situation perceived as "unethical conduct" or "reasonably tolerable" in the academic world, as the research efforts are hard to be quantified. How should I approach this?

The material you submitted for the project will presumably be important in any discussions as to who originated any ideas in the research.

It is very possible that it is unethical, but it would take a bit of analysis to clarify it. Your course professor is probably a good person to adjudicate it. I'd suggest that you take the problem to them, preferably in person.
Using other people's work without attribution is plagiarism.
Go see the prof.

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text:
Creating a StackExchange "Team" for an Academic class to replace the Canvas online discussion board
I am a community college math instructor.  We use the Canvas learning management system for our online courses.  Most of us use the built-in online discussion board in Canvas where students can share questions where I and other students can offer help and have discussions.  The discussion platform works ok but is lacking in so many ways.
I am a long-time user of StackExchange and find it very helpful for helping me find solutions to my questions in many domains.  It's helped me immensely and I hope I have helped others as well.  I find it very useful to have a moderator and rating system that incentivizes correct solutions and professionalism.
It looks like StackExchange offers something called "Teams".  I was thinking about moving my Canvas discussions to StackExchange.  My idea is to create a domain for each class... say "My Differential Equations Class (Spring 2022)".  Only my students would have access.
I would require a certain level of interaction every week for every student to ask questions and post responses to others.  As the moderator, I could control a number of aspects including editing and promoting better discussion.  It's nice that it is built into the service.
I'm not sure if this is a reasonable idea or not.  Has anyone else here tried this in an academic class?  I'm not even sure if "Teams" works like this.  Do you have any feedback you can offer?

Afaik, the default version of Teams does not support MathJax. I don't know if it's possible to buy this option. Otherwise, there's Piazza. I used it for a few years.

https://meta.stackoverflow.com/questions/406571/stack-overflow-for-teams-for-students

One more remark: Technical questions about Teams should be directed to https://meta.stackoverflow.com/ (e.g. you can ask there the availability of MathJax), and you might find of interest the above linked question by @nick012000. Here instead you might find feedback about the usage in class if someone has already tried.

If this belongs anywhere here it is on meta since it about using the site itself.

@Buffy This is not for Meta, absolutely, because it's not about Academia SE, the public platform. Teams is in fact the enterprise product. As I said in the above, the technical questions should be asked on Meta Stack Overflow (not our meta; this is requested by the SE staff), but questions about the overall experience are perfectly fine here (e.g. we have questions about Piazza). And as I interpret this question, it's more about the overall experience.

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text:
Why haven't we hosted research publications as repositories yet?
This just makes so much sense for several reasons:

Let's say I find errors in a very long research publication - A code repository like issue system would allow me to highlight this and notify the owner
Let's say I want to add to a research work incrementally in an effort to make it complete - A code repository like PR mechanism would enable me to publish my work and notify the author without "citing" the said work and having to mention all the details again.
Let's say I want to make updates on continued research and not just stop at one publications - A code repository like version control would allow making several releases based on work that could be published, moreover it allows maintaining a timeline of all releases for better clarity.

Every shortcoming I can think of can possibly addressed by treating research publications as repositories instead of standalone PDF documents.

What are your thoughts on this and has anyone thought of implementing this already?

Shouldn't one of the primary attributes of research be to enable collaboration after publication for the study of a subject?

Why haven't there been the tools to do that yet?

Would the repository only be open to peer-reviewed content?  Or, on the other hand, would it include all the miracle cures for cancer that now flood the web?  Experience with the social media sites shows that unless your comments are tightly curated, they will descend to name-calling and/or virtue-signaling in short order.

@GEdgar I think a tagging system could allow peer-reviewed content to coexist with non-peer reviewed content.  Maybe you want to see the author's latest thinking on a topic.  You can.  Maybe you want to see the author's latest peer-reviewed thinking on a topic.  You can.  Maybe you want to see my crackpot edits to the author's manuscript.  You can (but why would you?).

Because how do magazines that publish research made with goverment's funds make money then?
Sarcasm aside. I get you. Im in IT field, so I know that something like a github or googledocs would be wonderful for research and all, and it is, but there are many significant challenges. Just to name a few:

International cooperation.-  Science is an effort not of one country, and a paper on a published research might take upon the steps taken by a research done in a very different country.
Language.- As if country differences are not enough, a paper can cite another from another language, and even if the trail (like in Google citations) can name it, being able to create a clear research routes for various languages means at the very least the technical challenge of translating or having to correct stuff on various languages.
Authorship.- Not all researchers are considered the author, sometimes there are corporate authors.
Copyright and distribution.- Laws vary greatly from country to country regarding this, even within the same country by states/provinces; so research, even if public, would need some serious changes in regulations to not have troubles (also add the problem with magazines that charge money for access).
Connectivity.- The repository would have to connect to many databases with different characteristics that would mean a myriad of technical considerations
Accessibility of platform.- For this to be implemented for current journals the code of the repository/platform would have to be open at the very least so it can be adopted. That also means creating communities to work on it.
Lack of international standards agreements. There might be some common accepted guidelines for many things, but for many others there arent. I would like you to think how different can a mere scholar system be (I used to think sophomore was some kind of fungus.) Now think about all the differences in editorial guidelines for different journal even in the same field and how it would be addressed to technically reach an agreement that could be coded into a general standard.
Political challenges.

As @Wolfgang Bangerth said, there are some journals that already do that, but we are still ways off to go. Hopefully the world seems to be moving to more open science. I would like to know what doctors in other fields are experiencing too.

There are journals that do that. Here is one: https://joss.readthedocs.io/en/latest/submitting.html
In some sense, arXiv.org is also doing that, allowing to version preprints. It doesn't use a "repository" in the sense of git or subversion, but it allows you to keep track of different versions of a manuscript, and that's really what is key: Any system that allows you what's in a paper at a later time must allow identifying and accessing a particular version of the paper.

Thanks! I've looked through arxiv and it has done a lot of good in terms of no paywall peer reviews and version control but I still feel long term maintainability and collaboration tools are missing. For example, I was reading a great paper on ACM and I have a few questions and things I'd like to point out but there's no way to do that other than mailing the authors.

@RajeshS what’s wrong with mailing the authors?

Well you'd never know if something about it has already been discussed by someone else. I believe reading through the feedback on the publication can be incredibly useful as well. Just imagine, if this discussion was a DM instead of your comment.

Because we are stuck with an antiquated publishing system, which is very difficult to improve since it has been coopted by funders for deciding which researchers to support. Versioning and open collaboration would make it much harder to track authorship and citations, which are the currencies on which careers are built.
Still, the idea is very natural, and resurfaces regularly. See my 2014 blog post https://researchpracticesandtools.blogspot.com/2014/02/the-case-for-emancipating-articles-from.html , and my experiment with hosting a review article on GitHub https://github.com/ribault/CFT-Review . (So far there were only two minor contributions by others.)


text:
What To Do About An Apparently Non-Replicable Paper
I am a beginning researcher in a particular real-world application space of machine learning, with papers published in the application space, but not in machine learning itself.  I have identified a paper that is important to my program of research to replicate, have dedicated myself to its replication for a longer period of time than I wish to admit (even anonymously), and failed.
I am asking this question anonymously, and not identifying the particular application space of the paper (beyond the much larger "machine learning" domain) because the community of the application space is relatively small and I do not wish to identify myself or the authors of the paper I discuss below.
Some salient details:

I'm aware that some papers in machine learning are viciously difficult to replicate, even under the best of conditions.  It is easy to find discussion forum  comments such as "I tried to replicate X, spent months on it, got nowhere," or "I was only ever able to get Y to work by doing thing Z that wasn't in the paper."
Despite that, the machine learning community thrives on Github implementations by original authors, and Github re-implementations by students.  This research group has to my knowledge never published any code from any publication, and while some re-implementations of various papers from this research group exist, this one has none.
It seems, at a minimum, certain key details are absent from the paper such as hyper-parameters, learning rates, and other customary details.  Although in other respects the reported architecture is quite detailed, this does cause me to wonder if the model is unusually sensitive to the hyper-parameters, or if some other small detail has been left out.
A typical piece of advice given when I ask other researchers about this is to e-mail the original authors.  I have done this, as politely as possible (making the explicit assumption that I'm just missing something and asking very specific questions, i.e., about the hyper-parameters directly, so as not to waste their time) several times, and gotten no response at all, even offering to post my own re-implementation on Github, to their credit.  (I've sent enough e-mail that I fear one more will make me look like a stalker.)
Another typical piece of advice is, "Can you fix it and publish the new and improved version?"  Believe me, I have tried, both minor variations on the paper, and updating it with more recent machine learning techniques, with no useful results.  I have nothing publishable for my efforts.

Here are two final factors which complicate the matter even more in my mind (and which I think cause this not to be an exact duplicate of prior questions):

Although the lead author and their research group are well-regarded and well-published, this particular paper is published only on Arxiv  There is no peer review, no conference or journal, and there is an "at your own risk," factor involved.
Despite this, the Arxiv publication is gathering citations from other refereed publications, although it is not obvious to me whether the citing works' authors have been able to (or even necessarily tried to) replicate the results, either.

What can one, and what should one do, when one is Nobody from Nowhere as far as a research community is concerned, but is beginning to suspect that a cited but not peer-reviewed paper cannot be replicated?

Do your own results seem to refute the paper or support it generally if not specifically?

All but the last major stage of the approach works.  There is a technical name for the practical failure it exhibits, which is barely addressed in passing, and not by its technical name.  But the failure could be mine generally; or lack of parameters not presented (but necessary) in the paper.

I would suggest focusing far, far less on this non-peer-reviewed paper.
Publish the results you have. Use methodology that is as sound as you can achieve with the data and tools that you have. Cite previous work that agrees and disagrees with what you find. Contextualize your findings in an understanding informed by an entire body of work, not just individual papers.
The only time it makes good strategic sense to focus on replication of a particular result is if that result is influential and relied upon in practical use. A discerning reader of the literature will approach any single finding with appropriate skepticism.

What can one, and what should one do, when one is Nobody from Nowhere as far as a research community is concerned, but is beginning to suspect that a cited but not peer-reviewed paper cannot be replicated?

You could publish what you've discovered. One criticism you may receive is: The original work isn't published, so your results aren't interesting. You could defend against that, e.g., by explaining the interest others have in the original work (as illustrated by citations).


text:
How should I handle poor English in reviewing an article that claims to be proofread by two native English speakers?
I was asked to review an article written by non-native English speakers. I had never seen this before, but the manuscript includes a link to a certificate from a website called Textcheck that says:

We hereby certify that Textcheck has checked and corrected the English
  in the manuscript named above.
A specialist editor with suitable professional knowledge (M.Sc. or
  Ph.D./M.D.) reviewed and corrected the English. An English language
  specialist subsequently checked the paper again. The first language of
  both editors is English.

Unfortunately within the first few pages I'm already encountering clauses that make it obvious that this was not done to any depth. The issues are so blatant that even a quick glance by a native English speaker would catch them.
Should I point out major grammatical errors such as these in my review? Should I comment to the authors that they essentially got ripped off by this service (in more polite terms, obviously)? Should I comment to the editorial office?
EDIT: I also see that I can email Textcheck about the article. Should I do that? If so, what should I say/ask?

From the Textcheck website (under their "guarantee"): Please note that reviewers' judgment of English is very unreliable. Many reviewers are not native speakers of English, and unfortunately these reviewers often criticize English that is grammatically correct and well written. We hope that our certificate at the end of your document will help to prevent this problem.

@Kimball That takes some serious chutzpah.

You should consider the possibility that the manuscript could have undergone last-minute changes after the TextCheck service had completed its service. They would not have changed the name and there is no digital signature or hash that would allow you to check that the text has not been altered after TextCheck proofread it. I would not blame anyone, just state that the English is really lousy, possibly add these two and two more examples, and have the authors sort it out with TextCheck.

The plus side is that if Textcheck continue to attach this certificate to poor English, eventually it will become widely known that they are nothing but fraudsters.

I heard from an editor that these certificates are common, and totally worthless.  I forget which editor.

@Alexander: If we're exploring the possibility that Textcheck might not be a scam, I'd also seriously consider that maybe they submitted the document, received it back with corrections, and then submitted the original instead of the corrected version, with only the link included...

As an anecdotal side note: a colleague once told me of a review they did of a paper, also written by authors without native fluency in English. They found and pointed out a number of grammatical errors, and offered full, grammatically correct versions for the authors' free use.  A detailing of why the grammar was incorrect, and what the correct grammar rules were, was even included!  When the authors submitted a corrected manuscript, absolutely none of the grammatical revisions were made.  That reviewer lost their taste for offering such grammatical precision as a result.

Maybe you should write at the end of your review something along the lines "We hereby certify that Textcheck has done a poor job"...

Proofreading and correcting someone's language is a hard, tough job. Being a native English speaker isn't enough. You need to be a native speaker with a good grasp of the language, but then it also takes an enormous amount of mental strength. What you see written in black and white has enormous strength; the proofreader has to be stronger. From my own experience, being given a lengthy translation to my native language to proofread, after two or three pages of correction after correction I just couldn't handle it any more.

Refer the authors to this service.

These sites are usually dodgy.  They themselves are non-native speakers.  I had IEEE 'proof readers' changed a perfectly written article, after acceptance, into their rubbish and they had the audacity to change the facts in my paper to suit their 'understanding'.

https://academia.stackexchange.com/questions/147225/should-i-pay-for-a-certificate-showing-the-quality-of-my-manuscript-before-i-sub/147226#147226

You should not email Textcheck about the article. The journal review process should be confidential, and you should not take the liberty to violate it. You should put the quality of the writing in your review. If it's still bad even after review by this company, then those are the breaks. It sounds like it still needs some help.

And explicitly mention in the review that you are a native speaker and that you are aware the authors used the service. I'd go as far as advising the authors not to use that particular service again, since it clearly falls well short of what one would expect in a professional copy-editing service.

@SteveJessop, I'm not talking about the author breaking the blinding to find out who the reviewer is  nor the reviewing breakind double-blinding to find the author (though those are also relevant concerns), I'm talking about the confidentiality associated with the fact that these authors have a paper under review with this journal at all. A reviewer should not take it on their own initiative to break that by letting an external party know. Everyone involved has a responsibility to try to maintain the integrity of the process.

@BillBarth: sure, I'm just noting that publicly posting extracts from a work under review is already a breach of confidentiality, separate from the breach you're advising the questioner not to make. Hopefully that doesn't matter in this case, by itself, since nothing significant about the paper has been given away. But specifically doing so with your name attached risks reviewer anonymity.

@SteveJessop, oh yeah! That's a great point. He might want to edit that to anonymize and paraphrase the style.

@SteveJessop and BillBarth: What do you recommend I do? I tried to keep the article under review as anonymous as possible while still conveying how poor the English is, but I didn't think about how that would make the excerpts easily Googleable...

@CraigW, you could drop the excerpt altogether. It's not necessary to the point of the question.

@SteveJessop you probably want to remove that comment then, since the excerpt is still googleable from the text in your comment

I agree with Bill's advice from the previous post. If you email Textcheck then they will come up with some argument proving that they did a correct job, and moreover it's not you who paid them, so it's better that the person who paid them should contact them if required.
You should just indicate that the English used in the manuscript is sub-standard and can not be accepted in the present format. Though, this does not necessarily mean that you reject the manuscript. If you find that the scientific content is good enough then maybe you should indicate accept with major revision.

"If you find that the scientific content is good enough then may be you should indicate accept with major revision". True, but sometimes it is really hard to judge on the scientific content when you can't hardly understand what it is said...

True!! But if you have been asked to review a paper then for sure if not an expert, you still know enough about the type of work under consideration and hence you would easily be able to evaluate via figures and the confusing text the quality of science. Moreover if the author of this question has done the effort to post this question here, then it already shows the indication that the current manuscript has problems mainly in english only, otherwise it would have been rejected on the first instance only!!!

@ddiez The examples given in the question suggest that the scientific content is understandable, despite the bad English.

Absolutely true Saurabh and David. I was only pointing out that possibility regarding the quoted comment, which can be interpreted more generally than in the context of the OP question.

@ddiez. You have made some grammatical  mistakes in your comments above. e.g., "...what it is said" should be "what it says".

Just express your opinion, try and be objective and don't worry about what does not depend on you.

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text:
PhD student I am working with as an undergrad may pursue something similar to what my senior thesis is on, is this a conflict of interest?
I began researching for my thesis on subject X several months ago, and the thesis program is starting in a few weeks.
I did not tell the grad student at the old uni about this yet - because originally we were working on different things, his idea seemed cool, and naturally, I want my name on as many papers as possible. However, my adviser told me that my research idea may be enough to be considered a significant contribution in the field. A lot of people in research are interested in how X can be applied to different areas right now, but my idea on how to apply it is completely my own and unique.
I feel I should either only work on my thesis at my new uni, or email the grad student at my old one, let him know I am researching X right now, and that if he involves X in his research, that might not look good for me.
How should I go about this? I feel bad because the grad student invested time into teaching me for the last 4 weeks and getting me caught up, but I also want to do what's best for me - which is 100% pursuing my research idea.
The fact that my adviser thinks it is publishable and may make an impact in the field is rare enough in undergrad, while the grad student I am working with is not sure what exactly he's researching yet - and I fear that he will look into using X now, which might cross with my research.

Something confusing: in the earlier part, you say that the other method was/is X, and yours is Y. But then later you seem to indicate that your method is also X. Can you clarify?

Unless you made a mistake in writing, you decided to pursue X, which the graduate student was working on, after this presentation and a whole discussion on X, and the interest it receives? But you came up with a different way to apply X? Is that it?

Surely though, you developed this idea through exchanges with this graduate student. I think the high way to take is to collaborate on a paper, with you as the first author if it is indeed a novel way of applying X.

I don't think I explained well enough and confused myself generalizing. So I have worked with 2 grad students at my old uni. One asked me to do something for him, while reading papers for that, this inspired a whole new idea. I actually did ask him his opinion but he switched to a different research area and left the school.

I had my idea on X BEFORE the presentation. Yes, some UG are actually good at coming up with ideas - I know how rare it is, but I am an older student. He didn't even know I was pursuing it for my senior thesis. All of the sudden, it seems like he is interested in this area as well.

the grad student was not working on X, I guess I failed to word this correctly

From my reading, there is nothing wrong with what you are doing.  You can develop idea X on your own.  You should also familiarize yourself with the rules of co-authorship.  Australian universities follow the "Australian Code for the Responsible Conduct of Research" for example.

I simply don't understand the scenario. As far as I understand you seems to moved idea(s) from a PhD person / group / institution to your master thesis / new group / new institution. This won't be conflict of interest but it can be some sort of appropriation. To tell you if it is indeed the case one should know the scenario in details. The new supervisor might want to know it as well.

You don't gain ownership over an area of research by working in it. Issues arise when someone takes your ideas and misattributes them.

No.  One of the criteria for a problematic conflict of interest is that the conflicted person has power.  The PhD student does not have any power in this situation.
In general, collaboration is good.


text:
Does pure math have an application in communications engineering?
I am a communications engineering undergraduate, and I was thinking of studying pure math courses will this help me later on in graduate school, and if it will help what courses of pure math will be related to my major?

You may get a better range of responses to this question if you ask it on http://math.stackexchange.com/

You mean, like the stuff that this guy did?

@Willie Wong yes

Group theory has applications for error control codes.

The "pure math" label is very, very silly, ... especially as usually put in opposition to "applied math", ... when we're asking about applications to signals engineering, say. But, certainly, as in the work of C. Shannon (as @WillieWong noted), in the work of N. Wiener, and many others: yes, certainly mathematics is useful to communications engineers. Linear algebra over finite fields, Fourier transforms, and so on. So, abstract algebra, real analysis, complex analysis, functional analysis. And these have prerequisites.

If so, then it will be called "applied math". ;-)

I'm in a similar situation to you. I'm finishing my masters in digital communications and doing my thesis right now. Math is an issue for me definitely.
In my experience, a bit more complicated math is helpful if you're going to be developing systems that do statistical signal processing (which seems to be very popular now) and anything that has "smart" in its name.
What exactly do you need depends on what you want to study in detail. It might be a good idea to first dip your toes in the fields you want to be working with first and the pick math courses you want to take. You could try looking at some books or papers about say adaptive filters or modern receivers or estimation theory. This should give you an idea what's usually needed. If you're lucky enough to have approchable professors, do ask them about what will be useful to you.

I find Paul Garrett's recommended courses rather ambitious for a non-math major undergrad, if the context is the U.S.
You would be well served by covering most of the basic math classes needed for a physics or engineering major:

the calculus, including multi-variate
an intro to ordinary differential equations -- this is a classic course and will prepare you for the Fourier transform
linear algebra -- will make a lot of things easier once you've had this; also, as long as your course is rigorous and not too cookbook, you will gain mathematical maturity by doing lots of proofs
if you enjoy it, you could have some fun with a numerical methods class (although this is not a pure math course)
intro to probability or graph theory (for something totally different)
if you want more pure math, then take "advanced calculus" (but not without a rigorous linear algebra class under your belt)

If you like math, and want to take advanced math courses, it is quite likely that they will help you later in your career. Especially if you choose topics related to communications engineering. For example, the amount of probability taught in an intro to probability course is  insufficient for a lot of real applications. On the other hand, if you don't like math, I wouldn't advise taking extra math courses. You'll struggle to get through them and possibly forget everything you learned before you have a chance to use it.

authors: Макар Чистяков

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text:
Is it appropriate to submit a co-authored writing sample to PhD applications?
I will be applying to PhD programs in Psychology this fall. Currently, I am in an MA program where we will be assigned to draft a research proposal in the topic of our interest. However, There will be another student co-authoring this assignment with me (we must work in pairs). Is it acceptable or favorable to submit such draft as a writing sample?
If not, what do you suggest might be a good piece to submit?

Please ask one question per post.

I suggest that you don't submit a sample that was written jointly. It would defeat the purpose of the request. The reader doesn't know how you write. I suspect that it would be rejected by many (most?) places.
There are a lot of possibilities for what you might submit. An old assignment, perhaps. Or write up something specifically for this purpose. Perhaps you could write a proposal for some specific research that interests you, showing that you have done some background reading and are looking ahead.

OP: I would add that the last choice could be submitting that sample with an accompanying letter explaining the situation and digging in to the parts you were concerned most.


text:
Reference "private" lecture notes available for members of a different university
I'm writing my final dissertation and, among all the documentation I have read, I have consulted the private lecture notes of a course on the topic of my dissertation that is taught in another university (in another country) by a reputable researcher in the field of the dissertation.
A friend of mine was following that course last year and shared with me the lecture notes that are available online only for the students of that university (you have to login to access the resource). As I have used this resource I think it's my duty to reference it, however, since I shouldn’t have access to this resource in the first place, I don't know how to properly reference it.
What should I do?

Did you consider writing to the author asking for a copy of the lecture notes, or access to them (for personal use)?

If you had access, you can cite it (and should, if you make use of it). It may not be fully public, but you can still cite.
Of course, if this was confidential/classified material, that's a different issue, but if it's just lecture notes, the login probably just makes sure that people cannot just steal it and create unlicensed copies thereof. I do not see a major issue to use it as an aide-memoire or an additional academic source.
Example: Isaac de Novopeso, Lecture on Applied Brontomechanics III, University of Heavenly Masses, 1852. You could also look up how to cite lectures.

You mention that these materials are lecture notes. Lecture notes are not typically original, novel research, and generally cover what is considered to be common knowledge in the field.
So, my question to you would be what is it exactly in the lecture notes that you used?

If you are using a citation in the lecture notes to a specific paper (e.g. "Smith (2005) found that x > 3"), consult and cite the paper, not the lecture notes that directed you to the paper.
If the lecture notes helped you get up-to-date in the standard practices of the field so you could complete the work (e.g. an especially helpful set of analogies that really helped you understand how and why transregenerative epthelioid regression works with para-hypertransitive tensors across Garfieldian space), no citation is needed, though you could put in an acknowledgement thanking the instructor for the helpful lecture notes.

Common knowledge "in a field" is very different from "common knowledge".


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Meaning of bullet sign in citation number
I'm reading this research paper and some of the citations are marked like this:
[29•] or [29•,[30],[31•]•,[32],[33],[34]]
The bullet points are in superscript, as well as nesting in the bracketing. There is no legend for this symbol in the paper; does it have a standardised meaning?

interesting way is also this:
[[3•], [4], 4]

By looking at more recent papers from the same journal, for example this https://www.sciencedirect.com/science/article/pii/S1359029415000369#bb0140
it looks like these are commented references.
With one dot • , they are referred as

Of special interest because [...] It is where someone new to this area should start reading.

with two dots •• . they are referred as:

Of outstanding interest because [...]

Interesting, although not of immediate understanding.

This is not extremely common, but I have come across it in different journals, so I would call it "semi-standardised" as per the OP's question.

@StephanKolassa I agree, although it may depends on the field. Do you have an idea how to read the nested reference [[3•], [4], 4]  ?

No, that one is strange. Looking at the html version, I see that the 3 and the first 4 are hyperlinked to the references - but the second 4 is not hyperlinked. As such, I would assume this is just a typo. (How one manages to introduce this kind of typo into what should presumably be an automatic BibTeX/LaTeX run is not clear to me.)


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How to cite a paragraph from a paper with a citation in it
In my paper, I want to cite a paragraph from another paper that looks like this:

Universities are an ideal target for attackers because they have high bandwidth and open systems.“A university is not a high security area,” says Andreas Pfitzmann, professor for data security at the Technische Universität, Dresden.

How can I do that citation?

Normally, you would switch between double and single ticks for the outer and inner quotation, respectively.
Alternatively, for a quotation of the length you are showing, consider using a (slightly indented) quotation block.
I will look for some examples when I have a stable connection again.
Of course, you should also check the styleguide of your target venue, although in my experience, paper styleguides rarely mention such details/special cases.

Yes, i've never seen suck specific case... Thank you !


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Believe in yourself or your supervisor for your own PhD thesis when you feel it is ready for submission?
I am a PhD student. However I published more top-ranked journal articles than my supervisors within a 3 year period of time. As I am becoming more and more experienced, I feel uncomfortable whenever I talk to my supervisor for their comments on my PhD thesis. The comments are not penetrating and they do not seem to understand. It is hard for me to take their advice as I do not trust them enough academically. I told them I am not going to win a Nobel prize and I just want to finish my PhD to move on with my life, not a piece that I will be truly proud. Should I express my concerns to my supervisors openly by saying I am not comfortable with their advice, or what should I do with it? They are nice people but academically speaking, not strong enough.

I assume that, at least as a group, your supervisors have supervised (and completed) more PhD theses than yourself. That experience may count for something, even if you don't believe that they can compare to yourself academically.

Also keep in mind that the people who come to examine your thesis may be similar to your supervisors. If you can't convince your supervisors that it's ready, how can you be so sure that you'll convince them?

If your supervisors cannot understand your thesis it may need more work to make it clearer. Can you find out exactly what they are not understanding?

Ay, caramba. You already told your advisors that "I just a finished phd to move on with my life, not a piece that I will be truly proud", so, at the very least, telling them that you are "not conformable with their advice" shouldn't be too shocking for them to hear, right?

"Should I express my concerns to my supervisors openly by saying I am not comfortable with their advice, or what should I do with it?" No matter how good you are, that is the worst thing that you can do. It is their job to give you advice, and it is your job to take it into consideration. Telling them that you will not take their advice because you are better than them shows a lot of arrogance to which they will not react well to. A little humility goes a long way.

that is true. Thank for everyone's advice. In term of the content , they feel it is clear, but in term of the structure, they are not happy with it. I am doing a thesis by publication, so there are a number of repetition throughout as each chapter stands as a separate paper. Additionally, for each papers I do not like the directions they suggest as I feel it is good enough for a good journal. Sometimes, I feel that their advice is misleading... I think they are good supervisors but just not have enough confidence on what they offer...

Towards the end of your PhD studies you should be the ultimate world expert on the narrow topic of your thesis. You should be familiar with all published related research, and have added new knowledge through your own research.
It is your responsibility to convey that knowledge, in your thesis, in a form that other researchers in your area can understand. It is essential to getting your PhD that you convey it in a form that the committee that evaluates your thesis can understand.
If the examining committee don't understand it, they should reject it. At the best, your writing is not good enough. At the worst, fuzziness in the thesis reflects actual muddled thinking and the research needs more work to sort that out.
Regardless of whether your supervisor will actually be on your examining committee, they are the best surrogate you have for testing your thesis. If your supervisor does not understand your thesis, it is not ready to submit.
Looking at the bigger picture, the smarter you are, the more academically advanced you are, the more of your time you are going to spend explaining things to people who know less than you and need more explanation than you would. Your thesis is a good place to work on those skills, with an expert audience who will give feedback.


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Is reusing sources self-plagiarism?
I have a class that I have to research a topic on. It can be anything and all I have to do is inform the class about the topic. It's not super intense research, just a small amount, enough for a 5 minute presentation.
However, before, I had a research project that took up almost a whole school year about a topic we chose. It's a topic I'm interested in and I was wondering if it counts as self-plagiarism if I reuse sources from the old research project? Not all of them just a handful. It's almost all just facts and not much of my own analysis so would it be counted as plagiarism?
Does turnitin count it as plagiarism if they find 2 papers using the same sources? The thing I'm concerned about is we have to do an annotated bib and I took the sources from an old annotated bib. However the info paragraph I basically rewrote it all and its a lot more simple than my old one, which has a lot of specifics. Also all the sources I am using are on my old annotated bib.

Plagiarism while doing assignments is really too much of a concept

@yuq If all of the sources also appear in the previous project and both have been submitted to Turnitin, yes they will be flagged.

As a side note: If you are choosing classes where the homework is capable of being copy-pasted, then you have other problems. You should be picking classes that don't overlap so closely, and that advance you more.

Yes, they will be flagged by Turnitin. However, why don't you just cite your own research? In that case, it's not plagiarism because you cite your own work correctly.

Self plagiarism is when you use your old work without citing it. It can be avoided with citation, just as you would if the original was from another author. So, in this case, it would probably be considered to be self plagiarism.
However, you have another problem in that the professor may have wanted you to do something new, not to recycle work from the past. In that case, you could wind up in trouble even if you use proper citation of the older work. That would avoid self-plagiarism, but might not avoid sanction from the professor.
Ask the professor if it is appropriate for you to draw on old work for this. We can't answer for them, but do this before you make assumptions and end up in trouble.


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What to do when phd advisor wants me to work on side projects but i'm starting a post-doc?
I'm currently finishing up writing my PhD while starting a post-doc at another university in another country. The post doc is a great opportunity at a top tier university. Between finishing my dissertation, trying to get started in this new lab, and moving to an apartment in another country that requires I start from scratch, my time is super limited and everything is hectic.
I made sure my post-doc advisor was aware that I'm finishing my dissertation , and would be doing so for the beginning of the post-doc, from the get-go as I informed him during interviews for the position and when I accepted the job. He has been fine with this and held the position for me for as long as he could because as he said I'm a perfect fit for the position and he really wanted me to be his post-doc, so I'm super grateful for that. Plus, there is enough crossover in the project that my PhD advisor made him a collaborator on the chapter that I'm finishing up while starting the post-doc position.
My PhD advisor recently reached out to me about a side project I had been working on for him previously and had written up with me as the first author. This paper was rejected from the previous journal we submitted to and we received this notice around the time I was getting ready to move. Because of this, he offered to re-work the manuscript results/discussion sections after I re-did the analysis and sent him the new results, which I did. Now, he is saying that he doesn't have time anymore and that I need to set aside my work to make this a priority.
The other relevant background information is that my PhD advisor is in trouble with the university because he is so absent when it comes to his students. He had another PhD student who started at the same time as me defend her dissertation before she was ready, and the defense was so bad that department members outside the committee were asking how she was allowed to defend and it got to the department head. Now he is in trouble of losing teaching assistantships for future students. I have been independent for my PhD and have worked on many side projects for him. Just 6 months ago, again while I was trying to finish up my thesis because of the post-doc position, a similar thing occurred where I was asked to set aside everything to devote my time to a project I was a co-author on and it ended up being 2 months of re-doing the entire analysis, results, and discussion and with me being a co-first author on the paper, which was published after my rewrite. I have also worked on numerous other projects for him over the years. I have been very independent in my PhD, not relying on him for much as I came up with the question, methods, and interpretation of my PhD project - my independence (a byproduct of his absence) yet success with this project is a part of the reason why I got an amazing post-doc position.
I think realistically this re-write would be ~1-2 weeks and I know that I was first author on the manuscript and the major person behind the project, but I just don't have the time. I proposed to have a student from our collaborating lab that also did a lot of the work on it just finish the re-working of the results/discussion and to make him co-first author, but my PhD advisor wouldn't entertain the idea. I think he needs more papers coming from his students alone.
What do I do? Should I bring this up with my new post-doc advisor? If I do this I either won't have time to work on any new stuff with him or I won't be able to work on my dissertation and will fall behind there. Should I say no to my PhD advisor, and if so, how?

What about timelines? It sounds like you can't do the work now because you're busy, but there probably will be 1-2 weeks during your post-doc when you could do the missing work.

My initial response to my PhD advisor was to ask if I could do it in 4 months after I finish writing my thesis, which is what I’m currently focusing on doing outside of trying to start work in my new post doc advisor’s lab. He responded that it should only be a week or two but that he had discussed it with the other professor from the other lab and that we needed to resubmit now.

My worry with doing it now is that the 4 months is a strict deadline for me to defend so I absolutely can’t be late on that. Things tend to get pushed back with my advisor often - it usually takes weeks to get responses on anything. I really don’t want to jeopardize my defending in 4 months but I also don’t want to upset either one of my advisors.

One of my main questions , besides whether or not to do it, is should I mention this to my post doc advisor? And if so, any advice for how to approach that conversation?

It sounds as if your PhD supervisor is less than ideal. I would say your priorities should be:

Finishing the PhD dissertation so you can graduate.
Consolidating your postdoc position.
Finish the old paper.

Your PhD supervisor has different priorities than you, so you have to be the guardian of your interests.
You make sure to wrap up your dissertation first, because when you've got the PhD in your pocket that supervisor no longer has a hold over you. In a choice between the postdoc position and the old paper it sounds like you value the postdoc more. Finally, if the postdoc advisor is willing, finish the paper anyway. It's one more publication to your name for which you've already done most of the work. That it helps you not burn a bridge is a bonus.
Since you're trying to advance your own interests over those of your supervisor (as you should), be ready for some pushback. But it's hard for your supervisor to argue against working on your dissertation so focus on that.
EDIT to answer follow-up question.
A certain amount of discretion is called for when discussing this with the postdoc advisor. You shouldn't bring up your suspicions about your old supervisor, negativity generally doesn't help.
Rather, you can say that while you're excited about the postdoc position, you have some loose ends from your old position that you would like to wrap up. You did this research, and sunk a lot of work into it already. You'd rather not just abandon it, and your old supervisor is urging you to rework and resubmit. Then you ask if it would be possible to set aside some of your time to work on finishing it up.
Your situation is not really all that unusual; most academics have had some loose ends like this. Also your new advisor will be aware of the old supervisor trying to influence you, also pretty normal. What's important is that you keep your priorities straight: finishing the paper would be nice but it can't come at the expense of the postdoc. So ideally, you set aside a strict amount of time per week to work on it, and keep the rest reserved for your new postdoc work.

How would you recommend I approach my post doc advisor about this?

I am currently in a similar position to the one you describe, except that in my case I agreed to take on a brand new side project with my previous supervisor. I spoke to my postdoc supervisor about the project as soon as I started and received his go-ahead to spend some of my time working on it. In my experience, it seemed like my postdoc supervisor thought this was totally normal and expected after a PhD.
In your position, I would agree to the rewrite (after verifying with the postdoc supervisor that this is not an issue) because it seems like it will not be too significant a time sink - you already know the work and have a reasonable estimate of how long it will take. It is always nice to publish your work. Note that you do not need to spend the first two weeks of your postdoc on it - you can allocate some time each day to it and then you will still have time to do new stuff.
I have one caveat based on my own experience which is that even if you have permission to spend some time finishing up old work, it is quite difficult to commit to doing this because it feels like you are not putting 100% into the new project. It can also be tiring to have a task that needs extra work after hours when you are trying to get established in a new place. Thus, I would limit the number of "side projects" you agree to bring along from your PhD and try to make a realistic plan for how you will finish them quickly.


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Are computer skills degrading?
I teach masters level engineering students. I have observed that computer usage skills are slowly and constantly degrading among my students from year to year. Has anybody else observed this kind of effect?
What could I realistically do to combat this problem? I do understand that even if its not my job to do so I need to address the problems somehow. Unfortunately I am getting a bit frustrated to teach students how to graph a function, or numerically find the local minima etc. when i should be talking about formulating multibody dynamics for example.
How do I check that this isn't just a bias that I have somehow accumulated during the years of teaching? I am aware of the it was better in my youth bias. Frankly i dont believe i was much better in most aspects. But I sure knew how to use my computer.

Degrading from where to where? This seems likely to be closed for being too opinion based, but if you mean from year to year, I think so. We created an entire sequence of what turned out to be very popular courses because new graduate student users of our supercomputers couldn't use them (couldn't code, couldn't script, couldn't debug, didn't understand basic algorithms, etc.). Those of us who manage the systems and had graduate degrees were generally self-taught in the necessary skills.

@user37208 Yes im aware of this effect im trying to gauge whether im experiencing this or if it is in fact true.

@BillBarth Unfortunately we are in cost cutting mode so for us less is more.

@joojaa, oh, we didn't get paid to teach these courses, we did it, basically, pro bono.

What is it with the kids these days?!?

I could imagine that there is truth to the observation, but I wouldn't know whether there really is evidence to back it up. Of course, @BillBarth and I are from a golden generation that, when we were young, had access to computers but of the kind that had no graphical user interface, not a lot of games, etc, and so had to spend our time figuring stuff out and learn programming. The number of truly skilled programmers from our generation is really outstanding. Whether there is really a decline in skill between people growing up around 2005 or 2010 may be debatable.

Though it's just my personal opinion, I see no way to combat lax computer aptitude other than to make it integral to everything else that they take time to practice or explore the skills necessary themselves. Since solutions are readily available at everyone's fingertips with the transition from desktop to mobile computing, there's really no incentive other than "you need to know it to move forward," or some kind of self-motivation to just become better at computing.

And i think that out of the bunch there would be at least a handful who perform at a satisfactory level or higher, and you'll actually find that some circumstance like exposure to hardships while computing, the type of computing these people partake (tablet, desktop?), etc. greatly differs from those who need help with simple tasks. It shouldnt just be your personal bias, just a frameshift in how people are exposed to computers.

@WolfgangBangerth - Every time I read one of the seminal works from the 1960s, 70s, and 80s in CS, part of me wishes that I was alive back then to watch and work with those great minds.  They made it look so easy - I have to remind myself that even Ritchie and Wozniak and Djikstra "stood on the shoulders of giants".

@tonysdg: Yes, they did. I had no intentions of putting myself or Bill Barth in that category. Both of us grew up in the late 1980s and early 1990s when personal computers were around. Neither of us have accomplishments that come even close to those of the people you cite :-)

@WolfgangBangerth: Perhaps, but given that I've grown up in the late 90s and 2000s, and started truly digging into computers in the 2010s, you and Bill Barth are of just as amazing a generation as they were in my mind :) Just saying!

Maybe you could improve the question by specifying what field you want to teach exactly that would benefit the most from improved computer skills of your students and what computer skill you think are necessary for that.

IMO, it is the ubiquity of computers that has brought the level of computer skills down. If you got interested in computers in the 1980's you basically were a hobbyist who got in and taught yourself, and if you wanted to do something it required you to write some code or remember a bunch of keystrokes. If you were doing this, you were likely also inclined to select towards STEM. So the people you saw in STEM had above average skills. Now computers are everywhere. Everything is an App, and you don't really get involved in coding, so you aren't challenging yourself to think of solutions,

@AMR that may be. But as a engineer its not enough to use apps you must be able to see behind the apps and understand what they consist of.

I think you misread my comment. I am giving a plausible explanation for there being students with far better skills in the past and why you are seeing a degradation in computer skills; your conclusion is not a bias on your part. Another aspect is economic. We have an economy where in order to even have subsistence you need to get advanced degrees in highly technical fields, which many of the people you are seeing today would not have chosen 20 or 30 years ago.

@AMR Sure, i just commented that that is not enough, unfortunately. The start of the decline nicely coincides with windows 95 so this ease of usability is certainly the source of the problem.

And there in lies the irony. By the successful engineering of usability and enhanced user interfaces, you have made it more difficult to train a new generation of engineers... By the time you get them, I don't know that there is much you can do. Along the way, if they weren't "indoctrinated" into analytic reasoning and problem solving thinking, it will be very challenging to change the mindset they bring with them.

@AMR it does apply for other things too. Physical goods today are so well engineered that less and less people think of the internals anymore. Meaning its harder to teach mechanical engineering. Still we know how to teach that, we just dont know how to teach computer use for some reason. Even the CS departments do not, in fact they do more harm than good. Too academic that does not interest people outside CS branches. Not at least without a lot of background understanding on how it might help.


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Transferring to a PhD program I had been previously admitted to
I will be beginning my PhD (in a field that's halfway between social sciences and humanities) in the fall. During my application cycle, I was admitted to all three of my top choice programs, and was heavily recruited by all three - to the extent that when I turned one of them down, the admissions committee chair emailed my undergraduate advisor and asked her to try and change my mind. Eventually I committed to the school that I thought was the best match for my research interests, with one professor in particular I was extremely excited to work with and who was excited to work with me. This choice was a bit of a gamble- while the research going on here is probably the most exciting in my subfield at the moment, the program itself is pretty solidly second tier (as opposed to the two I turned down, which are definitely top 5) and fairly narrow in its focus (i.e., if my interests shift even within my own subfield, I'm not sure the department will be able to accommodate that).
Even with the potential risks of this program, I decided the research was fascinating enough, and I wanted to work with this professor and his lab enough, that it was worth it. However, since committing I've heard some things about the organization of the program as a whole, and specifically the advising styles of this professor and a second professor I would likely want to collaborate with, that really worry me. Also, I've had some conversations with my future advisor that similarly make me think that it may be a bad fit in terms of our working/learning styles. Basically, I'm afraid that I chose the wrong program for me and that I'll end up unhappy, unproductive, and (in the end) unemployed.
My questions, then, are if, after a year or two in this program, I feel like I have a bad "fit" with my advisor, am unhappy, and/or my research interests have shifted so that they will be better served by one of the other programs:
1) Is it generally possible to transfer, assuming that my academic and research performance at this PhD program are still very strong?
2) Is it possible that one of the programs I turned down in the past will accept me again? Or would the fact that I turned them down previously make them reluctant to do so, even if I made it very clear that I would definitely attend if accepted (I would probably only reapply to one university, so that I could say with confidence that I would attend if accepted)?
3) How seriously would this burn bridges with people at the program I'm currently attending, and the people they work with at different universities, if I did decide after a year or two that I wanted to transfer?

Related to your questions 1 and 3 (I think the answer to your 2nd question is most likely "it depends"): Is transferring to another university an option for an unhappy PhD student?

First of all...you haven't even started the program yet. Give it a chance. Go in with an open mind. Hearsay is unreliable and it's normal to have second thoughts about something once you've committed to it. So put the question of transferring out of your mind for now, and focus on getting fully integrated into your department and your program. If you're mentally one foot out, you might simply turn this into a self-fulfilling prophecy.
To more directly answer the questions:
1) Yes, it's generally possible; I have a couple friends who have "transferred" PhD programs. However, "transferring" usually just means reapplying to a new program; you usually have to start over. So if you've done 2 years elsewhere, it may mean absolutely nothing and you may have to retake all of your coursework. At best, you might get credit for one semester's worth, but you're probably not going to be able to pick up where you left off at the old program. Generally, you also need the support of your advisor at the Old Program. In other words, the advisor you are going to work with in the fall would need to write you a recommendation letter for the New Program. In some cases where the relationship has gone sour, students have successfully gotten letters from other professors in Old Program, but those professors need to be very skilled in explaining why the relationship went south (in a way that reflects positively on the student.)
2) Maybe. It totally depends on the department. If you were so good that they were recruiting you heavily, and you produced evidence that backed that up in your first year or two, they might be eager to take you again.
3) It depends on how you do it, and the reasons that you transfer, and how reasonable your advisor is. Most professors understand a transfer that has to do with a shift in research interests - if you came to study X with Professor Smith but Professor Smith leaves, or Professor Smith radically changes his research direction to Y, or you change your research direction to Y - explaining to your advisor that you have appreciated your time at Great U, but your research interests no longer fit the program and you'd like to transfer to Awesome U to work with Professor Jones in your area, usually engenders understanding.
In the not-uncommon case that your relationship with your advisor goes south and you're transferring not because of research but because of personality mismatch, that can burn some bridges. But they may be bridges that you have to burn if you want to retain your sanity. Only you can make that decision.
In the less common but still possible case that your advisor is simply a jerk and hates when his students leave for any reason, even a reasonable reason can set him off. There's nothing you can really do about that, but there are typically sympathetic other professors that you can turn to for support and recommendation letters.
And how you make the break also plays a role. These are obvious things, though - don't badmouth your advisor, don't badmouth your program, don't disparage your classmates or other professors. Stay positive and make the transfer about you, and not the program itself.


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Am I allowed to duplicate results from my own arXiv paper in a journal publication?
I had put up a paper on arxiv about 4 months back, which we had planned on submitting to a journal. However, before I submitted, we got some good reviews and ideas from a colleague at my university. All of the original results were correct and accurate, but now I would like to add some additional simulation results, a more detailed analysis, and also give an authorship to the colleague. However, in this time span, my arxiv paper has been cited a couple of times.
My questions are:

I would like to change the title of the paper and do it from fresh, and submit the newer version to the journal. In this case, should I just cite my arxiv article for all the background work, and just present the new contributions (which would be only 1-2 pages); or can I copy over all the content from my original arxiv article?
If the latter is possible, how do I indicate to others that they should cite the newer article and not the original one?

Field of research: At the interface of applied mathematics, engineering and computer sciences. Paper likely to be submitted to a SIAM journal.

Manuscripts in the arXiv are permanent and citable, but do not count as peer-reviewed publication.  Therefore, there is no inherent problem either with using your arXiv work as part (or all) of a manuscript submitted to peer review or with citing your arXiv work as background on a new work that builds upon it.
If you re-use your arXiv material in a manuscript, however, there are two additional steps that you must take:

You must make the source of the material clear, in both the cover letter and the document itself.  I personally like verbiage such as:

"Note: portions of this manuscript have been adapted from [cite]"

You need to check the policies of the venue where you submit it.  In some fields, such as computer science, most journals do not consider non-peer-reviewed venues such as arXiv prior publication, and so including such material is fine.  In other fields, such as biology, most journals do consider them pre-publication, and will consider it self-plagiarism.  These policies vary journal-by-journal, however, so you do need to check the individual policy.

In this answer, I'm assuming that the journals you are considering are not prejudiced against publishing preprints. (If this is not the case, I think you may have hard time publishing the content of the already-uploaded preprint, but this is likely largely dependent on the policy of individual editors and journals.)
If the journal is okay with regards to publishing preprints on arXiv, I don't see why they would mind having a "partial" preprint over there (as long as the "preprint" authors form a subset of the "postprint" authors, of course). But I want to say a bit more about your options with regard to arXiv.
I think one think you can do is to simply update the paper you have uploaded to arXiv, along with the added author and possibly other acknowledgements, and then send it to your journal of choice, and (simultaneously) simply replace the arXiv version with this new, updated one. I think this could be a good idea, particularly if the structure of the "old" part is left mostly untouched and you just add more content at the end (and maybe change the abstract and introductory parts a little bit). By your comments about the changes being only one or two pages, I imagine that this is the case here.
If the upgrade will inevitably disrupt the structure of the already-written part, then I think you should follow the advice on this thread (actually, you should probably see that thread either way).
I'm reading between the lines here, but I think you're thinking that what you don't consider replacing the arXiv article is because you want to change the title and add an author or because the preprint has already been cited. But you should know that:

You can add an author to an existing paper as well as change the title when replacing a paper.
arXiv keeps all versions of uploaded preprints with timestamps, so when someone follows a reference to (an old version of) your paper, they should be able to tell by the timestamp that the reference was to a previous version, even more so if the title has been changed, and if the structure (especially numbering) of the old part is left virtually untouched, it might not matter anyway.

Thanks a lot. I think you read the situation quite correctly. I want to upload separately because (a) 1 new author; (b) title change; (c) paper already cited. From what you said (a) doesn't seem to be an issue. However, my worry is that if I change the title, it might cause a whole lot of confusion when it comes to citations. Even if I change my title, will the citations carry over to the new title automatically?

@AravindRajeswaran: If the citations properly quote the arXiv identifier (as they should!), then yes, they will carry over in the sense that anyone who uses the identifier will find the new version of your paper: if you have a link like http://arxiv.org/abs/1506.00438, it doesn't care what the title actually is. If you're still worried about possible confusion, you can just do what F'x suggested in the other thread (though in that case, the citations will not "carry over" so much, but anyone who cares should be able to find the new version of the paper, anyway; I guess it's worse for h-index).


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Career in Mathematics as an Electrical Engineer
I am a university freshman with major in Electrical Engineering. My passion is pure math(topology, group theory etc). During my first semester I noticed that our math classes are not rigorous at all, focusing on approximations and practical purposes. My goal is to work on theoretical math research or mathematical Physics. Should I stay in engineering (and follow it with a math post-graduate) or switch to math major? In other words, is it possible to be applicable for research with a masters degree in Electrical Engineering?

If I may ask, how do you know your passion is pure mathematics? Were you exposed to it in high-school — perhaps in training for math competitions?

I indeed have some awards in math competitions, but that's not the case. I study stuff my own, and I 've been esposed to some ideas from areas like differential geometry, general topology, Galois theory, representation theory etc , and I find very attractive things like Lie groups, adele rings or hermitian operators and their relationships with other theoretical topics, like quantum mechanics or general relativity.. I have a deep desire of learning all those things at the highest level.

Family is undoubtetly quite important.. I 've thought of maybe doing research in another country in my first steps after PhD, and then returning back, or whatever comes up. Who knows

You say that your passion is pure math, so sure, that's what you should pursue, although there's no reason you can't do engineering as well in a double major. Regarding rigor - this highly depends on the class! A freshman calculus course will probably not be completely rigorous.  Modern mathematical rigor does not usually come into play until upper-level classes.  Do they offer classes like real analysis, abstract algebra, topology?  If so, they are likely pretty rigorous.  If such classes are not offered, you may need to move universities at some point if you want to do pure math.

And of course, the real answer to all these questions is "talk to an academic advisor" (or a math dept. faculty member) who can give you much better advice for your specific situation.

On the one hand, see https://en.wikipedia.org/wiki/Raoul_Bott ; on the other hand, keep in mind that very few people are geniuses like Bott.

In the US it is possible to switch after undergraduate, but I'll note that the focus of an engineering degree is very different from mathematics. I'd suggest that you switch as early as possible.
One reason that first year math isn't as rigorous as it might be, and not as rigorous as it will be later, is that those courses are intended for a general audience, including engineers, who have less need for a theoretical basis in math. The same will be true of early physics courses.
Outside the US it may be harder to change after an bachelors degree.
I'd suggest staying where you are only if you want a career in EE or at the junction of EE and CS. But your interests seem to be elsewhere.

"including engineers, who have less need for a theoretical basis in math": As an engineer, I beg to disagree. Engineers do need a theoretical basis in math, unfortunately universities are less and less willing to provide a decent mathematical curriculum to engineers (FWIW, when I studied engineering, the first- and second-year mathematics courses were virtually the same of those for mathematicians).

@MassimoOrtolano, yes, and for me. But Calculus was followed by a rigorous Analysis course. The mechanics were taught in the first courses, but the follow on courses provided the theory and insights.

Do you find possible the connection with pure math through personal reading while staying in engineering, in such a way that provides what is needed for PhD and research afterwards?

Certainly it is possible to learn. What is harder is to convince others that you have learned enough to get accepted. Having a university attest to your accomplishments makes it a bit easier. But you need to do a lot of work, just as if you were in class. Reading alone might not bring the necessary insights.


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Contacted by head of school regarding an issue - should I be worried?
I am a PhD student at a UK university. A small part of my time is taken up by (voluntarily) organizing a monthly seminar series. The seminar is open to all PhD students in my school, and is regularly attended by 30 or so students. I took over this duty in January 2018, before which time there were other student organizers.
Whilst I am an organizer (along with two others) of this seminar, all decisions that we take are checked with a particular senior member of staff - who I will refer to as Prof X. It could be said that Prof X is our organizational "supervisor". They check our posters advertising each seminar, our emails, etc. Very little happens without Prof X's knowledge, if not expressed permission.
As part of the seminar, due to the time of day and its duration, we order a certain amount of pizza to have in a break between talks. The money for this comes out of a particular part of the school's budget. We have always done this, as did the previous organizers. We have never discussed our budget for this pizza, or how much we "can" order. We have always presumed we are within budget, and had no reason to think otherwise. We consider that the amount that we order is entirely reasonable for the number of participants.
I received a surprising email today from my head of school - who I will refer to as Prof Y. This email requested a meeting with all three of us organizers, and explicitly stated that this meeting is due to the fact that our seminar is effectively running over budget, and moreover that this was not approved with them, the budget holder.
This email alarmed me for a few reasons:

Prof Y has, in the past, regularly corresponded with Prof X about matters regarding the seminar, which have then been relayed to us organizers. It is very out of the ordinary for Prof Y to email us directly. Prof Y has in fact never contacted us at all before this email.
Prof X was not CC'd in or BCC'd in to this email. Upon my contacting Prof X about the email, they expressed a great deal of surprise and some concern about the fact that Prof Y contacted us in this way. Prof X did then advise that I should attend the requested meeting.
Whilst we organizers are the ones who request the pizza order, we have no (and have never had any) knowledge of or control over our specific budget. I think it is reasonable to assume that Prof Y knows this, and it is therefore unclear to me what the nature of the discussion at this meeting could be.
Prof Y is head of department. Perhaps they have disciplinary action in mind, or something of the sort. I have no knowledge of procedures or regulations in this regard, and whether we organizers are liable to face any disciplinary action or on what level.

A further complication is that, outside of the organization of this seminar, Prof X is in fact my own PhD project supervisor - I consider them an excellent supervisor and am on very good terms. I am concerned that developments in this situation could effect this.
My questions are:

Could I be accused of misconduct?
Should I be alarmed about the email from Prof Y? Is it likely/possible that disciplinary action is on the agenda?
During this meeting, how careful should I be? Could I be in danger of serious repercussions here?

How much are you actually spending on the pizzas? I did a quick back-of-the-envelope calculation and figured it's probably around $150/mo. Is that really breaking the bank of the department's budget?

Perhaps Prof. Y heard you were ordering pizza with pineapple and wished to express strong disapproval.

@JairTaylor Perhaps Prof. Y is Italian?

I think you should be worried that you and your colleagues might have to go without pizza the rest of the semester if you've already (unknowingly) burned through the budget, and not much else.
You could also worry that in the future you'll have to go through a more formal approval process, which will probably loosen once whoever is involved in the approval gets tired of approving it every week and eventually delegates responsibility again.
To me it sounds like everything you've done is completely reasonable. It's somewhat normal for these sorts of things to fall through the cracks.
If there are any serious consequences that come about from this, then there is some deeper dysfunction in your department that is completely unrelated to anything you've done. There are plenty of things for a PhD student to be anxious about, I'd suggest trying your best to not make this one of them. Just show up to the meeting on time and be apologetic if necessary, and also be understanding.

Hmmm. Maybe take a pizza to the meeting as a peace offering???

@Buffy Only if it’s paid for out of his own pocket. It also may be inappropriate depending on how formal the department is.

I think Buffy is joking, but maybe it's important to make clear it's meant as a joke. Some people are more literal than others and it's hard to decipher tone in text even for those who are great at processing social cues.

"you and your colleagues might have to go without pizza the rest of the semester": And this became known as the moment where seminar attendance dropped :-)

Note that people going over budget happens ALL the time and should not be interpreted as malice.  (Worked in AP/AR finance department).  Especially if you have no means to know what your remaining budget is!

If you get into real trouble over too much pizza your department is doomed

"If you don't eat yer pizza, you can't have any pudding. How can you have pudding if you don't eat yer pizza!?" ... little known first draft to Another Brick In The Wall Part 2

@Spark Or has awesome pizza seminars.

There is a UK context to this situation which others may not have picked up on, and also some researchers within UK universities may not have been exposed to the current situation within their own institution.
Putting it bluntly many UK universities are under extreme financial pressures currently, due to various factors which (depending on institution) stem from changing demographics, changing fashions in subjects of study, political and governmental activity which has deterred large numbers of overseas students, league table statistics and the resultant intense competition between institutions for the shrinking pool of applicants. At the same time there has been previous and will be future industrial action by academic staff over pay, pensions and conditions which adds further to the pressure.
In several places voluntary downsizing programmes are in place and there is in the media talk of compulsory academic redundancies. As a result budgets are under microscopic scrutiny by the accountants and much activity which previous was considered "the norm" and funded for many decades past is now being questioned. Things like "postgraduate pizzas" are exactly the type of things that the accountants would find in their forensic reading of the books.
You will have done nothing wrong, and it is unlikely that your head of school is cross with you. It will be that they will have to gently explain the new environment and sadly ask you to consider running the seminar series in the new era of austerity.

Background Reading:
[1] The Guardian: Nearly 25% of English universities in deficit last year, figures show
[2] BBC: Number of English universities in financial deficit increases
[3] BBC: Universities at risk if they admit to cash crisis
[4] Daily Mail: Several UK universities are in such financial difficulties that they are close to bankruptcy, former government adviser warns

+1 for reasons that are obvious. It also clears up a bit my implied suggestion (in a comment) that Prof. Y is a bit of a micromanager with too much time on his hands.

But the government told us that austerity is over: "Sajid Javid said on Wednesday [4th September 2019] that the government could afford to “turn the page on austerity.”" - The Guardian.

You don't seem to mention that there is a huge oversupply of universities thanks to bad policy of previous governments.

@cal97g "intense competition between institutions for the shrinking pool of applicants" sounds like having too many institutions for the number of applicants.

Don't buy the line you are being fed. As a sector, UK Universities made a surplus of £2.3bn in 2016/2017. Wasn't able to find a number for 2017/2018 and 2018/2019, but if you look at hesa data (https://www.hesa.ac.uk/data-and-analysis/finances), that says that the average university made a £5m surplus last year. But those numbers cover a whole range of sizes from the tiny Hythrop College to the massive UCL. If you do a weighted mean by operating costs, you find the average surplus is £20m per year. Universities are not broke.

@IanSudbery Those sorts of averages have little to no meaning on a university, department, or professor level. Universities typically don't go to another university and ask them for pizza money. If your university has a deficit it doesn't matter much if others have a surplus, and surpluses may be necessary in any case for longer-term investments in infrastructure and such. A balanced budget is often not a healthy one.

The point is, if "nearly 25%" of English universities are in deficit, that means that more than 75% are not. And the numbers suggest that the 25% that are not are generally smaller, non-PhD awarding institutions. Yes its healthy to put a small amount into reserves each year. Infrastructure is almost always paid for by borrowing, even for universities that are in surplus. I'm not saying there isn't pressure on departments and profs to save money, but the narrative that univeresities in general are suffering a finance crisis is not supported by the facts.

A student-run seminar series that regularly attracts 30 students is something every school should be proud of.  I can't imagine that there will be any discussion of official sanctions.  I'm sort of amazed that the head of a UK school would personally involve themselves in anything like this.
I'd encourage you to go into this meeting with a completely open mind, but no fear.  You might even watch for opportunities to request a larger budget if you need it, but certainly be ready to say "I'm sorry I misunderstood the spending rules".

They may want to increase the pizza budget now that your group is so big. It's the least they can do.

I'm sorta thinking that they might want to put more supervision on the series, while trying to take credit for it.  Make it a little more official.

As a PhD student, you have no official access to departmental funds. If someone has given you a departmental credit card, they shouldn't have, and they are officially to blame and will probably be in trouble (irrespective of the actual facts on the ground).
Otherwise, someone, somewhere, is signing off on a form that authorizes the spend. Again, not officially your problem. Thus I'm pretty sure it is not possible for any formal disciplinary proceedings to be brought against you. In the very unlikely situation that you are threatened I would go straight to your student's union and/or the UCU, if you are a member (graduate students can join UCU for free) and request support.
But as I said, I think formal disciplinary action is very unlikely. If anyone is going to be in trouble, it's Prof X. But a more likely explanation is that your Prof Y is done this without thinking about it and the effect it might have on you.

"As a PhD student, you have no official access to departmental funds." Academia varies wildly across the world.  I am sure there are departments where PhD students can directly spend (small amounts of) departmental funds.

Phd students in my department definitely have been given at least temporary department cards

The OP states UK, and I am speaking from a British perspective - I know of no Dept that would be allowed to give students (who arn't employees or any sort of official of the Dept) a corporate card. Even faculty have to fill in a million forms and come up with a good justification to be allowed one.

Yeah to be honest it really just sounds like Prof Y was having a bad day.

@LightnessRaceswithMonica I think it's more likely that a finance person is bothering Prof Y about a budget issue and they just want to get it resolved so they don't have to deal with it anymore. It might be a bit complicated because the money might come from a rare slush fund that has fewer strings attached than the more typical budget items (alumni donations would be an example) - even though the expense is reasonable, sometimes the restrictions on how funds are used within academia are not.

@BryanKrause They should still have gone to Prof X though rather than cutting them out

Not just in academia, but in workplace generally, when a middle manager is not called to a meeting with his people, it spells trouble for the middle manager. Prof. Y is probably trying to understand where this budget overrun is caused and probably does not trust Prof X. Or it could simply be a case where Prof. X skipped some necessary step in securing your pizza funds. After all most profs are busy with more pressing matters.
This inquiry could be about how things work in the base level too, understanding the costs and what could be done to minimize it. This could happen in a situation where Prof. X is not very open about how things work under his domain.

I was about to post a similar answer. Another possibility is that Prof Y is in charge of the budget, someone pointed out the pizza scandal, he realized that they overspent, does not want to bother/annoy/embarrass Prof X and just want to tell them to stop spending on pizza and call it a day.

The meeting will answer your question.
This is a complex situation, and nobody really has the big picture. That is the case for you, and just the same for Prof Y.
Both of you had no problem with that situation.
Until something happened that caught the attention of Prof Y. It may be something trivial, like seeing some budget numbers that were not clear to him.
Now, the email is what caught your attention. And you found you have not the full view of the budget yourself.
The situation is at least similar to this.  There may be more factors like intentions, assumptions of intentions of others, irritating aspects and a lot more.
All the aspects you describe make the situation so complex that it is hard, if not impossible to predict what the whole thing is about.


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Should I cater to student interests?
I am a tenured full professor in the humanities, teaching at an elite liberal arts institution. Currently our department is struggling to attract majors and student scholars in our particular humanities field, for a number of reasons - the academic work is perceived as exotic, irrelevant vis a vis the more valuable STEM fields, and considered intellectually "useless" for those whose primary goal is "getting jobs" after graduation. I would still like to teach courses in my area, because I consider this to be valuable. My institution permits me to teach whatever I wish, but our students have requested courses that are more general and more suited for non-majors and non-scholars. Does it make more sense to offer courses for those few students who desire deep study in narrow topics, or should I cater to student demands for general classes that appeal to non-humanities undergraduates? I do not wish for my courses to be seen as irrelevant, but I resist "trends" and the constantly shifting and sometimes fickle interests of the students in popular subject matter.

Interesting question, but I have a hard time seeing how it can be "answered" here for you.

Can you specify in your post what kind of answer you're looking for? To some degree, this is a matter of personal preference and opinion, so it would help if you explained why you're asking us.

It would be useful to hear from other professors/academics in similar situations. The answer I am looking for is an "on the job" kind of response.

"Does it make more sense to offer courses for those few students who desire deep study in narrow topics, or should I cater to student demands for general classes that appeal to non-humanities undergraduates?" Certainly do both.  Of course the devil lies in the detailed implementation.

I like how you quote "getting jobs" like it's a superfluous thing to be worried about.

@Cape Code it is a longstanding question at some elite undergraduate colleges in the US among humanities and other faculty: "is the purpose of a college education to 'get jobs?" It may well be superfluous, as you suggest.

Some of the best lectures I attended were exactly for the reason that the lecturer was passionate about the subject. It's much better to have a "wow lecture" for a few than a "meh lecture" for everyone (of course, in case when the lecture is not mandatory).

I'm not sure what your discipline is, but I understand the situation you're describing.  Does your school have a general education-type program in which you could offer some tantalizing courses?  We've had a lot of success with a course on "banned books," "Shakespeare on Film," or "The Vampire Tradition."  Such courses, if interesting enough, might bring more students into your major.  I taught a "Fundamentals of Lit" class that was intended for non-majors, and I had Engineering and Computer Science students who told me it was the first time they'd read a story in college and they really enjoyed the class.
The other point you raise somewhat indirectly -- the value of the study of humanities.  This is one of those "don't get me started" kinds of topics, because I believe the value of it is tremendous in a number of ways, but most important to other majors is the increased ability to communicate effectively.  Business majors may get what seems to be a "good-paying job" upon graduation, but without the communication and critical thinking skills they would learn in the Humanities, they're not going to progress very far.

Very helpful. Thank you for your thoughtful response.

I spent a lot of time over the years thinking about these issues -- :)

This question seems too general for a proper answer, but here are a few comments that point to my belief in having to weigh options and make compromises:

As someone in a STEM field (pure math) at a large state school, I still find it difficult to some things I want to teach, even at the graduate level, and have to make comprises for what would best serve our students (or at least serve our students reasonably well).  This is not just about the level at which I can teach courses, but about what kinds of topics I can cover.
Interesting courses for non-majors can often attract students to take more classes in an area, possibly resulting in an increase in the number of majors, and thus more opportunities for advanced classes later.  This is one thing some departments focus on to help grow their major.
In many departments, getting enough students to run advanced courses is a challenge.  I don't know if this is a concern for you, but if so, you need to read the situation, because you may not even have the option to run the courses you want in the near future.  Related to the previous comment, one can often try to generate interest for a specific course by motivating it in a more popular introductory course.
I personally like teaching different things and experimenting with my courses, so often I will try to mix material that I like with the material that the students come into the class wanting to learn.  (And of course, I try to motivate this well.)
Different classes, as well as different majors, have different goals.  It may be okay to have some small specialized classes (and in fact good if there are a small but serious group of students who want to pursue these topics), but if all the classes in a department are like that with shrinking enrollments, the department will probably shrink too.


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What supporting documents to send along grad school application?
when applying to grad schools most university portals allow applicants to upload additional documents; I would like to know how can applicants make use of this opportunity and add documents to alter their status in the admission process.
though this question might be considered as not having a specific answer I must say: what type of content can be added to be considered useful. e.g. Drafts of manuscripts, research proposal (if it is not included in the required documents), other related works (such as projects, dataset, tools etc.), and CV (if not included in the required documents).

Ask them. I very much doubt there is a uniform document package requirement. If you come from a different country, the documents they'd want to see might be quite a bit more detailed than if you come from the same country.

there is no specific school or department to ask them, and it's mostly by your choice. and I don't think being a foreigner affects details of a document.

@adelrahimi, ask the school where you are applying to. They asked me for specific documents (including proof of being able to pay for the program and support myself) that I assume aren't required for US citizens. It was a long time ago, I'm not clear on details.