text:
What are author and journal rights after a article submission?
I am PhD student and I had submitted my manuscript by email (the journal has not online submission system) to one ISI journal in November 2014. After one month I asked about the status of my paper but they said that they have not received any paper. Then again they want me to try for submission.
However, before submission I asked the editor to announce the approximate time of publishing the paper if it is accepted. He said that they can not publish earlier than December 2015. Because I am in a hurry to publish may paper, I said them I will submit my paper to another journal. After that the editor promised me that it will be published in Issue 2 of 2015 and told me that it is accepted now. I trusted him and I submitted my manuscript to the journal.
Now after two months I asked about the paper’s status but unfortunately the editor said that my manuscript will be published at the end of 2015. I am very angry about this decision and I asked the journal to reject my paper urgently to let me be free to try for another journal. But editor doesn’t answer my mail.
I want now to know what are my rights now. Can the journal not answer my request? And can the journal publish pay paper without my agreement? I don’t want my paper be published in this journal. Can I submit to another journal?

The whole submission process sounds a bit strange, not to say dodgy. Did you at any time sign a transfer of copyright document to the journal you submitted to?

1) What is an “ISI journal”? 2) Your sentence “I assured him and I submitted my manuscript to the journal.” does not make sense – did you want to write “I trusted him”? 3) What field are we talking about here?

the journal name is "Journal of Water Chemistry and Technology", the field is environmental engineering and water and watewater treatment

It would be extremely wise to look at a journals publication policy before submitting an article, especially if you are in a 'hurry to publish your paper'.
Unlike most journals, this journal only seem to publish articles on issue base. There is no Online First. Getting your article in an issue is an slow process, in most fields this takes months.
In your case, being in a hurry, you should have gone for a journal publishing Online First. You should still be able to retract your article, but should mention this when submitting to an other journal.

Most, if not all regular journals allow you retract submissions at any time before publication, in which case you do not need to wait for the journal to reject your paper and a simple email that you retract your paper should suffice (even if they do not reply to it – make sure that you have proof that you sent that mail though). The details of this will be listed in the journal’s transfer-of-copyright agreement (or similar), to which you probably agreed at some point. If you did not agree to one, the journal cannot legally publish your article anyway.
That being said, there are some aspects of your story that indicate that the journal in question is not regular, but a predatory or otherwise shady publisher, in particular:

[…], I said them I will submit my paper to another journal. After that the editor […] told me that it is accepted now.

No reputable journal accepts papers just like that. I strongly advise you to make sure that you correctly understood this communication and also to check whether the journal is predatory. You may find relevant questions on this issue here under disreputable-publishers.
Finally , some sidenotes regarding your situation:

Depending on your field, one year from submission to publication may be the norm.
Many journals publish papers online months or even years before they are published in print. In most cases, an online publication (or even an acceptance) should suffice for your needs.
As already mentioned, it’s very unusual ask a journal to reject a paper. Rejecting or accepting a paper reflects the journal’s opinion (usually assessed with the help of peer-reviewers) on your paper. Asking a journal to reject your paper is somewhat like asking somebody to dislike the colour green. Instead, you retract papers from journals.

thank you Wrzlprmft, when I submitted my paper I only attached my cover letter which in it I had confirmed that my paper is not in under review or had been not submitted to other journal. your mean about "agreement" is this cover letter or the "copyright" before publication. I have not agree with copyright yet.

I am not sure whether there is a question hidden in there, but confirming that your paper has not been submitted to another journal is not a transfer-of-copyright agreement. (Be aware though that some journals consider this agreement implicit under certain conditions, but then this is stated somewhere.)

Very thanks for your useful answer, I have received an email from the editor that they retracted my paper, now I am free to submit my paper to another journal. But It was a good experience that I'll never submit my papers to journals those only work by E-mail and have not online-submission system.

The journal mentioned in the comments below the original question is published by Springer, which oftentimes guarantees some kind of quality. At the same time, the editor in chief and all members of the editorial board are from Ukraine -- a country small enough to make it questionable that they can have a sufficient number of internationally relevant researchers in a field like this.
In other words, it is a journal operated by a small group of people who are so close to each other geographically and organizationally that they cannot provide meaningful quality control and oversight over each other. This is, for example, visible in the fact that a large majority of the papers in the journal are by Ukrainian researchers. I'm not saying that these papers are bad, but it is certainly indicative that others from abroad do not want to publish in this journal. The behavior of the editor -- accepting your paper without any indication of review -- also does not install confidence.
So, you may be better off retracting your paper if you think you can get it published elsewhere. You should be able to do so by contacting Springer staff if you can't get to the editors.

Very thanks for your useful answer, I have received an email from the editor that they retracted my paper, now I am free to submit my paper to another journal. But It was a good experience that I'll never submit my papers to journals those only work by E-mail and have not online-submission system.

That journal really doesn't sound reliable. The main principle when submitting to journal is to confirm that the article is not under review by somebody else, so I am afraid that if you don't receive a final confirmation that they rejected the paper, it is better not to send it elsewhere.

thank you Sandrina, please let me know can author wants the journal to rejects his manuscript whenever he wants? or what are the rights of authors and journal after submission a manuscript?

Very thanks for your useful answer, I have received an email from the editor that they retracted my paper, now I am free to submit my paper to another journal. But It was a good experience that I'll never submit my papers to journals those only work by E-mail and have not online-submission system.


text:
If Trump was bad for science, why hasn't the rankings of universities based in the US worsened?
Follow-up question to If Brexit is bad for British science, why hasn't the rankings of British universities worsened?
For example, Berkeley for engineering and technology even managed to surpass Singapore's NTNU, going from the 6th place to the 5th, under the last 2 years of Trump's presidency (QS ratings).
Regarding Natural Science, both US and UK universities outperformed Japanese Tokyo University, which slide out of the top 10 in the same time-window.

How do you expect the answers to be different compared to the orginal thread about the UK leaving the EU?

@StephanZ. good question. I hope someone will come with the follow-up "If  was good for science, why hasn't the rankings of universities based in  improved?"

I mean there are exceptions where something big enough happens quickly where you would see it in the rankings (Russia 1991, Germany 1930s).  You also might see bigger effects in smaller countries that aren’t already atop the rankings, like Hungary, Lebanon, or maybe even Turkey.  And of course Kabul University.

I'm downvoting because you didn't cite anything for why you think Trump was bad for science. This matters because if the premise is false the rest of the sentence does not matter; furthermore if the premise is true then there are still different ways to interpret how Trump was for science - e.g. if he publicly denies climate change, that is arguably bad for science, but it doesn't directly affect the things that go into university rankings.

@Allure I do not need to explain the obvious. Anyhow, I put a big "if" in front, that is to be taken as an axiom, not an opinion, the question then follows.

In short, the ranking of the university (at least in the ideal world) depends on its performance, not on the support (or lack thereof) the society provides to it. Neither Trump, nor brexit directly changed the faculty composition, curriculum, or the student body at any of the US or British institutions. The incentives or punishments the government or the general public (right now you have to take into account both forces, at least in the US) impose on the educational institutions can change all three, of course, but it requires noticeable time, so the performance will react to them with delay and rankings will react to performance with delay as well, because they normally take into account the last x years, not the current second. So, just wait a bit to see the real effects of brexit and make sure Trump holds power for 10-15 years in a row to see the effects of Trump. Rankings are not stock market prices that are driven by changes in anticipation and react to any event immediately.
So, if you want to check your premise that something is good/bad for science using rankings as an observable, make sure that you maintain that something for a reasonably long time before taking measurements. The brexit will, probably, last though the particular economic hardships it caused may go away (after all, Great Britain is still a strong country). Will Trump last? All you can do here is to vote for him and for the change in the US law that would allow him to stay in power for more than one extra term. I doubt you'll find enough supporters for either of those ideas :-)

US universities are mostly private or run by states.  The federal government has very little direct influence on universities relative to what happens in other countries.  And most of the big ways that the federal government influences universities didn’t significantly change during the Trump administration (no giant cuts to NSF or NIH funding).  There were some decisions that had enormous negative impacts on specific scientists (most notably the incredibly cruel travel ban for Iranian scientists working in the US) but not much that you’d expect to dramatically move the needle broadly.  Certainly nothing at the level of Brexit.

There's also the fact that Trump is no longer president. See Much of the damage to science — including regulatory changes and severed international partnerships — can and probably will be repaired if Trump loses this November. Looking at that article it doesn't seem like Trump did much that directly impacts the factors looked at in university rankings either - things like CO2 emissions don't directly affect rankings.

Right, I mean the main damage was mostly damage to the US's reputation, which hurts recruitment.  For example, it's becoming less common for top German scientists to consider jobs in the US rather than Germany.  I know a number of people (both American and Canadian) who have moved from the US to Canada.  But there are so many good candidates and so few positions anywhere, that the effects are all going to be pretty small.  Honestly the first place you might see an effect in rankings is Canadian universities moving up (and Dutch and Irish universities moving up in Europe).

source: Stack Exchange

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

sort: votes


text:
As a Master Thesis supervisor, how should I assist students with poor fundamental skills (e.g., problem solving)?
I am currently working as a research assistant at a University and one of my tasks is to supervise the Master Thesis projects of students in our lab. Most of the projects I manage are related to Embedded Systems and Automation applications.
As part of my supervision, normally I dedicate an hour or two per week for supervision to discuss the development of their project and current issues. Most of the time their issues are related to a lack of technical experience on a subject (which was part of their Master's Course).
As sometimes, the problems are small I will dedicate part of my time to solve it with them. But from my experience, it seems that these issues keep upcoming due to poor research and problem-solving skills. As I am relatively new to supervising Master Students, I would like to know what are some of the key elements to assist them with these type of problems and up to what extent should I help them?

There are a range of possibilities, not all good. At one end of the scale you can just provide answers, maybe working out the answer for the student. This is the worst option considered here. Along the scale is your solution which is to solve it with them. Much better, especially if you let them lead. At the other (far) end of the scale is to simply provide them with some resource that is tailored to letting them do it on their own without further help. Even something like a section or even a page in a book. Or a search online that gives them help. This may be too little help for most students.
My own solution would be closer to the latter end, and exactly there with some students. Students need to gain insight and to do that they need to work through the crux of the problems they face. But sometimes they don't notice something that is blocking them. If you work with them a bit, asking for what they have done so far and why, perhaps you will get an idea about the nature of the block. If you can redirect them a bit, with a minimal hint, they will come out ahead in the end.
Students and some inexperienced instructors seem to think that the point of exercises is the answers, when in fact it is the learning that leads to being able to provide the answers. Keep that distinction in mind and also make sure your students understand that. Done well, it can also lessen the amount of cheating/copying that goes on.

To expand on this comment, I think it is important for OP to realize that what is an obvious block is not so obvious from the student's perspective. One of the things that OP can do as a supervisor is to help the student be more mindful and reflective of how they are approaching a particular problem. Perhaps the reason OP's student is having issues is because of something systemic with the approach the student is taking, but the student does not have the wisdom to recognize that yet. Place yourself into the students shoes, and try to adopt their perspective, it can be of help in guiding.

I suggest asking your supervisor about how you should deal with this problem. Provide examples of the questions you're fielding. Ask for help, don't simply badmouth the students. Your supervisor will know better than anyone on this site can whether the level of support you are being asked for is more than is reasonable.

I found with a masters research project, it works very well to break the problem down into small chunks, and give the student a week to solve each one. It may not be a week of work but there you go, its easy enough to tackle given the time frame.
Then, when they are done, they have gone way further than they could unsupervised. And they gain confidence (not all students at this level have confident problem solving skills, as they are still learning this).

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


text:
recommendation letter from professor who doesn't know me very well
A master's program that I want to apply to is asking for two letters of recommendation. I can get one of them, because I am very close with a professor that I'm doing a research project for, and I'm doing a good job in it.
But the second letter might be a problem. Basically, I have other professors and instructors to choose from, but none of them know me as well as the professor mentioned above. In their classes, I did well, but I wasn't top of the class.
There is one lab instructor that I had, and I always did very well in his lab (I'm good with hands-on work), but I don't know if he remembers me. He would always give me a bunch of extra credit for the lab reports.
Another professor I was thinking of asking is a statistics professor. I'm thinking he might be willing because at the beginning of his class, I was struggling, and failed the first midterm, but I studied and improved greatly in the end. I finished that class with a 3.5.
So my question is, how can you ask for a recommendation letter from a professor that doesn't know you all that well? I've seen others do it, but it always seems like they are the students who either did very well in their classes, or who have a much closer relationship with the professor.
Also, I'm on a time limit, as the masters application is due in about one month.
Any help would be appreciated.
Thanks!

Well, it's better than nothing. Maybe talk to them a bit and let them know you a bit more.

I finished that class with a 3.5 --- For many people (including me), this means about as much as saying you finished with a 92B-hw. Plus, was this an elementary (high school level) descriptive statistics course, a calculus based statistics course, a measure theory based statistics course, etc.? However, this issue aside, I think the rest of your question provides sufficient context and is sufficiently detailed for the question you are asking.

Possible duplicate: How can I get a reference letter if I was never "close" to any professors?

I think you have a couple of good options for the second recommendation letter:

Ask the statistics professor to write the recommendation letter. Struggling in the beginning, but overcoming the difficulties can be a good point in his recommendation letter if he perceived that situation the same way. If you ask him over the e-mail, please, give him enough information to connect yourself with a student he had. You don't want to write his recommendation letter, but want to give/remind him of certain facts (term, grade, progress, course contents, what you learned). Meeting in person will be probably even better, but be prepared to introduce yourself with some story and keep a piece of paper with the factual information you wish he uses in the recommendation letter. The professor will either decline (if he doesn't feel comfortable) or will become one of your references.
Ask the lab instructor. And follow the same procedure. The recommendation letter from him might feature your hands-on skills and ability to analyze the experiments, which is also valuable.
Find somebody outside of academic circles. It would be nice if you worked and volunteered somewhere and your manager is able to recommend you based on some other set of skills.

Again, none of those are ideal references, but usually, for a Master's program, people don't have reference letters that are from perfect sources. And your potential ones are certainly not bad at all. Especially, if they decide to write a good recommendation letter.

I was also planning to ask in person. I thought it would be more effective and more polite as well. Perhaps they do remember my face.
In regards to other sources from work, would it matter if my work has nothing to do with my major, electrical engineering? I only have had part-time jobs, but none of them are engineering related.

For other sources, it depends on what they can write about you. An excellent recommendation letter from a completely non-engineering job would be better than a dry paragraph from a professor that barely knows you (provided that at least 1 recommendation letter is from academic circles)

First, ask him/her if they feel confident they can write a positive letter. If they can’t, it’s usually apparent.
Next, consider how you would write a letter for someone you have a positive impression of but don’t know that well. You’d want some help. To do that, create a ‘packet’ of objective evidence - some papers you’ve written, synopsis of projects, a statement of accomplishments, and career goals. The willing writer will draw from that in constructing your letter.

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


text:
Is it acceptable to ask or present a recommendation letter from a professor who left the university?
I finished my undergraduate studies around 2 and a half years ago. I didn't directly apply to any university to continue my master's degree.
Recently, I decided to continue. I live in Lebanon and I was searching for some universities in the UK to apply for. I found some local agents that help students with their inquiries. They asked me to provide them with 2 academic recommendation letters or either 1 academic and 1 professional.
If anyone saw my answer around here would know that I am still in contact with one of my professors back in the university. That professor now left this university and even left the country with his family, yet we're still in touch.
My question is the next:
Is it academically appropriate to ask him for a recommendation letter? In case he did write me one, would it be legit to present it since he left the university?

Yes he can give you a reference.
But he can’t say he is still at X university , it has to be clear he has moved on just in case they try to contact him.
People move all the time...
Some universities still receive reference requests for professors who are no longer available (death, no contact etc) and organize another professor or the Dean to write a reference to help the student.

Yes, he can write a reference for you, outlining how and when he knew you as a student at his former institution, signing it with his current title at his current institution.  Happens all the time.

Mentioning that he was formerly a professor at the student's institution.

@Buffy  That's the "how" he knew the student.

Yes, but I think it should be explicit. It is possible to know a student otherwise, of course. The OP isn't in control of what is said, however.

@Buffy If indeed he actually held a professor title, I'm pretty sure he will know how to write an LOR.  I'm only a lecturer and I know how to do it.


text:
Results Presented in Conferences and Their Publication
I'm planning to go a large Earth Science conference (couple thousand attendees expected) that does not result in refereed publications. Some other fields (like Computer Science) have conferences that result in publications, but I'm in Earth Science and it's extremely rare our conferences result in publications. Only journal publications really count.
Questions:

As a student, I have unpublished results that I wish to obtain feedback/input on from experts in the field. But if I present unpublished results, what's to stop someone from stealing my work and publishing it in a journal?
For a different project I'm working on, I published my results in a paper, but I wish to obtain feedback for further work. However, when I submit a conference abstract, I need specify what percentage has been presented or published elsewhere. I hear that if 100% is specified, the abstract will likely be rejected. So it seems presenting published results is unfeasible, while presenting unpublished results is risky (Question 1). So now I'm confused: what do most researchers do?

Can you please say what field you are in, because the answers will likely vary by field (e.g., astronomers have very different practices than biomedical researchers)

Sure - I'm in Earth Science. I updated the question also.

On 1, if you present something at a conference, there will be witnesses that you presented it there, and you will have documentation of your work products on your computer, in your lab notebooks, etc. If someone does take your work from your talk and try to publish it, you can work with the journal editor when you discover it to prove that whoever it was stole it from you and have the publication pulled so that you can publish instead. You can also contact the employer of the stealer and have disciplinary procedures started against them. Stealing your work is not outright theft in a legal sense, but it is serious academic misconduct, and shouldn't be taken lightly by anyone.
Also, this isn't dangerous. As far as I know, this kind of stealing basically never happens. That being said, if you want to protect yourself even more, write up you results into a paper draft and get it submitted to a journal ASAP. If the work is under review, then you've got a lot more protection from having your work stolen.
As to 2, "I hear" is a bad standard to base your decisions on. Contact the organizers of this conference and ask for their advice. You might even link to the conference so that we can help you figure out what's going on.

Bill Barth, it's the AGU Ocean Sciences conference. I decided not to go, but thanks for the advice.

1) It does not happen often that researchers try to steal ideas. The risk may be higher if you are working on a very hot and competitive topic. How to protect yourself: try to publish your result somewhere by submitting a journal paper in the near future would be a good idea.
Besides, the risk is not just that someone may steal your work, but that someone  could do something similar but different that provides better results. Let say for example that some researchers see your method A at the conference that is unpublished. Then they publish alternative method B before you publish method A in ajournal and method B works better than your method A. In that case, it may then be hard to publish your method "A" This is why, it is important to not wait too much before you publish your work. This is true if you work on a competitive topic. On some topics, you need to publish very quickly otherwise other researchers will publish ideas before you.
2) Contact the conference organizers.  The % depends on the conference/journals where you publish. I have ever seen some venues/journals asking for 30%, 40% or 50% new content. It all depends. You need to ask if it is not indicated on the website.

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


text:
Author wants to withdraw or insist on re-reviewing at proof stage of publication
I am editing a small scholarly journal published by a learned society. One of our authors, after his manuscript was finally accepted for publication and he had signed and returned the publishing agreement (with copyright assignment), is trying to negotiate after receiving the first proof version.
He insists on adding new content and a new reference to the main text of the article, which I, as editor, will not allow. He is offering to resubmit the manuscript with the new content included, and to wait for the results of a completely new peer review. He is very persistent about including the new content which, I think, has no impact at all on the overall quality or on the conclusions of the paper.  The reference is a fresh (2015) self-reference, so I assume that he simply wants to increase the visibility of that other paper.
One of my main problem with the new reference (and the related content) is being to one of the author's own paper published in a predatory open access journal. The publisher is listed on Beall's list. When I pointed at it, he said that his paper was subjected to valid and rigorous peer review and other people's bad experience have nothing to do with the academic validity of that specific paper. I disagree, and as I am responsible for our published content I feel adding the new reference is a risk to our journal's reputation.
It would be a waste of our journal’s resources to disregard that we have the copyright of a manuscript, which we accepted for publication after rigorous peer review. We do not feel that we should comply with what the author wants, and we feel that we should publish the paper even if the author will not approve the final proof.
What do you think about this situation? I have a few other options, namely to reject the paper altogether and to go on with the new round of reviews. Both choices would make me feel being strongarmed. Any advice would be appreciated.

Can the new content be tacked on as a sidebar?

If were not in the proof stage I would suggest not to forbid citation of certain journals. That may be similar to encouraging citations from certain journals (the same publisher, for example) and that is clearly wrong. It may be a war against competing publisher.

I agree with @VladimirF: Considering where a citation points seems like a bad policy. If Springer forbids citations of Elsevier journals or the other way around, we would clearly not be better off. In your case, where the referenced publication was published should not be your most important argument. The remainder of the discussion remains untouched, of course.

At your journal, are the perceived quality of the citations always taken into consideration when deciding whether to accept a paper?

To the added information on Beall's list, you should be aware that list is not infallible.  E.g., http://academia.stackexchange.com/a/42387/19607 Have you looked into the journal and that specific paper in question personally?

@Mark Plotnic, Kimball: OC. The aforementioned self-reference points to a "policy paper" which enumerates and organize ideas about solving a specific problem -it is not easy for an external reader to decide if the paper itself is valid or not, as it essentially contains the author's (informed and educated) opinion on that matter. Before replying to the author I further checked two papers randomly from that issue and I found both being plagiarized, and because of that I doubt the seriousness of scientific control in that journal in general.

@Kimball, Mark Plotnick [continuing from the prev. comment] The policy paper in question is not plagiarized and, though I am not an expert on that topic, seems to be reasonable.Problem is I doubt that it received proper peer review from peers who are expert on the topic as the overal quality of the journal suggest otherwise. Yes, I've read other papers from that journal too, which are on a topic I am familiar with.

I'm not disputing your judgment of the lack of peer review in that other  journal.  I was just asking whether your journal already has a policy about this. If a paper cited a paper on arXiv, or on an author's own web site, or cited a  personal communication, would that also influence the decision about whether to accept?

If the author changed the reference to be to a copy of the paper on his web site, with no mention of the predatory journal, would there still be any objection to it?

@Mark Plotnick No it does not have. Usually authors can cite and draw information from anywhere they judge appropriate. We have many examples in published papers when references are to blog comments, newspapers, personal communications, white/working papers etc.

@Mark Plotnick No I would not object such a reference as the type of the source would be clear for the reader and would not simulate a scholarly journal.

@Wrzlprmft I don't think your edit was appropriate. The poster made a conscious decision to use a gender-neutral pronoun. It wasn't a spelling error. I admit I find "hu" silly and would prefer the standard singular they, but I don't think that opinion (or your opinion) justifies editing the post in a way that clearly contradicts the author's wishes.

@Potato: Ah, that explains the weird consistency. I didn’t even think that it might have been that. Anyway, given that it is hardly used (and certainly confusing readers), I do not think that it should stay. If necessary, use a singular they – at least this is somewhat common. Also, the author’s wishes are secondary on SE. To quote the FAQ: If you are not comfortable with the idea of your contributions being collaboratively edited by other trusted users, this may not be the site for you.

@Wrzlprmft You have a good point that it's very uncommon and may be (will be) confusing. But the author's wishes still have some force here. The edit should have kept the post gender-neutral. There's no good justification for gendering it when the author has very intentionally left it genderless.

@Potato: Feel free to revert it. As I said, I did not even recognise the author’s intention.

While you might be in the legal right, I think trying to publish when the author wants to withdraw is likely to be more trouble than it is worth for a small society journal.  You probably don't have the resources to get into a protracted battle if the author decides to be really problematic (e.g., a lawsuit).
As I see it, there are three reasonable approaches at this point, in increasing levels of assertiveness on your part:

If the new content isn't very big (e.g., a paragraph or two and the reference), just let it be; just make the change at the proof stage and let it stop being your problem.  If it really does make little difference to the paper, as you say, then this is a reasonable triage to do to get this author out of your hair.
Reject the paper and send it through a new round of peer review.  It's not too bad a waste of resources, particularly if you use the same reviewers, who will be able to just look at the new version in terms of its differences from the old.
Offer the author the choice between a final rejection (no resubmission will be reconsidered) and publishing as-is.

Which you choose probably should be guided by just how willing you are to invest your time and reputation into a battle with this author.  Some people are known and repeat-offending bullies, and it's definitely worth standing up to them.  Other times, you've got a person who is normally reasonable and who has just gotten a particular fixation on this particular issue and it's worth accommodating them one this one occasion.  If you do decide to accommodate the author, however, you need to make it very clear that this is an unusual exception and you will be holding them to much stricter guidelines in the future.

I think this is a great answer. The only thing I would add is for the publisher to add text to the publishing agreement that clearly says changes at the proof stage are not allowed except in the case of errors introduced during the editing and typesetting process.

@StrongBad: After all we know, such a term may be already part of the agreement.

Ok, it seems that I should add this information: One of my main problem with the new reference (and the related content) is being to one of the author's own paper published in a predatory open access journal. The publisher is listed on Beall's list. scholarlyoa.com. When I pointed at it, hu said that hu's paper was subjected to valid and rigorous peer review and other ppls bad experience have nothing to do with the academic validity of that specific paper. I disagree, and as I am responsible for our published content I feel adding the new reference is a risk to our journal's reputation.

@HunSoc Given that additional information, I would strongly advise going the route of another round of peer review.  If the publication is dubious, then it seems like the author might be perceived as trying to "slip it past," and the peers should have a chance to weigh in.  If they object, you can rightfully deny the new addition; if they don't object, then it's not the big reputation risk than you fear.

@jakebeal Yeah but since we blind papers and this is a self-citation, the reference would show as [item redacted] or sthing similar, so reviewers will not be aware of the nature of the journal to which the new reference is pointing.

@HunSoc The author is asking for one variation in procedure; you can say you will grant this extraordinary re-review if they'll allow some degree of unblinding.

@HunSoc: You said that the added content was okay.  Does this mean that you read the cited paper and found that the material in it is solid?  Or does it mean that the added material does not depend on the cited paper in any crucial way?  Or something else?

@Hunsoc I would say that you are using double blind reviewing in a suboptimal way then, as you are not allowing the reviewers to see information which can be crucial to reviewing the paper. As far as I can tell it is more common to hide the fact that it is a self citation.

@jakebeall yes, same thinking here

It would be a waste of our journal's resources to disregard that we have the copyright of a manuscript, which we accepted for publication after rigorous peer review. We do not feel that we should comply with what the author wants, but we feel that we should publish the paper even if the author will not approve the final proof.

I would absolutely recommend against this.  It may be legally acceptable, but I would consider it an immoral abuse of copyright.  There's a lot of debate about whether publishers should hold the copyright to papers and what the costs and benefits are, but I've certainly never heard the view that publishers should hold copyright in order to facilitate publishing the paper against the author's wishes if the author becomes uncooperative partway through the publication process.  I'm sure the author did not think of the copyright transfer as meaning the journal could simply publish whatever version it chooses in case of a dispute, and taking advantage of this technicality would hurt the journal's reputation far more than the author's.

The reference is a fresh (2015) self-reference, so I assume that hu simply wants to increase the visibility of that other paper.

If the other paper is unrelated, then this is worth arguing about (not because it's a last-minute change, but because inserting unnecessary self-references is itself problematic).  However, I see no good reason to object to adding a last-minute reference if it's actually on topic.  Surely the cost of making such a change is minimal, and it might actually be useful for readers.
The additional content is a more subtle issue.

He is very persistent about including the new content which, I think, has no impact at all on the overall quality or on the conclusions of the paper.

I can sympathize a little with the author, since this content might be worth recording in the literature but simply not publishable on its own (too short or too closely tied with this paper).  That's a reasonable argument in favor of including it in this paper, even if it doesn't improve the paper's quality or change the conclusions.  However, making nontrivial changes to page proofs is certainly disruptive.
I don't see reviewing as a real obstacle if the changes are modest.  If the author just wants to add some brief and uncontroversial comments, I imagine you could get one of the original reviewers to look them over very quickly and approve them as unproblematic.  Of course larger or potentially controversial comments would require serious reviewing.
If the other last-minute changes would increase the typesetting and copyediting costs, then you could ask the author to cover the increased costs.  (That may upset the author, but it's a traditional approach to handling this situation.)  You might also keep costs down by adding the material as a "note added in proof" at the end of the paper.
In any case, I'd explain to the author what you see as the problem here.  Disruption to the journal's internal processes, increased costs, the potential for an end run around the reviewing process, etc.  You might be able to convince the author by pointing out issues hu wasn't thinking of, such as "You might think adding two paragraphs on page 1 is no big deal, but the copyeditor has already spent time optimizing the layout and figure/table placement throughout this long paper.  I don't feel good about saying that needs to be redone just because you didn't submit a truly final manuscript when asked for one.  I can't run the journal effectively if the staff feel I'm wasting their time or not standing up for them."

Both choices would make me feel being strongarmed.

This sets things up as a power struggle between you and the author over enforcing the rules as you interpret them.  That sounds like an unnecessarily stressful and confrontational approach, and also one that is not likely to be persuasive to the author.  Your discussions so far have established that the author feels these changes merit an exception to the rules, while you are unconvinced.  Going forwards, I'd focus on what the underlying difficulties are, rather than whose will is going to prevail.

Ok, it seems that I should add this information: One of my main problem with the new reference (and the related content) is being to one of the author's own paper published in a predatory open access journal. The publisher is listed on Beall's list. scholarlyoa.com. When I pointed at it, hu said that hu's paper was subjected to valid and rigorous peer review and other ppls bad experience have nothing to do with the academic validity of that specific paper. I disagree, and as I am responsible for our published content I feel adding the new reference is a risk to our journal's reputation.

Ugh, that complicates things a little.  I wouldn't want to censor references based on where they are published (and in principle a reference shouldn't be viewed as an endorsement, despite the popularity of citation counting).  However, this makes me less sympathetic to the author.  I think referring to predatory journals would hurt the author's reputation rather than the journal's (except to the small extent that it lower opinions of this paper), so I wouldn't worry about this too much, but it leaves me feeling that the author may be pretty far out there regarding eccentricity or cluelessness.

I'm sure the author did not think of the copyright transfer as meaning the journal could simply publish whatever version it chooses that's not what he said. He said that the author did approve that specific version and later tried to retract it.

@Lohoris Exactly. True, I was and am annoyed by the possibility that I may have to put extra work on the reviewers and prepare a new proof, or loose this paper altogether if the new version will be rejected or the author withdraws (we already have a place for this paper in the upcoming issue, which will be published before a new round of peer review could finish). But what is perhaps the most striking is that the author seem to be neglecting that he even gave in writing that he approve the publication of the "finalized" version.

@Lohoris In my experience, authors have to sign off on the page proofs and have not given their final approval to the published version until that point, regardless of whether they have signed the publishing agreement and copyright transfer form already.  Authors may sign those forms early in the process as a sign of good faith, but if a dispute arises, it's not reasonable for the journal to say "Oh well, you already agreed to publish the paper, so we don't really need your approval for the page proofs."  (You can't even do this if the author is being difficult or unreasonable.)

I just wanted to add a third opinion: it is really not a good idea for you to publish an article against the author's wishes, even though you hold the copyright.  If you did this, then at best you would never have any dealings with this author again.  (In reality: that outcome must be acceptable and perhaps even desirable for you to contemplate this course of action.)  More likely, the author will complain about it to a smaller or larger number of people, creating a bad name for your fledgling journal.  For what it's worth, if I heard a story about this from an open access journal published by a regional scholarly society: I would not do business with you.
If I am honest, I didn't find your reasons for not publishing the change to be very convincing.  It sounds like you are viewing this as a power struggle with the author that you want to win.  You write:

He insists on adding new content and a new reference to the main text of the article, which I, as editor, will not allow.

Why not?  You don't really say why you care so much.

He is offering to resubmit the manuscript with the new content included, and to wait for the results of a completely new peer review. He is very persistent about including the new content which, I think, has no impact at all on the overall quality or on the conclusions of the paper.

If in your professional opinion the added content has no impact on the quality of the paper, then in particular it has no negative impact.  So what's the problem?
The offer to get a completely new peer review seems like a generous move on the author's behalf.  He's saying that he's not trying to sneak anything by you but rather wants to err on the side of going through the process thoroughly, even to the extent of having the publication delayed (surely) or jeopardizing the acceptance of the paper (possibly).  But because you feel the change is so minor, you can just bypass this entirely.  It seems to be matter of retypesetting the paper.

The reference is a fresh (2015) self-reference, so I assume that he simply wants to increase the visibility of that other paper.

This seems like a rather bad faith assumption.  If the author feels that his other
work is relevant, it contributes to the literature to have the citation appear.  In general, it can be tricky to get cross references in one's own recent papers right, and last minute additions can be very helpful here: if it's a 2015 publication then it is plausible that the author didn't have the full bibliographic data until now.

It would be a waste of our journal’s resources to disregard that we have the copyright of a manuscript, which we accepted for publication after rigorous peer review.

That's written as if you're conveying information, but to me it sounds like a dogmatic assertion about you've already decided to do.  What resources would be wasted by retypesetting the paper?  Let me quote from another answer which approaches this issue more reasonably:

If the other last-minute changes would increase the typesetting and copyediting costs, then you could ask the author to cover the increased costs. (That may upset the author, but it's a traditional approach to handling this situation.) You might also keep costs down by adding the material as a "note added in proof" at the end of the paper.

In other words: if it is really a waste of your resources, ask the author to financially compensate this waste.  Or tell him that you need to accommodate him in the most inexpensive possible way unless he is willing to financially contribute.  Either of these is so much more reasonable than publishing a paper that the author doesn't want you to publish.  You speak of being "strongarmed" but many authors would regard the behavior you're contemplating as an extreme example of that.  Can you not work with the author to come up with an outcome in which neither is strongarming the other?
Added: I just read the bit about the added publication coming from a predatory Open Access journal.  I think that probably should have been part of the question, since as my answer above indicated, the explanations by the OP didn't really explain the motivation.  This does.  However, I don't think it really changes my answer, except to say: either you have concern about the added content or you don't.  If you do, you should get it re-refereed.  If you don't, then the fact that the citation is to a not-so-great journal is really not your concern: citations should not be censored (which is not exactly what's happening here, but just to enunciate the principle) by the editor because they are unseemly to the journal.

"if it's a 2015 publication then it is plausible that the author didn't have the full bibliographic data until now." Though not having full bibliographic data isn't really an excuse: the paper could have been cited as "submitted" or "to appear", with the bibliographic data added later if it became available.

@David: Yes, that's true.

It takes two to tango -and tango it should be, and not tug-of-war.
You representing a collective entity (a journal), should take the high moral ground here, not the legal one. I would suggest to send the updated paper with a full copy of the other paper that the author wants to add as a citation, to the same reviewers, asking for their help, in the name of science (and anyway, since they know the paper, it should take them little time to judge the worthiness of the added material and of the citation). It is fair also to inform them about your concerns.
If they give the green light, the author's persistence would have been vindicated by the same people you have trusted in the first place. If they don't, you can tell the author that the new version did not pass the test. If then he wants to completely withdraw, so be it. You will have done what a scientific journal should do: give science a chance -and sometimes, two.

I am wondering not about the academic view (where clearly you shouldn't publish if the author doesn't want you to publish), but about the purely commercial view.
Up to some point in time a publisher wouldn't care much if an author withdraws. A bit later it becomes inconvenient because it's too late to find a different paper, and a 100 page journal might become an 80 page journal. Next stage is where the journal has been sold and the buyers won't be happy if they don't get the pages they paid for, or where buyers have been promised a great article about a subject and that great article isn't going to be there. Then a stage where the printer charges for the empty pages, and the final stage would be where the journal is printed, and withdrawing would mean to destroy the print run.
At the point where withdrawal causes the journal financial damage, the withdrawer has to take responsibility for this and face the damages. And if he wants to increase the visibility of his other paper by referencing it, he has to accept the risk that after withdrawing his first paper, it may not be accepted for the next issue of the journal.

At the point where withdrawal causes the journal financial damage, the withdrawer has to take responsibility for this and face the damages. Really? And if I find a mistake in my paper prior to publication, do I face a choice of withdrawing and facing damages or publishing to the detriment of science? Moreover, I am no lawyer, but given that a withdrawal request seems to have no legal standing after copyright transfer, I cannot see how one could possibly be liable for damages if one were to make such a request.

What happens if you find the mistake one day after the journal has been sent out to 1,000 subscribers? What happens if you find the mistake when printing cannot be stopped anymore? And when you say "the withdrawal request has no legal standing", that's what's being discussed here, whether the journal should accept the withdrawal even though the author has no legal standing or not. Clearly if I have 1,000 printed copies and you want to withdraw your article, I'll give you the choice of not withdrawing or pay for the 1,000 printed copies out of your pocket.

If the withdrawal, even if it occurs in or after the proof stage, is somehow connected to the validity or the reliability of the paper (f.e discovered error, compromised peer review etc.), it is in the best interest of the journal to not publish the article. Therefore, they should be thankful to the author for not letting them publish a questionable paper and should not demand compensation for economical damages. But if the withdrawal or forcing a re-review occurs for a reason which is not connected with the validity of the paper than the author should take economic responsibility.

authors: Vladimir F Героям слава


text:
What does "paper rejected provisionally" mean?
I submitted a paper to a prestigious control journal. The editor provided the following review:

The decision is that your contribution cannot be accepted for publication in [the journal] in its present form. It needs substantial revision in order to possibly become publishable. Overall the decision is paper rejected provisionally.

The editor has invited me to revise and resubmit.
Is "paper rejected provisionally" equivalent to "major revision" ?
Will you advise me to politely inquire the editor about it so that there is no confusion. I mean before revising I want to be sure that there is some chance that the paper can be accepted if I incorporate the reviewer's comments.

Why are you suppressing the journal name?

@Walter: Sometimes back I wrote a post mentioning journal name. I was told by admin/moderators that this site cannot comment on a  particular journal and suggested me to ask general question.

In case of this post, mentioning the journal name does not render the question non-general, though.

@Walter Does it add anything, though? Someone choosing not to include the journal name doesn't seem like a big deal.

Including the journal name is inappropriate.  It could allow a reviewer who happens to read this to identify a blinded submission, for example.

Journals use different rejection resubmission concepts.  It is whatever they say it is.

Could a journal be trying to game its statistics (about how quickly it accepts papers for example) by doing this?

@AndrewGrimm if a journal wanted to game its statistics, then couldn't the editor just order up a bunch of low quality papers (computers can generate them), submit them, and promptly reject them.

I've seen language like this before as well, and feel that it is unnecessarily confusing. Usually, what I have found is that it's effectively equivalent to "Major Revision."  Here is a good heuristic for distinguishing:

If they give you a date that they'd like to see the revised version by, then it's equivalent to "Major Revision."
If they don't give you a date, then you've been rejected, but they really are inviting you to submit a better version when you are ready.

They have given deadline. Also, there is a resubmission link given in the original submission account.

@RIchardWilliams Then it's just an awkward phrasing of a request for major revision.

As I said in this answer of mine there can be nuances to the awkward phrasing including who reviews the new submission and the submission date.

@jakebeal:Thanks for the earlier suggestion. Please suggest on the edit at the end of the post.

@jakebeal: I think one reasonable explanation of "reject provisionally" phrase is that "your contribution cannot be accepted for publication in [the journal] in its present form". provisionally means that the paper is rejected in its present form.

@RIchardWilliams I completely agree with you --- it's just that it's a fairly convoluted phrasing compared to a request for major revision, and causes confusion of the sort you experienced.

It needs substantial revision in order to possibly become publishable

That's sounds the same as "major revision" to me.

Is "paper rejected provisionally" equivalent to "major revision" ?

You're simply concentrating on the last thing written, not the part about "substantial revision", which is unambiguous.  All the "provisional" part is saying is that they're open to re-submission after a big rewrite and are not completely rejecting it (and you).  I'd actually consider it as a mildly encouraging choice of words.

"You're simply concentrating on the last thing written" Because that's the only part he doesn't understand! And I'd say that "rejected provisionally" is a very discouraging form of words. "Rejected" means "we don't your paper", whereas the intended message seems to be, "If you improve your paper, we might accept it."

@StephenG: What about the above comment ?

As an invited reviewer to some journals, my advice is to prepare a letter detailing a response to each comment and a major revision of the paper. The comments should direct you to what needs revising. Aim to do this as soon as you can. If there's a date, you must submit by that date. If there isn't, turn it around within 1 month. Good luck!


text:
How many places one should apply for postdoctoral position
I need a suggestion in applying for postdoc position in mathjobs. In general how many places one should apply ? I mean, can my recommendation letter writers get disturbed if I apply for too many places and ask them to send email to too many places ?
Any help/suggestions will be useful.
Thanks in advance.

You should apply all the places where you want to have a job, and no more.  That may sound flip, but there's no magic number; it all depends on how many jobs are the market and what sort job you would accept.

Thanks for the reply. I mean, can my recommendation letter writers get disturbed if I apply for too many places and ask them to send email to too many places ?

@Magicsowon This seems field-dependent. Many institutions won't even consider your application if it is incomplete, and will consider it incomplete if the requested number of recommendation letters has not arrived.

@RIchardWilliams If you're applying on mathjobs, your references only upload have to load their letter once and you can send it as many places as you want.  So that's not a concern.

@Magicsowon In math, that's a good way to torch your career.  People will read the letters if they are there, and if they are not, they will click to their next in a list of several hundred.


text:
Journal rejection after 9 months without proper review: why do journal editors allow this sort of rejection?
I came to know from a senior in my lab that he once submitted a paper in Applied Mathematics in one of SIAM journals and the review came after 9 months and the review was like the following:

Reviewer 1: The problem is well-motivated and the paper contains original results which deserve to be published.
Reviewer 2: The contribution of the paper does not satisfy the journal standards and should be rejected.

He showed me the reviews from his email.
Overall the paper got rejected saying that it is not good enough (quality wise, the paper is in the scope of SIAM) for SIAM. My question is that why to keep somebody waiting for 9 months for such rejection. Is the message that "Unless you are completely sure that it is a path-breaking work don't send to SIAM, otherwise you will not get any comment if the paper is rejected and hence it will be time waste ".
I am a PhD student, not aware of much about journals. Sorry if the question is inappropriate.

Were the reviews really one-liners, or have you summarized them? I would expect at least a half-page report for a paper that has been under review for such a long time.

One of article passed two reviews, but one of associate Editor was against the publication of works. So despite 2 successive positive reviews by 4 different reviewers my work still got rejected after 7 months. So dear it happens very often, don't feel discouraged, submit to another journal.

@FedericoPoloni: The 2nd review additionally pointed out some typos in the paper. The exact same paper got accepted in another Tier 1 Applied Math. journal.

A two line review is not a sufficient review, I am not in maths, but I will rank any journal that gives decision over total of 4 lines of review very poorly. This might happen due to working on a remote field and the editor couldn't find any willing reviewers for your paper.

Regarding the timing: You only get a decision when all (usually at least two) reviews are in. This means it is entirely possible that reviewer 1 sent their reply after four weeks, but reviewer 2a never replied -- nor did reviewer 2b, 2c etc., until reviewer 2f was pressured into giving a report on short notice (which they did) so you only had to wait nine months.

Also, keep in mind that your colleague probably shared this experience with you as a "journal horror story"; do not consider it as the typical outcome of a submission to a SIAM journal.

I don't agree with the modified title, my concern is not the rejection without any comments, it is the long time taken

This is actually pretty common with high-standard journals as the SIAM journals and this is one of the risks you need to know (and your advisor should tell you early enough).
The SIAM journals are really top notch for applied math,
and the top journals try to maintain a high standard and to only publish papers they deem to be good enough. Unfortunately, it is hard to tell the quality of a paper in short time, even for the editors (although a desk rejection happens). So they send them to reviewers for an in depth check and the state of things is that it takes at least a few month (and nine month used to be standard, but e.g. SIAM if working hard to reduce the time). If the reviews are only slightly non-supportive, rejection is likely. This is what happens at the "upper end" of publication venues.
So, I'd say that your conclusion "Unless you are completely sure that it is a path-breaking work don't send to SIAM, otherwise it will be time waste" is quite accurate. So, unless your advisor is very confident, I would advice newcomers (read PhD students) to aim a little lower in the beginning of their career and aim for faster and slightly less prestigious journals - if their work is great, it will be read and recognized (but don't aim too low, too).
As to the question whether such a reasoning for rejection and little to no comments are common: No, this is not really the norm, but happens from time to time. I would guess that also the editors are not happy with such reviews, but their choice would be 1) to forward the reviews as they are, probably with additional comments from their side, 2) neglecting the reviews and write something on their own (which would really be a large waste of time for everybody) or 3) ask for more comments from the reviewer or more reviews. Action 2) has the downside, that the authors would not even see that at least some reviewer was involved and 3) would take even more time and the only benefit for the author would potentially more detailed feedback. So, the editors go with 1). I can not comment on the question whether such a review leaves a bad impression with the editor and may remove the referee from the "favorite referee list".

Thanks for the answer. My point was that after 9 month I would expect some review which are not just typos in the paper. I mean the reviewer who said paper is good should also give comments on why he liked the paper.

With a little bit of sarcasm: Well, there also was the judgment that the quality of the paper did not meet the standards of the journal. I also would prefer some reason for a conclusion like that, but you will not always get this.

@RIchardWilliams There are many reasons not to like the standard peer review mechanism. But as always: You either have to follow the rules or to find another kind of job.

@J.FabianMeier: My question was is this the usual rejection letter (no comments) in SIAM journals or this is an exceptional case.

@RIchardWilliams oh, that's a little bit different from "My question is that why to keep somebody waiting for 9 months for such rejection." (I did not see the emphasis on "such"…). Will update my answer.

@RIchardWilliams you seem to think that the number of months equate to the number of lines in a review -- roughly speaking.  Reviewers don't spend 9 months writing reviews.  I would say the length of a review is more correlated with a reviewer's interest+expertise and how well the paper is presented.  Your paper might have gone to reviewers who are busy or simply not interested.   Also note that Reviewer-1, although is an accept, did not provide good reasons for recommending an accept.  Also, you don't know what was said to the editor in private by both reviewers.

@RIchardWilliams: assuming that the reviewer is male is, I believe, a manifestation of our implicit gender biases. I encourage people to think consciously about the gender pronouns they use (and why, especially when there's no evidence concerning gender), since STEM fields are already too unwelcoming to women.

My question is that why to keep somebody waiting for 9 months for such rejection.

You are mixing up two issues here, the rejection "without proper review" and the delay, and I think that's illogical and they need to be addressed separately. So first of all, it's not actually clear to me that it's fair or necessarily correct of you to say the paper was rejected "without proper review". There was a review -- two of them in fact -- you just don't like that one of the reviewers didn't think the paper was up to the standards of the journal. This is a perfectly valid and legitimate reason to reject a paper (one I have used myself on various occasions), and while the report could be a bit more detailed about why the reviewer doesn't think the contribution is important, it's quite possible that this is an entirely subjective matter and there's really nothing useful they could add in terms of justification. So in what sense exactly was the review "not proper"? Moreover, you seem to cite the facts that reviewer 1 liked the paper and that the paper was later accepted to a good journal as evidence that reviewer 2 was being wrong or unreasonable, but I see nothing of the sort; it is perfectly acceptable and reasonable (and common) for reviewers to hold different opinions. After all, if they always agreed, prestigious journals wouldn't have a need or desire to send a paper out to two separate reviewers, would they?
The second issue concerns the 9 month delay to get a decision. Again, I think this should be addressed entirely separately from the outcome of the review. It is in fact reasonable in my opinion to complain about such a long delay (and would be reasonable even in the case of an acceptance), but the conclusion you take away here is again incorrect. You ask:

Is the message that "Unless you are completely sure that it is a path-breaking work don't send to SIAM, otherwise it will be time waste".

Well, no, in my opinion the message is rather "if you really care that much about your paper getting accepted (or rejected) fast, don't send it to the most prestigious journals, which are precisely the ones that have to handle the largest number of submissions from all the other authors competing to publish in them." Keep in mind that the editors of those journals are very successful and (as a result) very busy mathematicians, their workload is high, and the referees they approach to review papers are also very successful and hence very busy mathematicians, who despite their own heavy workload are nonetheless occasionally shamed into agreeing to increase their workload further by accepting thankless and uncompensated refereeing assignments, in many cases out of a sense of guilt or because they are bad at saying no (a very common problem among academics btw). Is it a surprise that some of them might drag their feet in completing their assignment? No, it really isn't.
The bottom line is that if you can't afford to wait 9 months for a decision on your paper, you are free to send your paper to a predatory journal that will reach a decision (that is sure to be positive, another advantage) in a few days, or to a legitimate but less competitive journal that might do an honest job in more than a few days but in less time than 9 months. Yes, it sucks that the academic publishing system in math sometimes (not always) works this way and we haven't been able to reach a point where authors always get detailed reviews and in a reasonable amount of time. But that's life, and that's the best system currently available, and it's precisely the most prestigious journals that suffer from it most (statistically speaking at least; I'm sure there are exceptions). The best that you and your friend can do to change this is to be the change you wish to see in this world, and make sure that when you get requests to review a paper, that you deliver a great report and do it in a reasonable amount of time.

My point was that after 9 month I would expect some comments which are not just typos in the paper. If they are not interested they should reject the paper in 2-3 months. Also, when I said that the paper got accepted later in some other journals, I did not mean that the other reviewer was wrong. I just wanted to update what happened to the paper.

@RIchardWilliams as Prof.SantaClaus commented on another answer, there just isn't any connection between the number of months your friend waited and the length or quality of review you should expect. Moreover, I don't really see anything fundamentally wrong with a review that does nothing more than point out typos and provide a recommendation whether to accept or reject the paper. Perhaps it is not as helpful as one might wish, but it fulfills the basic requirements for a review. So I think your only somewhat valid complaint is about the long delay, but it's unrelated to anything else.

Based on your comments, you seem to really be asking whether the experience you have described is typical for high-quality papers submitted to SIAM journals.  I can reply based on extensive experience as both an author and a reviewer for those journals (primarily SINUM and SISC, both considered to be at the top of their respective fields).  The answer is unequivocally no, but I did have an experience similar to yours once.
Time for reviews to be completed
As a reviewer, when I accept a request to review for a SIAM journal I am given a 2-month deadline.  Of course, the journal cannot and does not enforce this, although they will send a reminder if I miss the deadline, which I sometimes do.  I can say that get all of my reviews done within 3 months.
Based on my experience as an author, many reviewers do take longer.  Nine months is not out of the question.  I usually send a polite request for an update to the editor when 3-4 months have passed, and I often get the reports within a month after that request.
Length and quality of reviews
The papers that I get to review from SIAM journals are almost always reasonably high quality.  My referee reports are typically 1-2 pages long.  I have on rare occassion written reports of 1-2 paragraphs for exceptionally good or bad papers, but those are probably less than 5%.
I submit most of what I deem to be my best manuscripts to SIAM journals.  The reports that I've gotten on my own papers submitted to SIAM journals are usually detailed and of high quality (though, like any referee report, they usually contain some things I don't agree with!)  I have occasionally had very short positive reports that were obviously based on a superficial reading.  I once got a very negative report (leading to rejection) that was ridiculously short and superficial.  In my case also, the same paper was later accepted by a good journal.

I had an experience when my manuscript was under "review" in a math journal for a much longer than 9 months timeframe before I received a rejection with a short absolutely noninformative and meaningless statement. In my opinion, it happens because many journals do not have Ethics Policy for Editors or something like Ethical Conduct for Editors. If journals will introduce and follow the Ethics Policy or Ethical Conduct for Editors, then these things will never happen again. I understand that many of us believe that it is unnecessary as it is supposed to be "by default" without any policy. However, this particular example explicitly shows that the manuscript may be delayed and improperly processed in review. If most journals have Ethical Conduct for Authors, then why it should not be for the Editors as well? Please leave your comments if you disagree with my point of view.

(1) a long delay before reply may be annoying, and may reflect a lack of competence on the part of the editor, but does not constitute an ethics violation (it may violate the policies of the journal, but I think you will find that even journals that state a typical time to first decision do not post this as a guarantee!); (2) while a long delay is an objective fact, an "absolutely noninformative and meaningless statement" is opinion-based. It would also be hard to consider it unethical, just (if I agree with you about quality) negligent or sloppy.

@BenBolker: I respect your opinion, but disagree with you. When review is delayed, this is not only discourages you, but also badly slows down your current research. And after many months (sometimes years) of delay when you finally receive so called "report" consisting of a few noninformative sentences, what would be your filling? I do not wish to anyone so unpleasant experience! Therefore, such a behavior of an editor, who knows very well that delay is destructive (and who ignores all your emails) cannot be in compliance with elementary Code of Ethics.

It's bad, but I don't consider it unethical within the scope of a journal editor's position. (Could be unethical in a broader sense of "behaviour to avoid because it harms someone else".) Fine if we disagree.

@BenBolker: Let me clarify. When editor delays for months and years and ignores all manuscript inquiries from authors, it is nothing but a disrespectful behavior (I hope you would agree about it). And a disrespectful behavior towards contributing authors is not in compliance with Ethical Code.

@BenBolker: And regardless if this is ethical or not, there should be Ethical Code for Editors anyway to prevent delays due to "negligent or sloppy" attitude of an editor.


text:
Does papers under review/revision has any value for faculty application in mathematics?
Does papers under review/revision has any value for faculty application in mathematics ? In detail, when reviewing faculty application does the committee checks the content of the papers or just checks the journals where it is published ?

Your paper is on ArXiv, right?

@Alexander Woo: yes

Yes. It's an anecdote but I got a permanent position pretty much because I had a paper under revision at a very top journal. It still doesn't count as much as a published paper, though.
One thing you can do is ask the editor if she/he would be ok with you mentioning it in a job application and whether you can pass on contact details so that the job committee can ask for confirmation. You also have to take the reports into account, moreover; an extremely positive report with some minor modifications asked is not at all of the same value as a lukewarm report with a lot of major modifications asked.


text:
Is publishing in open access journal a good impression?
Is publishing in open access journal a good impression ? I mean publishing in such journals (where one has to pay money), will it be valuable compared to other journals ?

A good impression in what way, exactly?

@Buffy: see the edit.

Say more if you can. Valuable? Do you just mean to your overall academic reputation or something else?

OA does not necessarily equal paying money (APCs, or article processing charges). There are plenty of free OA journals as well - and many closed access journals where you nevertheless need to pay APCs.

This is further complicated by the fact that nearly all journals that are not open access offer an open access option.  Simply liking open access does not help you choose a journal.

As a side notice, Springer-Nature recently made their journals OpenAccess for German scientists. Basically, with a right affiliation you publish in their journal and your magically becomes OpenAccess. (I understand, that you are asking about journals that are fully OpenAccess, and some are predatory. But having OpenAccess publications can also mean publications in hybrid journals.)

Please make your question less vague.

Might be some very small reputation boost if people can see all your articles are open access and available to anyone rather than being hidden behind paywalls.

It depends entirely on the journal. There are good and bad open access journals, just as there are good and bad closed access journals.
For example, in biology Nature Communications, Cell Reports, eLife, PLoS Biology and Genome Biology are all open access journals with excellent reputations.
PLoS One, BMC genomics, PeerJ, Scientific Reports are open access journals that have a reputation (earned or not) of publishing work which is sound, but maybe less exciting.
And then there are various lower quality open access journals that people might be suspicious of.
This is no different from closed access journals.

Nature Comms definitely gets you into 4* territory around here.

@Libor stretch? I'd say it has the best reputation on the list by far.

Nonsense, I've submitted to Nature Comms 3 times. The first two I got desk rejections. The 3rd paper we tried at Nature Comms has now been under review for 6 months and we are on our 2nd revision.

Maybe its field specific. The papers in my field in Nat Comms are generally very good. If you wanted something more like PLoS one, then you'd be look that "Nature" Scientific Reports.Its not like publishing in Nature or Nature Genetics costs any less than publishing in Nat Comms anyway really.

@Libor I've also thought about Nature Comms in such hostage terms, but that doesn't stop it from being a good journal, with a reputation for publishing a lot of great papers (indeed often ones that didn't meet the flashiness standards of the glossy journals).

For academic reputation purposes, publishing in a reputable open access journal is fine. I'm assuming that the journal goes through a proper review and editorial process and that papers might be rejected for quality or innovation reasons. Otherwise, it may be a predatory journal that just wants your money and will publish anything.
But it is the reputation of the journal and its adherence to norms that makes this valid, not whether the authors (or their grants) or subscribers pay for the costs, etc. of publishing.
In some ways, it is a (minor) reputation enhancement since you are doing something for the public beyond what is required by absorbing the costs.
But do a bit of investigation of any journal (open access or not).


text:
Structure of a review paper with author's unpublished data
I am wondering how to structure a review paper that contains a small portion of the authors' unpublished empirical research results. These unpublished data only account for maybe 2% of all the data cited in the review, and together with other's published data serve as evidence to some claims to be made. So should I introduce the detailed methodology of the empirical research in the manuscript or put it in the supplementary material? or do you have other recommended paper structure?

Introduction
Detailed review on the topic
Discussion
Conclusions
Supplementary material
Methodology of the empirical research

or

Introduction
Detailed review on the topic
Discussion
Conclusions
Methodology of the empirical research (use smaller font)

or

Introduction
Methodology of the empirical research
Detailed review on the topic
Discussion
Conclusions

"a review paper that contains a small portion of the authors' unpublished empirical research results. " That doesn't seem like a good idea to me. Including new results defies the purpose of a review paper.

I did upvote the comment by lighthouse keeper but if this is the only way to publish the results you perhaps might do it and refer to a brief but exhaustive extra paragraph at the end, after conclusion and before the refs list. Second way in your list, I see.

Let's talk about three kinds of papers that are commonly distinguished:

Empirical paper with original primary research
Conceptual paper with no empirical primary research
Review paper that synthesizes empirical and conceptual papers in the literature

Despite my simplistic categorization into three types of paper, this might be better considered a triangular spectrum and any actual paper falls closer or farther from any of the three points. All empirical papers have some conceptual development and some literature review; all conceptual papers have some literature review (but rarely any original empirical analysis); all literature reviews have some conceptual development (but rarely any original empirical analysis).
Your question seems to ask about if it is acceptable to write a review paper that, contrary to the norm, includes a little bit of original primary research. I have a two-sided response to offer you.
On one hand, in principle, if you consider paper genres as a spectrum, then you can do anything that you want that meaningfully advances your arguments. If the original research supports your reasoning, then it could be reasonable to include it.
On the other hand, there are risks when you deviate from established scholarly genres. I see at least two concerns with what you are proposing to do:

First, there is a concern about scholarly rigour. Presumably, almost all of the articles in your review are peer-reviewed. That is, they have been evaluated and approved by editorial committees with invited expert reviewers that are independent of the study authors. Thus, their reports should be given greater credibility. However, that is not the case of your original empirical research. It is your original work that has not passed scholarly peer review, yet you are offering it as evidence on par--or even with more weight--than published, peer-reviewed work. What you should do is to let your original empirical work pass peer review first before including it in a review of the literature. It is awkward mixing unscrutinized evidence (your original empirical work) with scrutinized work.
Second, I began with three common genres of work. The advantage of writing according to common genres is that peer-reviewers and editors know what to expect and know how to evaluate that kind of work. When you break from convention, you risk the high possibility that peer-reviewers and editors would not know how to properly evaluate your work. So, some might evaluate it as an empirical paper (where it would be considered far too light), whereas some might evaluate it as a review paper (where they would object to the original empirical work). You might be willing to take this risk, but you should not be surprised if peer-reviewers and editors have a hard time understanding what you are trying to do because of your break from convention.

Overall, I recommend one of two paths:

Do not include your empirical research in the review paper at all. If you say it only supports what the literature already says, then it adds little meaningful. In that case, it is not worth the risks of breaking from convention. But if your empirical research is substantial and meaningful, then you can submit it for peer review for publication as an independent article.
If you feel that the empirical research is not sufficient to be published as an independent article (or it is not worth your time trying to do that), yet it does add something meaningful to your review paper, then place it entirely in an appendix to the review paper. You are free to refer to it in the review as evidence, but the fact that you are placing it in an appendix meakes it clear that you do not give it the same weight as the independently peer reviewed work that you review.