text:
Manuscript evaluation for becoming an editor
I was wondering how editors evaluate manuscripts. They certainly do not have time to read the paper thoroughly. What are the key points to look for when evaluating a manuscript as an editor?

Different editors treat this differently. Some of the things I looked at:

Does it look like a serious research paper? If not, desk reject.
Does the paper pass plagiarism detection? If not, desk reject.
Is it plausible? The methods used should conceivably lead to the results. If it's not plausible, unless the authors provide a convincing explanation, desk reject.
Is the paper review-ready? A paper that has lots of typographical errors, has figures without axis labels, is written in incomprehensible English to the point where I cannot in good faith ask reviewers to wrack their heads deciphering the paper, etc - reject and resubmit.
Is it within the journal's scope? If not, desk reject.
Does the paper have anything interesting to say? Chances are I won't be able to judge the significance of the paper myself, but the authors ought to have written something in the introduction about why their research matters. Something like "this material is important because of [reasons]. Nobody has ever done [calculations] for this crucial property. We do it in this paper and suggest [methods] to make an even better material." would be helpful. If the authors don't give a reason for why their research matters, a desk rejection is more likely.
What tests did the authors conduct? How do the authors know their results really are reliable? If no error analysis is performed, desk reject. The same goes for any standard tests, e.g. before one can claim that a new drug is effective, I'd want to know if there was a control group, if the results are statistically significant, etc. If the authors do not discuss these standard things - desk reject.

Beyond this it depends on what the reviewers say. Reviewer reports can be very varied so it's hard to make statements about them, but the idea is the same: I read what they say and come to my own conclusions. It is possible that I don't understand what the reviewers or the authors are saying, in which case things can really seem like a coin flip. Peer review isn't a scientific process. As a personal guideline, when in doubt, I accept the manuscript. Another person might lean towards rejecting.

You find reviewers who look at the paper for you, and whose judgment you trust.

I feel like this misses that core of the question: "What are the key points to look for when evaluating a manuscript as an editor?"
Like yes, the editor finds reviewers to do the main part of the evaluation.
But they do some evaluating themselves, e.g. for things like desk-rejects

But what about when they reject before sending to reviewer? :( :(


text:
How can I proceed if my email is not working, and I am in the middle of creating proofs for my new accepted paper
I received an acceptance letter for my article and the letter said that the manuscript will be transferred to the production department and work will begin on the creation of the proof. They also said that if they need any additional information to create the proof they will let me know.
Now the problem is that my establishment email (the email that I was using to communicate) is not working because of problems with the university's servers, and I don't know how long it will take to solve the problem.
How can I proceed?

Has the problem been going on for days?

@Jon Custer, Yes.

Wow. Normally that might be cause for a celebration...

Many journals have an online system where you can log in and change the e-mail information. If not, just contact the responsible person (by using another e-mail account).

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text:
Meeting with Professor for letter of recommendation
I am applying for PhD positions. I emailed one of my professors asking them to write a strong letter of recommendation for me. I took two courses with this professor and I got an A- in both of them. The professor replied and asked me to meet with him.
What should I expect from this meeting? What kind of things will he ask me?
[I think I am asking something stupid but I really want to prepare myself before going in front of this professor as he's always very rude and angry]

Well, if the professor doesn't know you that well outside of the classroom, he might just want to get to know you a bit better so that any letter he may eventually write will be more meaningful for you.

You can expect questions about your plans, your interests, strengths you want the letter writer to focus on, any weaknesses in your application you may want to assuage, etc.
In other words, this sort of meeting is designed to allow the recommender to write you a better letter. This is a very good approach by the recommender - a professor who knew you more closely might not need such a meeting, but all this professor has to go by is your participation in his course, which may not be all that memorable. He may come across as "rude and angry" but in this context it seems he has your best interests in mind, so you should be very thankful. An alternative would be to write a curt, impersonal recommendation ("Of all the students I had in my Important Studies 301 course, my records show Luqman Saleem was one of them.") that will do you little good.
It may be helpful to bring along your CV as well for the professor to keep, if he has not asked for one already. Be ready to answer questions about why you want a PhD, your research interests, etc, and have a good reason for why you bothered to ask this particular professor - what skills or abilities are they best positioned to write about that will be important for the programs you are applying to?

Thank you. Professor exactly asked these things. Thank you again.

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text:
What to reply a PhD supervisor who says my chances of getting selected in this scholarship program are not very high?
I sent an email to a professor and asked him if there's any PhD  position available in his group. I also told him that I want to apply for SINGA scholarship program if he agrees to supervise me.
The professor replied:

My experience with the SINGA program is that it is very competitive.  Almost all successful applications have already published papers prior to application.  I do not believe your chances for getting accepted are too high.

I really want to give it a try. How should I reply to tell the professor politely to please support my application, and that I don't care if I get a rejection from SINGA scholarship program?
Also, I am writing a research article, and I am hopeful it will be complete within two weeks.

Have you worked for the professor before? Have you taken his class before? What do you want him to do to support your application of SINGA? Do you have backup plan if the application of SINGA is rejected?

No. I haven't worked with him before. Moreover, I am writing a research article. I am hopeful it will be complete within next 2 weeks.

How do you know your article will be accepted by journal/conference? What's your backup plan? Pay attention to his e-mail Almost all successful applications have already published papers prior to application

Well, nobody is sure that their article will be accepted. The only thing that I can say right now is that my current supervisor says that my article will be accepted easily.

I think it's a good idea for your current supervisor to say this in his recommendation letter.

I am sure my current supervisor will write this thing but first step of getting this scholarship is to choose a supervisor from host university and discuss a project with him. After that candidate have to apply on a website which require recommendations from my current supervisor. I just emailed this professor to ask if he's any PhD position or not and he replied me with this.

Related question:https://academia.stackexchange.com/q/90725/546

The professor is saying no. He is being polite about it, but he's saying he doesn't want you in his group. Arguing with him is not going to change that. (In fact it's more likely to solidify in his mind that you are a bad candidate, with poor social skills, who would be a poor fit in his program.)
Look for somewhere else to go.

From the parts quoted, I'm not sure that this a rejection to working with the candidate, but rather a "don't get your hopes up." I would be shocked if being a competitive candidate for a particular award were a requirement for working with him. I do agree that arguing on that point is unlikely to help; perhaps the best response is a simple, "Thank you for your advice about the SINGA. That probably means my time is better spent right now doing final edits on my research paper than on applying for that award."

(That said, I may be missing context: with the SINGA, is becoming a PhD student with that professor likely dependent on receiving the award? In the U.S., it seems like that is how an NSF postdoc award works (funding wouldn't exist otherwise for the desired position), but I have not heard of a PhD position being contingent on receiving an NSF predoctoral fellowship.)

I agree with iayork that your professor appears to be giving you a polite and implicit "no", framed in a way that requires you to read-between-the-lines.  However, he hasn't been explicit, and if you want to follow-up to get an explicit answer, you should feel free to do so.
If this is indeed a read-between-the-lines-no, then further inquiry into the matter will probably just get you a more explicit "no".  However, you could reasonably make your inquiry tangentially, by asking this professor for some advice on what additional work you would need to do to become a competitive candidate, and get to a level where he would support your application.  From his email, clearly one thing you can do is to publish some academic work; you could reasonably ask if there is anything else you ought to be doing to become competitive.

You reply: "Thank you".
It's rare that a professor will be so direct and tell someone outright not to try to apply for a given program/scholarship because they don't stand a chance. I don't know SINGA but scholarship applications usually require a lot of work on your end (and also from other people, like the ones writing recommendation letters). This professor is doing you a favor by telling you your time and efforts would be most likely better invested in something else. For example: becoming a stronger candidate, alternatively apply to a less-competitive scholarship.
Don't take it personally. There are many reasons that make some people eligible and most others not.


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When do recommenders get asked for references? How do they get asked?
I have decided to apply to a few faculty jobs, and all of my faculty references have agreed some time ago to support me (my masters and PhD advisors who I talked to a year ago).
I have submitted 5 applications so far and plan on submitting another 5 this season. But I am not sure when I should contact and ask my references to submit their reference letter.
Does the application system request their reference letter as soon as I apply? I have no idea if they've been notified of my applications. Is it okay to just apply first and then ask them for specific letters once the application gets reviewed (I'm sure that not all my applications will make it past the review stage)?
Does every application requires a reference letter, or do my references only get asked by the system if the application seems promising? Or should I email each of my references directly after I apply to request their recommendation letter, and if so, where do I tell them to send it?

You should contact your potential references now.  You need their permission to list them as references before you submit any applications.

Does the application system request their reference letter as soon as I apply?

Every department is different.  Some do, some don't.

Does every application requires a reference letter, or do my references only get asked by the system if the application seems promising?

Every department is different.  Some ask for letters for every candidate; some only request letters for candidates that satisfy minimal qualifications (like having a PhD); some only request letters for candidates that pass a more rigorous initial screening; some may even wait until after interviews.  My department automatically asks for letters for all minimally-qualified untenured candidates, but we only request letters for tenured applicants when we decide we want to interview them.

Or should I email each of my references directly after I apply to request their recommendation letter, and if so, where do I tell them to send it?

Every department is different.  Some will tell you to ask your references to send letters when you apply.  Most departments will ask for contact information and request letters directly from your references.
In any case, each department will provide their own instructions.  Follow them.
I've recommended the following protocol to my students for several years.  When you decide to apply, you create a shared spreadsheet (on Google Docs, for example) with one row for each application target, and columns listing the university, department, a link to the ad, instructions for submitting letters (as supplied by the department), submission deadlines, and each of your references.  Ask each of your references to indicate in their column of the  spreadsheet (1) when anyone asks them for a letter, and (2) when they have actually submitted a letter.  That way, you can keep track of the status of your applications and letters, your references have a unified record of where and when they need to send letters, and your references can be properly (but not too publicly) embarrassed if miss a deadline.

Thanks @JeffE for the detailed information about how your students manage their spreadsheet.

It depends on each institution.
In some searches, the online application system submits a reference request immediately after you apply for the job.
In other cases, the search committee will ask for recommendations only if you are short listed.
In other cases, you have to submit the letters with your application.

is this also the case for adjunct faculty?

Yes, all of these options are also possible for adjunct faculty applications.


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How do I correctly show price differences in academic writing
I am writing a text about a new technology in electronics systems.
Here is a problem that I am addressing in the text:
There are people that want to use high frequencies in electronics, but at higher frequencies our connectors become more expensive.
I want to give an example using numbers so that the reader can fully understand how much more expensive it becomes when using higher frequencies. I plan on comparing the prices of connectors capable of operating with current frequencies, and then comparing the prices of connectors that would be needed to operate in higher frequency bands.
There is not really any existing research giving a comparison between price and frequencies. What is a good way to do this? Or is it okay to leave it without any reference since it is just in the introduction?

Well you definitely need a reference because I am very confused.

You'll need to clarify what you're trying to ask here. I've voted to close in the meantime.

I don't know about a metaphor, but this seems to be about not being scalable or the law of diminishing returns.

Hmm. It seems like with my metafor, I made it unclear what I want to ask. I'll try to change it.

You could look up some real prices to show the reader the difference, and cite the sources from which you get the prices.

Another option if you can't get exact numbers might be to cite the reason why the connectors are more expensive (e.g. more expensive materials, lower tolerance for manufacturing defects) and then ball park the increase cost.

It appears that there exist connectors that have different specs as regards operating frequency, as well as different prices.
Simply stating two pieces of actual data "Connector A operates at 10-frequency and costs 100, while Connector B operates at 20-frequency and costs 150" is enough as an example to show that higher-frequency operators cost more to purchase.
If this is all you want to convey to the reader, you're done. You could mak it a bit more elaborate by trying to find a rough quantitative relation, if it exists, say "from the available market data, roughly speaking it appears that doubling the frequency increases price by 50%".
But all these are purely descriptive. To my economist's mind, the real question is "is it worth it, to operate at higher frequencies?"
What do we gain, if anything, by operating at higher frequencies? More volume of work, however it can be defined? More reliability? More safety? What? And, if we gain anything, is it worth the increased cost?
You just entered cost-benefit analysis, which is a much more complex task than simply stating some price & specs data.

Thank you for your answer. Given those connector costs it is not worth it and is one of the reasons why we are not using the 20-frequency applications, but my research is on an alternative option, which could result in it being viable.


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Should arguments based on the proponent's gender be used in a grant proposal?
Recently I have reviewed a project from a female proponent. Among the scientific content there was a section about the under-representation of women in a specific field - saying that, on top of all the scientific justifications for the project, it should also be approved to support women in that field.
I know that in some countries, e.g. Germany, gender is often considered a tiebreaker as affirmative action in order to support women in science. However, in this case there is no such policy in the call guidelines.
Is this kind of argument appropriate in a grant proposal? Should it be a criterion to be taken into consideration?

What do the funding agency and proposal guidelines say?

@JonCuster Nothing related to gender or any affirmative action.

Is this a young investigator type of award that is partially driven by the “promise” and characteristics of the individual?

@Dawn It is a postdoc project for individual funding. Young and not-so-young researchers are eligible to apply.

Yes, I meant academically “young” not of a particular birth cohort.

@Dawn I meant both. Any phd holder can apply.

By "proponent" do you mean what I'd call "principal investigator" (PI)? Does this jargon vary by location?

@Reid a proponent is someone proposing a project. It is more general than a PI, since it could be applied for someone presenting a project for PhD studies.

So the project is from the same woman that is saying to favor her due to her sex? And not only did her just say informally this but actually wrote it down in the scientific section? That sounds quite outrageous. It could be something that you might evaluate, but being told what to do in that way seems like the author of the project is a weak candidate trying desperately to get the grant. Research should be about merit, so someone trying to dodge that with her sex doesn't sound like an exceptional candidate.

Is the question of under-representation of women a valid scientific subject for that field (e.g. sociology)? I.e. how closely is under-representation of women related to the proposed scientific study?

@cbeleites it's a completely abstract field of physics.

Please can you clarify whether the request for affirmative action was from the applicant themselves, or from someone else in your organisation/department?

@Graham from the applicant.

@Bakuriu Questioning whether the candidate is weak because they wrote the statement is also "quite outrageous." External reviewers should judge the science on its own merits and ignore the statement [and note that they might be biased against the candidate given the statement was written, and try to correct for that bias].

@Bakuriu "...but being told what to do in that way seems like the author of the project is a weak candidate trying desperately to get the grant. Research should be about merit, so someone trying to dodge that with her sex doesn't sound like an exceptional candidate." Your conclusion about the potential weakness of the candidate is a bit unclear. I would say that nobody knows. In the worst case, just ignore it. Otherwise, it's a reality that women are especially promoted in science in many regions. That may just reflect this.

@WetLabStudent Ignoring a part in the scientific section creates a second bias! Scientific parts in proposals should be judges as a whole, in the absence of further instructions as in OP's case.

@Trilarion A good candidate should not need her or his sex to get the grant. Using her or his sex to get the grant is only showing that the proposal by itself is not good enough. A good candidate knows that and will avoid writing down such a thing, especially in the scientific section of the proposal. The committee might take that into account according to policies or the members' consciences. Writing it down in that way seems like the candidate is aware of the weakness of his or her proposal and is trying to find something to make the committee feel bad for a rejection.

Comments are not for extended discussion...

@Bakuriu "Writing it down in that way seems like the candidate is aware of the weakness of his or her proposal and is trying to find something to make the committee feel bad for a rejection." It would be quite an obvious try, easy to see through. I would not see it as that negative. And indeed sex is nowadays one criteria for some grant applications, mostly the grants that aim at supporting women in science. Don't know why you insist this is nowhere the case.

@Trilarion I'm not intending to engage in this discussion, so this will be my only comment about it.  As a matter of fact, she is not a weak candidate - on contrary! She made valid points using statistics and connected that with the impact for a more equal society. Bakuriu, I can't understand how can you say that someone you don't know is a weak candidate or not. You never saw her project at all. This discussion is useless, nonsensical and there is nothing to do with the question.

This does not feel like something you as an external grant reviewer should really care about. The gender of the applicant may or may not be a tie breaker (or even a major factor) for the jury, but they will know which it is. If gender is a factor in the evaluation, they will also be acutely aware that the applicant is female, because either the system or an administrative person will have flagged the application as coming from a female applicant. No need to tell the jury that this is indeed a female applicant.
In consequence, I think you should simply ignore this part of the application. Keep in mind that as a reviewer, you are not deciding on the application - you are merely laying down the facts (e.g., related to the scientific quality of the proposal and applicant) so that the jury can decide based on their own strategy, criteria and availability of funding.
Side remark: note that even should you disagree with the notion that the gender of the applicant should play a role, you should resist "mentally subtracting some points" because the applicant even brought it up. It's not your place to decide if gender should or should not be part of the evaluation. If you would decide to judge the proposal more harshly to counteract a perceived undue advantage, you yourself quickly become part of the problem. Nothing good can come out of that.

I think my question is right to the point. I don't know how you felt some bias from it, but you are wrong. Feel free to edit the question and cut the parts you sense some bias - I'm not a native English speaker. In my opinion, affirmative actions are important in science.

@TheDoctor Fair enough. I want to leave the remark in as I think it may be important for other readers, but I removed a suggestion that you specifically felt this way,

@TheDoctor I should also say that there is, upon second reading, nothing specific in the question that I object against, but many discussions in the recent past (which often start with innocent-but-actually-loaded questions) have made me wary and suspicious. I apologize.

This does not feel like something you as an external grant reviewer should really care about. - I would think this would depend on the review guidelines.  Yes, if you were specifically told to only evaluate the intellectual merits of the proposal, but perhaps no if you were told to also account for impact to the scientific community.

@Kimball Yes, this is my point too!

Re your side remark, suppose they used another suggestion of bias. Maybe "hire me because my dad runs the department", for example? Anyone asking in their application for undue bias has to damage their chances, because of lack of professionalism. All women/PoC/pick your underrepresented group do not expect handouts. Given equally-qualified candidates, I'll happily engage in positive discrimination myself (by policy, or just because I value a diverse team), but they can't presume to tell me how to do my job in selecting them.

@side remark: resisting to try to counterbalance the bias with a different kind of bias is a noble goal, but it may be impossible due to the way humans work. People do it without even realising it and even with best intentions not to do so.

what troubles me is the following: as a reviewer you are asked to judge the scientific part of the proposal. The problem is that within the scientific section it is written that the reviewer should be biased based on the gender of the candidate. In this particular case I am not sure that ignoring deliberately this part can be a good strategy, since scientific sections should be judged as a whole for every candidate. Otherwise, you create a 2nd bias by choosing the subsections to judge the proposal.

"not your place to decide if gender should or should not be part of the evaluation" - that's of course up to the review guidelines. Nevertheless, as OP clarified the proposal topic is in abstract physics and thus not on a topic that is itself related to gender studies. Thus, I'd consider "mentally subtracting points" for not being concise: the proposal is not totally focused on the (abstract physics) point but contains irrelevant matter. Just as I'd do for anything else irrelevant to the proposed topic (in the "science section"), or any other paragraphs that should be in another part.

The answer invariably lies in the instructions the funding institution provides.  If instructions have not been provided, and you don't know how to appropriately review  -- as with any other review issue, contact the program officer, or whoever is managing the review process, and ask.
I haven't seen processes that use this information for general science grants, but such issues surrounding diversity efforts are often fair criteria in things like training grants (e.g., the NSF GRFP review process: https://www.nsfgrfp.org/applicants/application_components/merit_review_criteria), so it wouldn't surprise me if there were situations where such considerations are important.

I think there are situations where this information is relevant.
First, as you stated, there could be explicit notes in the call which signal that one of the goals of the funding is to increase the diversity of the field.
Second, you might be asked to evaluate the "promise" of the applicant, or the potential of the applicant to significantly impact the field. This might be common in a "young investigator" program. In this case, I think information about an applicant's individual characteristics and their ability to impact the field as a member of a diverse group might be relevant (in addition to the project's impact on the field of course).
Third, the evaluation guidelines might include some criteria looking for the impact of the proposal on a broader set of institutional goals. For instance, we have a faculty research fund at my school, and one of the criteria is "impact of the project on the university." In this case, if one of the university goals is better representation, then funding this project would advance that. I basically think of this as a PR criteria.
In other situations, where you are only asked to evaluate the intellectual merits of the project itself, this information would not be relevant.

That may depend on the grant proposal regulations and the nature of the project.
If the project is specifically about something that needs funding to support women in the field, such a statement might be considered auxiliary to the scientific background.
If the regulations, as stated in question, do not mention anything related to gender or affirmative action, such statement should carry no weight beyond that which is already provided through the scientific background.
Professionally speaking, providing such arguments in a grant proposal can be a slippery rope. Provided that neither of the above is the case, she is basically asking you to favor her proposal based on a criterion that is not stated in the relevant procedure and that other applicants, consequently, don't have, thus treating them unfairly.  Also, depending on regulations, if such a grant proposal was refused, she might be able to challenge on the grounds of sexual discrimination and if it was accepted, some other party might also challenge the decision on the same ground.

(Thanks for the clarification.)
It is entirely inappropriate for a candidate to try to use their gender this way in their formal application. If she happens to be the best candidate, she has created a context where she can be seen by others as only having been selected for her gender. And if she isn't selected, she's created a context where she can claim sexual discrimination. This is completely unprofessional.
As experts in the field, selecting who goes forward, you can choose to bias your decisions in favour of women or other under-represented groups. This could be formally stated, or it could be by informal agreement amongst yourselves. The candidate could even mention this jokingly during an interview.
Putting this in their application though - just no. You don't put the people assessing you in that position.

I'm surprised that this is currently the lowest-rated answer. The applicant is brazenly demanding a sexist bias in her own favor! I thought society was beyond that kind of thing now?!

@Vandroiy A smart applicant would keep it verbal. Even better, a smart applicant would say in the interview, "Hire me because I'm female. I've had to work harder to get here than your other applicants, and I'll keep working harder." I'd respect that a lot, and it certainly would count in their favour. I want smart, determined people. The OP's applicant though - hell no.

@Vandroiy The first paragraph of current top answer is a much better answer to such a brazen demand. This answer seems to assume the applicant should be wary of reviewers' feelings when applying, which sounds irrelevant. Graham, so you're saying it can be said out loud, but shouldn't be put in writing ? Why so ? If it's true, why wouldn't them write it down ?

@NikanaReklawyks Verbally, it can be taken as a joke. I'm fine with applicants having a sense of humour. Also my example about "I had to work harder" - using it to show not just a sense of humour, but demonstrating determination too. That kind of thing translates really badly in writing though, because someone could misunderstand it as having a grudge against "the system". Application forms should be cold hard facts, not personality-based. The interview process is where you add your personality to the facts.

@NikanaReklawyks The biggest problem though is an unprofessional attitude. Presuming to tell the selection team they should bias their selection process unfairly in your favour - that's seriously unprofessional. Not as much as a bribe or "my dad owns this company", but it's still not acceptable.


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What is the point of questions asked in a mathematics master thesis presentation by the professor?
A student working on a master thesis in mathematics will have to present it at the end of the semester in front of the professor.
The professor will ask several questions during the presentation, what is the intend of those questions?
Basically, what is the professor trying to achieve through those questions?
Does he want to see whether you are the writer of this thesis and that you didn't have someone else do it for you?
Does he want to know whether you understand the concepts you are presenting? ( I am guessing yes, since this is the point of a master thesis after all)
Does he want to know whether you can use the information in your thesis to come up with other conclusions, not mentioned in the paper?
Perhaps give you some short mathematics exercises he expects you to solve during the presentation.
Can you explain what is the point of those questions?

If a presentation is good, audience members might even ask questions because they are interested in the answer personally.

After some decades of naively thinking that the point of an exam was the exam itself ... I've finally realized that the largest point is to give students a motivation to study/review/think.
So the point is that the student knows, in advance, that questions will be asked. And that not being able to respond will be, at least, an embarrassment. So the student makes sure to improve their ability to answer relevant questions. That is the real goal. :)
And, for that matter, one's advisor should not allow the exam to take place until they are confident that the student is adequately prepared. There's scant purpose in carrying out an exam wherein a bad outcome is predictable (except, conceivably, in extreme cases where the student is really not working hard, is disinterested, uncooperative, yet somehow doesn't realize they should leave the program voluntarily...)

Often there will be a committee, and not just one professor asking questions.  In some institutions, any faculty member can attend and ask questions.
The principal reason is to be sure you do understand the concepts you have presented, which has the added effect of reassuring them that you actually did write the thesis.  They may also probe for broader, more general understanding of the subject matter of your degree.
Your thesis advisor or committee chair can help you prepare for the oral examination part of your presentation by giving you advice on how to prepare.  It may be possible for you to attend the thesis defenses of other students to see how they are conducted.  If so, I urge you to do so.

I can't know what the practice is at your particular university, but that kind of public presentation is common. Other faculty and students may be invited, and may come. The forum gives the student a chance to explain to the audience what they wrote about, what they learned, and why it's important and interesting. Unless there is some doubt about the correctness of the thesis or some doubt about the references the questions are likely to be open ended and straightforward.


text:
Citing a Matlab live script
How do I cite or reference Matlab live script? I want to cite/reference a Matlab live script that is published on my university's homepage. How to do that correctly?
The script has a detailed explanation of the algorithm’s steps and I want to skip this explanation and just refer to that.

What citation style are you using? MLA? APA? ACM? IEEE? AMS?

I don't know what to use. @JoelReyesNoche

In general I would give the URL, the date accessed, and as much information as is available (date written, author, institution, etc.).  Can you give a link to the URL in question so we can see it (if it's publicly available)?

If your focus is the algorithm instead of the particular implementation, it is probably better to look up a paper / textbook explaining it and cite that.

Your problem is unusual, but it helps to work from first principles, namely that the main purpose of all citation systems is to allow a reader to locate the source to which the author is referring. That is true for a thesis, journal paper, conference paper, or blog.
You don't say what it is that you are writing but if you are writing a thesis for a university, then my experience would suggest that there will either be university-wide rules that govern the citation format in different disciplines at your own university, or there will be at least discipline specific conventions or customary styles, suggesting that an advisor or professor could guide you on the appropriate format.
If, on the other hand, you are writing for a professional journal and the journal style guide does not give enough guidance for your specific source, then I would suggest the following. First, determine whether the journal style uses a superscript in-text citation system (such as  Vancouver), or whether it uses an author-date system, like this (Jones, 1988). Once having done that, your problem is simplified in two ways. First, you can insert a superscript at the appropriate place in your text or a simple reference of the form (MyUniversity, 2021). Next, in the reference section, you include as much detail as needed to explain the source. For example, following a pseudo-APA style:
My University. (2021). Matlab source code from the web page entitled "This is where I got my source code". Downloaded July 7th, 2021 from URL http://example.com.
If you are submitting a journal paper, the advantages of this approach are (i) it is not seriously going to affect the chances of the paper being accepted, (ii) the reviewers will be able to locate the source, (iii) the reviewers might suggest how the reference ought be formatted, and (iv) if your paper is accepted, an in-house copy-editor will likely have the last word on the formatting of the reference.


text:
Are my chances of getting into a PhD program better if I do not need funding?
I searched the site and couldn't find any information on this topic so I thought I would ask myself.
I have been at work for quite a while now and am fortunate that they have offered to support me while I pursue a Physics PhD in the United States. This would mean that I would not need financial assistance while I completed it. I was curious if this would increase my chances of acceptance at my target universities in the US or would it have no bearing on the outcome.
Following up on this, should I mention that I do not need funding in my statement of purpose/personal statement or would it be a faux pas?

Edit:
Thank you everyone for providing information. Yes Roland, it is very similar to a industry stipend but only living expenses/tuition would be covered. With respect to programs, Looktook, I am still in the beginning stages of the application process and haven't narrowed down my target schools, if that is what you meant by your comment. Thank you Buffy for clarifying, so it sounds like my situation is more of a good bonus to have but isn't a reason for me to get too comfortable. My place of employment is outside of the US and they do not have a pipeline to any particular University but thank you for your insight Jon. Fourier, I will keep that information in mind. Once again thank you all for sharing your insights.

Does your company have a pipeline to various schools. Once upon a time, IBM supported students were highly regarded as pre-selected as suitable candidates in several programs. Your mileage may vary.

You need to specify which program. Because they are different

(My context is math at an R1 in the U.S.)
Our usual admission criterion is on merit first, and then have number of admissions limited by our capacity. The point I want to make is that "capacity" does not only mean "number of Research Asistantships or Teaching Assistantships or Fellowships" we have, but, also, on the number of faculty we have as mentors and advisors.
This does presume that faculty behave responsibly toward their PhD students! :)
But, still, yes, there might be a small marginal benefit to have your own funding. Make this clear in your application. But, again, funding is only one part of admission criteria (at least for a responsible department, as opposed to predatory, trying to generate as much tuition as possible without offering much in return).

Is it true that some R1 math PhD programs pick PhD students with the expectations that they won't finish and that they will be used as cheap TA labor?

This would depend on the place and probably isn't uniform for physics in the US. In most places the funding decisions and the acceptance are done separately. If you don't qualify when needing funding then funding isn't going to help.
There may be a few positions (spread over a lot of places) where it might matter if the lab you join is grant funded.
If you enter with an MS it might be more helpful, but less so if you apply with only a BS, as most students do.
In other fields it wouldn't matter at all, since most doctoral students are funded as teaching assistants. But some lab sciences will be exceptions.
But the more important thing is to have a good application independent of the funding. They would rather take a good student that needed funding than a mediocre one who doesn't.

"They would rather take a good student that needed funding than a mediocre one who doesn't." This is totally wrong, all the engineering departments at my uni are happy to admit anyone who pays. There is always room for more, if you have the cash.

@FourierFlux, that would seem odd for a doctoral program. If I accept your statement I wonder if your university is so bad that it doesn't attract enough qualified applicants. Alternatively, is your opinion of engineering so negative that it biases your outlook? In any case, the OP is looking to study physics, not engineering. And in the US. You don't indicate where you are from, but "uni" is typically a UK abbreviation. And, by "totally wrong" do you mean "never correct".

For non-ivy universities the graduate program tuition is a money making operation, even a state school has huge tuition costs. Most programs are more than happy to take people's money, space isn't an issue. I even met international graduate students who clearly had no place in the graduate program but the university actively lowers their standards for them since they pay the most $$$. If you're semi competent and willing to fund yourself you will definitely get into a state school. Maybe not the best one but you will get in. This doesn't mean I put will graduate of course.

Yes, but make that clear in your application or email a professor directly.


text:
Suitable citation style for dealing with many de-identified sources, interviews and personal correspondence?
Background:
I am writing a paper analysing various organisations that I need to de-identify.
For my analysis I need to cite three types of sources:

Publicly available published works that identify the organisations (e.g. reports by the organisation, peer reviewed works that assess the performance of the organisation, etc)

Interviews I have conducted with the organisations where I need to de-identify the organisations.

Personal correspondence (emails) with the organisations where I need to de-identify the organisations.

For the sake of explanation, lets pretend that "Organisation A" is Google (in actuality this report has nothing to do with Google). I have undertaken an interview with Google (that needs to be de-identified per ethics approval), had personal correspondence by email with Google (that needs to be de-identified) and also I want to cite public reports Google has published.
The problems:
When combining these three types of sources I end up writing sentences like this:

"Organisation A performed well against validity metrics (interview
with Organisation A), sufficiently against accuracy metrics (personal
correspondence with Organisation A) but poorly against correctness
metrics (Google et al., 2020).

Problems with that include:

When I am analysing publicly available sources alongside interviews I essentially re-identify the organisation. It is obvious in the above sentence that Organisation A is Google.

These sentences are really ugly with all the interjections of "(personal correspondence with Organisation A, 2021)" and "(interview with Organisation A, 2021)".

The questions:

How should I deal with citing these three types of sources without re-identifying organisations?

Is there a citation style that will make this less ugly? Maybe something where personal correspondence and interviews can be references with a superscript or similar? At the moment I am using Vancouver and I don't think it is the best choice.

Thank you kindly for your assistance.
Edit: clarification - even though I know that it is not necessary to reference your own interviews in the text of your study (i.e. interviews that have been undertaken pursuant to a description in the methods section), I would still like to find a notation style that allows me to intermingle interviews, personal correspondence and public documents in a way that is visually clean but also shows where information has come from (i.e. not ugly in the way I have described above). This issue is almost separate and apart from the issue of deidentifying sources.

What did the IRB that approved your interviews suggest?

They made no suggestion re this.

Ok. There's typically no need to cite your own research in your writing using a "citation style" - that's for citing other work. You might use it if you were referring to interviews that are published in some way, of course. Your methodology should make clear that you've used interviews to draw your conclusions. But you need to work through your IRB on this - whatever suggestions you might get here are still things you need to run by IRB if they've decided things must be de-identified. Probably you can't make comparisons like you want to if you don't have approval to release the IDs, though...

(not even without connecting specific Org A to Org A... even if you just use Org 1 2 3 for the public data and Org A B C for the interviews, even being able to know that the orgs are the same identifies them)

Yeah, I will certainly be running everything past the relevant IRB, I just want to see how other people would approach this problem to get some ideas.

Okay, great. We frequently get people asking here that seem to have absolutely no idea what they are doing with human subjects stuff so I always get a bit nervous about it because of how much trouble people can get into when they get ahead of themselves. I think your question (2) is very easy, but your question (1) may not have any good answer. Good luck!

Thanks Bryan. Yeah I am new to human research, but working within a more experienced group. I just want to be able to bring some ideas to the table in terms of how to proceed. Do you have any suggestions re question (2)?

See my comment above: you don't need to "cite" the things that are not external resources. Just be clear in your writing what you're talking about.

Thanks Bryan - much appreciated.

You don't need to cite your "data" every time you mention it
Assuming it is okay to identify the institutions in your study, I would recommend that you cite the published reports and other public works from these organisations (using standard citations), but for the remaining material you can consider this as part of your "data" and you can just mention how it was collected in your methodology and not cite it each time.  The results of the interviews you conducted, and any correspondence dealing with follow-up questions are essentially just the recorded "data" for your project.  You should save this material in an appropriate form with your institution, and it should be available to researchers on an appropriate basis having regard to privacy, etc. (which might preclude access).
For example, in your methodology section you would describe the interviews you conducted in sufficient detail for the reader to understand the methodology; it would then go without saying that the results in the interviews are recorded in your data for the project and you would have no need to cite any source when you set out the results of the interviews.
If you want to completely de-identify the institutions then you would not give citations to their policy documents, but you would note that internal policy documents were the source of the metrics (and in your internal data you would record the sources of each of the metrics for your own use).  Alternatively, if it is okay to identify the organisations in the study, but you want to de-identify their results (so you give results that are not matched with organisations), you would cite their materials in your methodology section to establish the relevant metrics, etc., but you would then de-identify in your results; you would have no need to re-cite those sources there.  If the internal policy documents are quite voluminous (and I can imagine they would be) you could put your citations in the methodology section in a table.  For example, you might do something like this:

Methodology
We did a series of interviews with employees at ten institutions: Google, Apple, IBM, ... .  Performance metrics were taken from internal policy documents at those institutions; see Table X for sources for each institution.  Questions for our interviews are shown in Appendix B; these were supplemented by correspondence to clarify policies, metrics, etc., where needed.
Then later...
Results
For purposes of de-identification we have randomly assigned our organisations as Organisations A-J, and they are described with these labels in the results and discussion.  ...
Organisation A performed well against validity metrics, sufficiently against accuracy metrics, but poorly against correctness metrics.

I agree with the responses above. Once you identified and cited the sources of the data, statistical/qualitative results don't need citations because you found them.
In terms of the citation style, I think you are asking the wrong question. Whatever journal you plan to submit the article, you should follow their instruction about the style.


text:
Can we apply to the Marie Curie postdoc fellowship with two supervisors at two different universities?
I'm thinking of applying to the Marie Curie postdoc fellowship.
My topic is a interdiscipline, two professors from two universities both participate in.
One of them can be the supervisor from the host organization, but can the other professor also involved in the the application?

Have you tried reading the provided documentation?

There's also a less known Global Postdoc fellowship that is made for this purpose: https://marie-sklodowska-curie-actions.ec.europa.eu/actions/postdoctoral-fellowships. Conditions apply (see below).
Global Postdoctoral Fellowships. They fund the mobility of researchers outside Europe. The fellowship lasts between 2 to 3 years, of which the first 1 to 2 years will be spent in a non-associated Third Country, followed by a mandatory return phase of 1 year to an organisation based in an EU Member State or Horizon Europe Associated Country. Only nationals or long-term residents of the EU Member States or Horizon Europe Associated Countries can apply.
I don't know if this applies to you, though.
P.S. There must be, in any case, only one main PI or supervisor for bureaucratic reasons. This was some time ago for me, but it was not possible to have them both with equal role.


text:
Why would a grad school make admission offers prior to the deadline?
The University of Illinois physics PhD deadline is January 15th. When I submitted on January 1st I got an email confirming submission and it included the following:

"Committee reviews will begin immediately after the application deadline, January 15 for Fall term. Admissions decisions are typically completed by March 15 for Fall admission. Decisions will be sent to you via e-mail."

However, the GradCafe results board shows that multiple applicants received offers within days of applying.
The more I think about it, the more this doesn't make sense for the program to do. Aren't they missing out on potentially more qualified applicants who are busy and haven't applied yet (deadline isn't for another 5 days)? What if these offers they are sending out BEFORE the deadline are accepted? They are reducing the number of spots in their program.

Actually, I'm very surprised that a place like UI would do this without publishing the fact that it is an option. Rules at State universities are usually pretty strict.

What do you mean by "it is an option."

...publishing the fact that early acceptance is an option. In the US there are some rules about "fairness" that might be breached if this occurs without notice.

Sending offers too late to a very good applicant also involves the risk that the applicant will accept a different offer, and the university will lose out. Very good applicants also tend to receive many offers, so this risk should not be underestimated.
Similarly to the case of hiring employees at a company, if a university wants to admit the best students, the optimal strategy would probably be to make sure to admit the very best applicants as quickly as possible, while delaying the decision for the "good but not best" applicants until the end of the deadline, in case someone better shows up. The difference between study programs and hiring processes is that universities have plenty of statistics from previous years that let them know what a "great" applicant is and what a "good" applicant is, so the could optimize this process much more if they wanted.
In the German system, some universities have this explicitly built into their admission procedure. For example, at the Technical University of Munich, great applicants are immediately admitted, and good applicants are invited to an interview:

In the initial stages, the grades you obtained during your Bachelor's program, as well as your written documents, will be evaluated using a point system. Depending on the number of points accumulated, applicants are either immediately admitted, rejected or invited to a 20 minute admissions interview carried out by the department faculty.

In the US, I see this more and more.  It puts a different flavor on student visits, which have trended towards organized events for a slew of students at once.   It means the students can ask questions of a different sort when face to face with faculty members, and the departments work on wooing the good students.
It's a horse race.  Departments don't want to lose good students to other schools just because they want to make a decision with the acceptances they're already holding.

Can you elaborate a bit more? I'm not sure what this has to do with student visits. Moreover, I still don't see how admitting students prior to receiving all applications is worth it. The students admitted still have until April 15th as per the acceptance date resolution.


text:
When applying to grad school, how can I address having failed a core course before retaking it?
I failed a crucial course for my major that serves as the foundation for many other core courses.
I retook the course and got an A, and have kept straight A's in my upper-level courses since then.
Question: What can I do to mitigate the fallout from this?
According to graduate admission committees that I've spoken to in the University of California system, this is a potential deal-breaker, which is why I'm a bit worried.

Almost certainly "admission committees" in "the University of California system" [of 10 campuses]. Will suggest an edit.

In what year is this course generally taken? E.g., failing Intro to Physics freshman year will not hurt you if you got As in the upper-level courses; failing quantum is a much more serious problem.

@cag51 The original question statement specified it was an upper-level class that they failed-and-retook, though I like the more general wording and how your answer addresses both cases.

Possible duplicate of How does the admissions process work for Ph.D. programs in the US, particularly for weak or borderline students?

You can address this in your statement of purpose.
If you failed an intro-level course during your freshman year (e.g., intro to physics), no one is likely to care; straight As in all the core classes prove that you know your stuff. You can mention this in your statement of purpose, but I would do so only as an aside -- maybe even humorously.
If this course was a junior-level course (e.g., quantum), then this is a bit more serious. You should definitely devote ~3 sentences in your statement of purpose explaining what happened. It is a bit strange that you would get straight As in all the other courses and an F in a separate course, so they'll be glad to see a reasonable explanation.
My concern is that they may assume the anomalous F was due to cheating -- so I would definitely give an explanation that they can buy, rather than letting them make their own conclusions..

I failed a crucial course for my major that serves as the foundation for many other core courses.

This by itself shouldn't prevent you from attending grad-school.  Good students fail courses sometimes for a number of reasons, family emergency, taking too many classes, working too many hours at a job, etc.

and have kept straight A's in my upper-level courses since then. [...] this is a potential deal-breaker

I feel there is more to this situation than a single failed class.  Is your GPA in line with the published average of an accepted grad student?  Were you a middling freshman student, and got serious as a Junior?  Does your transcript bear out that this one class was a fluke, or does it show a return to an old pattern?
If you have a good overall GPA, and good letters of recommendation, then I don't see why an admissions committee would dwell on a failed and re-taken class.
By "graduate admission committees" did you do an interview with the faculty members of the department in which you will be working?  In general, you submit your application to the university, which then filters base on minimum GPA and test scores, and passes it onto the department you applied to.  Did you talk with someone in the department you'd like to attend, or a person in the admissions department?

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


text:
Not submitting reviewed manuscript
I have just addressed reviewers’ comments to one of my papers. I am the first author and did most of the job.
One of the authors does not want to resubmit. They offered no explanation and have been avoiding me. How to behave in this case?

Please do not vandalize your own question. Please see here for an explanation, and some possible alternatives.

Did your co-author tell you why he/she does not want to submit? They may have a good reason and it may be worth for you to listen to it carefully and take it into account.

The problem in the question changed a lot due to some edits. Right now it sounds as if one of the co-authors doesn't want to give his/her approval for submission, which is a completely different problem than the initial problem where co-autor said to submit, but apparently didn't.

Ask both the editor and the colleague to change the corresponding author to yourself. Make it one mail to both parties. Explain in the mail that there has been a mixup and you want to correct it. You don't need details in a first correspondence, but supply them if required.
Hopefully the journal's procedures will permit this and hopefully your coauthor won't cause a stink.

In fields of research where corresponding author has a lot of prestige, this would be very dangerous advice.

To complement Buffy's good answer, here's a potentially more diplomatic option: You could email the editor the revised manuscript, indicating that your coauthor had resubmitted it previously but apparently something had gone wrong on the way.
You could even inform your coauthor about that action beforehand, without necessarily having to wait for their response/approval.
This might be slighly less confrontative then asking to transfer the corresponding author, in which case the editor might check with your coauthor, causing a potentially awkward situation.

@neutroshock Now resubmitting as a single author does not sound like a smart idea. Basically it means that either this or the previous submission was unethical.

@neutroshock No, it is not, but this does not justify you submitting the same paper on your own.  Unless, of course, the other author did not contribute enough to be a coauthor, in which case they shouldn't have been a coauthor on the first submission to start with.  Unethical behavior is not made ethical by other unethical behavior.

@neutroshock Anyway, it seems you had recurring bad experiences with them - so you should stop publishing with them, and potentially tell your peers.

@neutroshock I think this is more tricky than you would like it to be.  But it feels that the ethics of this would be another question.  (Might have seen some similar questions here.)

@neutroshock As I said, which action is ethical etc. is a matter for another question.

No need for a rant here.  But consider that you submit it with you as a sole author and the new referee happens to know that this used to be a work with two authors: From a preprint you posted (did you?), from a conference talk, or it might even be the same referee as for the original submission.  What would you say if the referee wrote the editor that the very same paper used to have two authors, and one apparently was just taken off the paper?

Well, the reviewer from the previous submission of the manuscript could complain as well, if he/she is to review it again.

No, I'm talking about the very same paper, which you submitted with two authors and for which you apparently got referee reports (since you are talking about a revised version)?  Imagine the other journal sends it to the very same referee.

Being upfront about it to the editor is certainly the safest (and ultimately best) way: The editor might disagree, but for sure you don't risk being accused of any kind of dishonesty.  I think this is clearly the best option! (And then I also wouldn't see any ethical issues.)


text:
How is the corresponding author on a (math) paper typically chosen?
I am preparing a joint paper with my mentor. I am a math postdoc. How is the corresponding author generally chosen? What are the benefits of being the corresponding author? Is it better for a post-doc's career if they are the corresponding author?

As Ben Linowitz points out, the situation can be very different in other countries. In many places in Asia, for example, the significance of a publication on one's CV goes like this:
     publication as first author ≥ publication as corresponding author > publication as any other author.
The assumption here is that the first author contributed the most, while the corresponding author is the PI. Obviously, this should not apply to most mathematical publications where the authors are listed alphabetically, but university guidelines often do not take this into consideration...
Some countries will even put a quantitative value to this statement, explicitly weighting your publications based on the authorship order (in addition to other factors such as the impact factor). Here's an excerpt from Taipei Medical University's promotion standards (PDF):
        Rank of author                       weighted points (A)
----------------------------------------------------------------
first author or corresponding author               5.0
2nd author                                         3.0
3rd author                                         1.0
4th or lower rank author                           0.5

In some cases things get even weirder — here's an excerpt from the regulations of Seoul National University (PDF):

Score of each research publication stated in Paragraph 1 of this article is as follows:
  1. Single author: 100 points
  2. Two authors: 70 points
  3. Three authors: 50 points
  4. Four authors or more: 30 points
   If applicant, however, is the first author or the corresponding author in a publication with three or more authors, he/she is entitled to 70 points.

Curiously, sometimes a corresponding author is worth more than first author. The Academic Ranking of World Universities, compiled by an agency in China and arguably one of the most influential international university rankings, uses the following scaling:

To distinguish the order of author affiliation, a weight of 100% is assigned for corresponding author affiliation, 50% for first author affiliation (second author affiliation if the first author affiliation is the same as corresponding author affiliation), 25% for the next author affiliation, and 10% for other author affiliations.

As you can see, there are often advantages to being corresponding author in such cases. Universities can offer additional incentives (e.g. monetary) for being first or corresponding author on high-impact publications, which often leads to more arguments and occurrences such as six "joint first" authors or, similarly, multiple "co-corresponding" authors on a paper.
Anecdotally, I would say that in non-Asian countries, such weighting is also frequently done but on an implicit basis, and is significantly more field-dependent. (For instance, the Korean university regulations do not distinguish between different fields, and I am unsure if different departments can have different rules — if not, I encourage every mathematician named Aaronson to apply for faculty positions in South Korea immediately.)

Essentially all the pure maths papers I've seen lists authors alphabetically. This is independent of what country the paper was written in. Any ranking system that ignores this is producing random noise or worse when applied to maths departments.

@DavidRicherby: Absolutely.  Nevertheless, such systems are used, and affect many mathematicians’ career prospects.

I don’t think linking to an undated document on some web server in a language that’s not Korean provides sufficient evidence that this is how Korean universities evaluate their faculty’s work in the context of pure math, where (as @DavidRicherby pointed out) this data would produce a completely nonsensical result. Your extraordinary claim that Korea and “many places in Asia” are bureaucratic to the point of insanity requires extraordinary evidence. I’ll believe it when I see more convincing proof. Until then - downvoted.

To answer your questions in order, and based purely on my own experiences (in pure math in the UK).

Some reasons for choosing a particular person as corresponding author might be:

they are more experienced in dealing with journals
they are less experienced and so need the experience
they happen to be less busy at the time of submission
they are more junior and less busy in general
they are more senior and so their affiliation is unlikely to change (and they're not likely to leave academia)
they volunteered
it's their turn
they are the most organised
they know how to format the paper to the journal's requirements

The main "benefit" is being in control of the process. The non-benefit is that it is extra work - even if it doesn't make much difference to who actually implements any changes the journal asks for, you probably still end up emailing the other authors to say what needs done, writing the response to reviewers, checking proofs, and various other small things.
No. The reasons for being corresponding author or not are very varied, and either largely irrelevant or things that are more obvious from other factors anyway, so it's not useful information. IMO it would look very weird to specify on a CV which papers you were a corresponding author on, and I doubt any committee would bother to find this out. It would perhaps be preferable to have been corresponding author at least once, but in pure math people will generally have some single-author publications and so this isn't an issue.

The only "benefit" that I can think of of being the corresponding author - if you can call it a benefit - is that it prevents underhanded actions by coauthors. Sometimes, people from different groups and motivations, who are possibly at odds with each other, end up co-authoring. Or - an estranged pair of advisor-advisee. Some of the authors might suspect the others of being willing to compromise the paper somehow (obviously I'm being vague since this is inspecific.) The corresponding author, however, has control over communications with the venue, so s/he can exercise effective veto power over steps s/he disapproves of.

@MorganRodgers: Let us not speak of such atrocities :-(


text:
Getting into new PhD after failing comps
Last summer I failed my comps/quals of my PhD program. I did not have a chance to take a second try, as my spring semester grades were poor. The first semester (fall) was good, though.
I could not fully concentrate on my studies during the spring semester as there were some family issues in my home country.
My advisor believes in me and said I should continue my studies. I am still very much motivated to do research in my area.
There are couple of concerns, though. How will my poor performance in the spring semester (and consequently failing comps) affect my chances into getting to another program? How should I approach my personal statement?

what do you want to achieve in life? What is wrong with staying in the current program? What is your location in the world? What is your area of reserach?

@aaaaasaysreinstateMonica I want to become a strong researcher in development economics as it is the only thing that I want to do in this life. I am from central asian country.

Two bits of advice.
First, your SoP should be as positive as possible without hiding the setback. Talk, as usual, about your goals and how your preparation makes you a likely success.
But, I think more important, use your adviser's personal/professional contacts to help get you in the door somewhere. The advisor, even beyond a LoR, can boost your chances if they are willing to speak to others they know who can help you.
If you say "I failed comps, but ..." it is an entirely different thing than a professor saying "He failed comps, but ...". The professor is putting their reputation on the line for you. It is likely to be respected.

I agree completely with Buffy.
RE the SoP, I would add:

You need to spend a paragraph to address it honestly. They're not going to admit you until they feel like they understand what happened, so you want to give your side of the story. In particular, you should honestly answer why you think you will be more successful someplace else.
But don't dwell on it or make excuses. Your SoP is not the place to do a lengthy introspection or post-mortem.
If you can summarize the problem at home in a sentence or less (e.g., "my father died"), that is probably worth doing.
If you can take responsibility for some aspect of the failure in a sentence or less (e.g., "I didn't spend enough time studying for quantum"), that is also probably worth doing.


text:
What is the meaning of the two numbers in the paper identifier of EDAS?
I have submitted a paper to a conference via EDAS. The conference asked me for the "paper number" in its own registration form (independent from EDAS).
On EDAS my paper has an identifier composed by two numbers, in the form #XX (XXX..XXX), where the Xs are digits. What is the meaning of the two numbers?
I went quickly through the EDAS glossary, but I did not find the answer.


text:
Addressing age, resume-gaps and non-related job experience in a research job interview
I spent 7 years after high school working in hospitality, customer service, and semi-skilled manual labor. I returned to school got a bachelor's and later a masters, and now work in a research lab.  I do not include any of my pre-respecialization work experience on my resume or LinkedIn. I also do not include my high school graduation date. As such, someone reviewing my resume could mistake me for a different candidate, one who was more focused and went right into the field. In some scenarios (application/interview), I do not do/say anything to discourage this assumption. I have a youngish face, though in terms of energy level I'm sure it comes through. Obviously, co-workers have an idea.
I feel that some cases of respecializing are respected, such as transitioning from one trained, professional role to another. People change, and taking steps to align your career with your priorities and interests, if these fall out of alignment is looked at favorably. Meanwhile, "menial" jobs (retail, customer service, food service, construction in some cases) regardless of the reason a person might stay in these jobs, are a looked at as lost time, and in most cases, are best glossed over or avoided.
Anyone have thoughts on this? If your resume/publications/accomplishments etc. do not suggest your age, should you fake it where you can? (as many people are most productive early on in their careers, ageism, etc)

Depending on the job you're applying for, your "menial" working experience might be a big plus on the soft-skill side. You know how to deal with people, how some things work in the "real" world, etc. Sure, this wont give you much bonus in engineering or chemistry research, but e.g. in humanity related researched, your experience might help you.

One option is to put in a single job call "hospitality, customer service, and semi-skilled manual labor" covering these dates.

It depends on what you mean by "fake it". You need to be honest, but you don't need to volunteer things that aren't required. Nor do you always need to give the most complete possible answers.
But honesty is required.
I think most people will accept you as you are, not looking for ways to put you down over issues like age. There are exceptions, of course, but more people "do the right thing" than not. And a lot of people will have gone through some of the same things. Not everyone's path is smooth.

I think you are looking from a subjective perspective.
Everyone perceives from a different point of view. For example, your work in "hospitality, customer service, and semi-skilled manual labor" moved to research, it shows that you have the ability to adapt to the new environment, which is a good thing in research.
Sell your past with better words rather than hiding it.
Be honest! there must be a post/job that will appreciate your "agility".

To this I'd add that someone who can survive in the hospitality business probably "adults" very well.  this is a plus.


text:
How can I find out if New York State's Department of Education accredits more than just high schools, and if there is a list of their institutions?
I'm looking into schools that are accredited. I saw that NY state department of education gives accreditation to institutions, but I simply cannot tell if this is only for high schools. Also, I can't find a list of the high schools they accredit.
How can I find this information?

You are correct that the states accredit secondary education. They don't accredit colleges and universities, but have some say in policies.
Accreditation in the US is handled by private agencies that are, themselves, accredited to the US department of education. Most of these are regional and accredit most of the colleges and universities within their region. There are a few specialized agencies as well, but they, too, require accreditation from the US department of education.
On the other hand, the states can permit universities to offer certain degrees. So, a university, to offer a doctoral degree in a given field, needs something like a license from the state. But we have fifty states and so I can't guarantee that this is a uniform practice.
Most universities will have a web presence that makes their accreditation prominent. They will probably name the main accrediting agency and link to it.
See: https://www.chea.org/regional-accrediting-organizations-accreditor-type
And one university has the following information: https://accreditation.umich.edu/history/
And some fields have separate accreditation for programs.

States really only have say over majors/degrees at state-funded schools, and that is mostly to concentrate funding to support one viable program vs multiple sub-par programs.

@JonCuster, actually that isn't true. New York has control over doctoral programs even at private universities. You need state permission to offer a PhD in field X. I have direct evidence of this. The university was accredited and allowed to offer PhDs in some areas, but new programs needed vetting. But other states have their own rules on such things.

I'm having a hard time believing that New York would tell Columbia "no" - they have no real leverage and would quickly lose any PR battle over it. The SUNY system, CUNY, and the state-supported portions of Cornell they have leverage over.

@JonCuster Still, it happened. But you have caught part of the reason. Some of it is political. A few schools can apply a lot of pressure on the state agencies.

it also turns out that universities have leverage over both the state and accreditation bodies, so it cuts both ways. One state told a university it would stop giving teaching credentials to their liberal arts graduates (who did a lot of un-credited work on things like practice teaching) unless they implemented all the 'how to teach' courses in an education degree. The state backed down after every school district who had hired such a student told them they were being stupid.


text:
How to politely ask the editor to freeze my submission
I am facing an inconvenient situation that I will try to explain as well as I can. Here is my case:
One and a half years ago, I submitted my paper to Journal A. The reviewing process started and I managed to convince three out of four reviewers. All of the reviewers asked the editor to accept my submission. The last reviewer asked me to include an unusual comparison method. I refused to add the non-standard method and the reviewer ask the editor to reject my paper which he did immediately. Being shocked, I wrote an email to the editor asking him to give me a chance to correct the misunderstanding. Not receiving an answer to my email, I decided to submit my paper to Journal B. After a while, the editor of Journal A sent me an email telling me that he has decided to give me another chance. Now, I am facing an unintentional double submission situation. My paper is "With the editor" on Journal B and hasn't yet been sent to the reviewers. Considering that I spent so much time convincing the reviewers of Journal A, I don't want to miss the opportunity of revising my paper in Journal A. Yet, I don't want to mess things up with Journal B because they are a very reputable journal, and I want to work with them in the future.
Now, I want to ask Journal B to freeze my submission to prevent from double submission problem. My problem is that I don't know whether they will understand me or not.

How would you recommend that I write an email to them?
Is this kind of situation normal?
Will they black-list me?
Will they understand me if I write them honestly?
Will I lose my chance of submitting other papers to any of the Journals?

Both Journals are very reputable journals and I don't want to get into any problems with any of them.

My first impression is that journal A messed up by having weird communication and not sticking to the standard process. If I was the editor at journal B, I would be very sympathetic about your situation. However, what precisely is the nature of the "other chance"? Have you asked for a chance to submit another revision?

@lighthousekeeper He has written that I should prepare a comment to the reviewer. Then, he will ask the handling editor to communicate with the reviewer and if needed they will reopen the review.

If the review at journal A would not be reopened by your "other chance", then there's no need to communicate with journal B until you have an acceptance. If you get the acceptance at A, you can withdraw from B, and explain to their editor that journal A went out of the standard process and accepted your paper after earlier rejecting it.

@lighthousekeeper Would they blacklist me? Could you please leave an answer addressing my questions?

@lighthousekeeper, this is poor advice. You suggest leaving it open with two journals. The answer of Allure is correct and much better advice.

@Buffy "Leaving it open" is not a formal status - one is always open to consider submitting a paper at any journal. The rule is that a paper may not be under review at two journals at one time. But the paper has already been rejected at A.

@lighthousekeeper What is there for journal B to be "sympathetic" about here? Journal A rejected the paper. The OP then submitted it to B. Now, A have said "OK, you can resubmit it to us if you want to." They have not said they will accept and publish it! It is entirely the OP's decision whether to stick with B or withdraw from B and resubmit to A, but the OP has to choose one or the other, they can't ride both horses at once.

@alephzero I agree with you. I don't want to ride both too. I want to find the best way to ask Journal B to withdraw my submission. I have papers that I want to submit in Journal B later. I don't want to make them angry with me.

What does it mean for "A to give you another chance"? Same reviewer? Different reviewer? Different revision conditions? Rereviewing from scratch? Demand that you fulfil the reviewer's condition? My reaction would be very different in each of these scenarios.

@CaptainEmacs He has written that I should prepare a comment to the reviewer. Then, he will ask the handling editor to communicate with the reviewer and if needed they will reopen the review. (Same reviewer)

@alephzero No, A has not said "you can resubmit" - please see the clarification in the comments. They have said that OP can send them a comment which they will forward to the reviewer.

@Sajjad Well, then it's anyone's bet if your comment to the reviewer will convince them. However, as B has not sent off the paper to the reviewers yet, you could tell them that you submitted to B, after journal A rejected, but now A has decided to offer to reopen your review (don't mention A's name). And ask B for how to proceed - whether to freeze or to withdraw, but without losing the opportunity to ultimately submit to B. If they say that you have to take a decision, you know where you stand.

Write to journal B and say you are withdrawing. You don't have to give reasons, although you could say the submission was premature if you want to. That's all there is to it.
Nothing much is likely to happen with the second journal, since it's fairly common for manuscripts to be withdrawn. Furthermore the status is "with editor", which means they've done almost nothing to the manuscript yet.
Edit: I would not suggest telling journal B that your paper has been rejected by journal A. See:

[What'd you actually highlight would be]: Your paper has been rejected by another journal before (not a good sign; think of it as "if we publish it now, we're actually publishing another journal's rejects, and we're supposed to be a good journal!!")

@Buffy Will I be able to submit my papers to Journal B, if I ask for the withdrawal of my paper out of "premature submission"?

@Sajjad sure, why not?

Well, they might think that I wasted their time. I submitted the paper to Journal B on Friday!

@Sajjad the longer you wait, the more of their time you're going to waste. As I wrote, they've done almost nothing to the manuscript yet.

You are right. That's why I tried to ask you as soon as I could. Actually, the paper's status changed to "With editor' just today. As I said, I don't want to lose my chance on submitting my next papers to Journal B.

While I wouldn't yell about a rejection from the mountaintops, I'm also not sure it needs to be quite as hush-hush as that quote suggests. Anyone editing a mid-tier journal must know that a) people submit elsewhere and b) papers get rejected for all kinds of trivial, even spurious, reasons.

@Matt OP did say both journals A and B are very reputable, though.

I think the best is somewhere between the suggestions by Anonymous Physicist and Scott Seidman. Namely, just write to the editor of B and state only the bare facts that are necessary for the editor to know:

Dear Editor, I had submitted paper X to you after receiving a rejection from another journal. However, some time later, they sent me another email saying that they might reconsider their rejection. Due to that, I can no longer proceed with my submission to your journal, and would have to withdraw it. Thank you.

I do not think you should be embarrassed for something you did not do wrong, and it is very important to state that the first journal rejected your submission before you submitted to the second journal.

If you really want to stick with journal A, simply say:

Dear Editor B,
Please withdraw my paper "papername" from consideration.  I am sorry for the inconvenience.  I am making this request because the editor of another journal has changed their mind.

Do not tell B who A is.  Do not resubmit to A until B has confirmed withdrawal.

I worry that your formulation leaves the impression that the other journal has accepted the paper. That might not be what you want to convey, especially if it also conveys the impression that it was doubly submitted in the first place. Even less of an explanation might be better.

I'd like to make a point that the other answers aren't touching upon.
You're in a situation, a double submission, that some could interpret as an ethical lapse.  Clearly, this was not your intention, and you thought your paper was no longer encumbered by the first journal.
You need to approach this from the perspective of "If this blows up, I may need to be able to show a communication trail to my Dean that clearly shows my trying to resolve the screwup, regardless of the cause of the screwup".  The safest way is to assume that down the line, your Dean may be reading every one of your communications on the matter, and thus your communications must put all temptation to investigate further to rest.  You need to be clear and unambiguous.
I'd try "Dear Editor B.  I submitted the paper to you after receiving communication from Editor A that my submission was no longer under consideration.  After that communication was received, I received a message that Editor A revived my review, thus this paper is currently under review by two journals simultaneously.  I'm somewhat embarrassed by the situation, and I apologize for the inconvenience, but I would like to withdraw my paper from consideration, and might resubmit it later pending the outcome of my other review."
Collect ALL your communications about this paper to date, along with any response you may receive, and save them.

Should I include journal A's name?

No need to do so.

Nor the editors name.

I still prefer the formulation of @Allure. Any "reason" given could just get in the way. In the worst case, considered to be a "cover up". Keep it simple and clean. But the other advice, of keeping a paper trail, is very good.

This is clearly not a double submission.

@AnonymousPhysicist  I disagree.  Editor A currently thinks it's under review, and Editor B is in the process of scheduling it for review.  If the author takes no action at this point, there is a chance that the paper be accepted by both journals.  How is that not a double submission, regardless of how it arrived at this point.    Moreover, should both journals actually accept the paper, how would you like to be the one making a semantic argument to your chair that it wasn't a double submission?

@Buffy -- I'm marginally in disagreement with that.  Yes, there is a small chance that it confuses things, but when I cause somebody extra work because of anything perceivable as a screwup (and I'm not completely willing to let the author off the hook here), I lean toward providing explanation and an apology.  Also, the letter I suggests clearly documents a chain of events in case anyone is looking at it later, as I describe.  I prefer to have the situation self-document, as opposed to having to explain my actions that aren't apparent in the record.

@ScottSeidman No, editor A rejected the paper.  Please check the question.  "ask the editor to reject my paper which he did immediately."

@AnonymousPhysicist I understand that just fine.  It would mean zip should the paper be published twice.  Regardless of how it got there, the paper currently stands as double submitted.

This is a tough situation, the cause of which is mostly the poor behavior by Journal A.  I say "mostly" because of the following point:

Not receiving an answer to my email, I decided to submit my paper to Journal B. After a while, the editor of Journal A sent me an email telling me that he has decided to give me another chance.

It is well known that journals can take a long time to respond to authors' queries (what often seems like -- and probably often is -- too long).  To have a conversation like this with an editor, in my experience one must be willing for it to take up to a couple of months.  Do you as the author have to wait that long just to continue the conversation?  No: you can end it at any time by informing the editor that time constraints have forced you to move on to another journal.
In this case you left your query with Journal A open while submitting to Journal B.  Is this a double submission?  No, because the status of your paper with Journal A is "rejected."  But it does leave the door open for something like this to happen down the road.  You probably should have expected to hear something back from the editor eventually; in my experience, that has usually been the case.
Again though, the primary culprit here is Journal A, who seems to be behaving badly: spending a long time processing your paper, rejecting because of a suggestion made by one referee was not followed, while three other referees recommended publication, and then not addressing your concern about this in a timely manner.
I think it is ethical to withdraw from Journal B and resubmit to Journal A.  This would be ethical independent of the timing, but because you only submitted to Journal B on Friday -- c'mon, they have not done anything much with your paper since then.  I don't think you need to say anything about why you are withdrawing the paper, and I don't think they will ask or care.
I think though that the situation where you withdraw from a second journal to revive business with the first journal is a suboptimal one, to be avoided if possible.  I mentioned above what you could have done to avoid this situation and should (I suggest) do next time.  I did want to put just one word in for staying with Journal B.  I don't know the particulars of your situation: the relative merits of the two journals, how much time you're likely to lose by starting over with your particular paper, and so forth, so staying with Journal A may well be the best decision for you. But again, they've behaved badly.  On the one hand, everything else being equal it is best not to reward those who have behaved badly.  On the other hand, maybe they will continue to behave badly: it could be that after six months, Journal A decides to re-reject your paper because of the same critique by the same referee, right?  You have to decide how likely that is to happen and how you will feel if it does happen.
Good luck.

What you've quoted though follows after "I refused to add the non-standard method and the reviewer ask the editor to reject my paper which he did immediately." so the last communication received from Journal A was a rejection, followed by a lack of reply to the request to reconsider. I wouldn't give Journal A any benefit of the doubt.

@David: The problem is that it can be hard to tell how long to wait for a reply from an editor in order to be sure there is a lack of reply.  I have gotten replies after up to two months.