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PhD admissions - (undergraduate) credit/no-credit influence on acceptance
I plan on doing a PhD in computational linguistics, which I intend to start in about 3 years. I have one more year of undergraduate study, and 5/6 of the courses remaining are for my minor in Applied Linguistics.
I plan on taking 2/6 of those classes as credit/no-credit (CR/NC) because I'm also working two jobs, and worst-case scenario I'll fall behind in these classes, but not so far behind that I wouldn't pass with 75% (and still receive credit).
aeismail says in one of her answers that:

Admissions committees do not place as much weight on courses outside the major as courses in the major. If you are a physics major, for instance, a C in a US History course is not going to be as problematic as a C in electricity and magnetism.

These CR/NC courses are not in my majors (Computer Science and French), so I don't think that they would raise flags to admissions committees, but I also don't want admissions to think "oh he seriously slacked off his last year of undergrad!"
Do admissions committees care about CR/NC courses in undergrad?

I think the quoted answer would be better if it said "If you are applying for a PhD in Physics". Regardless of your major, your performance in Applied Linguistics classes is very relevant for a PhD in computational linguistics.

https://academia.stackexchange.com/questions/85755/how-do-pass-fail-classes-look-to-phd-admissions-committees

I wanted to expand on the point made by @StrongBad in the comments.  Even if the courses in question are not offered through the Linguistics department, any grade in a course that is closely related to the proposed graduate program will be weighted much more heavily than a random course taken for general-education or general-interest purposes.
For example, when I was on a graduate admissions committee in physics (during my grad student days), we did look at the student's performance in mathematics classes.  These courses didn't carry as much weight as their performance in physics classes, but a C- in multi-variable calculus or linear algebra would be troubling.  Seeing a "pass" indication in such a class would make me wonder what happened there, and would make me concerned that the student didn't really get everything out of the class that they would need for graduate studies.  Even if these classes weren't required for the student's major (an applicant who had majored in chemistry, say), it would still give me pause.  In effect, it's better than nothing, but not much better than that.
If I'm reading your post correctly, you're proposing to take Computer Science classes pass/fail and then apply to a program in computational linguistics.  I'm not a computational linguist, but this seems like a bad idea to me.  On the other hand, you might be able to get away with taking a French class pass/fail, since the skills you would be learning in that class are not as directly related to computational linguistics.  (At least, they wouldn't be if your classes are anything like my college French classes were.)  And if the classes are completely unrelated (a class in History or Economics, say), then it's probably fine to take those pass/fail.
On a related note: if you do decide to take these courses pass/fail, you should be absolutely sure that you can still complete the proposed minor.  Many institutions (for example, mine) do not allow you to count pass/fail courses towards an academic major or minor.  Check with the department in question about this, if you haven't already.

Thank you for your elaboration Michael. I would be taking the Applied Linguistics courses as pass/fail, not the Computer Science courses. In fact, I complete the French and Computer Science majors this semester. I was curious how application committees would view a couple CR/NC courses in the minor; I should have elaborated that the two courses I would take have nothing to do with my area of study (the courses are in sociolinguistics and English as a second language). There is also no violation of university CR/NC policy here either. Would any of that alter the info in your answer?

My general advice is still basically the same.  The deciding question about whether to take the courses CR/NC shouldn't be "are they in my minor?", it should be "how relevant are they to my proposed graduate program?"  If the courses are completely unrelated, you can get away with it;  but the closer they are to your proposed graduate program, the worse of an idea it is.  I'm not a linguist, so I'm not sure what the answer would be for the specific courses you mention;  you should really ask a professor in your department for field-specific advice.

Alright, I understand :) I will ask the linguistics professors that I know just to be sure, but by the course descriptions they have zero relevance. Thank you for your very helpful advice!


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Why are journals used in modern scientific academic research?
I am new to research and I have yet to internalize the concept of journals and their utility in archiving scientific literature.
Almost all the papers I have read recently are from this website called arxiv. Arxiv calls itself to be a preprint archive. Anyone can upload a PDF file to the repository and it counts as a valid research. Large companies like Google and Facebook post all their research here. The research is peer reviewed, It does not have the tyranny of a fixed format and the publishing is instantaneous unlike journals which are painfully slow. It is also open access and unlike open access journals it does not cost a fortune to publish a paper.
My question is, why were journals used to begin with? Why are they used now?
I have heard some people say that if a paper is not published in a scopus indexed journal then it does not have any value. Then why are so many people publishing here? As far as I know citations from arxiv are picked up by google scholar.
EDIT: Ok, so the entire system is a huge mess.

https://gowers.files.wordpress.com/2012/02/elsevierstatementfinal.pdf
http://www.michaeleisen.org/blog/?p=1439
https://arxiv.org/pdf/1204.1351.pdf

ArXiv is not peer reviewed.

"the tyranny of a fixed format" sounds a bit bombastic -- it isn't such a big deal in practice.

You may find the following related question useful: Why do we not reinvent the journal system?

"it counts as a valid research" - that's in the eye of the beholder.  There isn't some universal "valid/invalid" flag attached to any given piece of research.  For instance, most university faculty will find that arXiv posts  will not satisfy their employer's expectations for their research.

"The entire system is a mess" is an overstatement.  Don't despair.  The system certainly has flaws, and some people feel more strongly about them than others, and are more vocal.  But for a lot of other people, the system works reasonably well and its flaws do not interfere with research in a serious way.

OP, I honestly believe you chose the wrong answer to accept. While inertia is always a factor inhibiting social change, ArXiv is not an alternative to publishing in journals, for reasons mentioned by @TobiasKildetoft and most of the other answers.

@NateEldredge Many researchers (me included) would disagrees with your statement. The system is a mess. This is not an overstatement. Not everybody agrees, of course, but some would argue that this is akin to Stockholm syndrome: people got so used to the mess that they reflexively defend it.

@KonradRudolph Accusing people who defend a system of having Stockholm Syndrome really isn't constructive.

@DavidRicherby I’m not accusing, I’m trying to explain something (to myself and others). I’m not mad at Nate, I just think he’s wrong, and in such a way as to be hard to grasp for me: To many scientists, stating that the current publishing system isn’t a mess just flies in the face of overwhelming evidence. Incidentally, I don’t think it’s wrong to defend the current system, either. But defending doesn’t mean not acknowledging that it’s broken in very fundamental ways.

Why are so many people publishing [on ArXiv]?

You have to be careful with terminology when making statements like that. ArXiv is certainly "publishing" in the literal sense of "making public" but would you say that you'd "published a book" if you'd just put it on your website? Probably not.

My question is, why were journals used to begin with?

Because they predate ArXiv and the web by hundreds of years, though the format has changed over time.

Why are they used now?

Partly through inertia, partly through a lack of alternatives. On a purely scientific level, ArXiv itself is not peer-reviewed. On a non-scientific level, ... People have an intuition about the quality they expect from a paper that appears in a particular journal and we don't have alternatives that allow us to make this kind of judgement. Correspondingly, certain journals have quite a lot of prestige, which is important for students early-career researchers who are looking for promotion; a large fraction of papers have at least one such author. It's easier for people like Tim Gowers to work outside that system.

Additional context for the last sentence: Tim Gowers (the author of one of the linked posts) is an extremely famous mathematician. An abbreviated listed of his accomplishments include: the Fields Medal (the biggest award in mathematics), membership in the Royal Society of London, a professorship at arguably the best place to study mathematics in his country and a consensus top 10 pick world-wide, and a Knighthood for his accomplishments in mathematics.

I think his blog is excellent and take his ideas about mathematics culture quite seriously, but at the end of the day when you’re the kind of person who can walk into almost any university in the world and tell them that they now employ you, it’s a lot easier to disdain the prestige system than it is for most people.

First of all, ArXiv covers mathematical disciplines (specifically: Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics), not all academic fields. So, the question, which seems to pose this as a general inquiry about the need for journals, is overly broad in the context of offer ArXiv as an alternative.
Second of all, ArXiv is not peer reviewed. Therefore, consumers of the information need to be a bit more careful than when they're referencing information that has gotten past an editorial board and at least a couple peer reviewers. That's not to say that erroneous material doesn't get past peer reviewers (it does) but there's just more quality control in a peer reviewed paper than an unreviewed paper.
Third, my impression of ArXiv is that people upload their stuff there to make it available sooner while they pursue publication in a peer-reviewed journal. It is not meant as a publishing destination, but rather a repository to speed up dissemination of the information for those who may want it sooner.
Fourth, in my department (I'm in a science discipline, not math), getting tenure requires publishing in peer reviewed journals that are indexed by something like Pubmed. Book chapters and unpublished reports (which is what I'd consider an ArXiv paper) count very little toward fulfilling tenure expectations.

I feel compelled to say that things on the internet are literally "published". I'd hate to see that word corrupted to mean only "peer-reviewed" or "passed the gate-keepers", etc. And for many people with tenure, now that we have the internet, what's the point of continued status-seeking? It costs time and effort, as opposed to actually doing the work.

Is peer review even necessary for computer science? If the code runs then yay otherwise boo. Also as @paulgarrett said its kinda superficial. Cyclic if you think about it. All good papers are published in good journals, good journals publish good papers.

@SouradeepNanda I am afraid that what's superficial is your view of computer science.  It's about far more than "does the code run".

Yes - computer science (my area of it, at least) is about proofs, not code. Even if you're looking at code, the fact that it runs does not in any way imply that it will always give a correct result.

@SouradeepNanda if anything, whether or not the code runs is the least important bit of information. A valid algorithm with a syntax error in its implementation is still useful, while a perfect implementation of a crappy algorithm is pointless. Nevertheless, the later runs while the former doesn't. In any case, the vast majority of scientific output is not algorithms and isn't something that can "run".

Physics and quantitative biology, at least, are scientific, not mathematical fields. The difference is whether things can be proven in the mathematical sense or they have to be observed empirically and reasoned about using mathematics. You cannot ever prove anything about the natural world.

@terdon For very large chunks of computer science, there is no code to run.

@DavidRicherby yep, that's precisely my point. The code is usually secondary or not even there.

@terdon I'm making a stronger statement. Much of computer science is not about code at all, to the extent that saying that "the code is not even there" is a bit like saying "the bananas are not even there." It's not that these researchers have code but don't put it in their papers: there never was any code because the work has nothing to do with code.

Accuracy is only one aspect of a paper.  There is also making sure the document is readable, that it appropriately references earlier works, and so on.

@paulgarret: status seeking is unfortunately necessary, as status determines how the (limited) available funds are distributed.

@Gerhard, some status is necessary, sure, as in many endeavors, but I'd hope that there is a viable notion of "sufficient amount" of status/money/whatever, as opposed to "getting as much as possible".

+1 for noting arXiv isn't universal. Almost none of the papers I read are on arXiv.

Peer review, as the others have said.
Mathematicians can consult dozens (if not hundreds) of false proofs of the Riemann Hypothesis on Arxiv.  Such things are (mostly) rejected by the journals.   Journals which publish them soon get a bad reputation.
Imagine if all the amazing new health claims form the Internet could not be distinguished from serious medical research!  (For many people I know, that is unfortunately already the case.  But those who care can try to find which of those cancer cures have at least some actual evidence for them.)

There is not a lot of junk math on Arxiv.

@MilesRout... Yes Archiv.  For fun I just browsed there.  The most recent proofs of the Riemann hypothesis are dated March 15 and March 13. Some wiseacre once said that the Archiv category math.GM stands for "garbage math".

Journals, in the past and today, are not just printed material - they're social institutions of the community; and publishing in a journal is a process that involves:

Peer review by such specialists in the field as the editor/editorial collective/steering committee deems appropriate; and
Editing of the paper: Content-wise and typesetting/graphics-wise and language/style-wise. It could be editing due to reviewer comments by the original authors or by professionals employed to assist with the journal.

You don't get that on ArXiv, and you only get that partially (or almost not at all) in conferences.
The use of journals as publication venues is also a form of filtration / selection, even from among papers which would merit reading given endless time and attention. In the past, publication in a journal was often the difference between a publication coming to people's attention at all (ignoring personal contacts); but these days, it's still the case in most disciplines that there's much more awareness of what's been published in journals than of what one could find using an web search engine.

In some fields, conferences serve this role as much/more so than journals, but you can just apply this answer to submitting papers to those conferences - whose proceedings are like a sort of a journal too.

Regarding getting peer review and editing feedback from journals more than conferences, that must depend on the field.  I've been involved in many CS conferences whose reviewing processes are more rigorous than most journals, including some reviews that will note every last grammatical mistake and typo for the benefit of the authors.

@FredDouglis: Well, that's true, but you can count the proceedings of those conferences as journals in the context of OP's question.

Perhaps.  If the real question is "why peer review versus arXiv," that is a different point entirely.  I originally read the question as given: why should we still have journals in the modern age?  And that is a good question. The role of journals has evolved.  In fact some conferences (e.g., VLDB) have moved to a "journal-first" model in which papers are submitted to a journal and selected papers are invited to be presented at a conference.

PS.  Why can't I tag einpoklum?  It disappears.

Thanks Nate.  I'm relatively new to stackexchange from the standpoint of active commentary.  I would have expected an alert saying it was removing the name, and not silent edits.

+300 this is the correct answer.

@CapeCode: Yeah... not that DavidRicherby's answer is completely without merit, but it's the minor aspect of the truth IMO. Thanks for the vote of confidence :-)

The big problem with Arxiv is something you mentioned in your post:
"Anyone can upload a PDF file to the repository and it counts as a valid research. "
There are thousands and thousands of papers on arxiv which are somewhere between junk and complete nonsense. To convince yourself just look at the many "proofs" of the Riemann Hypothesis and, if I remember right, there are also "proofs" that RH is false.
The same problem also appears with some journals. The simple fact that something was published in a journal doesn't make it true. There are a lot of predatory journals which would publish anything for money, and the quality of their papers is even lower that the worst things on arxiv.
But there are a few journals which try to control the quality of the published research. They are not foolproof, and they sometimes publish bad or wrong papers, but the chances of that happening are typically much much lower than the chances of a random paper from arxiv of being junk or wrong. While not perfect, peer review can catch many mistakes and comb out many low quality papers.
As a researcher, knowing that a paper was published in what I know to be a serious journal, compared to just put on arxiv (see (*) below for extra comments), gives me an extremely important piece of information: I know that if I read the paper in detail, and try to understand it fully, it is less likely that after couple weeks I discover on page 64 that the author does something completely stupid and unfixable and nothing works.
Peer review in good journals it gives me better chances of not wasting large amounts of time for nothing.
(*) Often, if I am familiar with the work of a certain mathematician, I don't need to rely on this type of information to know what to expect. In that situation, what I know about his work combined with a fast read of the abstract and maybe introduction can tell me if the paper will be interesting or not. But things can be tricky if I come along a very long and technical, potentially interesting paper from an unknown mathematician.

Maybe Nick is from a Slavic country?  Anyway, when he says "There are few journals" he means "There are a few journals".  Not the same thing at all.  English is weird like that.

@GEdgar Not slavic, but English is my second language :)

You claim that this is a problem. But most people who use/understand preprint wouldn’t agree that it is a problem at all. So what if crap is uploaded to arXiv? It only becomes problematic if that crap somehow is thought to have the same validity as good research uploaded there. And this isn’t how preprint servers work. The fact that there’s no gatekeeping is intentional, not incidental. Institutionalised peer review is often upheld as the only valid form of scientific assessment but that’s nonsense.

@KonradRudolph For my area (pure mathematics) there is a much more subtle issue which is the problem I refer to. For long technical papers, in can take months or even years to really understand if it is correct or not (Mochizuki's proof of the ABC conjecture was posted on arxiv almost 5 years ago, submitted for publication, and there were many workshops and conferences dedicated to this particular proof and nobody completely understands it yet, might take few more years) . This also makes the peer review take much longer in my area, and makes arxiv problematic.

@NickS I don’t understand the jump from “makes peer review take much longer” (agreed) to “makes arxiv problematic”. arXiv is an archive, it does not in itself confer any status to a publication. The status comes from how the paper is regarded by professionals (= peer review). If anything, early publication and wide dissemination helps make this peer review more thorough because more experts get timely access to the results.

@KonradRudolph With the Arxiv, there is too much of a risk of investing months to read something, and discover that it doesn't work, and that you learned nothing new. And with long technical proofs, the devil is always in small details, you cannot catch the mistakes unless you invest the effort....And unfortunately, in mathematics an "almost right paper" is not much better than a crap paper.... When reading things from Arxiv, I am never concerned about the crap papers, but I am concerned that the paper I read might be "almost right".

@KonradRudolph Exactly my point: Arxiv without dissemination is not that helpful. And how do you disseminate? In mathematics, most conference presentations are 1 hour long, and they are definitely not enough to understand the details. The only way to make sure that things are right, is to read carefully the entire paper, i.e. to peer review it...

I am probably not making my point clear, but the question is asking (at least my understanding) why Arxiv is not enough, why do we need journals. I think we both agree that without dissemination Arxiv is useless, and at least in my field, conferences are a good way to get people familiar with the theorems you are proving, but not good enough to make sure that the proofs are correct, which is essential in mathematics. Also, in mathematics, the status is not really how the paper is regarded, the status is either right or wrong.

@KonradRudolph I think we should make the distinction between peer review and journals. arxiv is not enough because we need peer review. journals currently provide the best/most convenient form of peer review but it's not that we need them. we could do a post-(arxiv)-publication peer review on a platform like scienceopen.com after which the authors upload a new version of the paper on arxiv. to choose reviewers the authors could just ask the editor directly instead of via the journal.

It's all about scientific communication.
Once opon a time ... researchers wanted to share and discuss their findings with each other. At the beginning, they talked and wrote letters, since there was only a small number of researchers in each field.
With a more and more educated society the research communities started growing. Letters were no longer sufficient, because only a small amount of people could read and interact. The solution was to publish the letters, i.e. allow several print copies which could be distributed to several researchers and/or research institutions.
Letters were mainly like writing down an idea and/or conclusions as a starting point, waiting for the input of one or two collegues/recipients, pick their ideas up and answer to them again with a letter.
The communication via published and widely distributed letters was no longer as interactive as letters. The published research/text was no longer a starting point of a discussion, since a discussion only worked by publishing an answer and waiting for the published reply of the initial author. Each publication had to be printed and send per Mail.
This process had three major disadvantages: (1) It was expensive, (2) it was very slow and (3) since there was no longer a specific recipient which was required to answer, some letters were never discussed/questioned.
Journals shifted the discussion with some colleagues to the time before the publication of the letter/article. This is what we call peer-review. It solved the three disadvantages by being less expensive, by allowing a faster interaction between author and reviewers (only letters between author and reviewers) and by ensuring a critical examination of each published research/text and therefore its quality.
Today ... print publications are more and more vanishing and online/digital publications are the majority. Although the current peer-review process has its problems and issues, it still has the goal to ensure the critical examination of the published research/texts. This is what repositories without peer-review like arXiv can't ensure.
There are several approaches to solve this problem, since there are problems with peer-review and publishers. Some researchers and research societies start their own open access journals where researchers publish and review for free, i.e. research coordinates its own communication without the need of publishers. Another approach is to peer-review after the publication. This is also a community approach but might end up with articles without peer-review, since there are no specific recipients/reviewers which are required to answer. This approach reintroduces disadvantege (3) to the communication process.
In general, most researcher would say that articles that are not peer-reviewed are not quality proved which means that a reader always has to check and validate what is written in the article. Since there are problems with peer-review, most researcher would say, that you also have to check and validate what is written in a peer-reviewed article. With this in mind, one could argue that both ways to publish are equivalent.
Looking at the great picture one could describe the current system of scientific communication as ... let's say ... problematic. Publishers are trying to make money. Funders want to save money. Institutions want their researchers to publish a lot, to be cited a lot and to publish in reputable journals, which are most of the times defined by the impact factor that privileges journals that have been around for some time. Researchers want a wide distribution of their work and good jobs which is most of the time depending on their publication list, the impact factors of the journals they published in and the h-index.
Long story short, the whole system is stuck.
Coming back to your question ... Publishing on arXiv is fine, if your research topic is represented at arXiv. It's also fine to publish on any other (maybe institutional) repository without peer-review. Unfortunately, the current system might penalise this due to the concentration on journals, publishers and bibliometrics when it comes to evaluating research/researcher.

Why were journals used to begin with?
Before journals, scientific work was disseminated through books.
And this was fine for many centuries. However, after the Scientific Revolution, as scientific work and consequently publishing were gaining momentum, the format of books and book publishing was simply becoming impractical.
Scientists needed frequent, periodical publishing of regulated works, i.e. something akin to a scientific news service. And this is how scientific journals came to be.
The format of scientific journals has noticeably changed over the years, but the core idea of periodical publishing of new scientific work has remained the same.
Why are journals used in modern academic research?
We still use journals for at least a few reasons.
As @DavidRicherby has mentioned in his answer, inertia and lack of significantly better alternatives are two major reasons.
But the biggest reason, in my opinion, is simply money.
There is just too much money in current academic publishing, e.g. Elsevier had a net profit of £1.014 billions for 2015, and this creates all sorts of barriers.

The last paragraph makes no sense.

@CapeCode It makes all the sense. When you make billions and have no other stake in the system (the management of Elsevier are not scientists), having all these resources at your disposal to guard your profits and keep the status quo is really no joke. And Elsevier have time and time again proven this through their business model, e.g. by spending millions actively working against the Open Access community and other viable alternatives to the current publishing model.

Ab-surd. Open access is a goldmine for publishing. Elsevier is not "working against it" they're jumping on the bandwagon. Imagine, infinite papers, no desk reject, academics only worried about getting their stuff published and funding agencies allocating budget for "article processing charges".

@CapeCode I agree it's absurd but there we are. Journals took ages to accept open access, just as the music industry, for over a decade, struggled idiotically against commercial file sharing. Journals see open access as a competition, even as they begrudgingly embrace it. That's a simple fact.

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How might I improve my math department as an undergrad?
I am an undergraduate math major at a small state university in the US. Our math department has about 20 tenured/tenure-track faculty, including applied mathematicians and statisticians. We have only 3 current NSF grants, two in statistics and one in biomathematics. According to MathSciNet, only 4 of our faculty have published something this year. Additionally, our current department head mainly does applied interdisciplinary research, but I suppose it is not rare for math department heads to be in some kind of applied math field. To be fair, my university was founded less than 50 years ago, but I still want my department to become better.
Is there anything I could do as an undergrad to help improve my department? It's hard to say exactly what would make my department "better", but to be somewhat vague, I would consider research productivity and funding to be important factors to improve on.

"Funding" in math is a very volatile, and often irrelevant measure, especially for "out-state" places. It is not clarifying to think in such terms, because of all the skewing. It's not that the money is "really necessary", so lack thereof won't impede anything... apart from maybe having largesse to throw around... yes, to undergrads, but, ... More to the point would be militating for more-advanced courses to be offered. Pushing for this would help in many ways.

Paul, do you mean that I should convince my department to acquire more funding to go towards offering more rigorous courses (e.g. proof-based linear algebra versus applications-based linear algebra) or more upper-level courses (i.e. end of program courses besides the typical topology, analysis, and abstract algebra courses)?

Both less cook-book oriented, and higher-level. (I do think it is a mistake to exaggerate "rigor" in lower-level courses.)

@Matthew, MathSciNet isn't a good way to judge research activity: there can be very long delays -- a year, even more -- between math papers being written and their being listed on MSN.

Is there anything I could do as an undergrad to help improve my department? It's hard to say exactly what would make my department "better", but to be somewhat vague, I would consider research productivity and funding to be important factors to improve on.

There's not much you can do as an undergraduate to help improve research productivity or funding.  It's not clear whether the department wants to improve in these ways, or should want to: there's nothing wrong with focusing on teaching.  Even if the faculty do want to become more research active, or the administration wants them to, it's not easy and there's little you can do to make it easier.  I'd be careful with how you frame things, since you could easily cause hurt feelings by giving your professors the impression that you consider them substandard.
Instead of focusing on what might improve the department in some abstract sense, I'd focus on what would create a stimulating, exciting environment for the current students.  You don't want to be too demanding, and some things just might not be feasible, but it can't hurt to ask what could be possible and what it would take to make it happen.  You could look into various sorts of activities:

Advanced courses or independent study.
Undergraduate research supervised by faculty.
Informal mathematical activities: math club, Mathematical Association of America student chapter, Putnam team, etc.

If all of these things are regularly available, then your department is doing pretty well.  Otherwise, you could try to initiate or reinvigorate some of them.  You aren't likely to get clubs or courses for just one student, so you'll probably have to gather some other enthusiastic students.  This may be the biggest way you could contribute, as a catalyst to bring together a group of students the department hadn't realized wanted or needed these activities.

Thanks for your answer!
I was also thinking I could convince my department to apply for a NSF Research Training Group grant or to host an undergraduate math conference for the benefit of our math undergrads, but it would make sense to start with the suggestions you mentioned.
I expected that I wouldn't be able to do much in the way of research or funding for my department, but I'll still leave this question open to see what others may suggest.

Just to add to this excellent answer, if you don't have one already, I suggest starting a student seminar series. Work with other enthusiastic students to organize a weekly (or whatever) seminar where the students give talks on various topics. This is beneficial for all of the students involved, and the faculty may take an interest as well.

+1 For Jeff's suggestion. Organizing seminars is perfect for an undergraduate, and can go a long way towards generating excitement about research projects in your department.

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How significantly does the salary amount for tenured faculty impact the quality of a deparment?
I mean both the salary a department offers to new hires and to already hired faculty members. I would prefer answers specifically about math departments, but I would also be interested in answers about departments in other STEM fields as well as other fields such as the humanities or the social sciences.
My motivation for this question came from another question I asked recently on another website. I had asked specifically how math departments improve and received the answer that with enough money, a math department could hire and keep the best researchers in some specific field. Now I'm asking here to confirm that that is indeed the case for math departments, but I am now also interested in seeing if this applies to all departments in academia in general.
EDIT:
I cannot give a specific criteria for "quality" as I assume this may vary from field to field. What I can say somewhat concretely, though, is that research productivity should be weighted above attention to teaching. Of course, if a department happens to have one or two extremely productive researchers in some specific field but does not offer a PhD program, then I would not considered that department a top department.

There are several main financial factors faculty candidates must consider when weighing offers:

Salary and resultant standard of living
Overall compensation package (health, retirement and pension, other benefits)
Institutional support (resources, personnel, infrastructure)

The first two are with respect to the financial resources committed directly to the faculty member; the last is the amount of resources committed to the professor's working group. It is difficult to say how much the different factors are weighted, as this is highly subjective and personal.
However, I would caution against considering absolute salaries as a metric; salaries always have to be considered relative to the cost of living in one's environment. (Would you rather have $50,000 in New York City or $40,000 in Akron?)

I know people who have changed their mind about where to go for ~20% increase in salary.  It wouldn't make them go to a terrible place instead of a great one, but it was enough to weigh advantages.  I also know people who have not changed their mind about where to go for a >30% increase in salary, but that this was viewed as somewhat surprising by people who heard it (given that the places were otherwise not that different).
Based on this very limited data set, I would speculate that in the 20-30% range you'd have substantial power to attract faculty members a tier higher than your reputation would otherwise allow.

Your first paragraph is valid anecdotal evidence, but I would strongly caution against generalizing as you have in your final sentence without at least some source to back you up.

@eykanal - I think my language was appropriately cautious.  It's clearly anecdotal, I clearly spell out it's a limited data set and that I'm speculating.  If anything, all the warnings serve to emphasize the fact that you shouldn't trust this, rather than just leaving people to draw their own conclusions on the basis of the numbers I gave.  I hope there's an answer with better data (or better anecdotes), but this is nonetheless more than nothing.

I hear you, and that's why I didn't downvote. Personally, I would have left the speculation "as an exercise to the reader", but I guess it's a matter of taste.


text:
Somebody used recommendation by an in-law – should I report it?
I recently learned that a friend of mine was accepted in their master’s program to become a therapist after multiple denials throughout the past years. They tried again this year with an additional recommendation and finally got in. They shared that one of their letters of recommendation was submitted by their in-law, a counselor, whom they listed as their mentor.
I just do not feel like this is right and am torn between reporting it or just not saying anything. They don’t feel as if they did anything wrong and to be honest I’m not sure if they did because I’m not up to date with these kind of things but it doesn’t sound right.
Any insight on what I should do would be appreciated.

What is your relationship to these two people? What is your relationship to the university?

How do you know that their in-law did not disclose the nature of their relationship?

@wrzlprmft: not sure about the "without disclosure" part in the title; that does not seem to be established.

@cag51: I interpreted “listed as their mentor” as this, but yeah, strictly speaking the asker doesn’t know and should clarify. Anyway, the entire question becomes moot with disclosure, so for answers there is little difference between no disclosure or unknown disclosure.

@cag51 this previous revision says "The individual also mentioned that the familial relationship was not disclosed in the letter, and they advised altering the last name on the application and social media accounts to avoid any apparent connection. According to them, this was within guidelines."

@muru Good find. I wonder why that key information was removed. Buffy's answer makes a lot more sense with this context.

I'm -1, as the asker edited out relevant details.

There is probably nothing to do here. A "mentor" is not a formally-defined thing, and if their in-law is involved enough to write a letter of recommendation, the term "mentor" seems like an apt moniker.
The mentor should have disclosed the relationship in their letter of recommendation. If they didn't, that is likely a breach of ethics on the recommender's part. But, for all you know, they did disclose it and there is no issue. Even if they didn't, there is no reason to think that the recommendee did anything wrong. Even if the recommendee did do something wrong, getting their admission rescinded at this point would probably require evidence of "gross misconduct" (such as if they were specifically asked about recommenders who were family members and they lied about it).
Unless you have a lot more information that you didn't share with us above, it seems like involving yourself in this is much more likely to ruin your relationship with your "friend" than it is to correct an injustice.

As in-law is rather broad, the severity of this conflict of interest can broadly range from the recommender being slightly more welcome at family reunions to ensuring the future of recommender’s child who is the recommendee’s spouse.
Given that you asked this question, I assume that the conflict is on the severe end of the spectrum.
In general, there is strong consensus that letters of recommendation from close relatives are a bad idea and problematic, see, e.g., this, this and this question and the references therein.
The easiest solution would be if  the school explicitly states what degrees of relationship must be disclosed in recommendations or completely preclude them, so I recommend to check this before anything else.
If they don’t, this might be one of those things which is easier to navigate over a phone call to the admissions office (or similar):
You first describe the situation as if asking for yourself, and ask whether it would be problematic.
Only if it is, you continue to inform them about your friend.
That way, you can also ensure your anonymity as much as desired (which should be no problem since they have to independently verify your claims anyway).
You have to eventually sort out the ethics and your allegiance to your friend yourself, but here are a few considerations:

It is not upon you to decide whether there is a problem, but on the school:
If they decide that all is fine, you’ve done whatever duty you could possibly have.
The one thing you can do wrong here is to waste their time with frivolous hints (which I assume you don’t).

If the school acts upon your report, what happened likely was actually problematic.

Places in the school are probably limited, so while your report might thwart your friend’s career, it also enables somebody else’s.

Well, it certainly isn't right. And deception in a therapist seems a bit dangerous. More than a bit, actually. The in-law has also acted unprofessionally. Would you trust either of them with important personal matters?
But, raising the issue with the university will likely affect your relationship with the person if the university acts on your complaint, which they might not. If they act, they might not be able to hold your communication in confidence. But it is unlikely that they would or could act on an anonymous complaint.
People can change, however, and the masters program might have a positive effect on that person's attitudes about what is right and wrong. I don't have high confidence in that, however.
Whether you act or not might depend on what you might know about why they were denied entry previously, and on what you know about their general ethical behavior or lack of it. You do suggest that there was also deception involved.

I doubt that a university would/could act on an anonymous complaint. You would probably need to be known to them. Whether they reveal your name depends on a lot of things, including legal issues.

"it is unlikely that they would or could act on an anonymous complaint" -- why? In this case it does not require trusting the source of the complaint. All the pertinent facts (the contents of the recommendation, and the fact that the writer was related to the applicant) are independently verifiable by the university if they care to look into it. An anonymous note would just be bringing their attention to these facts. If the info is wrong, or if there are mitigating factors unknown to OP, then the university can disregard. ...

... If universities impose a policy of never acting on anonymous tips even when there is evidence  that does not depend on trusting the veracity of the tipster, then they should realize that they will miss important issues due to reluctance to report with a name attached for exactly the reasons you cite.

@nanoman, anonymous complaints are hard to act on as the recipient of the complaint has no way to judge motive of the complainer. And, they might also find it hard to discern the truth of it if people have been lying to them already. "Just who is lying to us here" might be impossible to know. Hence, reluctance, at least, about accepting anonymous complaints unless they come with hard evidence.

I am suggesting that in this case the motive of someone flagging the issue is (or should be) irrelevant -- either the recommendation violated the rules or it didn't. You say "unless they come with hard evidence" -- are you thinking that somehow OP is the only possible source that can attest to how the recommender and applicant were related? It seems likely that in a note, OP could helpfully point the university to publicly available documentation that indicates a relationship between these two people, at least at a level of plausibility that would justify further investigation.

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


text:
Should I send an email to the editor-in-chief regarding the delay in receiving the editor's decision for my submitted research paper?
I submitted my research paper to a Springer journal called Electrical Engineering a few months ago. After exactly three months, I received a major revision, and the editor gave me 14 days to send back a revised version of the manuscript and a point-by-point response to a reviewer’s concerns. I sent what he asked for within the recommended timeline.
It’s been a month and five days, and I still haven’t received the editor’s decision. Although the status is peer review and Your submission has passed technical checks as of 06 Mar 24, the editors’ decision can take several weeks as they may consult peer reviewers. I have sent an email to the journal’s editorial-office assistant to inquire about this, but she keeps copying and pasting the same response, stating that I have to wait for the editor’s decision.
Now, Should I send an email to the editor-in-chief, or it is not recommended?

You should stop emailing them and wait at least another few months. The following is a huge red flag:

I have sent an email to the Journal's Editorial Office Assistant to inquire about this, but she keeps copying and pasting the same response, stating that I have to wait for the editor's decision.

Even though they ask you to respond on a fast timeline, they cannot similarly force the reviewer to respond immediately, and you are certainly not in a position to force the editor or reviewer to act on such a fast timeline. After your revisions, the paper would go back to reviewer 1, who is probably some overworked professor in the busiest time of the academic year. They will hopefully look at the revisions over the summer. If you keep emailing the editor, office assistant, and editor in chief, you will alienate them. Since it took 3 months to hear back the first time, I think you could check in after 3 months again. But please do so tactfully and recognizing that the people you're emailing are doing their best.  As an author, I once waited 18 months for a first referee report. I once had a positive referee report, made all the changes they requested, and had to wait 9 months for the editor to accept the paper. Waiting is completely normal at this stage of the publication process, so please find a way to wait.

Thank you so much for taking the time to answer my question. I will wait a bit longer, but as a PhD student, publishing my first research paper is mandatory for defending my thesis. That's why I'm feeling a bit rushed.

@Gomasha if it got to the point where the delay was hampering your ability to graduate, then your advisor could write to the editor and try to smoothly get the paper unstuck. But, I'd only use that in case of emergency. Waiting is the better option.

Without wishing to seem unkind: the fact that your thesis defense is contingent on getting this paper published is not the journal's problem.  Your school has decided to outsource (part of) their assessment process by getting the editor to do it for free.


text:
Problems with supervisor – Should I listen to myself or just follow him?
I started a PhD in September of the last year at a European university in the field of engineering. I was very enthusiastic about it because I really worked hard to obtain this opportunity and I won three positions in total (the one I choose in the end and other two).
The project where I am now looked amazing, there were also the possibility to go in another country to do some experiments and it was together with other industries and university. I enjoy the spirit of "science is done together" and so I believed that here I could find my happiness.
I started. I found troubles in understanding the content of the papers I was reading. This because I am a civil engineer and the project is more in the field of mechanical/material engineering. It took me a while to really start to understand also the language of my other colleagues and I am still working on that. I realized that my supervisor has a hands-off approach, so he does not have the expertise in my field. I started to feel a little bit alone, doubting that I could really do something good without a real technical feedback. I talked with a friend who is doing a postdoc and he told me that this situation is quite normal and the really valuable skills that matter are the ability to work alone and independently. I understand that, but honestly it is far from the motivation that I have to do a PhD: I do not do it to become a professor; I do not do it to become a manager; I just want to give a little contribution to science, and I do not think that as a young PhD student, I am able to understand everything without support.
My supervisor cares about documenting everything that is done and about writing. He is obsessed with me to writing a perfect report each time. I understand that, on the long run, this is important because I can forget the details, but I have to say that it stresses me a lot: I would like to spend more time doing something good rather than writing every single detail. This approach is due also to his lack of knowledge, since he needs me to explain everything I do.
During last month our relationship became worse: He says that I have problem in understanding (in the civil field), and honestly I do not think so. I am just not very good in the writing part, because I am not used to write a lot and I also do not really like it. There are some postdocs in the mechanical department working in my field, and I tried to ask my supervisor if I could collaborate with them, but he denied this in a kind way. He said that we are independent and we “do not need them”. However, I need them. I need some support during this initial period of the PhD.
Some weeks ago I asked the head of the department if I could get some support because of the interdisciplinary nature of my PhD and during the meeting he said yes. He then completely changed in a subsequent meeting with my supervisor and me: He changed his mind and both of them had my last report printed. They pointed out every mistake. For example, in a table there was a typo because I had missed a zero in a number. Maybe I am superficial, but why is doing a mistake is so serious? Why do they have to make me feel not good enough because my report is not perfect? My supervisor is lacking in a lot of things, but he will be always right.
In the end of the meeting, they told me that I should be “more critical” but they believe in me. Honestly I do not believe in these words from my supervisor. It is not that he tells me what I did wrong, it is that sometimes I find him mean in the way he tells me things.
I have applied for other projects. I won a position in the UK one week ago, in a good university, and I was shortlisted two times in another very good university in Europe. The position in UK is sure, while the other one no. I would like to go, but I feel bad about myself. What if is it me? What if I am not able to pursue a PhD? Talking with other students in the departement, I found out that also other students had problems with him and some of them have left. Two who stayed say that they hope I will make the right decision so I will not feel bad like them in the following years.
How can I approach this situation?

Hello there und nice to see you in this forum! This seems like a good question, but it is too long and not good formatted. Also you should ask a clear question, not for comments. Maybe you can refine the question in this way? This would br nice, otherwise we should not answer it. I hope you enjoy your stay!

in a table there was a typo because I missed one zero in a number and so the measurement was wrong is not serious? In the real world you could be fired right on the spot.for this.

@scaaahu: In the real world you could be fired right on the spot.for this. – Depending on your country’s labour laws, you can be fired for anything. However, any reasonable company will have better ways to avoid errors in critical data digitalisation than fear of being fired. For example, if critical data really has to be digitialised by hand, have at least two different people digitalise it independently.

You do not like to write -but much of academia is precisely about communication. You need to learn to write well and communicate well. Errors: there are subtle, forgivable errors that happen. However, if you make them regularly, it means that your supervisor has to check everything in detail and cannot trust what you say. A supervisor needs to be able to trust his student that they invest attention to detail and do not make many errors, and, if they make errors, that they capture them quickly and put measures in place to mitigate them or avoid them next time. So, what is your precise question?

@scaaahu: This may be, but this then seems to be a horrible company nobody should want to work for anyways. Mistakes can happen - and this company has no better process to prevent them than to let it happen and fire the person on the spot?! Horrible. Which country?

"Missed a zero in a number"  I once had a student complaining that gave zero points on an answer that was wrong by a factor 1000. I offered 0.001 points. Or, yet another analogy, would you be upset if your salary is missing one of its zeros (or any other digit) before the comma?

@cbeleitesunhappywithSX: I do not understand this sarcasm. I asked for opinion because I am not sure of my approach, and I think my supervisor has his own reasons. However, I don't feel I am working for a company, I am sorry.

@Elen: no sarcasm here. The student fundametally did not understand that having the correct digits in the correct order, but the comma in the wrong place is a serious mistake. My example with your wage was meant to make you aware that you probably wouldn't think it negligible if the university wires you 137.49 € instead of the 1370.49 € you should get. But that is actually much less serious than the potential consequences of me (or my student) being wrong about an order of magnitude in our chemical labwork or you as civil engineer being wrong about the payload of a bridge: those may have

... irreversible consequences. I do see one potential source of misunderstanding between you and your supervisor here: you write that you need supervision which the supervisor is not giving. The supervisor may be looking at you as a fully qualified professional in engineering. I.e. you are not only allowed to, say, construct bridges or machinery that has similar safety requirements but you are actually expected to work with the care that is necessary for someone potentially entrusted with such work. "Hands-off approach" and supervisor+dean pointing out that mistake as serious are consistent

... with such a misunderstanding.

@Elen, when I was a fresh PhD student, I had the same feeling. Until my professor told me when I said I did not [yet] feel qualified for something: "You are a fully qualified professional since your Diplom [Master] - with all the rights and duties." - which got me thinking... Legally, my PhD does not allow me to do anything that I wasn't allowed to do after my Diplom. Of course you are not experienced yet - but you should be professional.

@cbeleites unhappy with SX: I am not saying I have the right to be unfocused, but I think I do have the right to have doubts and to do mistake not knowing how to conduct research, because it is not easy. In this moment for example, I would like to write an email to my supervisor with my ideas about some experiments we did, but I am too afraid of his reaction. I feel judged, I do not think this should be the feeling when you are doing a PhD.

Partially a duplicate of: https://academia.stackexchange.com/questions/11765/ive-somehow-convinced-everyone-that-im-actually-good-at-this-how-to-effect

If you're unhappy where you are and aren't getting support even though you've asked for it, and you've been offered a position elsewhere, I think you know logically what you should do. You should take that new position and hand in your notice to your current supervisor as soon as you can. Make a clean break of it and try to have some time off before starting the new project.
That's the logical thing to do. Emotionally, however, it's not so easy. You've spent a lot of time on your current project and worked hard, with little help, in an unfamiliar field. But don't fall foul of the sunk-cost fallacy: the belief that it's worth continuing to invest in something that's giving you no return, just because you already heavily invested in it. It very often isn't.
Finally, while you say you don't enjoy writing, the ability to write clearly and accurately is really important in research. Having very good written English is a must if you want to complete a PhD in the UK. The sooner you accept this, the better. Learning to critcally read and edit your own work is something your department or university can help you with; at my institution there is an "academic skills" office that provide help with writing, presentation skills etc to anyone who needs it. I recommend you seek out such help wherever you end up. Hopefully the more you write, the more you will come to enjoy it.

Thank you for your comment. Yes, I am aware about the writing part and I also do not feel strong about it. I know it is logical to think to leave, but it is like I am not ready to leave this place, because beside my supervisor, I have a really good relationship with the other people and I also do not know how it will be in the new place. I have no guarantee it is gonna be better.

@Erik No, I do not see myself happy working with him and if I had the chance, I would change supervisor. I had the chance to talk with the supervisor in the UK and he seems really nice and he is an expert in his field. We wrote a proposal together and even if I did mistakes in that text, he was very supportive and he was aware of the effort that I made to write it. I really appreciate this kind of behavior from a supervisor, because I can learn without feeling terrible. However I do not know him well, so this could be a wrong impression.

@Erik No, but it's a good idea to ask them. I have other two possibilities but both of them are not sure, since there is a selection process that is "on hold" for the pandemic. For one of them I visited the lab and the campus, since the professor invited me to join his group for a day. I had good conversations with the professor, he seems amazing and a highly intelligent person.


text:
What are best practices for designing publication-quality figures?
I am a postgraduate student in mathematics. I am writing my thesis, for which I need to prepare some Matlab plots and figures. I had sent some plots to my supervisor, and he suggested to use black for the line color because most  journals want to make sure that plots look good when printed black-and-white.
I am curious to know some other advice for figures like line width, styles, colormap for surface and contour plots, the figures’ dimension, etc.

These days it is not unusual to have the online version (pdf) in color, but a print version be in b/w because of costs. So it is more a question of making a plot that is clear in both b/w and color.

Why is this question specific to MATLAB and not figures in general? Have you looked into the (vast) amount of guidance that exists about making figures?

You can get a lot of what you are searching for with a quick Google on this question. Just experiment, see what you like, look into principles of design in academic figures too - there is plenty.

I edited the title to generalize beyond Matlab, since your question is about typesetting generally rather than some particular issue that Matlab presents. But, the community may decide your question is too broad -- as others have said, the visual arts is an entire discipline, so it will be hard to give a comprehensive answer here.

This question should be closed as too broad.

Someone general advice:

do a Google search. There are already plenty of articles talking about all different aspects of creating good figures, and they probably do a better job than my answer here.
experiment. Just create a figure and look at the font size, linewidth, color selection and arrangement, etc. If you have an average person's understanding of aesthetics, you should be able to spot issues in your figures. Print the paper out, and see if everything is legible.
imitate. Find papers in top journals and important dissertations, and see how other people create figures. I am not in mathematics, but if you look at Science, Nature or top journals in my field like Physics Review Letter, you should get a good sense of the elements in a graph, how to convey data and ideas effectively, and how to make a graph look great.
look up guidelines. Journals in my field often have a very specific style guide (like this), which can be a very useful reference. They can include things like "minimum linewidth is 0.5 pt" and "font size must be greater than 18 pt". They are generally good guidelines to follow.

Some specific things you can look into:

Don't be afraid to use large font size. They are probably not large enough.
using colors, and especially color maps, is tricky. There are many considerations that you may not be aware. You can easily find advice of how to use colors, and there are websites that help you select colors, so I will not repeat them here. Here are some discussions on colormap:

A Better Default Colormap for Matplotlib
Rainbow Color Map Critiques: An Overview and Annotated Bibliography
Color Map Advice for Scientific Visualization
A survey and task-based quality assessment of static 2D colormaps

make things simple. Don't overcrowd your figure.
use annotations where necessary. A figure with adequate annotations will often explain itself, even without captions.

Additional resources:

Look up a book named "Trees, maps, and theorems" in which there is a chapter about figures. (I have been to a great talk given by Jean-luc Doumont about how to give a good presentation.)
Figure Design (MIT EECS Communication Lab)
Choosing color palettes (Seaborn)

Nice answer! I updated the question title as you suggested, and removed the corresponding paragraph in your answer.

imitate – I cannot support this as it is and recommend to apply some caution. Sturgeon’s law applies strongly to scientific presentation and many bad practices are propagated “because everybody does it”. In particular, I find most figures in Science and Nature horrible, mostly because they are way too much crammed due to extreme space restrictions, but even apart from that they do not strike me better as figures in other venues. Thus a crucial step before imitating is to ask yourself whether what you imitate is actually good.

In particular, Matlab's font sizes in figures are notoriously too small. If I see a figure with an unreadable axis scale in a talk, I can be 99% sure that it comes from Matlab.

@FedericoPoloni In my experience, this can usually be mitigated by shrinking the size of the output figure via PaperPosition. In other words, it's not that the font is too small, but that the figure is too big for the font.

At its heart, every figure tells a story. Before you worry about the "polishing" details, you first need to make sure that you're organizing the information to tell the story as clearly as you possibly can.
A classic book on the subject, which I have found very helpful, is Edward Tufte's "The Visual Display of Quantitative Information." This has a lot of great first-principles concepts for communicating information with figures, as well as a lot of great examples of figures that do well in doing so.
When you are working on your own figures, try playing with different arrangements and densities of information within a figure.  Our first instincts are often wrong, so try splitting dense figures into separate charts and try combining figures together.  Likewise, our eyes like to move in lines, so try shifting locations and orientations of objects in diagrams into different organization (e.g., vertical, horizontal, circular) to minimize overlapping lines and to bring the most important conceptual relationships into simple and salient geometric relations with one another.  Color is another valuable dimension that you can use to organize relationships, whether to make certain things pop or to turn a bunch of individual lines into an organized gradient whose gist can be grasped with a glance.
Once you've got the core narrative elements of presentation sorted, then you can think about how you might want to polish the figure by adjusting fonts, line weights, colorblind compatibility, etc. Most modern software, however, starts you with pretty reasonable defaults for fonts and colormaps, so you may not need to worry much about those. Matlab, for example, has switched to parula, which is designed to work well for both colorblind viewers and greyscale printing.


text:
How does author-initiated peer review differ from double blind peer review?
Some journals (example) today ask the authors to initiate a peer review rather than initiating a blind peer review themselves.
Are these articles different in terms of quality and bias?
Are these articles accepted by experts/professors/scientists like regularly peer-reviewed articles?

Like the OP, I am in math and computer science. The situation described is not normal at all. For the vast majority of journals, the editor will choose the referee(s). Only once in my life did an editor ask me to recommend a referee, after the editor had failed to find anyone to referee the paper (that was for a CS paper submitted to a math journal, hence the difficulty).
It seems clear to me that allowing the author to choose the referee would subvert one of the main purposes of peer review. You could expect that papers would face less scrutiny on average, that more errors would get published, and that overall quality might suffer.
That said, because this practice is rare, probably most academics would not even know that the paper they are reading was peer reviewed in that way. I doubt it would truly affect whether or not others accept the paper as correct. Because we mostly communicate by preprints anyway, most readers already check papers for themselves, even if those papers have never been peer reviewed or published.
Still, all things being equal, as an author I'd recommend leaning away from journals where you pick the peer reviewer, because long term if that information gets out, that journal might be viewed with suspicion, and having published there might be held against you. Sure, it's tempting to publish something with less scrutiny, but we all know that publishing in vanity press can hurt you more than help you. The risk is not worth the reward. Best to stay with the normal publishing model, and only consider moving to new paradigms once you are already established.


text:
One week for minor revision: Indicator of predatory journal?
I submitted a paper to a journal (which was on Beall’s list ten years ago). It got accepted with minor revisions, but they gave me only one week for the revision. Should it be a concern for me if this a standard operating times for making revisions?

We do not like to evaluate individual journals here, one reason for which is the one you mentioned, namely that the information gets outdated (see this FAQ). For determining reputability in general, please see this question. I therefore reduced your question to the second one, which is one that we can actually answer.

It might not be "predatory" under the most common interpretations, it could just be low quality. Only you know exactly what journal you submitted to, and why you thought that was a suitable venue.

You can't begin to answer this question unless you first define what "predatory" means, and spoiler alert, that word is not well-defined. These days you get people calling X journal/publisher "predatory" for all sorts of reasons, including:

That it charges APCs
That it solicits submissions
That it has high profit margins
That it is based in Egypt (Beall himself suggested this was an "indicator" when discussing Hindawi)

Given the diversity of definitions, it's nearly certain that someone somewhere will say that one week for minor revision is an indicator of predatory journals. Of course, it's equally certain that someone somewhere else will ask if you're trolling when faced with the same question, since according to them, predatory means [insert reason here that is thoroughly unrelated to the one you gave]. Therefore, the title question is unanswerable.
What we can answer unambiguously is:

Should it be a concern for me if this a standard operating times for making revisions?

When the publisher is heavily prioritizing processing times (not all do), then yes, this is standard. If it's too fast for you, just ask for more time; you can expect the request will be granted.

Do you have a reference for the claim that Beall called a journal predatory for being based in Egypt?

@FedericoPoloni I don't think Beall made that particular claim, but he did suggest that being based in Egypt is "bad". Exact text would be difficult to find since the website is defunct now, however. I referred to it previously here (second last bullet point): https://academia.stackexchange.com/a/115704/84834.

Searching the Wayback Machine I found this article: https://web.archive.org/web/20131005233414/http://scholarlyoa.com/2013/04/04/hindawis-profits-are-larger-than-elseviers/. Beall wrote: "Is this the future of scholarly publishing, dumbed down and offshore?" So he didn't directly say that being based in Egypt is bad, but did suggest that not being based wherever he was is bad.

@Allure Beall was at University of Colorado Denver at the time. Anyway, in the comments to that post Beall maintained that he considered Hindawi "borderline" rather than "predatory". Unless you have better evidence for the claim, I would suggest removing that bullet point altogether.


text:
Is talking to a professor about personal issues acceptable?
I've been struggling a lot recently with stuff thats been going on, I'm in therapy and receiving help but I'm still having a really hard time. I have a professor who's always asking if I'm doing okay even though I've never told him anything about what's been going on. The other day he came up to me and told me if I needed anything, or even just someone to listen, I could come to him. I kind of want to talk to him, but I'm scared of bothering him and I don't know how I would go about it.
If I should talk to him, should I go to his office hours and ask? Or should I send an email because he doesn't have office hours for another week?

Is the professor the same gender as you? If not, I'd be more cautious. Emotional intimacy can have side-effects.

"Acceptable" to whom?

Obviously, how you approach this will depend on what your relationship with the professor is like. That they have personally asked how you're doing is a great sign that you aren't an anonymous face in a large lecture hall. In many ways, having yet another person to talk to---even if it's just a brief session to unload your worries---is hugely beneficial. Pain festers in isolation! I would wager that most any professor has seen the gamut of student depression and other life circumstances. You will not be the first student they've had who has struggled. From their comments, it seems like they suspect something is troubling you and want to check in and see what support they can give.
However, there are some power dynamics at play that are worth acknowledging and considering.

Particularly in the US, professors are considered mandatory reporters. As such, they are required to notify the appropriate people in some circumstances (e.g., Title IX violations, crimes, imminent self-harm, etc.). Be aware that they may not legally be allowed to keep your conversation confidential.
Outside of mandatory reporting, know that professors have to strike a balance between being compassionate and caring versus the needs of their other students and university policy.
Professors will often be aware of resources that you are unfamiliar with on campus---from counseling services, to support groups, to tutoring services. This also cuts both ways: professors are not licensed therapists and cannot supplant the role of one. They are, however, genuine humans with human emotions and compassion.
If outside circumstances are impacting your classroom performance, then this is an excellent reason to reach out to your professors. I would much rather be alerted early, even in vague terms, that there are external factors at work, than learn at the end of the semester after I've assigned grades. It is much easier to work out a proactive plan (such as meeting regularly, building a schedule for catching up, or even filing an incomplete grade) when there is time left to work with. If you think you're falling behind, talk to your professors as soon as possible. Many are very accommodating and receptive. That being said, this should not be considered an expectation and professors must always balance what is fair to the entire class.
Choosing whether to reach out via email or in person (during office hours or similar) is highly dependent on you. If the idea of talking about your struggles in person is overwhelming, then a vaguely worded email can be sufficient to clue your professor in---never feel like your are forced to share more than you are comfortable with! It is not your professor's job to decide whether your problems are "bad enough." If you just want to let them know that you're struggling and need help, then don't feel pressured to say anything more than that! However, if they seem receptive, even general details of what you're dealing with can help steer the conversation and course of direction. If you're up for it, having a face-to-face meeting can be more productive (again, doubly so where your professor has strongly hinted that you are welcome to come by even if you just need someone to talk to).

+1 for bullet 4. Give faculty and yourself a chance to work out a proactive plan that can include decisions points (when to 'give up' for that semester or when you promise to drop other XYZ activities because something has to give).  While trying to be accommodating, faculty need to balance what is fair to entire class.  That is easier to plan as a fair process when it is discussed earlier (rather than begging for special consideration at end of semester).

Although I'm not from the US, I have never heard of professors being "mandatory reporters" before.  Can you provide a link to any documentation showing their obligations?

@Ben Go to the website of any US University and search for "Title IX Compliance," and look around for policies relating to faculty & employees of the university. For example, MIT: https://titleix.mit.edu/faculty/responsibilities , Cornell: https://titleix.cornell.edu/reporting/staff-and-faculty-duty-to-consult/ , Univ of California system: http://sexualviolence.universityofcalifornia.edu/faq/responsible-employee.html

@Ben Broken link---even Title IX Administrators and AITXA need their cut these days. The closest I'm immediately finding is https://www.atixa.org/higher-education/

He's already said he's OK with it, so yes, it's acceptable.
You can probably do either method to talk to him. The difference would be whether or not you're face-to-face. If you're able to talk about your personal issues without breaking down, then face-to-face is also more personal. However if you think you're likely to, e.g., spend most of the time crying or tongue-tied, you might want to use email instead. It's up to you.

All professors should be able to have this sort of conversation with students, and should regard it as part of their duties. It's a key skill for anybody in a teaching profession.
Academic culture being what it is, not all professors do welcome this kind of conversation. Some still view teaching duties as an unwelcome distraction from the "real work" of research. (Some people really are much better suited to research than to teaching; others just don't try.)
But it sounds as if your professor has a better attitude. If you feel that it would be helpful to talk to him, you should definitely not have any guilt about "bothering him" - this is part of his job.

Talk to him - as the other answers point out it may be part of their job.
My point is you can ask a friend / best friend / collegue along as a witness, moral support, friend, shoulder to cry on etc. I even say to students to bring along someone - this works for both “sides” - either they sit in the room and don’t contribute or they help “fill out” the conversation.
Depending on the location then he may have to report - usually to help get further action to your benefit - I have asked students “can I take this situation to X for you” to help get a solution - had both yes and no answers...
Do talk to someone though...

Talking to a Professor, indeed anyone is acceptable to guide you with personal problems.
Caveats are in this increasingly competitive world include:
- Privacy, can this person possibly use this information against you;
- Look at the persons credentials to answer your questions, are they widely respected and indeed qualified to answer you - in the field specific to your 'personal issue'. Your professor maybe a great physicist, but are they expert in handling divorce, death, bullying etc; by way of example.
- Don't put ANYTHING in writing, unless it is briefing your legal counsel.

Perhaps your cautionary answer would be a good one to add in how "mandated reporting" (U.S. term for concept to which Brian Borchers alluded above) often kicks in. In many places a faculty member must report if there is risk of harm to anyone or evidence of abuse of a minor; learning of some other situations (sexual harassment or assault) may also trigger this, so keeping certain statements generic may be wise unless you want the professor + university's help in dealing with an issue.

This is really more of an extended comment.
Some information about your relationship with this professor, or lack of it, would be helpful and probably relevant.
Similarly, some information about what kinds of issues you are dealing with would also be helpful and probably relevant.
Have you ever spoken to this person individually? If not, what interaction have you had with him? Also, what are you expecting from a conversation with him? It is worth giving a little thought to that. If you are just looking for a sympathetic person to talk to, you hopefully have other options - friends, family etc. If you are looking for a trained professional to help with psychological/mental issues, the professor is clearly not that. If you need someone who can possibly help with some academic-related issues. then it might be reasonable to talk with him. But as others have mentioned, be careful. Don't assume the professor is your friend, just because he seems friendly and sympathetic.

Do not offer anything you are not willing or able to fulfill.

With respect to this claim, when the professor offers you such personal conversation they shall be able to handle it.
It is acceptable to accept such offer but be careful what you want to say and how you want to say it. Remember, what has beet said cannot be unsaid.
The fewer details you disclose, the better. If they want to see detailed picture, they'll ask. If you want to share, you'll answer.

I find it highly upsetting and uncomfortable if a student introduces themselves with their personal problem. This happens all the time around the end of a semester. In a class of about 200 students, I get dozens of emails that open with the details of a personal tragedy and then tell me they need an extension. It's not that I think students are lying (I always assume they're not). It's that the volume of tragedies from strangers is a lot to process and handle. I do not like doing it, and sometimes even dread it.
On the other hand, I know tons about a few students and bend over backwards to help them through their problems, about which I know all the details. These students are not strangers to me, and we had a pre-existing academic relationship and rapport before problems befell them. I see helping them as part of my job. I do not feel this way about strangers.
In this case, you are being given a wide open invitation to seek support from this person. You are absolutely welcome to take it, and I encourage you to do so. Not all Profs are willing or able to hear your problems (I am one of those people if I do not know you already), but you can always assume that, if the invitation is extended, we 100% mean it.


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What kind of content should one avoid when publishing (math) notes online?
I am a math undergrad doing an independent study course this semester, and I want to practice my math exposition skills by publishing some reading notes online.
I'm guessing I shouldn't publish my solutions to problems (or examples) from textbooks, and the notes I publish should be made from more than one text to avoid ethical and copyright concerns, respectively. I'm assuming coming up with similar but distinct problems and examples will at least address the first issue.
That is my situation, but to make this a broader question, what things in general should one avoid including when publishing notes online? By "notes", I'm also referring to lecture notes as well as other expository articles published for free access online.

You should cite all the books and notes you are reading. The point is to give credit where credit is due, as well as to be forthright/honest about where you got the ideas and information.

First do some examples from textbooks (with proper citation, many places prefer 'Harvard referencing' for that sort of thing), then expand upon them by posing similar problems that demonstrate the same (or similar) principles. That way you are including existing sources whilst providing additional information and demonstrating comprehension.

Copyright protects published texts and images, not the underlying ideas. A concept such as a "Fourier transform" cannot be copyrighted, no matter how it's written or described. However, what you cannot do is republish the material that's been put under copyright without obtaining permission, or demonstrating a clear fair-use case. For instance, one or two short, relevant quotations that are properly cited in a 50-page manuscript will not get you into trouble. Reprinting larger amounts or more complicated material (tables, graphics, etc.), however, should be done via a copyright request to the publisher.
You cannot reprint the text of problems that have been published elsewhere (unless, of course, it's sufficiently generic that it could be found in multiple books. For instance, the following text would not likely be copyrightable:

Prove that a connected open subset of R^n is pathwise connected.

for the reason that there is no "unique" or "original" content here; literally any book in the field could pose the same problem in exactly the same way. However, a longer, more detailed statement of the problem, guiding you through specific steps, would probably not be publishable.
On the other hand, the solution of such problems, so long as they represent independent scholarly work, need not be "suppressed." Again, copyright applies to the authors' wording of the solutions of the problems; the method for solving them cannot be copyrighted! If you solve them yourself, and publish your own solutions, that's not violating copyright. (There is the issue of making the lives of future students easier, because you're publishing solutions online that they could plagiarize from, but that's a separate issue from if you're allowed to publish such material.)


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Curriculum Vitae advice for PhD (non-US)
I am asking this on behalf of a relative of mine. He has a PhD with a concentration in Policy Analysis and Environmental Science and is trying to get a position in either a university/public sector or the private sector (research/policy analysis). He has been searching for a while and has had little success and is getting pretty discouraged. I recently looked at his CV and it seems like it needs a lot of improvement.
There is the catch though: he is not able to look for a position in the US at the moment due to visa requirements. Therefore, he is limited to looking outside the US (anywhere really).
Does anyone have any recommendations or advice as far as CVs go for academic positions outside of the US, particularly Canada or Europe (what should be avoided, what helps/hurts your chances, etc)? Any advice regarding online resources or CV editing services that cater specifically for someone with a PhD would also be appreciated.

I'm afraid that we don't do shopping recommendations, sorry.

Any advice would be very much appreciated as well!

I think with an edit this could be on topic. Most universities provide career services and help with that type of thing.

@DanielE.Shub Thanks, I edited the question a bit. My personal experience as an undergrad with the career center was pretty negative. They have a very cookie cutter approach that's helpful only if you are starting from scratch. But then there is a difference between undergrad and graduate cs I am sure, and every university is different.

What did his PhD advisor say when he asked for help?  (He did ask his advisor, didn't he?)

@daedalus I think Policy Analysis is the problem while Environmental Science would be helpful for him to find a position. Has your relative tried to contact a US institute to sponsor J-1 visa (visiting scholar) for Environmental Science ?

@scaaahu why is policy analysis a problem?

I could be mistaken. Doing research on policy analysis is one thing, working for policy analysis is another. I am not sure any organization would hire a foreigner to participate in the local policy analysis.

@scaaahu That makes sense, since laws are obviously different everywhere. But I would think a lot of his work would be applicable outside the country, as it has to do with optimal taxation and environmental regulation (from what I've seen of it).

As for working as a visiting scholar on J-1, that is exactly what he is doing at the moment. But unfortunately that's coming to an end this year.

While people often spend a lot of time tailoring the format of the CV, the two most important things are: do you have the experience the employer is looking for and can the employer easily find it. So while I agree that career services often suggest a cookie cutter CV one size fits all mentality, it really is a pretty god approach.
Unfortunately what really helps you get a job is a strong track record and not how that track record is presented on the CV.

Thanks, here is a two-fold follow-up if you don't mind:

What is the perceived difference between published/refereed  articles and, for example, conference papers/articles in academia? What if the person has not published many articles in a journal but has had a lot of conference/other presence?
The same thing, but considered for a position in a non-academic area

(1) That depends on the field.  (2) We don't know.

In principle, there isn't that much of a difference in the structure of a CV for US-based positions versus positions in other countries. There are a few items related to HR-type issues that you would never put in an American CV (such as photo, citizenship status, date of birth, marital status, or number of children) that can appear in an international CV.
However, there may be issues with respect to the kinds of positions that your relative is applying for. Are they appropriate with your relative's accomplishment level? (That is, you're not applying for a full professorship in Germany directly out of graduate school, or the like.) Plus, there is always the issue of demonstrating a match between the candidate and the position in general, as well as the quality of the work being performed.

Thanks. Its kind of a long story here but I'll try to be concise. He has been in academia all his life, but he received a PhD in Physics from a university in Ukraine. He had a decent body of published research and was an assistant professor before pursuing re-education in the US (life and prospects in Ukraine are pretty tough for academics). He has since received his Master's and PhD in public/envr. policy in the States, but he hasn't published that much here. Obviously now, applying in the new field, no one cares about his previous Physics experience, sadly, and that makes life difficult...


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How should I write literature review for a paper that is an extension of my own research paper?
I am a Masters student in Computer Science. I am planning to write two papers. The first is based on computer simulation and queuing theory. I have written its literature review and everything else. The second paper is parallelization of my first paper.
I am just making the code for my first paper parallel in my second paper. The problem is I don't know what to write in the literature review section as this paper is just an extension of my previous paper. I can't write about past attempts at computer simulation and queuing theory because I already wrote about it in my previous paper. I also can't write about previous attempts at parallelization because nobody has tried to parallelize my work before and I don't think it would be relevant to list other parallel speedups in the literature review of my paper. What should I do?

I think the best approach is to think of them as two completely separate papers. When you write the second paper you should write it as if you have read but not authored the first. You therefore need to add the necessary background and literature review to make it stand on its own. The reason for this is that anyone who finds your (second) paper once published will not necessarily know of the connection, may not have read the first, and will need a reasonable introduction to the subject.
So, each paper should be an entity of its own. The only clear case where this may not be necessary is if you publish two papers back to back as part 1 and 2 of a series with the same main title but differing sub-titles. Then it is clear that the papers belong together and you may expect people to note and read both papers to a larger extent.

I was talking about literature review.What do I add in the literature review section of my second paper if all it does is parallelize the first paper's code?

@iOsBoy That is what I am talking about as well. You need to provide a literature review (background) that is appropriate for the second paper and necessary to make it stand on its own. The basic thinking is that each paper is its own entity. Readers will not necessarily read the papers in the order you wrote them. But, you should of course make the coupling between them clear in the papers.

tl;dr: Lock the first paper out of sight.  Write the second paper from scratch, including the literature review.  Add cross-references.


text:
Acronyms at the start of a sentence
I was wondering if there was a rule regarding the use of acronyms at the start of the sentence in Journal Papers.
If so, is there a difference between the state of use of that acronym (i.e., whether it is being referred to as a noun or verb st the start of the sentence).
According to my understand and research, it seems that it is not advisable to start the sentence with Acronyms, however, there is no set reference for it.
Note: the use of that acronym is deemed necessary as it repeats over 10-15 times in the entire manuscript.

The first time the acronym is used, it should be fully written out*. For example:

The Special Executive for Counterintelligence, Terrorism, Revenge and Extortion (SPECTRE) organization features in a number of the James Bond films.

After that, it's perfectly acceptable to use it as the first word in a sentence:

SPECTRE is led by the notorious supervillian, Ernst Stavro Blofeld.

As for whether or not it's acceptable in journal papers -- I'm currently in the middle of reading a paper from a top-tier computer science journal that frequently uses acronyms as the first word of the sentence:

"...for code isolation. CERE finds and extracts the hotspots of an application..." (1)

It's perfectly acceptable (at least in English) and encouraged, especially if it makes the paper easier to follow.

*As pointed out by NateEldredge and aeismail, there's an element of subtlety in this rule. If something is common knowledge in your field -- for example, most computer engineers know that "CPU" refers to "Central Processing Unit" -- you can choose to skip the acronym if you want. The same goes for well-known/standardized unit abbreviations (as your audience in a journal paper would likely know what those abbreviations mean).

"Write out on first use" is hardly a universal rule, though; it tends to be ignored if the acronym should be common knowledge.  Or are you saying you write "Our computer has a 4.2 gigahertz (GHz) central processing unit (CPU) and 700 megabytes (MB) of random access memory (RAM)" in all your papers?

@NateEldredge: GHz and MB are units, not acronyms, and therefore do not need to be written out. As for the "true" acronyms and initialisms, the rule should be "expand if they're not in everyday use in your field."

@NateEldredge: That's a good point that I didn't catch; I think aeismail nicely addressed the subtleties that I ignored. Though depending on the audience, I might still write out some of those acronyms (journal paper, probably not; post on the academic blog I'll someday get around to, perhaps). In my time as a grad student, I've discovered that common knowledge isn't always that common, even within a field.

I suspect some (maybe most) acronyms are more well known than their full version.  What is a "Central Processing Unit"? Oh it is a CPU ... why didn't they just write CPU?

@aeismail Are they not in fact acronyms of units?

@TobiasKildetoft: They are neither acronyms (which can be pronounced like a word, such as SPECTRE) nor an initialism (which cannot, such as FBI). They are symbols representing the full unit name. However, many SI units should be familiar enough not to need formal definition.

@tonysdg Thank you for the detailed response. I think it would have been of valuable information, from my end, to state the Journal was in Geotechnical (Rock/Soil) Engineering. On that note, reading online, there seems to be a trend of avoiding acronyms at the start, like in APA writing style from example. However, there seems to be no real YES/NO answer for this. Its more of what is common nowadays...

@NateEldredge Thank you also for your valuable inputs.

@AlyAbdelaziz: The only thing I'll say is that ultimately, you should do whatever makes your paper more readable. Formal writing styles be damned -- the goal is to inform your readers. Everything else is secondary. That doesn't mean to ignore writing guidelines -- like the APA's -- which aim to support that goal. But they're just that -- guidelines, meant to be broken if necessary :)

@tonysdg you convinced me with the "guidelines are meant to be broken" :)

In biomedical research you should always introduce an acronym in full at first use. Even if you add an accompanying acronym/abbreviation table, this rule still applies.
In addition, even if you have introduced an acronym earlier, you should not begin a sentence with the acronym.
These is a realistic example:

The management of coronary artery disease (CAD) has seen momentous
  improvements in the last decades. Specifically, percutaneous coronary
  intervention (PCI) and coronary artery bypass grafting (CABG) appear
  to improve symptoms and prognosis of patients with CAD, at least in
  selected high-risk subjects. Coronary artery disease remains however
  an important cause of morbidity and mortality, giving the aging
  population...

Some journals enforce even stricter rules. For instance, this is an excerpt from the American Journal of Cardiology guidelines for manuscript preparation:

Abbreviations are permitted, but usually no more than 5 or 6 per
  manuscript (at the Editor's discretion), and then they must be used on
  every page of the manuscript after they are initially spelled out
  (followed by the abbreviation) in both abstract and introduction.