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A typo made it through the process of one of my publications, and it's bothering me
It's a very simple typo (a misspelling of the word "frequently", one letter off), but it still bothers me that it made it into the final version. Not sure if the copy writer introduced the error later. There's also a missing close quote somewhere in the manuscript. Do minor typos like this affect citation count or credibility, or are they relatively ubiquitous? I'm also a bit angry that the journal staff couldn't help me catch them (since I'm a single author working alone and paid a hefty publication fee). Is it worth trying to change (or even possible to change)? What's your experience/advice with this?

I've seen dozens, maybe hundreds of typos in published papers. I don't think it matters at all. I've even seen well-cited papers where the main result has a typo in it that changes its meaning!

Most publications of any non-trivial length contain at least one typo, probably more. Literally no-one is going to think "gee, this person wrote fequently instead of frequently, better not cite this paper or give it much credence". It is not the publishing staff's job to catch your typos, so being angry at them makes no sense.

@AdamPřenosil Actually most reputable journals employ copy editors, and catching your typos is explicitly part of their job.  Unfortunately, many commercial publishers (even those of top journals) now outsource this work to very low-wage and low-quality providers.

@DavidKetcheson introducing typos isn't part of their job; that doesn't stop them doing it! That's especially true with technical terminology now that the copy editors have next to no familiarity with the subject matter. I've also had editorial staff completely change the meaning of an equation (by choosing to typeset a prefactor of "⅓" as "1/3" before an opening bracket, they moved the numerator to the denominator - we ended up with the rather ugly "(1/3)(...")

As a certain ice princess suggested, let it go.  Your paper was written by a human.  Humans make mistakes.  I do not think that you are ever going to find a corpus of text written by humans which doesn't contain many little errors like this.  This is why many authors and publishers keep lists of errata.  It isn't a big deal, and practically no one cares.

This is an April Fools right?

Don"t worry, these things have freqwently.

With every paper I've ever published, when I go back and read it after a year or two I find things I'm not happy about. Typos, paragraphs that aren't as clear as they could be, repetitive phrasing, points that should have been made but weren't... Perfection is unachievable, but no-one other than you will ever give it a second thought.

@DavidKetcheson But even when they do not, it is almost inevitable that an error or two will slip through the cracks. Proofreading is hard. (I say this as someone who does copy editing and proofreading for a particularly persnickety academic publisher.)

@knzhou [citation needed]

Do minor typos like this affect citation count or credibility, or are they relatively ubiquitous?

They do not. At all.
Many, many authors are absolutely terrible at writing, with tons of grammatical, spelling, and punctuation errors. This is not, by the way, exclusively (or even mostly) an issue when the authors speak/write English as a second language - people who speak/write English as their first (and sometimes only) language frequently overestimate their own writing ability and don't proofread as well as they should (or at all). Also, plenty of researchers are just plain terrible at writing, regardless of what language they're doing it in. Lots of terribly-written-to-the-point-they-are-difficult-to-understand papers that don't have any sort of evidence of proofreading or copy-editing still have citation counts in the dozens. So long as people can understand the paper and think the results are important, it will be cited.
Very, very few people will even notice, let alone care, let alone hold it against you, that you have a few minor typos. I know it's frustrating to look back at your work and see the imperfections, but this is the kind of thing you should let go.

In a print journal it won't be changed or even addressed, I think. It is too much work for too little benefit. Similar if not identical for an online publication. An editing process can actually introduce other errors in some cases.
You can, of course, inform the editor, but the decision will be theirs. If you have a personal website somewhere you can keep a list of errata there for your various publications. That is more common for books, though.

As you say, too much hassle too little reward.  Another point to keep in mind is that even small changes like this, when made after publication, require a new doi.

Meet me, the person who submitted his life achievement paper to a super prestigious journal. My family was proud. My colleagues were jealous.
And then my name, John Döe, was spelled in the article in the journal as

John Derroroe

This trumps all typos in the world.
To answer your question: no, it does not matter at all, there are plenty of typos in articles - and some of them change sensibly the meaning of some information. Yours is not in that case.

Please do not worry. No one will care.
As well known to historians of General Relativity, even Einstein made typos in his works.
Like, e.g. a lost factor of 1/2 in his celebrated work on the Mercury perihelion advance,
see arXiv:2111.11238, page 69, note 20.
Big deal...


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If you introduce an abbreviation/acronym in the abstract, should you reintroduce it in the introduction to be safe?
For instance, say I introduce the term "macular degeneration" in the abstract and follow it with (MD) to establish the abbreviation. Should I just use (MD) from then on, including in the introduction? Or is the abstract often read separately and the reader expects all groundwork to be laid from scratch in the introduction, including re-establishing what the MD abbreviation means? Alternatively, I suppose you can avoid all abbreviations in the abstract and establish them for the first time in the introduction. Which is most standard/correct?

I'm sure I'm in the minority here, but I abhor the use of unnecessary acronyms. It's two words; you might as well write them out. Should you insist on using the acronym because "that's just what everybody does," I'd suggest writing it out a few times in the introduction before switching over to the acronym. Your readers may not be as used to that particular acronym as you expect, and seeing the concept in full more than once should help reinforce the concept-acronym association in their minds. By no means should you introduce the acronym in the abstract and assume everybody got the memo.

I would just reintroduce it. What's the harm?
Journals typically have a style guide for how they handle abbreviations, so ultimately you can follow whatever their guide is.
APA also recommends redefinition:

If an abbreviation has appeared in the abstract as well as the text, define it on first use in both places.

One reason is that an abstract might also appear separately from the full paper, so it needs to be "complete" in some sense.

If you use the abbreviation in both places, then define it in both places. On the other hand, it’s seldom good to introduce an abbreviation you aren’t going to use; if you’re not going to use it, then there would need to be some other (good) reason to introduce it.

I second this answer. I also tend to reintroduce acronyms and abbreviations in the Conclusion, as that section sometimes gets read separately. Figure and table captions may need introductions of acronyms and abbreviations, too, as figures and tables should ideally be self sufficient. Perhaps this is too much, but I would rather err on the side of being too explicit than not explicit enough.

Some folks will read only the abstract, others will dive into the paper, and yet others will read both. It’s a matter of taste in the end. I’d say lean to the side of the reader’s convenience as you see it at this point of your career. Your style will change over time.

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At which stage do you pay the article processing fee for Elsevier journals?
I recently had a paper accepted at an Elsevier journal, and am currently waiting for the typesetting process to start. Since it's open access there is a charge for publishing, yet I haven't seen where to pay. Does an email come after the typesetting process with details for payment or am I missing something?

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arXiv delays by putting paper on hold
How common are arXiv delays? (putting a paper on hold status?). I have recently (yesterday) submitted my first paper on arXiv, it was supposed to show up a while ago, however the status of the paper was changed to on hold. How common is this? Also is it because I'm submitting my first paper on arXiv?
Also how many days does it generally takes for the paper's announcement after on hold?

Does this answer your question? Submission on hold on arxiv


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How to deliver google scholar alerts at specific time
I get google scholar alerts at all times of the day. This irritates me because it comes up as an email, I dont have time to read it, and then I forget about it.
My only reading time is Friday morning so it would be great to get my alerts at 8.00am on Friday morning as that would be consistent with my workflow.
The question is therefore can I get my alerts delivered on Friday 08.00 and not before then- a kind of weekly digest?

What is the point? You can just not read them until Friday morning.

Create a filter to add a label to the emails.
Then every Friday you can read all the emails marked with that label!

This is definitely a good start. Honestly, I wish I had a way to prevent myself from clicking on these labels the moment something shows up, though!

Good answer.  @AJK - I use Thunderbird and gmail together.  My "favorite" folders are displayed normally, but what I can do is, on Friday, toggle over to "All Folders."  This would solve your problem.  Alternatively you could subscribe to Google Alerts with a different email account, which you would only read once a week.

There is no option to change the frequency of the Google Scholar alerts that you have subscribed to. It is better to ask the Google Scholar support team directly. You can only change the number of results that you want to see a list in your email.
I understand that it is sometimes annoying looking at 3-4 emails daily on various topics. If you are really not reading the list and not following the work, it is better to unsubscribe (or 'Cancel') the alert by logging into your account.

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IS the IJSER.org journal fake?
I have submitted my research paper inot a journal IJSER.org . But I don't know whether they are fake or not. Have any idea about this Journal?

IJSER is not listed in SJR, so be careful.

This journal is not indexed in Thompson Reuters JCR, despite their claim to have an impact factor of 3.8, and was listed in Beall's list of predatory journals. Draw your own conclusions.

The best approach is to read some past articles and see if they appear to meet an appropriate standard.  If you have enough professional experience to write a publishable paper in a field, you should have no problem making such a judgment.  IJSER's papers don't look very good to me...

The Impact factor doesn't look like legit and as stated by others it's not on the TR list of journals. In personal experience, this journal is kept on spamming my email inviting me to submit a paper. So, for an advice find other journals with good track record (i.e. studies, authors, etc.). :)

It calls itself the International Journal of Scientific and Engineering Research (emphasis mine), and it published the following paper:
Nishad, T. M.  "Origin."  International Journal of Scientific & Engineering Research, Volume 8, Issue 7, July-2017, p. 1163.  PDF.
I quote here the abstract and an excerpt:

Abstract— In this paper the application of Soul Sets in Theology is introduced. Based on reference of various Holy Scriptures, a link among
  some religions is derived.Using that relation, the generalized concept of God is discovered.

Theorem 1: Origin O intersects with A.
Proof: To prove that Origin intersects with A, It is
  enough to show that there exist a soul object
  x € O ∩ A.Consider a name of God “wadud”, The
  stem of meaning of which is Love (say x) having
  full judgment. Then x € A.It is obvious that Love
  is a soul object. Since it has full judgment,
  x € O.Hence x € O∩A .
APPLICATION IN THEOLOGY

Theorem 1 helps a Devotee to identify the soul
  objects in A and try to implement in life.
[...]

I rest my case.

You have to admit that using the euro currency sign for the "element of a set" relation is a creative touch.

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How to draft a recommendation letter for myself after professor asked me to do so
I asked a professor I have been working for about a year to write a recommendation letter for graduate school. She agreed but says she usually ask students to write for themselves and she will do some editions on it.
I was supposed to ask her for a template at that time... And now I have no idea how to draft one for myself. Anybody has any advice?

@scaaahu: I don't think this is a duplicate. The other question asks whether or when it is acceptable. This question asks how to do it.

It would be helpful to tag this question with your country, and - even more importantly - with the intended country of destination for the letter of recommendation. As outlined in a great answer by Massimo Ortolano, typical LoRs, and thereby, expectations to what an LoR should contain, vary considerably around the world.

@O.R.Mapper Actually, I was going to use Points to remember when having to write recommendation letter yourself as a duplicate. I don't want to retract the close vote because we already have many questions and answers (you pointed out one of them) about writing rec letters yourself.

Professors often do not have time to write a recommendation letter. Sometimes, they do not know the student well so they ask the students to write a recommendation letter for them. However, universities are aware of this form of "Ghost writing" and they can recognize ghost writing pretty easily. I would suggest to read some recommendation letter online and then try to write one for yourself.
If you are working with your professor for some time, try to write about the project in the recommendation letter. Try to write what you are doing in the project and what is your contribution in the project. Also, try to discuss your differences with other project members (if you have any). If you have taken any course with the professor, then try to discuss the course's interaction from the professor's perspective. If you won any awards, you can also discuss that from the professor's prospective. I guess the best idea is to read about some recommendation letter and then try to write your own.

Could you qualify your answer with some location where the guidelines you point out would apply? As outlined by this answer, for instance, a European LoR recipient may just expect to be told that "that you had worked with this person and that they are not that bad", rather than an elaborate discussion of the project, the precise contribution, and the differences with other project members. Different expectations may exist in yet other parts of the world.


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Applying PhD during the last year of master studies
I am a final year master student and currently I am working in my thesis (I have done about 70% of my work).  My graduation will be expected to be latest in this August.
I have published several publications during my bachelor degree.  However, I have not published any single publication during my master studies (my supervisor has a plan to publish a paper based on my thesis works).
Is it possible for me to apply for a PhD studies with stated condition above (I haven't get master degree and lack of publication in my master degree.
In addition  I do my bachelor and master thesis in different subfield. I will plan to take a PhD in the same subfield as my master studies. So I can say I dont have any publications directly related to my planned PhD studies.

It is certainly the right time to be applying. Don't delay.

You can definitely apply. If not now, then when?
The number of publications doesn't matter that much because the number is just a number; it doesn't reflect the complexity or difficulty of the research you did. I would fully expect that the publication resulting from your Masters studies will be more substantial - i.e., involve more work, with more robust results - than those you did during your Bachelor's.
If it still troubles you, remember there are people who do PhD studies without having published any papers in the past,


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Is it OK to have side projects during grad school and how can I get on?
I think the title is pretty self-explanatory. I am very happy with my current research topic but I would like to have some side research. Is it OK? And in case it is, how do people get those projects?

Are you talking about side projects that require lab equipment and funding?  Or just side projects that you think about in your off hours, where you need no equipment.

It's perfectly ok. In fact, I'd say it's a good idea to work on things that don't directly contribute to your thesis: you learn new things, you gain some valuable independence from your supervisor and your mind and creativity can be refreshed by tackling a new problem. Just don't let it become your priority, or I guess your supervisor might be unhappy.
People start side projects on their own, based on their own ideas and interests, or by meeting others and having interesting conversations. This can be as simple as chatting to someone at lunch in your institute, in the bar after work or at workshops and conferences.

Make sure your advisor is happy with your progress. And, it is good to finish your degree having a notebook full of unfinished work for the future.

@Buffy I think we need a new nickname for you: Fastest Gun on the Web ;)

I don't think this is a valid answer for many students.

@ScottSeidman, can you say why? Some who can't handle it are unlikely to try it, I think. Do you still see harm if the advisor is happy?

No, I don't see harm if the advisor is happy, but the answer isn't "Yes, so long as your advisor is happy", -- it's simply "Yes".  I have no idea what this student's background is, so "this student is probably OK for this" is perhaps too ambitious.  Also, there is occasionally a disconnect where a student just misperceives a mentors outlook, believing that all think their performance is fine, when some think it isn't.

This is going to depend on your whole performance as a student, and whether adequate progress is being made toward your primary project.
The better part of valor is to ask your mentor or committee, if you have one.  Those are the people monitoring your progress.

I agree that the advisor needs to sign off. I also found it useful as a doctoral student to keep a notebook of ideas/problems that would be worth following up later. These naturally arose as part of my research and jotting them down gave me a pretty big future work agenda. They were mostly just "what if... were changed to ...". They didn't distract from the work for more than the time to capture the idea so I wouldn't forget it.

And, I think that a person who would ask the question (the OP here) is probably in a good enough place to at least consider it, with caveats, of course.


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Is it OK to propose to present research in a conference as a grad student?
I am a first year grad student, studying abroad, and there is a conference in the country where I am from which I think can be a good experience (I have never presented in a serious conference) to present the  research being carried in my group. Is it OK for me as a student to propose my supervisor to present our research there?
A bit of context: there are like 8-9 people in my group, I thought of attending the congress as I would probably be in vacation anyway there, so my group would not have to cover the travelling expenses. The only thing is that I dont think that anyone from my group would travel with me, as my country is like 20 hours away from where I'm pursuing my grad studies.

Unpublished oral presentation. But my question was more inclined towards if it's okay to ask my supervisor 'permission' to present? I am new in the group and I don't know if it's a good option to seek for conferences or if I should expect my supervisor to tell me

The answer is simple. Discuss this with your supervisor.

I mean ask him without looking pretentious. "Would it be a good idea if...."

Yes of course! I would love to go, but I wanted to know whether asking could be seen as 'pretentious' or something. Thank you!

Some of the best conference presentations I've seen are from first year grad students. I think it's great to get a feel for the process as early as possible and should speak to your advisor, who would probably be a co-author on the abstract submission. Even if you don't get selected to speak, it's good practice for learning how to apply to speak at conferences.

Thank you for the advice! :D

Yes it is fine to submit to a conference as a student. But it is up to the committee whether your paper/proposal is accepted. Some conferences have special sessions for student work, actually.
It is also fine to seek advice from your advisor on this. In particular, you might get good advice about whether your work is actually ready for presentation.  But, in general, don't hesitate to ask.
Make sure you give proper credit to the others in your group.

Thank you for the answer! But my question was more inclined towards if it's okay to ask my supervisor 'permission' to present? I am new in the group and I don't know if it's a good option to seek for conferences or if I should expect my supervisor to tell me @Buffy

Thanks for the advice!


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Can I ask a postdocter candidate to write a recommendation letter for applying to graduate school
I'm working in a lab as an undergraduate worker. Can I ask one of my lab member who is a postdocter candidate for a recommendation letter?

Please clarify what you mean by postdoctor candidate.

I am guessing OP referring to the Post Doc researcher working in the lab.

See this answer

You can absolutely ask a postdoc (or even a PhD student) for a letter of recommendation! It happens pretty frequently :)
If you're debating between asking the postdoc or the professor (PI) in charge of the lab, it depends on your interactions with each of them and what you think they might have to say about you. A letter from the professor may hold more weight due to their reputation--if they can actually say something meaningful about you. If you think they would just give you an obviously impersonal form letter, it might be more valuable to get one from the postdoc who actually worked with you and can provide a more detailed and personal recommendation.
If you're applying for a position in the same field as the postdoc, also consider whether that postdoc is already making a name for him/herself, or if the professor is new and hasn't developed much of a reputation... that might further weight the value of each of their potential letters.
I'd suggest asking the postdoc who they think would provide a more valuable letter, as they will know your research field and professor much better.

Yes. Especially, a postdoc that has worked closely with you, and may have a different perspective than your professor. Whereas the professor may be involved in broader planning and thinking, the postdoc may have spent many hours with the student in the lab, analysing data, etc. Therefore, letters from professor and postdoc could complement each other and work very well.

You can ask, but he/she might not be knowledgeable in writing nor in a position to give you a recommendation letter. You should ask the professor leading the lab, their words would have greater weight when it comes to review boards.


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Should I publish work from my undergrad now that I am in graduate school and no longer working in the same field?
During my undergrad (past 3 years) I worked in a niche ecology lab and during the time generated some data. The work I did was not exactly groundbreaking but I think it was solid publishable work and could find a home in a decent journal.
My PI is encouraging me to write up my work and submit it for publication in the next few months but I have just started graduate school and am working in an entirely different field (Biophysics with a sprinkle of cell biology).
Considering that I expect writing up the work for publication will be a significant undertaking (seeing how it would be my first time writing a paper for publication), and the disparity between the subject of the paper and my current/future research, would it be worth the time commitment to follow my PIs advice and write the paper? Would there be any real benefit for my career in a different field if this work does get published?

At the beginning of a career, a paper is better than no paper at all, even if in a different field, and the experience that you can gain by writing this will become quite useful when writing your future papers.

The experience of having gone the whole way through the publication process is very valuable and will benefit you when you start writing up your new research.  In the long run (say by the time you'd be applying for tenure-track jobs) having a publication in another field won't help your CV much because people are looking at your research program.  But in the medium-term if you apply for postdocs you may not have many (or any) actual publications (given the time it takes to write-up and submit research) and it's going to make you look better because it shows to potential supervisors that you're responsible and capable of completing a project.

You beat me to essentially the same answer - so I'll just up-vote yours. My earliest publication is in a different field which is rarely cited, but it was good experience to go through the publishing process.

I guess it would be good to have the experience. Thanks for your advice!

As a side note, I'd also add: you did some research, why would you hold it back from the research community instead of going the last few steps?... There's hopefully some emotional benefit to you in contributing to the science corpus, even if it may only be a tiny piece this time.

Yes. Future employers in general like a longer publication record. (You also may end up working in another field or fields from that of your degree.) It also helps to go through the publication process.

I presume you can use the experience you get from creating the publication in your current job. The data may be totally different but the process will be almost the same.


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How knowledgable do I have to be when I start a phd?
Say I wish to pursue a phd in some CS related field. How knowledgable do I have to be in the field I am pursuing? I'm asking because some things happened recently that led me to doubt myself:
I have been doing some machine learning research for the past year and I'm working towards a first author conference submission (as an undergrad). As I was drafting my paper, my professor asked some questions about the project I'd done - such as why I chose certain methods over others, or why I choose a particular parameter for my experiments and more. And I realised that I couldn't answer them. See, in my project, I didn't create anything new. I simply took existing methods and applied them to a relatively unexplored research area, which means that I was just following what other people did. To take something and apply it somewhere else doesn't really require that much knowledge in my opinion. I've been reading papers, trying to explain why some methods outperform others and often times I do not fully understand them. The high level logic maybe I understand, but certainly not the in-depth algorithms or implementations.
I feel as if I know nothing about this field (and I probably really don't know much). Yet, my professor offered me a phd position. I feel like he was placing too much confidence in me. Have I managed to fluff my way through this project, or is this something that happens to other people too? Especially those who completed their bachelors and went for a direct phd.

I barely know anything about applied probability and optimization but that's where I am. You'll learn about the subject area as you move along.

With a few rare exceptions, first year phd students are mostly useless :)

You might want to read about impostor syndrome. The feelings you describe are sadly quite common amongst PhDs and academics in general.

Talk to your potential advisor. If possible, organize a meeting and have a chat. Granted, the formality of the occasion will depend on social norms in your country, but it should be possible to have an open conversation about any apprehensions you have about the position. If nothing else, the conversation will give you more information about what to expect during your PhD, which is not an outrageous request.

Obligatory imposter syndrome link.

The advice from @WillR is right on target.  Or you could talk to the graduate program director.  Send the person a copy of an unofficial transcript and ask if there are any gaps in your coursework. // It will be interesting for you to come back to this question a few years from now.  Hopefully at that point you will be used to thinking about those things (e.g. why did such-and-so method outperform this other method) and will have an easier time with professors' questions!

It is very appreciated for your honesty. In my knowledge, I have seen many students they join PhD courses having very little knowledge in their field. Also, many join in new fields without having any proper/concrete ideas. However, their interest to learn, hard work and self confidence all together help them to achieve a PhD and a great career ahead. It is also worth to mention that each PhD student must face lots of ups and downs. However, their self confidence and interest to do something new helps to overcome all the down situations.
So first of all, you should never loose your self confidence at the very beginning. It is very well said that "it is never too late to start". You will get enough time in PhD to learn many new things including your objectives. Moreover, it seems you have got a very good and inspirational professor. So there is no doubt whatever knowledge you have now, it is very much enough to pursue a PhD in your area of interest. Good Luck!!

It appears you may be suffering from 'imposter syndrome' - welcome to academia! This particular ailment is widespread, I'm afraid.
Especially as an undergrad, no one expects you to be an expert. That's why you go to graduate school. The fact that your advisor asked those questions suggests he/she thinks highly of you, and suggests he/she may be a good advisor.
Now, and in the future, use these situations to identify holes in your knowledge, then fill them.


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Converting URL to DOI
I'm currently trying to get published journal information (author, title, date published etc) automatically from webpages. I'm trying to avoid scraping since this is against most publishers ToS. The best solution I have so far is:

Get <title> tag from page at URL
Search CrossRef for matching title. Get DOI of top result.
Get the rest of the information from CrossRef

Unfortunately sometimes the wrong journal article is chosen when searching CrossRef. This especially happens with newer publications which have a DOI, but don't seem to show up on CrossRef search at first.
I've also tried using Regex to find a DOI on the page, but this comes up with all the DOIs listed in the references as well so this doesn't help me.
Since the DOI points to the ultimate URL, is there any way to reverse the process to get the DOI from the URL?

Hm, good quetion. The CrossRef API does offer a "link - URL" field, but one cannot filter by that. - Anyway, I have two questions: First, if you do that "automatically", why is it not "scraping"? It does sound like webscraping to me. Secondly, can you link us to an example? Is it confined to just a specific publisher? Or are there many publishers and many journals you address? I think there should be another technical possibility to obtain the data you need.

Both are valid points thank you. @anpami It's true that getting the title is scraping, but this is the minimum to get basic information (and acceptable to search engines) so this has been deemed okay. An example is this publication: https://www.cell.com/molecular-cell/fulltext/S1097-2765(21)00327-0 however note that the top result on CrossRef search is different: https://search.crossref.org/?q=The+SARS-CoV-2+RNA+interactome&from_ui=yes
Daniel-Hatton The use case is not purely research (this will output to a website) therefore I'm being very careful about minimising scraping

It turns out the process seems to be far less trivial than one might expect.
There is a comprehensive write-up entitled URLs and DOIs: a complicated relationship describing all the intricacies.
It seems it should be feasable to resolve at least the URLs of scholarly articles to their corresponding DOIs, but even this is currently not deemed doable.

In order to find the Landing Page for every DOI, we would have to follow each and every individual link. This is not practical at scale, and impossible in some cases. We therefore can't, and don't attempt to discover every landing page URL ahead of time. Our process instead tries to look for possible landing pages and then connect them back to DOIs.

If publishers would refrain from obvious misbehaviours such as indefinitely deploying internal redirects instead of updating the DOI resource URLs or even worse breaking basic HTTP functionality by using HTML redirects or even more worse using JavaScript-based redirects and/or requiring cookies or using some other bizarre means of breaking the web then the task seems rather doable, deliberately ignoring the corner case of DOI aliases for the moment.


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How often is transfer of Copyright to University required to submit PhD Thesis?
My university apparently requires Ph.D. students to transfer copyright of their thesis completely to the university. The copyright agreement, as written, seems to prevent them from publishing the work elsewhere after the work is submitted, as it only permits the author to reproduce sections of the thesis for "personal use."
I want to prepare an argument for my university that copyright to a Ph.D. thesis should stay with author, (but that the university should be granted unlimited permission to reprint or distribute the thesis, etc., as may be the norm in international universities.)
In most US and Canadian universities, how common is it for a university to require Ph.D. Students to transfer the copyright of their thesis to the University? Can anyone give me a partial list of any universities with this policy.

You can find some university policies with this Google search: site:.edu thesis copyright and intellectual property policy

Good for you. The US institutions I've been part of leave the copyright with the student. I was actually required to register my copyright in my thesis with the US Copyright Office.

Decades ago I remember having to sign a paper to allow Michigan Microfilm to make copies (delegating them the right, not surrendering it). I really can't see why the university would demand that - probably some lawyer got involved.

Note that even when the policy specifies that the copyright has to go to the university barring justified circumstances, it is often possible to just keep the copyright without giving a specific reason (example: MIT).

Without the copyright agreement in question, it's hard to be specific to your situation. Nevertheless, this sounds quite odd - while it could be the case, I think you've either misinterpreted it or left out a vital piece of information. In particular, the following, if correct, is extremely disconcerting:

The copyright agreement, as written, seems to prevent them from publishing the work elsewhere after the work is submitted

This could potentially limit your ability to publish your thesis as academic journal articles after you've assigned the copyright (On the other hand, since these are rarely word-for-word from the thesis, you may still be OK. Ask a copyright lawyer.)
Typically, there is some transfer of rights from the student to the university, for a few reasons:

So that the university can keep a copy in the library, allow people to consult it, provide to other institutions via interlibrary lending systems
So that the university can provide a copy online, via their institutional digital repository
So that the university can provide the thesis, or details thereof, to external indexing systems and repositories (e.g. EThOS)

Typically, the student/supervisor can request temporary or permanent embargo of these rights if there's an appropriate justification. Some (non-exhaustive) examples:

To allow time for the preparation of journal articles/monographs from the work contained in the thesis
Releasing the thesis would violate third party copyright on material that is integral to the thesis
Releasing the thesis would create some risk to the supervisor, student, institution or a third party
Releasing the thesis violates confidentiality/non-disclosure agreements with a third party (e.g. an industrial research sponsor or interview subjects)

Finally, there may be specific restrictions on an individual's project (this is sort of covered by the last point above). Most commonly, these would be industrial/third party sponsors who own the IP generated in the project and don't want it republished for all the world to see.
I am wondering if you are confusing some other, specific, restriction for a general policy? For instance, if you have an industrial sponsor, you may have assigned the IP arising from your project to them. Although such an agreement would usually exclude the copyright on the thesis per se, it would include a confidentiality clause for the thesis because the other IP in the thesis (potential trade secrets or patentable IP) would belong to them.
Typically, you would expect to assign your university non-exclusive royalty-free rights to your thesis.


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Don't PhD programs in Europe always inform the application result?
Earlier this year I applied to 3 PhD programs in physics in Europe, and one (Germany) informed me they can't provide me a PhD position while the other two (Germany, Netherlands) didn't inform me their review status or decision. I afterwards sent them e-mails to inquire about the status but they didn't reply me.
Last month I applied to a PhD program in physics in Europe again. The program (Germany) doesn't specify when they will inform their decision and how they will inform the applicants. It has been 3 to 4 weeks since my submission of the application. I haven't got any of their notice and wonder whether they will eventually give any notice.
So is it a common convention of European PhD programs that they don't inform all the applicants the application status and those applicants who don't get any notice can just automatically assume they are not admitted? I don't like this way because the application is not an effortless process. To apply to a PhD program, I spend much time to check its research profile, including the publications of the principal investigators therein, to compose the essays they require. Therefore I expect each program I apply to informs me the definite result.

I am not sure about NL in particular but unfortunately in general it is quite common in EU (also for PostDoc where the effort is larger in general). No matter how big effort you and the professors supporting your applications put, nothing can guarantee any answer besides an initial ack, and sometimes not even that!

Yes, unfortunately this kind of thing happens often in Europe.
Some years ago I sent a candidature for the Francis Crick Institute (UK) and in the public notice it said explicitly something like:

"We will contact the candidates we are interested in before the date
  X. If you do not hear back from us it means you were not selected."

I also had submitted a candidature for a Max-Planck program (Germany) and received a standard email. But with a note that explains why they don't give further informations about the candidatures:

P.S. I have a personal wish: Please refrain from further enquiries. I
  am the only person dealing with 1000+ applicants and I simply can't
  answer such enquiries.

However, in Portugal they usually are very transparent with this kind of process. The candidates are seriated and they ask for every candidate to reply an email in agreement with the results. If the candidates didn't agree they have 15 days to complain. In the absence of a reply and a complaint, the process is put on hold for 15 days and then they atribute the fellowship.

The websites of the programs I applied to never have statements similar to what you describe. The automatic confirmation mails also don't mention about how and when they will inform the result. One program just said selected candidates will be invited for interview on (a date). However, I think the number of applicants should not be an issue for notice, because they can just send automatic mails to those they don't admit, just like they send automatic mails to referees requesting reference letters.

Wow! Portugal has that kind of practice I have never heard! So they send mails including the reason they are rejected for the applicants to complain in case they are not convinced by the reason? But what's the meaning of complaint? Can it lead to change of decision? Usually an applicant is rejected just because there are other applicants better than him even he filfills all the requirements and the positions a program can provide outnumber the applicants.

@Captain I agree with you. The email with the "P.S" I described above was an automated rejection email, I think that this should be the minimum to be done. Not receiving any response at all is somewhat rude. In Portugal you can disagree with the evaluation, they need to justify why the other candidate is better than you. If they made some mistake on classifying the candidates and the candidate point out it can change the final classification and, consequently, the fellowship attribution. This how it is done in Brazil too.

Sorry, I found I wrote something absurdly wrong above. I don't know why I would typed that way; probably yesterday it's too cold so that my  brain didn't function well. What I meant is the applicants outnumber the positions a program can provide. On the other hand, how do you know that rejection mail is automatic? The rejection mail I received never wrote that way. Instead, it was usually atached with something like ``We hope you will find other suitable place for your PhD." I can't tell whether this kind of mail is automatic or not.

The program I was affiliated with in Europe had a lengthy admissions process—it could take months to decide on an applicant, and thus it would take time before we felt comfortable notifying declined applicants, if we felt they were qualified.
Clear-cut rejections, though, were handled much more efficiently.

If that's the case, they can show the review status in the personal homepage where we submit the applicatoin so that we can login to check the status anytime, like when we submit a paper to a journal for them to consider publishing.


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Can a research paper be accepted if its results are very close to previous works but are not better than those?
There are different metaheuristic algorithms for evaluating optimization benchmark problems, some give better results than others and some don't. If a novel metaheuristic has a very close fitness function value to another algorithm created before, let's call A, but is not better than the fitness value of A, what could be the outcome of peer-review process? Would you accept it or there is a rejection possibility for the paper if you were one of the reviewers? Can you explain it by showing an example if it is affordable?

It is possible, but unlikely that such a paper would be accepted unless it shows some significant advance other than just the result for this particular application. For example, if the methodology were sufficiently new and different and had applications elsewhere, then a knowledgeable reviewer might recommend acceptance. But the reviewer would probably need significant expertise to judge this.
What you describe doesn't seem to fit that characterization, though there isn't enough detail for an analysis here.
A technique that gives additional insight into a class of problems would qualify, if it is noticed.
So "novel" need to be "novel enough" or "significantly novel" to pass the bar.

Thank you, what do you mean by having applications elsewhere? can you clarify a bit on it?

Mostly applications to other similar (or not so similar) problems. In math, for example, a new proof technique might be more valuable than the theorem it was used to prove. A new proof of an old problem might be very novel and valuable. Or not.

Thank you, got it.

It is not possible to reduce the entire scientific value of a work to a single number. Even in industrial settings, there is rarely a universally applicable fitness metric by which all approaches may be evaluated: some may be less accurate, but also less computationally expensive, some may be better suited for a specific subclass of problems, the list goes on.
Some researchers in ML lean towards the leaderboard approach to algorithms and models ("if it is not ranking high, it is useless"). At the same time, if everyone was competing on the same leaderboard, we would have maybe 50 papers a year, not tens of thousands.
So even if your novel metaheuristic does not beat SOTA performance, it still is useful. Beware of low-hanging fruit though: if you fail to take the next step and it is trivial (examples may include combining this approach with an existing one), you will essentially get scooped. Good for the overall scientific progress, not so good for your career.

So do you think leaning towards the leaderboard approach is considered by researchers or caring about the novelty is a priority for them?

It is ultimately on you to explain why your approach is useful. At the end of the day, the venue you will try to present your work in, be it a journal or a conference, will be thinking "why would our readers/attendees find it useful?". Leaderboards are kind of a shortcut, even if the researchers would ultimately see some proposals as an attempt to game the leaderboard itself and not as a bona fide solution to an original problem. But there are many more ways to explain and support usefulness than just "it ranks as #1 at XYZ leaderboard". And it is your job to do so.


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Can i define a new problem other than existing problems in a field and propose a novel method to solve it?
I am putting my effort into proposing a novel method to solve a set of new problems in my field which have never been defined and solved before. These problems are almost similar to existing problems that are solved by different methods proposed by researchers over a long period of time. However solutions for the new problems are different than those of existing problems and also these new set of problems will be evaluated by existing methods for verification of my novel proposed method. My question is that: Is this considered a contribution or not? Can reviewers point out that why am I not solving a set of famous existing problems with my novel method?

You can always define new problems and provide answers to them. It's your choice what you do with your time and intellectual ability.
The question you don't, but should, ask is whether that meaningfully advances science. In my field of computer simulations, for example, you can always come up with a new finite element and then ask the question of whether it converges. That is, in principle, a valid scientific question that can be answered. But I suspect that few will care because there are already a million finite elements and we have very good existing methods -- we don't really need any new ones; as a consequence, you would probably have a hard time publishing this work in a good journal.
In other words, when you ask whether you can define variations on previous problems and propose solutions to them, the answer is "yes" -- but you are not entitled to anyone caring about these variations, or entitled to get them published. That depends on whether these problems are of practical relevance or otherwise of interest to your community.

If you can successfully do that, and few can, it would be a good thing.  Reviewer reaction can't be predicted in advance, however. But a good reviewer should, with suitable hints from you, say in an introduction to a paper, be able to make some judgement as to the possible impact and importance of new ideas.
In math, for example, variations on a theme can be welcome (as was my dissertation). And new proof methods can give insight beyond the specific application. A reviewer skilled in the general topic area should, in principle, be able to recognize this.
Note that both novelty and potential impact are important here. Some new but trivial variations might be interesting but only require a few moments of thought and a smile or two, but have no lasting impact on a field.
So, "can you do it" is subtle. You "can" if you are able, but it also requires that you meet some general, perhaps diffuse, criteria of impact. Neither of these can be predicted in advance.


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"Decision in process" after the median number of days from submission meaning
My manuscript went from "With the Editor" to "Decision in Process" after I submitted it to a journal, which had a median decision time of 10 days. After 18 days the status changed to "Decision in Process". What might this imply? If it was intended to be rejected within the 10-day period, shouldn't they do so? Why is there a status change after eighteen days?

Please learn the meaning of "median". If there are three papers and one takes six days, one takes 7 days and one takes 5 years, then the median is a week. Most such statements from editors and publishers, generally, are literal statements of fact. Even beyond that whatever they "intend" may not be what they can achieve in any particular case as decisions are made by individuals.

Does this answer your question? https://academia.stackexchange.com/questions/148382/editor-invited-to-decision-in-process

An 18-day desk reject is normal . A two-month desk reject is a torture!

If the median is 10 days, that means that half of decisions take longer than that.
Plus, among the half of decisions that get taken in 10 days or less are presumably all the desk rejections that happen within two days. So conditional on not being desk rejected, median time to decision may be a lot higher.
Finally, time to decision is a discrete variable with support on the nonnegative axis. Such distributions usually have a mean (much) larger than the median.
Bottom line: the elapsed time, in itself, is no cause for concern. 18 days is actually easily a case of "the editor in chief got a case of COVID, couldn't work for a week, and is now slowly digging through their accumulated work". I would not yet start contacting anyone.


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Is excluding some parts of proposal in Phd. dissertation acceptable?
Is this situation considered acceptable, wherein a PhD. student has submitted a research proposal for evaluation and the proposal is approved by committee members, but due to some reasons (which are actually admissible) the possibility of conducting some part of what is mentioned in the proposal is quite out of reach in practice (it was realized after a series of experiments proved that doing this part of proposal in practice is not possible),so student decides to remove a part of the proposal in their dissertation?
If yes, does this have to be mentioned in the dissertation? Can it have bad impacts at the dissertation defense?

You need to mention a country.

It might depend on where you are doing the PhD, but, as far as I was/am concerned, it should not matter. The proposal is written at the beginning of a PhD project and, as such, many things can change which have a serious impact on your ability to do what you originally suggested. I think everyone knows that you have to just go where the research takes you—if you find that you proposed something that turned out to be impossible, that is just how it is.
Also, unless things are done very differently in your country than mine, your examiners will never see your proposal, they will only ever see your thesis; they will never know what you intended to do at the beginning of your project, and will only care about what you accomplished by the end of it.
So, assuming your supervisor and your graduate research school (or whatever department handles the PhD students at your university) are happy with your progress, there should be no problems.
However, you will only know how much it matters for sure if you ask your supervisor, because random people on the internet cannot give you any reliable advice.

Experiments that all go according to plan are, well, boring and don’t lead to new insights.

What country are you in? In mine, my committee approves my proposal.

Let me rephrase. I know this isn't a country-level rule, but in my program, my committee was the one that approved it ... so please add some details.

@AzorAhai-him- You missed the part where I said OP should ask their supervisor this question. It does not matter what country either of us are from, because the answer will be entirely dependent on the OP's individual circumstances.

@isolatedmatrix No, I didn't. I asked because it would be useful for all readers to know where your perspective is from, as you've stated quite strongly that "your examiners will never see your proposal," and I have no basis to understand how "very different" my country is from yours, because I have no idea what it is.

This depends very much on the customs and regulations of your institution.
In general, Ph.D. quality research cannot be planned ahead and it is understood that the outcome can be quite different from what was anticipated when the Ph. D. proposal was submitted and defended.
In general, it is the job of the Ph.D. advisor to interact with the student in order to guide them exactly on issues like this. It could be that in your institution, the committee is taken this place. My expectation as a Ph.D. advisor would be that I would be informed and asked for advice when the direction of the thesis changes dramatically. One important aspect of leaving out parts of the work is that what remains might no longer fulfill the requirements of a Ph.D. thesis.
To summarize: The proposal and the Ph.D. thesis are often very different. However, there should be guidance provided for these changes. If guidance is not sought, the Ph.D. student might find themselves with insufficient work for a Ph.D. Besides, it is the advisor's responsibility to guide the student.
It is hard for me to imagine a situation where a student would present a thesis for approval without interaction with the advisor (or who-ever or what-ever takes the advisor's place).


text:
How should I ask permission for using tables or figures from published papers, in my own paper?
If I find myself in a situation where I want to incorporate a table or figure from a previously published paper into my own manuscript, and I am unable to modify the content of that table or figure in any way, I need to know the proper procedure for requesting permission. Specifically, I would like to understand how to approach a journal or the original author of the published work to obtain the necessary authorization to use their tables or figures in my own research paper. What steps should I take to ensure that my request is clear, respectful, and compliant with copyright regulations?

In almost all journals, you will find a link on the article page that will allow you request to permissions (see screenshot from a Wiley journal). Depending on the copy right settings of each article, the process to obtain permission will be different and the requests from the copyright holder as to what you have to write on the reproduced figure or table will vary as well. But normally you click on the link and the system will guide you through the process.
For some open access publications, it is enough to state the open access license that is given at the article, and you do not actively have to ask for permission to reproduce. But in those cases I would always check the extent of the open access and what it permits, as there are differences.

You need to ask the copyright holder, which may be the author(s) or the publisher. If you start with the author it might be easier to navigate, but they may not be able to actually give permission. They can, if needed, point you to the publisher.
You can also start with the web site of the publisher which may have the information about the path to follow and who to ask, perhaps.
There is no special etiquette for asking other than being clear. Giving a sentence or two about your own work, especially if it is an extension might be useful.


text:
Is it acceptable to respond to a reviewer by indicating that their request is practically unfeasible, while providing valid justifications?
I am currently addressing feedback from a reviewer regarding my paper, in which the reviewer recommends comparing my results with those of other similar studies. However, such comparisons are not feasible because, although the suggested studies bear some resemblance to my work, they differ in key aspects that preclude direct comparison. Would it be appropriate to communicate this concern to the reviewer, supported by valid justifications, or might this approach lead to negative perceptions on their part?

"Infeasible" to me means something like "that would cost a million dollars and take four years," not "these studies are different in key aspects." It sounds like you should explain what the differences are, what comparisons aren't possible, and what are.

@Azor Ahai -him, In a straightforward manner, the studies proposed by the reviewer address discrete values, whereas my research focuses on continuous variables. Consequently, a direct comparison of the results from these two types of analyses is not feasible due to their inherent methodological differences.

Not necessarily. You can definitely compare a study of people with ADHD to those without and a study of people where ADHD was measured dimensionally. This sounds like a time to deepen your understanding of the field. As a reviewer, I would not be impressed with a claim that "comparing these studies is infeasible because one is continuous and the other is discrete."

@Azor Ahai -him, The distinctions between continuous and discrete values significantly influence the outcomes of both studies, rendering direct comparisons problematic. This fundamental difference in data type and analysis methodology creates a scenario akin to comparing apples and oranges, as the underlying assumptions, statistical treatments, and interpretations of results differ markedly between the two approaches. Thus, any attempt to juxtapose the findings of these studies would not yield meaningful insights.

Did the reviewer say "directly compare"? You have inserted the word "direct" here. Did you ask ChatGPT for help with that comment?

Yes I did. The reviewer did not ask me to "directly compare" the results of both studies. However, I am not sure that explaining the whole situation here to the reviewer can result in a bad interpretation for him about the paper or not.

Not particularly interested in talking to ChatGPT. See ya.

"although the suggested studies bear some resemblance to my work, they differ in key aspects" This does sound like a comparison of the studies.

I assume you're using ChatGPT because you're not confident in your English language skills. Unfortunately using ChatGPT is likely to make up and add new details to your writing which confuses you and everyone else. Don't ever use ChatGPT when you are unable to personally verify the output in detail. It's rude to waste other people's time with ChatGPT hallucinations.

What you wrote is already a comparison. You could add a couple of sentences to your paper explaining why other studies are different and preclude direct comparison. If you think these previous works are relevant, they could be cited in this way.

If you feel that you cannot or should not make changes to respond to these comments then you need to explain why, more for the editor than the specific reviewer. It might be a judgement call in the eyes of the editor and it could go either way.
I can't predict the outcome and it could be anywhere from acceptance of your argument to rejection of the paper. But, yes, it is appropriate and necessary to respond in some way to reviewer comments even if you don't change the paper. Don't just ignore the comment, even if you think it misplaced.


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How to judge whether my application for the NSF graduate research fellowship is competitive?
The rules have changed recently, and students can only apply for the fellowship once.  I've done some interesting research over the summer with my advisor and we got some interesting results, but I don't know how "small" or how "big" my research progress is for the fellowship application.  I don't feel that I have additional ongoing research ideas that can stretch out to a 2 or 3 year time scale, at least not without my advisor's input.  Basically, I still feel too inexperienced to have that kind of foresight, and I'm wondering whether that means I won't be able to send in a bona fide, competitive application.
I could, however, use my advisor's ideas for future work on our summer project, and those ideas would conceivably take a couple of years to work on and materialize.  But would that be stealing from my advisor, and me taking his ideas to another university / lab?
I haven't had this conversation with him yet, because I want to think about it a bit on my own first.


text:
I believe a portion of a paper I am coauthoring is false
I have mildly contributed to a research project which is now ready for publication.
However, I am convinced the treatment of the experimental data is wrong.
I shared my concerns with the PI of this project and shown him why I believe this was not correct. Yet, I only made him doubt and he still wants to publish it as it is. This treatment of the data is not necessary to reach the conclusion of the paper which still holds with more standard data analysis, but it looks less fancy. Now what should I do ?

should I go ahead and work on the publication ?
should I withdraw from this project (which is a side project for me) ?

On the one hand I still believe the conclusion of the paper is true and I could use an additional publication on my CV. On the other hand I feel it is dishonest to publish something which I believe is not true.

Welcome to Academia SE. Please be aware that we cannot weigh different aspects (ethics, your CV) for you. You probably get a more helpful answer if you ask for ways to achieve a specific goal such as ways to get your part published without facing ethical issues. Note that you can [edit] your answer.

Your sense of academic integrity is more valuable than a line in your CV. If you feel strongly enough about it to post this question, perhaps you should drop out. Doing so might cause the PI to reconsider the issue. It is of course easy for me to say this. Only you know all of the issues involved.

I would also say it depends on your field. For a straight philosophy (the discipline) paper, don't have your name on anything you don't fully endorse. For a 1000+ author physics paper, I would never assume any author of the paper endorses its every word as dogma.

You seem to be giving two stories: you note that you 'still believe the conclusion of the paper is true' but you then note that 'it is dishonest to publish something which I believe is not true'.  If the issue is simply the handling of the data analysis (with alternative paths leading to the same conclusions through more or less fancy approaches), I might suggest a compromise. Add a footnote at the presentation of that analysis indicating that conclusions remain even under a more conservative statistical analysis.  If the journal allows, you can elaborate a bit there.  That way, you've solidified that you understand there are multiple approaches, but the conclusion is robust to that. This might be even more convincing.

Before signing or withdrawing, I prefer to keep discussing those matters until a decision is taken which everyone can defend. If this isn't possible you will have to weight the pro's and con's, and how you feel about having a paper with your name that you cannot stand behind (if that is the case).
One option could be to not be named as author, but instead in the acknowledgement section - especially if your role was a minor one.


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Switching paths very late
I am going to graduate this spring with a BSEE, but I have realized only now that going into the engineering industry is not the direction I want to take my life. After doing some deep introspection I realized that what I really want to do is go into academia, specifically in mathematics. Luckily, I had at least some foresight early on and picked up a minor in math. Ideally, I would like to finish the degree path that I an on and move straight into a masters program and then hopefully, eventually a doctoral degree program. However, after reviewing the requirements for acceptance into and curricula of several major math graduate programs and even the graduate program of the state school I currently attend, I am wary that, despite the amount of mathematical knowledge I have gained from my minor and what I have gotten from engineering, I am not well enough prepared for graduate school or to even get into a program.
So my question is should I still apply to graduate school despite these misgivings or would it be a good idea to switch majors/pursue a second bachelor's before I think about applying for graduate school. I am not unwilling to spend the extra time and money to do so but at the same time I am wary of doing something this drastic so late into my undergraduate career. Although one thing I am certain of is that this is indeed the path I want to take.

First of all, don't be too worried, switching after the Bachelors is not "very late" and happens more often than you seem to think.
Now for your question: I would first try to find a university/program you like to join. Maybe even more than one, in case that you don't get into your first choice.
Then, you should contact the advisor(s) responsible for this program and ask them your questions. The requirements are a little different for every program, some offer the chance to catch up on missing courses during the program, others require it before the program or don't offer it at all. Thus, we can't really give you a general answer here, as every program handles things a little different. But, as I said in the beginning, it is not entirely uncommon for students to switch paths, so most program advisors should be familiar with such cases.

Indeed. My grandfather was a mining engineer, but after retiring decided to go back and get a Masters degree in archaeology so he could work on some of the local 'digs'. So, changing course in your 60s isn't late...


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Is the approval of a co-author required after submitting a paper to a journal?
After submitting a paper to a journal, usually an email is sent to the corresponding author and the co-authors, wherein it demands the approve of them for their contributions to the paper. If the corresponding author and all of the co-authors except one, have approved their contributions to the paper by the link provided in the email, can it cause some problems and issues in the initial screening stage of the paper, such as obliging the corresponding author to get the approval of the co-author who did not approve his contribution to the paper before any further action or decision by the journal?

I'd expect so. Otherwise it would be pointless to ask for co-authors' approval. (Not every journal does that though.)

It's entirely up to the individual journal how to handle that situation.

@ChristianHennig The question is at what point does it make a difference? A journal could reasonably go to pre-screening or perhaps review before a missing approval would hold things up. The majority of cases are overlooked e-mail type issues, not actual authorship disputes.

Can you email that coauthor with a reminder that approval is needed?

@Andreas Blass, Sending an email to inform the coauthor which hasn't approve the paper is possible, but i want to know what happens if the journal does not receive the coauthor's approval upon the submission/before the assignment of an editor to that paper?

Some journals, such as the one you've submitted to, require explicit approval from all co-authors, other simply assume implicit approval (which can be problematic if an author later states they don't approve). But obviously, all authors of a manuscript must approve of it, since they are ultimately responsible for it.
Clearly, in your case, approval of all authors is required for the submission to proceed. There are two scenarios.

Your co-author simply forgot to approve and/or is currently unable (on holiday, offline etc) to do so. In this case, you simply have to wait this out.

Your co-author genuinely does not approve of the paper. In this case, the paper should never have been submitted. I recommend to retract the submission and seek to alter the manuscript such that all authors approve of it, then re-submit. This may not be easy, if there are opposing opinions, but even that can be resolved by giving space to all such opposing opinions (and stating that the authors couldn't resolve this issue between them -- I have seen this in published papers). Ultimately, if one person cannot be made happy, they may/should consider to withdraw their authorship.

I can't say about the situation you describe, but in the setup I'm familiar with, approval by co-authors is implicitly assumed. You email all coauthors to say a manuscript has been received, and you cc them in decisions or status updates, but you don't expect a reply from them, and you assume that if they do not approve they will notify you.
Because approval is implicitly assumed, it's possible to proceed directly to peer review before every co-author responds. In fact, if you are after shorter turnaround times, you can reasonably send the manuscript for review while waiting for the co-authors to respond.
Of course, if there is a "I did not approve of this paper" reply, then the manuscript is immediately put on hold while the authors figure it out.


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Leaving PhD in the US and moving to Japan?
I am PhD student at a US university (QS ranking>500). I have completed my 2 years here. I am thinking to quit the PhD here and move to the University of Tokyo. The reason behind this is my PhD advisor, his lack of supervision and biasedness towards other students has compelled me to do this. I feel discouraged and demotivated most of the time.
I have talked with one professor from the University of Tokyo, he is happy to take me. He is a renowned person with a lot of research papers and citations.
Do you think leaving the US and moving to Japan is a good idea? Many of my friends think that the US has better opportunities, but the Univ of Tokyo is one of the best world universities.
PS I am not a US citizen.

Is it possible to work with someone else at your university? Maybe you could switch or have a joint adviser (two people supervising). That would be easier.

I think there is a missing step in your reasoning between "my PhD advisor isn't great" and "I'm going to move to Tokyo." :-) [More concretely: are you a Japanese citizen? Do you want to work in Asia long term?]

In any case, only you can decide whether this is a good idea for you personally, but you might check out our archives, such as the analogous question for India and this one about Asia generally.

Hard to answer. But Tokyo univ. is probably better, in general and on paper, than a rank 400-500 QS University.

Even ignoring the big question about "why Tokyo", how can you be sure that a high profile professor in Tokyo will be more helpful/involved than your current professor?

It's hard to give advice only based on the information provided in the question. It looks like  OP is merely thinking about the prestige of the University and professor, and does not have any particular love for Japanese culture/language. If this is the case, OP is going to find themselves deeply isolated and depressed in Japan. Living there requires a SERIOUS commitment. Anyway, for the time being it's impossible for foreign students to enter the country due to COVID restrictions (if I'm not mistaken, only students with a MEXT scholarship are allowed). I think OP needs to reconsider.

The University of Tokyo is an excellent institution, but my understanding is that whether or not you are Japanese can make a big difference in the quality of your experience there.  If you never been to Japan (or East Asia more generally), you may find it challenging to fit into the culture, even just at the University.

Is there somebody you trust you could talk this over with? This is something very much too complicated for a post here to give you good adivce. In two minutes of thinking about it I cam up with 50 questions that might affect the choice. My guess is it would require an hour or two conversation to get a good handle on it.

This question is impossible to answer sincerely because it depends on a lot of other parameters of which we have no knowledge.
However, judging by the limited information you provided, and only by this information, I would say that doing a PhD at Tokyo University with a professor you get along well, is clearly much better than doing a PhD at a "QS rank 400-500" university with a professor you definitely do not get along well.
Tokyo University is the top university in Japan, or among the top, and this provides you both the infrastructure to do excellent research and the prestige to be able to continue further in your career.
Comment:
I disagree with the comments provided to your question, depicting the life in Japan as potentially challenging for you. The OP has written explicitly that they are not a US citizen. Therefore, there is nothing that hints to the fact that Japan would be a "foreign and strange cultural experience", while the US would not be a strange and difficult cultural experience for them.


text:
Undergraduate thesis credit is too expensive. Can I turn my thesis into 1-2 research papers & publish instead?
I’m a highly competitive (currently undergrad) student with the end goal of getting a position in academia. I’m about to graduate undergrad this summer; afterwards, I will do a Fulbright research grant, and try to apply for the top graduate schools.
Now due to the difficulties of the semester, I couldn’t finish my thesis in Spring 2021 but instead moved it to Summer 2021. Normally my scholarship (fully paid, public university) would cover tuition fees. However, this scholarship has just ended for me and will not cover the summer fees. And I’ve realized that the summer tuition for this one thesis credit — in which I’m getting minimal guidance from my busy advisor and am taking no classes — is $1,750.
I do have enough money saved to cover this, but it’s really a stretch. I’m kind of pissed really, paying this much money for literally a thesis credit is insane!! However I see my education as an investment. I really wanna be super competitive, and if doing a thesis is part of that, I’ll go hungry to make it happen.
But at the same time, I’m really doubting whether a thesis will be so much better than  turning my topic into 1-2 research papers. Plus I’m about to do a year long Fulbright research project, which I think will overshadow my senior thesis anyway?
Can you guys help me sort this out? Any advice is helpful!!! I’m so angry my public university is so exploitative and not sure if I should buy into that.

Can you take an incomplete for your spring credit and finish it over the summer?

Can you really get one or two research papers out of your (as yet unwritten) thesis, especially without good supervision? In my field, it's unusual for an undergrad thesis to contain anything novel. You might be underestimating the task.

Hmmm. Not sure how your university is "exploitative" after providing you a free education. Why the whine?

@Buffy The OP didn't say their university provided them a free education.

@AzorAhai-him- ... "fully paid, public university" ...

@Buffy That doesn't imply the university provided the scholarship ...

If you don't finish the thesis will you still graduate? Everything in your future depends, most likely, on graduating.

If you can publish your thesis in a journal, you should aim to do so regardless, and in addition to a thesis (if you choose to write one). Papers in a good journal are more highly regarded than a thesis.
Writing an undergrad thesis might increase your chances of grad school admission. If you have papers accepted into good journals, I doubt an undergrad thesis adds much to your application. However, most undergrad theses are not good enough for a journal publication (although yours might be).
Your thesis advisor is probably willing to help you continue your thesis research and/or turn it into journal papers even if you are not enrolled as a student.

+1 without support from a thesis advisor it's highly unlikely OP will successfully publish anything in a reputable journal.

The possibility that your advisor likely (?) does not care about your enrollment status is worth looking into, I'd think. They'd probably help you in any case, and you'd probably need their advice to manage to "conform" to publication standards in your field.

They are probably "willing" but not necessarily able.  They likely have a large workload.

I would recommend you try to separate your anger from the practical problem you face. Even if in your judgment your university is screwing you over, I'd recommend you decide based solely on what you think is in your best interest.

Talk to your supervisor. They might be willing to help you supervise your thesis on an informal basis, and/or help you turn it into publications, even if you don't enroll. Conversely, even if you are willing to pay tuition, your supervisor's obligations likely ended with the spring semester, and they might have other plans for the summer.
In either case, I'd recommend that you make a plan to have something concrete to show for your work, and that you consult with your supervisor. Good luck!

This does not answer the question.

Several things about the question are unclear, but...

If the thesis or corresponding credit is not required to get the degree, do not pay the $1750.  You will no benefit from paying it.
Do publish your work if you can publish it in a reputable journal or conference.  Check with your advisor before you try this.
Probably your advisor will be writing a letter for you.  If so, do finish the thesis and send it to your advisor.  Do not expect your advisor to help you finish the thesis; presumably, if you do not pay the $1750, the university will require your advisor to do something other than help you with your thesis.  This does not mean your advisor will not help you, but you should not expect it.

I would be very surprised if the university forbade the advisor from helping a student who is no longer formally enrolled. Especially during the summer, when faculty members often aren't even being paid.

Seconding @academic's objection: I'd be mildly amazed if a university or department therein attempted to prohibit faculty from assisting more-or-less students trying to do research. The question of enrollment is hard to see as critical, because none of my collaborators in my own work are "students enrolled at my university", etc.

@academic I did not say the advisor would be forbidden to help, simply that they would be required to do something else.  I am assuming that, whatever the workload model, the advising duties are part of it.  If advising is officially decreased, some other workload will be added.  We do not know if the faculty member is being paid during the summer, but the sort of faculty who advise theses are much more likely to be paid during the summer than those who do not advise theses.  If the faculty member is not being paid, then they should be able to do something other than advising.

@paulgarrett Again, I did not claim there was any prohibition.

@AnonymousPhysicist, understood. But/and a too-casual reader might misunderstand... (As usual...)... which might be the operational point... The longer I live, the less I seem to understand of people... :)


text:
Rejected short paper accepted as poster
I am a 1st year computer science PhD student. I recently submitted a paper to a large conference LBW that was rejected (with fair comments), I re submitted with changes to a smaller conference short paper track but it’s was also rejected (not as fair comments imo). However, they have accepted it as a poster where I would need to condense the paper from 6 pages to 3. The paper would still be included in the proceedings.
I am a bit conflicted on what to do, this would be my first publication. A few academic staff are telling me it wont be worth it as poster publications are the lowest peer reviewed paper and during COVID it is unlikely the conference will be in person (but not impossible as it is still 6 months away).
I would like to publish but is it worth looking for a different conference instead? I would also need to re submit the smaller paper in a few days.
Any advice is greatly appreciated.

This really depends on so may specific factors individual to your case that we cannot sensibly advise. Your academic advisor is really your best bet. And if that doesn't satisfy you, engage with your immediate local environment.

Actually, my advice would be to do it unless it would interfere with more valuable work.
For many students, the value of a poster session is to get some disinterested people to look at your work, ask some questions, and give you some feedback. Some of that feedback might be valuable in extending and improving the work. That, alone, has value. I remember some (face to face) poster sessions that were real posters and the people were doing interesting things. I don't know if I helped them or not, but their needing to try to explain their work to me and answer my questions had some value in solidifying their work, I think.
Not earth shattering insight, probably, but exposure and feedback are good.


text:
How to identify potential advisors for a masters program in the US
My apologies if this question is asked elsewhere or is extremely trivial, but I couldn't find a satisfactory answer anywhere...
I am currently a math major (US university) in my junior-year, looking to apply to a computer science masters program in the US later this year.
I've heard from many different sources that in general, it might be beneficial to reach out to faculty/professors before I apply (given that I genuinely have something meaningful to ask or talk about).
But... I don't really understand how to find these faculty/professors? I understand it will be different for every program, but in general how would you tell which professors are advising masters students?
I guess this question just boils down to my lack of understanding with the advisor-student relationship in a masters program. For example, is every professor required to take in masters students every year? What about adjunct/associate/assistant professors?
In the universities I plan to apply to, I have identified some faculty whose research I find interesting, but I can't figure out if they advise masters students, as they only list their PhD students on their websites. Should I just contact them, and ask if they advise masters students?
Thank you!

"Should I just contact them and ask if they advise masters students?" Yes! Unless you have a crystal ball, that's the only way to find out :) You can search on here for info on how to write emails to professors and get an answer, e.g. https://academia.stackexchange.com/questions/90725/how-should-i-phrase-an-important-question-that-i-need-to-ask-a-professor.


text:
Should I mention that I am an undergrad researcher for a lab in the postgrad program I want to apply to
So I am currently a rising senior at a college in the US (which I will call "UNI"), and preparing to apply to grad schools. Furthermore, the college I currently go to (UNI) also happens to be my dream school for graduate school.
I have been working at a lab here at "UNI" as an undergraduate researcher in the field I want to go to graduate school for. I find the research topic very compelling, and as far as I know, the lab which I am working at is one of the only labs in the US focusing on this specific topic.
I would love to continue to contribute to research in this field for graduate school, but I'm not sure if I should be mentioning this in my application to "UNI".
I'm mainly concerned that it will be frowned upon by the admission committee because I'm leveraging connections (to the lab here at "UNI") which other applicants NOT going to this school won't have access to.
Furthermore, as far as I am aware the professors don't have any say in which applicants are accepted, so the professor in charge of the lab won't be able to put in a word for me either.
What would you all recommend I do? Should I emphasise this point in my application (I.e  that I found a lab here which researches a pretty niche topic that I am very interested in, and that I have already done some undergraduate research for), and if so, to what extent? Should I mention it in passing or really emphasise it as the main focus of my application?
Thank you in advance!

I agree with the two now-existing answers that it would not be frowned upon and that you should mention it, but I'm not sure whether it should be the main focus of your application. Wouldn't the graduate selection committee already know about you, or is your department so large and/or undergraduate participation in research in your department so common that this is not necessarily the case?

You should get your supervisor's help preparing your application.

I am not in the US, but I don't think that mentioning this will be "frowned upon" as if you were having an unfair advantage in relation to the other candidates. You are not doing anything wrong or illegal by doing your undergrad research there: I actually think it is an advantage, as it shows you're motivated by the subject. If I were a part of the committee, I would see that as a very good thing.
Regarding the emphasis, I don't know about the other things you have on your CV, so I can't tell what is more or less important. I would advise you to mention it as an important experience that qualifies you for the postgrad program - be proud of it!

My advice is that you should certainly mention it. I suspect that if you apply to some other university you would certainly want to mention your undergraduate research. You should do just the same for admission to your own graduate program. It would be expected, I think.
If this is for doctoral study in the US, note that professors do, in fact, get involved with admissions. Students are admitted or not on the advice of a committee that is largely (or wholly) faculty. Not everyone is involved in any given year, of course.
Other students at other universities who are applying to yours will certainly mention any research experience. You aren't taking advantage.
Your letters of recommendation might have extra weight since the committee members know the writer, but this also happens generally when faculty have wide circles of contact/collaboration.
Just. Do. It.

Admission to masters programs may be more pro forma with faculty less involved, but the same advice applies here. Someone needs to finalize the acceptance based on what is in the written materials as interviews are much less likely.


text:
Bad undergraduate grades, decent research experience, what are the chances of PhD admits?
I'm an undergraduate student in Electronics and Electrical Engineering but am more interested in research in computer science and have decent research experience. I have done a summer internship at a very reputed place in France and our work during the summer was published and we also won Distinguished artefact award at the conference. I'm now writing my thesis at a prominent computer science research institute in Germany with a senior researcher and now am thinking about pursuing PhD. But I don't exactly have good grades and people have suggested to go for a masters to improve my academics but I feel like its the same issue there as well, isn't it the same case for masters? I need good grades to get accepted for a decent masters program so I don't see how it helps me.
I would really appreciate the community's help and advice on how best to proceed for this.

It would help if you could specify some countries where you would want to do your master's or PhD. In Germany, you would typically do your master's before the PhD anyways, and admission to a master's program isn't as selective as for a PhD.

you need to read program requirement, what is GPA they require for adission

I am writing as a American about American universities in case you want to apply here.
A Master's Degree is basically a "halfway" step toward a PhD. That is, it requires two years instead of four (or more) after an undergraduate degree.
As such, a Master's degree represents a lower risk for a university. In your case, they're dealing with a student that has a weak academic record and a strong work record. They are also, potentially, dealing with a "late bloomer."
So the feeling at a Master's Program might be, "let's see if this strong worker can fix his academic record. If he can, that's great, and he can go on to a PhD. If he has the same problems in his Master's work as in his undergraduate work, that's two years, not four that were wasted. (One year, if you are asked to leave the Master's program.)

This is true in the US. In Europe, there is no risk to the department to admit someone as a master's, since master's degrees are part of the "undergraduate" sequence.

@aeismail: I added a new first line to limit the advice to American universities.


text:
Validity of an Indian 3 year undergrad degree in the U.S
I am doing B.Sc (Hons.) Mathematics from University of Delhi, India. The duration of the course is three years. I am looking forward to get a MS or a MS + Ph.D. from the states in Pure or Applied Mathematics. So far,I know that validity of degree is subject to course and University. Do the following Universities consider a 3 year undergrad for their MS or a MS + Ph.D. in Maths?

MIT
Stanford
Harvard
Ivy leagues

P.S : I know I can get a MS in India and then apply for a Ph.D. from the states.But I would like to know about this so as to plan accordingly.

Have you contacted those universities and asked them?

Ya. I did so. I am just waiting for a reply from maths dept. of MIT. Meanwhile I thought to inquire about it from here.

According to MIT:

Graduate student applicants, who are not citizens or permanent
  residents of the US, must have a bachelor’s degree or its equivalent
  from a college, university, or technical institute of acceptable
  standing.

Therefore, if your undergraduate degree is a legitimate degree, then yes, you can apply for those programs. However, it does not guarantee acceptance.
I'd imagine the same applies to just about any graduate program in the US.

The fact the Bachelor's degree of US is of 4 years while a typical Indian one is of 3 years brings the confusion. Some of them do some of them don't. If someone belongs to these universities could help, that will be really nice.

I don't think length of study matters that much. A Bachelors degree is a Bachelors degree (assuming it's legitimate). I got my Bachelors in less than 4 years and it's just as legitimate as someone who spent 7 years getting their's.

It does. Many of them require basic 16 years of education (10+2+4) for graduate admissions.

That's interesting. I don't think I've seen that before. Not really fair for child geniuses then (not me).

Yeah. In my case it;s (10+2+3) 15 years. So I am not sure whether they'll consider me or not.

@yasir What do your three numbers represent? I would spell mine out as 13+3: public school and then college.


text:
Changing fields in postdoc. Whether or not to pursue another postdoc at 35
This is my story. I did my PhD in neuroscience (took me 5 years), with no publications during my PhD, but got my PhD thesis published 2 years after graduation as a first-author Nature Medicine paper and a Nature Communications coauthorship. I also have a few other coauthorships in smaller journals. I had a very bad experience during my PhD, mainly due to my supervisor and neuroscience research dynamics in that particular field, so I quit science and took 10 months of holidays after my PhD (I was very depressed and had enough savings). Nevertheless I always loved science. For many years I have been interested in evolutionary genetics, and even during my PhD I was reading more on evolutionary genetics than on my own PhD field. By the end of my long holidays I got the opportunity to do a postdoc in evolutionary genomics in a small research group (this was 2 years ago). I was not convinced because I thought I would have a similar experience as during my PhD. Finally I took it. I learned programming, data analysis and bioinformatics from scratch, following tutorials on internet. Now I am extremely happy and I feel that I found what I was looking for all these years. We are about to publish a PNAS paper (where I am first author) and I am thinking in applying for another postdoc in this field in a big lab to start in 1 more year. I would really like to get a faculty position in this field some day, and I don't care if it is not in a top university (I also cannot, most likely). But I am 35 years old, so by the end of my second postdoc I could be 38-39. So my questions are:

Am I too old to start a second postdoc, considering my story?
How much can changing fields affect my chances of getting a faculty position in the middle term?

I am sure there are many people around the world with so different stories, so I would really appreciate to read some opinions.

Possible duplicate of Is doing two PhDs a good path?

Read the answer to that question and consider your position. You've taken time off and recharged and refocused. I would argue that it is never too late, but you want to maximize your opportunities given what you have (a Ph.D in Neuroscience). Although I am not familiar with the field, what is stopping you from collaborating and working with researchers within Evolutionary Science?

related https://academia.stackexchange.com/questions/23613/are-old-35-faculty-candidates-discriminated-against-all-over-the-world

I hope it is not too late - I started my first post-doc last year at 35.

@geometrikal I also started at 35 and had no issues.

@FrankFYC Doing a second PhD is a completely different proposition to doing a second postdoc -- almost nobody anywhere in the world does two PhDs but there are fields where it's common to do multiple postdocs. So I don't think this is a dupe at all.

@DavidRicherby You are absolutely right. I completely misread that question. Although I hope the answer in the question helped.

@FrankFYC No worries. But I doubt the other question is much help, since the answer to "Should I do a second PhD?" is essentially, "No, that's a terrible idea" but the answer to "Should I do a second postdoc" is, in many cases, "Sure, why not?" Anyway, no harm done.

Ask yourself what the trade-off is. There are basically three possible outcomes: (i) You quit now and do something else. (ii) You take the postdoc but don't get a faculty position after that, so do something else. (iii) You take the postdoc and do get a faculty position after that.
The way you describe it, you love doing what you do. So options (ii) and (iii) involve doing something you really enjoy, with the possibility of being able to do that for your entire life. In the worst case, you only get to do it for a few more years.
Options (i) and (ii) involve having to find a different job. The only reason why (ii) would seem to be a bad choice would be if you think that the job you can get after another postdoc is worse than what you could get now. But I don't really see why that would be so. So the long-term prospects for (ii) are no worse than for (i), but (ii) involves doing something you enjoy.

I assume that for most employers, hiring OP after choice (ii) is less desirable than hiring the equivalent of (i) plus four years in professional experience in the industry, except for the very few cases where the new postdoc is in a field the employer is highly interested in. In this sense, I think the long-term prospects for (ii) may well be (but don't have to be) worse than for (i).

I agree that that is likely statistically true, but maybe to a degree that in individual cases might be hard to determine. I bet that the standard deviation is quite large. Maybe more measurable would be the fact that you start with a starting salary four years later in your life, and will lag by these four years till retirement. This may add up to a sizable sum -- but does that outweigh the joy of working in a field you love for a few extra years?

Ask your coauthors what they think. Clearly you have the chops in your chosen field to first-author a publication in a top-tier journal. You're already doing what you want to do. I'd say put yourself out there for faculty positions and see who bites. Use your coauthors for references.