How do I approach a professor from another university?

I'm playing professor psychology here; may serve as another approach for you to think about.

If it's an experienced professor and the school is large, your cold calling e-mail may not stand out (unless you have some stellar skill sets or experiences.) If it's a relatively new professor, hiring someone outside his/her school may be a deterrence.

My suggestion is this: talk to your school to set up a cross-registration arrangement and take a course at the state university. Preferably, take a course that is taught by the professor with whom you would like to work.

This gives you a few edges: you'd get to see if commuting to two campuses work for you, you'd get to check out all the resources and feel the campus culture there, and you will get to know the professor better, and be able to make a personal contact with him/her. Get a good grade, and use the semester to build a relationship with the faculty there.

Once the professor got to know you and understand your aspiration and capability, it'd be a lot easier for the professor to engage and make a decision.


How to deal with consequential rounding errors when verifying the works of others?

Now, I doubt any decent teacher would discard this result as wrong

I'm generally considered a decent teacher, and, yes, I'd consider that result partly wrong and I'd remove a mark or two, because students, especially from certain fields (e.g. engineering), should learn to get the values right, also, not only the math.

There are mathematical tools that allow to evaluate the effect of rounding errors and to deal with uncertainty of parameters in general: if in an academic paper, the authors overlooked the effect of the rounding errors (getting the wrong result or suggesting a model excessively sensitive to the parameters), I'd suggest to reject the paper asking for major revisions, pointing out at the proper literature.


Rejection from a legitimate journal, with reviewers recommending me to try a Beall's list journal

I am quite new to academia, is the above considered normal practice

No. This is abnormal and unacceptable for a reviewer or editor to suggest this.

  Any advice of what I can do?

If the journal you submitted to really is legitimate, contact the editor and escalate this. Simply point out that the review you received pointed you to a predatory journal, and ask if the editor can reach out to the reviewer to see if this was a mistake.

  Update: I found that a member of the editorial board of the SCIE journal, is also in the editorial board of the Beall's list journal.

This is a red flag, and the review you received is another red flag. These red flags suggest that the journal you submitted to is not reputable. I would check with online journal ratings, impact factor, etc. to make sure you are not already submitting to a very low-quality journal (even if it is not predatory).


Getting a Phd abroad: is there any chance?

Getting a Phd [outside of Greece]: is there any chance?

TL;DR: Yes

  I think i have built a pretty good CV for my level (and young age) with good grades, numerous poster presentations and 4 peer reviewed publications in well known journals in my field.

Many universities will accept PhD students without any publications, so - with 4 peer reviewed publications - you seem like a good candidate.* You don't say how good your grades are, PhD students will typically be amongst the top of their class.

*I cannot answer specifically for  Earth Sciences.

  Is it possible to find a PhD in a prestigious University [outside of Greece], based
  on a good CV with degrees (Bsc, Msc) from Greek University?

Yes. You mention, during the last couple of months i am trying to find a PhD opportunity, has your search been unsuccessful? If so, why?


Research proposal for a pre-defined PhD topic

I would ask the professor who encouraged you to apply what the best strategy is.

In any case, a good idea is to take the topic proposed in the list you mention and write about that. Make it your own. Try to develop your own approach to the topic. Elaborate more on what needs to be done. Explore some related work a find out what has been written. This will help demonstrate that you have what it takes to be a (top) PhD student.

Avoid simply writing a personal statement on top of the research proposal. They probably want to see how you think about the research topic and would approach it.

If possible, get the professor to help you out. Not by doing the writing, but by providing comments and possibly related work. (Note that professors are busy, so s/he may not have time to do this.)


Follow the conventions of your target journal or conference. The most reliable predictor of how a title will be perceived is if other papers at the same venue have had similar titles.

Specifically, your question Are titles written different for different areas of research? can be answered with a clear yes. For example, compare the following programming languages and neuro-imaging venues.


Can an editor examine a PhD student whose manuscript is under review in their journal?

In the US system, my main concern in such a situation would not be conflict of interest in the thesis examination but rather would be conflict of interest in the journal reviewing process.

In the US system, a good advisor generally ensures that the examining committee are people likely to approve if the student does good work (e.g., no philosophical enemies) and ensures that the student does not go up to defend until they are certain to pass.

Members of a thesis committee are thus typically either members of the same department or close external collaborators, who should typically be barred by conflict of interest from handling a paper from that student at a journal in any case.


Do university accept a Mechatronics Engineer undergraduate to do Masters in computer science?

This will depend entirely on the University. My University, for example, does not look at whether you have a degree in CS, but does look at factors they feel influence whether you are likely to complete your Master's in CS. Those include your GPA, if you've completed certain core upper division CS and lower division math classes, and your GRE scores. Each year they accept the  students most likely to complete the degree.

Ultimately, you will need to contact the CS department of universities you are interested in, and ask them their policy. You will probably find a low GPA is more of a hindrance than the lack of CS degree. When I was looking at US universities for my MS, I didn't find a single one that said my undergrad degree (in math, not CS) would be a problem.


Should honorifics be included in acknowledgments?

In general, when in doubt, you should use the name of the author as it appears professionally. If the person in question publishes under a particular name, you should use that. The only exception is if you and the author have an existing relationship outside of this, in which case it is appropriate to use a less formal name.

You do not normally need to include honorifics ("Prof.", "Dr.", etc.) unless specifically asked to do so.

This leads to the final point: if you have any questions about how someone should be credited in an acknowledgment, ask. They'll generally be more than cooperative.


pros and cons of submitting a conference paper in first round vs second round

The conference's important dates precisely mention both dates, namely the first and the second submission rounds. Although I understand your worries, I do not explicitly see on the CfP that the two overlap.
So I would suggest you to move as you planned. But! In any case, since those sensitive matters are not well defined, you can easily send an e-mail to the respective organizing committee/program chairs with your question. Thats what I would do if I were you.


What are the downsides of using arXiv references instead of conference/journal references for the same paper?

Using arXiv instead of a conference / journal reference has an obvious disadvantage: readers won't know that the paper eventually passed peer review and was published.  This is important context, especially if they want to cite the paper themselves later.

Using arXiv in addition to a conference / journal reference might make sense, but some might consider it redundant.


Often, people confuse the protections of the freedom of expression in various forms as protection from judgment by others rather than protections from government (and sometimes employer) sanction. In a free society, you have the right to express the things you want to express on social media (with a few key exceptions), but you do not have the right for that expression to not influence the opinions others have of you.

It seems like you've run into conflicts based on not knowing the boundaries of this principle. Therefore, stepping back from social media seems like good advice from an academic perspective.

You'll have to weigh for yourself whether this advice is too stifling on your personal expression. Some types of expression may be too valuable. However, if you make that choice you have to understand that it comes with consequences.

Social media is not a venue through which you get to have a pulpit without taking a risk. You can reduce the risk through anonymous accounts or by sharing among friends rather than the general public, but things you post on Twitter are no different in principle from things you stand and shout on the street outside your university buildings.

I personally am not opposed to working with people who speak their mind publicly, but there are certain things, such as those that are racist or sexist, those that are homophobic or transphobic, those defending or supporting certain types of crimes, etc, that for the sake of my own expression I will not tolerate. Just as some will choose to use their freedoms to express those opinions, I will use mine to avoid working with them as long as I'm within the law.


I am sorry for your experience. Regarding the naming issue, I think that it is alright and no one will comment about it. You do not have to email that person again.

Regarding the publication, You should not be silent. It is an authorship dispute. If he published them in a peer-reviewed journal. Email the editor in chief all the documents, the LOR that indicate your role. You do not have to be silent if he stole your work. He is abuser and thief and that it should not be acceptable in academia. Stay safe and strong. You are not wrong. He is the jerk.


PhD admissions - Contacting multiple profs from the same university

I think there are no answers yet on this question because there is no problem here; being interested in two different research groups is acceptable.  In fact, interest in just one group increases your chances of rejection since that group may be full.


What is the best way to explain unrelated work in a Masters application?

It is unclear whether you are applying for a coursework Masters or a research Masters. If it is a research Masters, applying for a project that straddles across three disciplines seems unlikely (political science/international relations/public policy).

Coursework Masters tend to not have a high selection process as coursework Masters tend to be funded by the student compared to a research Masters.

So if it is a research Masters that you are applying for, then evidence of the ability to do research would tend to be the focus. If you have done an honour thesis during your law degree, that would be significant useful. If you have done extensive research and wrote long form analysis as part of your role as a corporate lawyer, then that would be relevant too. Some lawyers have written submissions or in-house publications, so that would be good evidence of your work.

Being able to show that you are able to engage with difficult political science and public policy issues would be useful as well.  You have done international relations in your undergrad but you may not be as convincing in the areas of political science and public policy especially at a research Masters level. Extra-curriculars would not be that convincing, unless it is extra-curriculars that has produced good work such as an editor of a student journal or publications that potential supervisors that are able to examine.


Publishing in 'leftist' journals or book projects: Impact on career?

There is nothing wrong with communicating your research to (a part of) the general public. In all likelihood public funding was used to pay for part of your research or used in your university, so it is only fair to give something back when you can. I would not hide it either, that only looks suspicious. Instead I would just add a section to your CV for communications with the general public. It would often be viewed as positive, though other things like publications would be valued much higher. Who knows, maybe you will end up in a very close race some day and that little extra is just enough.

If those pulbications have nothing to do with your research than those are just your private actions as a citizen. You don't need to mention those in your CV, but I don't think they will be held against you.


In Europe it is somewhat common to apply directly to professors for a PhD project

I cannot speak for the whole of Europe (and I think you'd get better answers if you'd narrow down your question) but at least in Austria it is usually required that you apply directly to professors; you can only enroll at the university for the PhD program if a professor is willing to advise you (there are other ways, e.g., if you enroll in a graduate school type program; but they aren't all that common).

I know that in several (central) European countries, at least in Computer Science, it is very common to approach the potential future advisor before applying formally. A formal application is nonetheless necessary, since you will usually be employed by the university. In some cases, open positions are only announced once the professor has found a suitable candidate - so there might be (and there usually are) opportunities even if there are no listed open positions. If the professor already knows you (from courses or a thesis project) it shouldn't be a problem to talk about PhD opportunities. If the professor doesn't know you, it shouldn't be a problem either; but you should be able to show real interest in the subject.


What things can I do as a job market candidate to gauge the internal political culture of a department that is hiring?

One measure of the politics within a department is the faculty member's attitude towards collaborations. When I was touring grad schools as a prospective PhD student I remember interviewing with a faculty member. I asked her if she collaborated with other faculty within the department or other departments. She answered dismissively and instead asked me why I was interested in asking such questions and why it mattered whether she was involved in collaborations. If you get such a response, or sense such attitudes, this might imply there is an unhealthy dose of hostility or competition between faculty within the department.


I have an article in the field I am just interest and has no overlap with my major. Should I mention it my SOP?

I wouldn't mention it. As Chris C states in the comments, it is not peer-reviewed and is not directly relevant to your area of future research.

My answer would change if the article were peer-reviewed and/or published in a journal, however. I think demonstrating that you have the ability and motivation to submit an article for publication is a positive attribute for a potential graduate student, regardless of whether the paper is in your field of research or not. For example, my first publication was not in my current research area, but several reviewers of my application later told me that just having a published paper set me apart from other applicants.

Since you claim that at least one person in the field finds it interesting and that the topic is new, why don't you want to publish it? Is there a way to at least submit it for publication before your applications are due?

In my opinion, it is a little dangerous to put unpublished articles on a SOP or CV. A reviewer might arrive at the (potentially false) conclusion that you're trying to pad your CV or SOP with articles that may never actually be published, which can hurt you. Others might wonder why you feel that the article is important enough to include on a graduate application, but not be important enough for publication.

Overall, I think the safer thing to do is omit it for now. If you end up moving forward with disseminating it further, then I would consider mentioning it.


How important is to maintain an online/digital presence for a graduate student?

Yes, it hurts your chances. It does not make you unemployable, far from it (I have recruited post-docs without web presence): when you apply for a position, your application file will include all the information that should be necessary for the hiring committee to decide, so they do not strictly need to see your webpage. As long as you appear on the departmental or group-level web listing of researchers… (otherwise it just looks weird)

However, look at the bigger picture: you're trying to make yourself a name in academia, so why do something that prevents it to some extent? There are good reasons for people to look up your webpage:

They saw you name, and wondered who you are, where you are, what you do.
They want to see what you have recently published, and find it easier to have it grouped on your web page that through a citation database (where your name may not be unique)
They know you, and thought about you for an open (or soon-to-be-open) position, and they want to check out if you have moved, if you recently accepted a position, etc.

So, there are two things that are absolutely needed:

People need to find that minimum amount of information about you when they search your name, and possibly some research-related keywords. A personal webpage, even a terse one, may be better for that than your departmental web page.
Your list of publications

As for myself, I maintained a webpage composed of exactly 1 HTML file, including:

my name
status (“PhD student at South Laponia U.”)
research keywords, link to my publication list (ResearcherID)
link to my CV (so I lied, I have a second file on that website: my CV in PDF format)
email address
link to my departmental website.

That's it. (It used to host my Master's thesis, but it is now hosted on an open archive, with a link from my publications list.) No picture of me or my pets, no blog/tumblr/twitter, no social websites.


Publishing as an undergraduate student: can/should I list my university affiliation?

Ask one of your professors or the administration about what the best course of action is.

Most likely, you should publish as affiliated to the university as the work was conducted while you were at university. In any case, you have nothing to lose by doing so.


What is the role of a University Archivist

In general, an archivist is someone who preserves records and artifacts of the university's historical record. The part that probably varies from institution to institution is which objects are retained.

For instance, some might keep minutes of board of trustee meetings, letters to the president or chancellor, and other records, while others may choose not do so.

As a further example, the Yale University archivist has the following responsibilities:

Works with the schools, departments, and offices of the university to appraise the records that they create in the course of their activities and to select those that need to be preserved for future use;
Works with students, alumni, faculty, and friends of the university to collect papers, graphic materials, audio recordings, and objects that document Yale life and history;
Promotes, supports, and sponsors programs and activities that contribute to accessible information, interpretations, and research on Yale history.


how not to burn bridges between two academic jobs?

What stood out to me is:

  This same institution has already booked me for some partial hour lecturers in a couple of courses.

Have you, in any time, either written or orally, communicated with institute B indicating that you will take up the position (even just the part time one)? If so, the polite thing would be to honor this commitment with Institute B, even just for one term (if you really want to work at Institute A, you can try to talk to them to see if they can arrange for the offer to be deferred for a year or a term).

If you have not indicated to institute B that you would take up the position, and they, without your knowledge, advertised you as a part-time lecturer for their courses, I would be very, very wary of joining their faculty. It is simply not the case that a department can strong-arm a potential hire into working there just by listing his or her name on a website.

Aside from the above: the job market is competitive. It is expected that you will be looking out for your best interest. As long as you have not made any formal commitment to either of the institutes, you are free to choose which one to affiliate yourself with in the future. If you really prefer the offer given by Institute A, you should just be honest and reply to Institute B and say that Institute A has given you a better offer and you regret that you will not be able to work for Institute B.

This really should not be a situation that counts as "burning bridges". From your description it sounds like just the normal competitive hiring process. If the administrators at Institute B are the type that will hold your declining of their offer against you in the future, I really doubt you will want to work for them anyway. (That just doesn't sound like a healthy work environment.)


Just missed grad school application deadline..what can I do?

I just missed the my grad school application deadline....... This is the biggest and most serious mistake I even made in my life...

If that's really true, then what a great life you've had.  You'll bounce back from this and be back to sunshine and roses sooner or later.

  [D]oes anyone of you know if the department would accept my late application in this instance?

Of course not [i.e., we don't know], because you haven't told us what department you've applied to.

  Is there anything else I can do?  I am even too shamed to contact my prospective advisor regarding this situation.

Taking you at your word, letting shame prevent you from talking to your prospective advisor is the biggest and most serious mistake you've ever made in your life.  Don't do that.  Talk to your prospective advisor as soon as possible.  (There is no need to write about it in a panicked or alarmed tone.  If this really all just happened in the last two hours, it is quite likely that you'll hear from the admissions personnel as well.  But calmly informing your prospective advisor of the situation will be helpful.  If she tells the department that it was not your fault that your application was not submitted on time, it can only help your case.)  If it's very soon, there's at least a reasonable shot that this can be straightened out.  The worst case scenario is that you may have to apply elsewhere or up to one year later.  This is suboptimal and you should do what you can to avoid it, but it would not ruin your life.  Really.


Should I switch to PhD or graduate with a Master's?

You shouldn't stick around for a PhD because you're afraid to do something else. A PhD is something that you should do because you're motivated to use the skills you acquire in the PhD in your later career (either as a researcher, or in a research-oriented field).

If you're not excited about being a PhD student, then it's not worth it in the long run to be miserable for several years of your life to obtain the degree. Moreover, because the PhD can limit your ability to take certain jobs—because of the perception of overqualification—if you're not motivated, don't do it.

In other words: Choose to do something because you want to be there—not because you're afraid to be somewhere else!


Moderating online education forums: delete, snip or leave rudeness?

Snip the last part out, send a private message to the poster reminding them of the behavioral standards expected in the course forum.

I don't see any reason to remove the whole post, if there are parts that are appropriate. Removing the whole post makes it seem like your motivation is to punish the poster, rather than to keep the forum professional and constructive.

I would recommend against leaving rude comments there until/unless someone takes offense. This is a forum that is hosted and moderated by you, not your students. It is your responsibility as an educator to create a constructive learning environment (to the extent that you can). It's not your students' responsibility - they have to be responsible for their own actions, but they shouldn't have to be responsible for making you respond to other students' actions.


Relevant math courses for theoretical physics/applied mathematics?

Although the name is not explanatory, a course in "Lie theory", or "Lie groups and Lie algebras" would be very helpful: this is about the influence of large-ish (certainly not finite) symmetry groups, such as rotation groups ("orthogonal groups"...), and more.

Also, "functional analysis" is very hit-or-miss, depending on what one wants. What a potential physicist would want would be "operator theory", especially "unbounded operators". Also, probably, "distribution theory/generalized functions", to be able to cope gracefully with things like Dirac's delta "function". (E.g., to not be at the mercy of semi-ignoramuses who'll happily rant about the non-existence of such a thing, and/or insist on describing it in ways which horribly obscure its utility and sense...)


I can only speak for myself, and I'm just a postdoc.

I would be indifferent if someone pointed out one or two typos; on the one hand that's helpful, on the other a bit pedantic.

However, if I received a "Word doc containing all the typos and mistakes [you] could find" in a 90 page document, I would be delighted and grateful.

As an aside, I'm currently working through a textbook to brush up my statistics skills. I'm trying to collect the mistakes that I stumble upon in order to send them to the author once I've finished the book, so he can correct them in the next edition.


Is having a specialised PhD topic a pitfall when applying to be a lecturer of STEM education, even with relevant practical experience?

Is having a specialised PhD topic a pitfall when applying to be a lecturer of STEM education? [with teaching and research duties]

I would not call it a "pitfall," per se, but rather you'll have to do some convincing that you're qualified to research in the field of education. I applied for a couple of similar positions (with somewhat similar experience and education as you, though with about half the number of years teaching high school), and the guidance I received was that I needed to demonstrate that I had a "research arc" (or research strategy) that was consistent with the research goals of the position. Having a good deal of teaching experience may have given me an edge as far as the teaching duties were concerned, but I only had one publication in the education pedagogy realm, and that (among other things, presumably) was not enough to make me competitive for the positions (i.e., I didn't get the jobs). In fact, it probably was the case that most applicants for such a position spent time teaching at the secondary level, and my experience there was a wash.

Bottom line: if you are asked to write a research statement, make sure it is highly targeted towards the position, and try to have a long-term approach to the research question or questions you discuss. Relating it back to your hard-science degree may be difficult, so leverage as much of the teaching experience you can to inform the statement.


what steps to take when research result is patentable

If what you have is potentially patentable do not publish any critical element before filing the patent application or you risk losing eligibility due to existence of prior art (even if it is yours!).

Be aware that your university may claim ownership of the IP since it concerns ideas that you got in the context of a project while they were paying you (my university would claim partial ownership). This need not be a problem, as this also means they get to pay the piper. This is not necessarily an issue since, if your name is on the patent, you are entitled to a slice of the cake.

You should really talk to patent experts. Your university probably has them. Most universities have a dedicated tech transfer office (TTO) which handles patents, spin-offs and industrial collaboration. They have the expertise to guide you in such endeavours.


Is it common for doctoral dissertations from for-profit schools to be unavailable?

I don't know about for-profit universities, but the practice at "good" US universities is generally as follows.  Before being eligible to graduate, the student must submit a copy of the dissertation to the library and to ProQuest.  By default, after being processed, it is then immediately available to the public from both sources.  (In some cases it might not necessarily be available online, or might require a fee, a visit to the university's library, or an inter-library loan request.)

The student may be able to request an "embargo", in which case access to the dissertation's text is restricted for a period of time.  For example, this could be used if the student intended to commercially publish the dissertation or related material.  At my PhD institution, this period can be up to 2 years; any longer embargo requires the special approval of the graduate dean.  Even in such cases, I would expect that the library and ProQuest would still show the dissertation in their catalogs; they just wouldn't allow access to the text.

In your case, "embargo" sounds like the only possibly legitimate explanation. But if the student graduated several years ago, or if the university library and/or granting department cannot confirm the dissertation's existence, I would declare shenanigans.  (Maybe NSFW).


ACM templates have a number of different options, and it's quite easy to not select something in the variant options that is desired by the particular SIG that you're dealing with.

Double-check the options, and if you still can't figure out how you aren't in compliance, the only thing to do is to write to the folks who sent you that message with a polite question along the lines of:

  "To the best of my knowledge, I am complying with the template.  Can you please let me know what you see that needs to be changed?"


For faculty positions: Cover letter vs. a letter of application

Cover letter = letter of application.  It typically goes: "Hi, this is who I am, this is where I got my PhD, I have published here.  Let me tell you a little about my research.  Let me tell you a little about my teaching.  I want to join your faculty because of this reason.  kthxbai"

It should be two pages, single spaced, maximum.  Use letterhead if you've got it, but keep in mind that letterhead is only used for the first page; the second page, if you have a second page, is on regular paper.


Can I have the same project as another master's student (same experiments and results) and we both write two different theses?

Bring this up to your university and be open about it. Make sure your supervisor knows you are seeking extra guidance. This is very sketchy but not necessarily bad.  If you think about it, some grad work may rely entirely on secondary sources or data collected by others.  The challenging part here is that you have the same project, not just the same data.  Working together on the experiments isn't the problem - I had some masters students work with me on my experiments - writing the same thesis "in your own words" is the problem.
If you are both going to draw the exact same conclusions and do the same analysis, then there is an issue.  You both need to be able to distinguish between your specific contribution and your specific methods.  For instance, just having a data set in common doesn't mean much if you analyze it for property A using method X and your partner looks into property B using method Y.
To be more concrete, you and I might run the same survey, and to save resources we run it with the same participants, but you are looking at socioeconomic status as an indicator of academic success and I am looking at a correlation between socioeconomic status and academic preparedness.  We will look at different things, probably have different literature reviews (at least partially), and definitely make different conclusions.  No worries here.  We'd just acknowledge that the survey was run cooperatively.
The problem is that, during your defense, you have to be able to defend what you personally did.  You can give credit where it's due, but if it turns out that your thesis is only half yours, then giving the degree is going to be difficult.


How to deal with grammatically incorrect suggestions from my advisor on master's thesis?

It will be helpful for your advisor if you give a list of changes, and where they were implemented in the text, together with your new version of your thesis. That way (s)he won't have to read your entire text again and can just foucus on those passages that have changed. That document would also be a logical place for mentioning the changes you did not implement and give the reasons why you did not do so.

Your advisor will probably be very familiar with this way of working; this is how we respond to reviewers when we sent articles to journals. So this should not feel strange or offensive to her or him. This does not mean that (s)he will agree with you, but that is something you can talk about at the next meeting.


Is it professional to have a "cited by" section of a personal website?

For any well established research, they will usually have quite a large number of citations, which would make a "cited by" section would be exhausting to maintain and large beyond meaningful readability.  A better route is to link to an database that actually engages in curating ones citations, such as Google Scholar.

I do, however, sometimes see people maintaining a collection of notable articles in non-scientific media.  These are not normally picked up by citation databases and are valuable for showing that work is having impact outside of the scientific community, as well as (sometimes) providing a nice introduction to the work.


How many hours do PhD students work as a TA (total)?

So are you saying you will only be TAing for 10 hours weekly? And you are unhappy about that?

This work load depends on the university. Some schools are notorious for loading graduate students with lots of TA work. Where I went to school, I had to TA for 20 hours full.

So if you are only required to work for 10 hours (and are getting paid for 20), if I were you, I wouldn't complain about it. -:)


Does it cost universities less to teach online?

Consider the University of California system as an example: of its core funds expenditures, three quarters goes to employees, and most of the rest is student financial aid. Only 6% of the costs go to equipment, utilities, and similar.
Now, some portion of those employees would also become unnecessary if they did away with a physical campus entirely, but most are still needed to operate the organization. In the case of an institution like the UC system, remember also that much of the physical campus is also not devoted to instruction, but to research and other non-instructional activities, and these have continued in many cases (albeit with reduced capacity) through the pandemic.
In short: in the near term, most universities' costs are almost entirely identical while teaching online.  In the long term, even if they shed every physical aspect of instruction, the costs would not go down all that much unless the institution was radically restructured to greatly increase the numbers of students per instructor.


How important are my grades to the rest of my PhD career?

As far as your research stature is concerned, grades would matter least of all, below other non-academic stuff as your soft-skills, your personality etc. There are a number of reasons for this:

No one cares about your GPA once you are a researcher! While it certainly looks nice to have a stellar GPA, it's the work that you do and where you publish that would matter. Look up some resumes of notable faculty in your field - how many even list their MS/BS grades?
I might even say that your adviser would not be too happy if you have a 4.0 GPA - as it means you are spending time on perfecting your grades which is more profitably spent on research! I actually have read this on a faculty/university webpage - would post the link once I dig it up. EDIT: Haven't found the faculty website link yet, but here's a couple from an established source, phdcomics - enjoy!

PS: I'm actually waiting for JeffE to comment on this: His credentials are such that I'm not even qualified to state them, and he himself claims that he had the lowest undergraduate GPA amongst any professor he's ever met!

EDIT: I'm talking about grades in subjects that you have to take as part of requirements of grad school - you would be expected to master the subjects that are directly required in your Ph.D research thesis, so your adviser would expect great grades in them naturally!

tl;dr - They don't matter (as long as you clear all your subjects!)


Is it appropriate for a professor to give the same exam to two different classes 2 weeks apart?

I deduce that one section is taught in French and another section is taught in English? The tests should be given in the language that the class is taught in. However, if there is reason to believe that all students are fluent in one language (e.g. English), it is debatable whether the language of the exam is actually of consequence.

Does your university require all students to be competent in English (or in French)? I guess it could be argued that students who only speak English should not be required to take a test in French.

Seeing as this is an engineering course, it would seem that there would not be a significant advantage to students who attend the French section versus the English section.


Does a high score in Math subject GRE helps in applying to a Finance PhD program?

While a strong GRE score certainly won't hurt your chances of admission, I think that in general students place too much emphasis on test scores relative to their actual importance in the admissions process.

The only case where this will make a substantial difference is in an "edge" case—where you're on the borderline of being admitted or not and the small "bump" could cause a significant change in the outcome. (If you were a clear admit, the GRE score won't make a difference, and if your candidacy is otherwise weak, a strong GRE score won't rescue it.)

As for how to highlight it, I would just put that information in a "miscellaneous comments" section of the form, if it's available.


Is it convenient to ask the journal's editor for two additional days to complete a review?

Getting a review in two days late for a journal article is pretty common. I wouldn't worry about anything less than being a week late. For conferences, deadlines can be tighter, but 2 days is nothing. Ideally you would let the editor know your review will be a couple of days late, but even if you didn't, it is not the end of the world.


Conducting a training seminar without projector

Put your seminar material online, and just have people view it at the same time as you talk. It can be any easily readable format, like PDF file or simply series of web pages. If you are not sure that people will follow, just put large bold numbers on each page, and announce what page you're at when you change page. (A bit like kids' audio book!)

Either that, or hard copies of the material.


Knowing that most students submit assignments right around the deadline, is it advisable not to set deadline that is very late at night?

First of all, I think the distribution that you're seeing is not very unusual, and indeed looks very similar to the distribution of times that I see coming from mature scientists submitting conference papers and grants.

It is simply that people, including your students, tend to overcommit themselves and to underestimate the difficulty of work. When that is combined with tasks on which there is a flexible amount of effort that can be invested (e.g., quality of work on an assignment), it is generally the case that "this work is done" is an ill-defined notion, and instead it gets triaged at some point of time shortly before the assignment.  Better and more prepared students (or whoever) simply climb farther up in quality before triaging.

Given that, I generally advocate for a policy of "tight deadlines, lots of mercy."  That means setting the deadline slightly before when you really want the assignment turned in, and then being very liberal about accepting requests for extension up until your secret "real deadline."

Addressing your specific question about timing, I think that if you want your students to get more sleep, moving the deadline up a couple of hours is a totally reasonable tactic: given the phenomena at work, it is unlikely to affect the distribution or quality of the assignments you receive.  Depending on how your automated system works, you may also be able to explicitly support an official deadline of 10pm, with the de facto ability to leave the submission system open longer to receive the main tranche of "just a little bit late" assignments.


You should also consider registering for an identifier, such as ORCID or Researcherid. This way you can have an additional layer that relates your profile with your work. It is used in many submission websites and it is becoming quite common for funding agencies to require such a profile when submitting applications as well.


How to cross-references sections in a thesis?

Intuitively, it's a matter of taste.  Both are indeed correct.

  As discussed in the Discussion section/Section 3.4

But the former is less usable, because finding the Discussion section is harder than finding Section 3.4, so I strongly advocate the latter.


What to do if predatory journal won't withdraw paper after acceptance?

There are three issues here.  Have you signed a publication agreement, have you paid them, and has the paper actually been published yet?

If all three have happened, then you are probably stuck.  Retracting a published paper is a big deal, since it involves
changing the permanent scholarly record, and you can't do this just
because you regret the choice of journal.
If you have signed and paid, but the paper has not been published yet, then legally they have the right to publish it but you may
have a chance.  An ethical publisher would not publish a paper over
the last-minute objections of the authors.  (Of course the publisher
would be legitimately upset with the authors if there wasn't a
compelling reason for the withdrawal, but they wouldn't insist on
publishing anyway.)  Unfortunately, there's no reason to expect that
a predatory publisher will behave ethically, but it can't hurt to
ask.
If you have signed but not paid, then you have some leverage.  Legally they may be able to demand payment, but actually suing you
would be more trouble than it is worth.  They probably don't want to
publish the paper without being paid, so you may be able to negotiate
a withdrawal.  On the other hand, it's conceivable that they would
publish the paper in order to strengthen their legal/ethical case for
getting paid.
If you have not yet signed, then there's nothing they can do, since publishing the paper without your permission would be a
copyright violation.  You should be polite but firm, and they will
have to accept that you have withdrawn the submission.


What is being done to make the academic environment more women friendly?

I imagine actual studies will be few and far between - they'd be difficult to conduct, and I suspect the reasons behind many of the outcomes would be near impossible to establish with a degree of certainty. For example, if a woman leaves academia because she got saddled with tons of committee work, student advising and other activities, and is denied tenure, was she just unproductive? Did she get saddled with those duties because she is a woman?

Beyond funding initiatives, which StrongBad discussed a bit, I think there are some very serious "quality of life" considerations that impact the retention of women in academia:

"Mommy Tracking" (A "mommy track" is when a woman is put on a particular career trajectory as a result of having, or planning to have children. While it may involve flexible work arrangements, it is often at the expense of her professional career and may involve limited advancement opportunities, being regarded as "less serious about research", etc.) While now notorious enough that it ought to be a thing of the past, penalizing female academics for having children - or the possibility that they might have children - forces women to make a Family vs. Career choice that most male academics never have to make. Faced with this dilemma, some female academics will choose family, resulting in a higher attrition rate among women. Worse, some promotion committees, etc., will effectively make the choice for them.This report goes over some of this.
For those female academics who do have children, consider providing things like breastfeeding rooms or daycare at major conferences.
Actively questioning our own implicit biases. If your field has a large number of women in it (like my own), the panels at conferences, the awardees, society officers, etc. should have a fairly large number of women in them. Even for fields with less women in them - if 10% of your field is female, but none of your invited speakers for a major conference are, that might indicate some implicit bias in how people construct panels, think about the luminaries in their field, etc. Looking at things like panel composition and asking "Do we have any women? If not, why not?" is a useful exercise. Note this is not a quota system. The answer may be that no women applied for an award this year. Or that everyone who published on this aspect of a subfield this year happened to be a man. But it also might not be. This kind of thing will impact both the careers of the women chosen, but also allow women who are junior in the field to see "people like them" as big names in the field, which has been shown to be important.
Stemming from the above, avoid tokenism. The female faculty you do have shouldn't have higher burdens of committee work, etc. because "We need a woman on the X committee and you're the only one" while their male colleagues are left free to do research.
Make academia unfriendly to sexist statements. Actually speak up when you hear them. Don't dismiss it as "Oh, X doesn't have any social skills, but they're a brilliant researcher..." when it's driving away other brilliant researchers who don't want to be treated as if they are sex objects (unwelcome flirting, comments on their appearance, etc), or have their accomplishments and contributions dismissed because of their gender.


How long do PhD students typically take to come up with their research proposal?

If you are talking about the writing of a formal proposal document, the rules vary from department to department. If you are talking about the idea for a project, then that needs to be developed very early on—the tentative idea should already be in place by the time work starts.

In my department, for instance, students had roughly one year from the completion of the qualifying examination to submit the research proposal. This was a fairly substantial document (25-30 pages). Other schools I considered required the submission as late as the third or fourth year (in what was nominally a five- to six-year program); in that case, the research proposal was almost a first draft of the thesis, as it was typically anywhere from 50 to 100 pages in length!

In my current department, students receive fellowships to work on projects with their advisors. In such cases, the advisor typically plans the basic outline of the project, and the start of the work plan. Later years are left for the student to devise.


How to check how fast the review and publication process in a journal

In mathematics, the AMS publishes an annual report in the AMS Notices with data on how long journals take from submission to final acceptance (in addition to other things).  The most recent edition of this is here.


Is peer review process by the US Department of Energy, Office of Science anonymous?

I haven't submitted grants to those departments, but for most federal grants, the researchers applying are not blinded. The reviewers for other departments are also often not blinded, but you have to dig to find who they are- for instance, for the NIH you find the study section that will review and find the list of who is in that review group.


How can I change the assignments in the syllabus in a way that is fair to the students?

Since the assignments did not go as intended, and it is obviously not the students' fault. I would just turn this part of the grade into extra credit. For example, students who did the assignment get +2.5 points added to their final grade, and those who didn't, don't get anything.


University-wide use of cracked OS and software – how to fix this?

If you suspect pirated software is being used, you can report it either directly to the software publishers themselves, e.g., to Microsoft, or you can file a confidential report online with one of the various software industry trade groups, e.g., the BSA Software Alliance or The Software & Information Industry Association.  (SIIA offers rewards.)

Realistically, it's the publishers' responsibility¹ to protect their intellectual property, not yours.  So once you've made a report, I'd let the matter drop.  The publishers' attorneys will take it from there.  They know how to fix blatant cases like the one you describe.  Typically what they do is offer a carrot and a stick, the carrot being a very attractive "get well" price to replace all the pirated software with legitimate copies, and the stick being the threat of a lawsuit.  The objective isn't always so much about getting paid for software previously pirated as it is about turning pirates into paying customers, changing their practices to ensure they always buy legitimate copies in the future.

¹ “It is the responsibility of the rights' holders to register, protect, and enforce their rights.”


Any reason not to apply for funding as a grad student?

Reward to ratio of the application. If you already have some funding, and the additional funding is small compared to the time required to apply for it. For example, you have an NSF fellowship at ~$30k/yr, so it might not be worth applying to $2k scholarships which take a week or two of time.
Reward to ratio of the work. You don't want to take on a new project.
The project isn't relevant to your line of work.
You aren't qualified (GPA, citizenship, or status limitations)


What to do with someone that cheated their way through university and a PhD program?

He literally had someone else take the exams for him

If you wanted to speak out, that was really the right time, not so many years later when damage is done and every accusation is virtually unprovable.

  His doctoral thesis was weak and the defense round wasn't difficult.

There are many weak PhD theses around, and it's up to the universities and to the defense committees to decide which level of weakness is acceptable before rejecting a candidate (gosh, if we were to object to any "weak" degree...).

  Do I tell his employer? Do I tell the university? Do I let it go?

You let it go because, as you said, you've nothing to prove your accusations (and the university would have no interest in undertaking an investigation after such a long time without any evidence to start with). And he is now in industry, and it's up to his employer to decide whether to promote or demote him according to his work performance and to decide whether the PhD title is just a vacuous document in his hands.

Different is the case where, for instance, you can prove that a student cheated by plagiarising other works. Here, there is evidence that can be used to revoke a degree, as it happened in some cases.


How to talk to other UG researchers and/or PG researchers?

In my experience, researchers who are genuinely interested in the same topics as you will be happy to discuss them regardless of whether you're at the same stage of education. Push yourself to attend events that challenge and inspire you, whether they're mainly attended by graduate students or by undergrads, and don't tell yourself that you're an intruder there. Most people won't be thinking about whether you're an undergrad or a postdoc; they'll just be listening to the ideas you exchange. As a graduate student myself, I love working with undergrads who are motivated and excited about research. Of course there will always be some people who think they're above you simply because they have more credentials, but that's their problem, not yours.

Asking people about their own  research can be a great entry point since everyone likes to feel that what they're doing is appreciated. Check out a poster session on campus and find a few posters that you're interested in. Eventually you'll start a great conversation with someone. Be patient and don't give up!


From conversations with a mentor who was the editor-in-chief for a major journal, if you take the responsibility seriously, you need to have enough of an understanding of the papers assigned to you to figure out which referees will be suitable for a paper, while not taking so much time to read it that you can't process all of them for lack of time. As mentioned above, you need to at least a "high-level" read of the paper before assigning it to the referees. If the paper comes back with mixed reviews, it probably requires a careful re-read; if the reviews are uniform in recommending for or against publication, then it may not be as critical.

However, the editor will want to read papers when revisions come in, so that may mean going through a paper several times during the course of the review process.


Is it possible to get application fee refunded from PhD programs that miss admission decision deadlines?

You do not a have a leg to stand on, legally, morally or otherwise.  The thing you should actually indict them for is not responding to your emails. That is rude; I think you should probably accept that as an implicit rejection.  If they were still thinking of admitting you they would have checked on your status by this point.

The issue with your argument is that it doesn't actually follow the text of the resolution.  The binding part of resolution you cited says "Students are under no obligation to respond to offers of financial support prior to April 15."  So, schools have agreed not to withdraw an offer because you haven't accepted it before April 15th, and not to try to hold you to an offer you've accepted if you change your mind before April 15th.  The school in question has held to their end of the bargain perfectly, since they never made you an offer.

The resolution says nothing about the school having to make a decision before April 15th. Of course, schools are well aware that it will be much harder to get people after April 15th, so they make an effort to make offers earlier. However, this is not a deal, this is the department acting in their own self-interest.

Unfortunately, there's too much uncertainty in the process to guarantee you'll make all offers before April 15th.  After all, you have some plan for what your incoming class will be, you make offers to many more people than that, and you hope that you guessed the yield correctly.  If the people who've already been offered admission are waiting until April 15th to make up their minds, you're then left with a great deal of uncertainty as the deadline approaches, since it will be a big problem if your incoming class is such bigger or much smaller than you planned.  Thus, there often are people who you are not sure you want to reject, but not sure you have the money to fund.  In my department, we still have a number of people waitlisted, since we haven't filled our class yet.  Usually, such people will be formally notified they are on a waitlist; I think again, that's in the department's self-interest and helps clarify things for the student.  So, again, it's likely this is an implicit rejection, which for whatever reason they haven't bothered to formalize.


Are Doctor of Arts (D.A.) degrees in math taken seriously?

If the NSF (National Science Foundation) doesn't recognize a degree as a Research Doctorate, for whatever reason, the holder's opportunities will be limited. For example, most colleges and universities in the US expect faculty to do at least some research at some level. The required quality varies widely.

Tenure in the US is determined by faculty committees. If one or more members of your committee doesn't accept the quality of your degree for whatever reason you will fare poorly in attaining tenure.

Finally, when you apply for grants you are expected to list your "highest" degree. If a "doctorate" isn't recognized as a Research Degree by NSF, you might need to list an MS as your highest degree. This can be devastating if you don't expect it.

For the D.A. degree, NSF recognition as a Research Doctorate ended in 2003.

Note that the above is directed to anyone who would want to pursue this degree now or in the future. Consider the above issues. However, it says nothing about the quality of the people holding the degree. Many were unfairly left stranded, unfortunately, by NSFs change of designation.


Is there a convention regarding frames around plots in engineering?

There is no convention or guide on this, at least none with appreciable universality. Having said that, one doesn't need a style guide for things like this.

The intention is to be clear to the reader. Minimalism or any other aesthetic ideal is secondary. In engineering, the values on graphs are potentially of interest, not just the trend. So a reader could potentially want to know the value of y(x), and your graph of y vs x should make it as easy as possible for him/her to do so. The top and right  axes make it easier to read out values, because (a) you now have two sets of axes to check your value against, (b) a point on the top-right is as easy to read as a point on the bottom-left.

Given that, I wouldn't recommend removing the frame or the ticks on the frame.


Is it reasonable to ask a professor about the strength of a recommendation letter (after they have submitted)?

It would be quite acceptable to ask for a copy of the recommendation letter (although your professor is not forced to supply it). That is probably a more reasonable request than asking if the recommendation is strong, which may require the professor to justify the recommendation.

Once the recommendation is submitted, you would also be entitled to request a copy directly from the institution you've applied to, as this is covered under the Data Protection Act.

Now, as someone who both writes references for students and reads them, I can tell you that the norm in the UK is for them to be restrained and factual. References that are full of hype are generally treated with suspicion.

Academic referees in the UK are also rather limited in what they are allowed to say. There are generally university guidelines which dictate the format. They usually have to be internally signed off before they can be submitted. Then a copy is kept on file.

Choosing referees is something that needs to be done carefully. Even with the best will in the world, an in-demand professor is not likely to be able to give this their full attention.

During my busy periods, when I was writing references for students regularly, I could get up to 20 requests a week. Normally, I'd have to write those in my free time, in the evenings. So, even though I would want to do my best for every student, references for anyone other than students I'd worked very closely with would become necessarily formulaic.

Choosing a referee who has had the opportunity to get to know you, who you have impressed in some way and who is not run off their feet with other activities is generally a sound strategy.


How to get rid of excessive 'silly' mistakes?

First, stop thinking about "Tier A" or "Tier B" or whatever "tiers" -- it's another kind of a silly mistake. You have the whole Internet in front of you, so gaining knowledge anywhere is not an issue.

Next, after supervising many different students, I tend to believe that some people are inherently unable to be meticulous. We indeed should discipline ourselves, and simple tricks do help. The best one is to write, put aside your writing, do something else, re-read later carefully and fix.

However, in general I think the best advice is to focus on your strong parts. Yes, perhaps, you won't win a medal for attention to details. So try to train yourself to the best of your abilities, but think what kind of future job/career would not be too demanding in this regard. Exams are quite artificial situations, hopefully in "normal" life you won't have to do often something quick and correct while the clock is ticking.


Citing the same idea in different studies

Of course! If you write multiple papers in the same area, you'll cite many of the same papers in each paper. No one should be required to know your history of publication to get a fully account of related work from one of your papers.


Stuck with a mediocre topic for my master thesis

An emplyer won’t necessarily be concerned with the topic of the thesis but how you functioned and completed it.

Most employers look for capability and capacity...


2 majors with average grades or 1 major with excellent grades?

I actually have doubts that those two majors are "related". It sounds like a statement from someone who knows only a little about either. The thought patterns and insights are very different. It isn't a question about accumulating things, but about how the things fit together.

Note that academia is about specialization - more and more the farther you go. But at the beginning it is natural (and good) to be undecided and hence flexible.

You can do well (most places) with a double major but you have to work a lot (a lot) harder. Mathematics itself is a flexible position from which to go forward, as it is applied in many fields. The most flexible field (IMO) is actually philosophy, but that is a different discussion.

I'll note that you don't have to decide early to accept one field and reject another (or others). If you develop a career you can branch out into other things that interest you. But you need to start from a solid base.

But if you want to establish a solid base for doctoral study, a single subject with great grades would seem to be the best choice, by far.

I don't know the rules in Germany for doing two MS degrees simultaneously. The thing I would suggest you be very careful about, however, is how much "double credit" you get for overlapping courses. If this is a common thing to do, then a given course may "count" in both degrees. Otherwise, you may actually be required to repeat things, or, more likely, to substitute elective courses for those you have taken in another degree. Just be sure of the rules and be wary about 25% "overlap".


Is it possible to become a professor in a field where you don't have a PhD degree?

Yes, it is possible to cross over between different fields following the PhD-level studies. However, in general, this tends to be more applicable to "interdisciplinary" fields that can fall into multiple disciplines. For instance, the engineering department I studied at hired people with PhD's in applied mathematics and physics, because their research fields—in fluid mechanics and interfacial science, respectively—meshed well with the research interests of the department.

To give a counterexample, however, it will be much harder to make the case for a high-energy physics person to move into another discipline, just because it is so strongly identified with physics.

Thus, if you have a PhD in a field such as mathematical economics or econometrics, it will be a lot easier to make the lateral shift. However, if you're in a more "traditional" subfield, that move becomes much more challenging.


What points should be included in SOP if the target program is industry focused and not researched focused?

Here are some stuffs, could which be deserving to be taken into account:

Explain about the expected contribution of this program to pave your
way for the future professional career.
Elaborate on any related working experience to the concept of the
program.
Illustrate the intriguing points, corresponding to the program, have which stimulated you to pursue it.
Pinpoint any presentation within the technical workshops around the     program's subject or any research-based experience, to depict your
related coherent background.
Mention your potential ideas to commence a business, based on the
acquired technical and professional skills, stemming from the
program.
...


how to specify 'pseudo-random seed' in publication, any reference?

If you are aiming for your results to be completely reproducible, you will need the random-generator seed, however you will also need the source code (unless you use only one predefined method in a very clear way) and sometimes even other information such as the version of employed software, operating system, and hardware specs. The random seed is of no use to the reader on its own, and hence there is no point in mentioning it here.

In most contexts, I would only state in the main text which realisations are identical.
That you control this with seeds (instead of say saving and loading them) is a technical detail that should have no relevance to your results.
I would put the seeds together with the source code and other relevant details in a supplement (or similar).
At most I would mention the specific seed when referencing this supplement in a way that makes clear to the reader that this information only makes sense together with the supplement:

  The results in Fig. 2, 3, and 4 were obtained for the same realisation of the topology (Supplement A, seed 1010) to validate the scheme.


Generally speaking, if you wish to be involved in designing, proposing, and interpreting experiments, you need to be a PhD. (This isn't specific to synthetic biology.)

That's not a hard and fast rule. There are certainly Masters and Bachelors out there who will propose experiments and do analysis, and any organization worth their salt will consider intelligent proposals for experiments from technicians. However, a PhD is usually taken to be the sign that someone is capable of designing and executing an independent research program. -- In some respects, that's what a PhD degree is. It's a certification by your peers that you are able to intelligently propose and carry out an independent research plan that is sufficiently novel. (Cue grumbling from older PhDs about the dumbing down of modern degree programs and lack of intellectual rigor these days.)

So that's where the line is usually drawn. The PhDs design the experiments, and the Bachelors and Masters (and lower-ranking PhDs) carry them out. The Bachelors and Masters may do some routine post-analysis, but ultimately they hand the results back to the PhDs to interpret and plan the next round of experiments. It's not that you can't find positions where Bachelors or Masters are significantly involved in planning and analysis, it's just that if you want your primary responsibility to be planning, you should probably shoot for a PhD.


Is it a red flag if the justification for my research (why it is likely to matter) is popularly sourced?

Research need not be completely inward looking: a snake eating its own tail. All applied research, in fact, is rooted in real world concerns. The fact that the questions have been little studied in the past is not a reason to avoid them in the future.

In fact, "its interesting" is enough of a justification for a lot of research, whether theoretical or applied.

And having a potential application immediately may make it more interesting, actually.


"Decision pending" means that the decision... is pending. They haven't decided yet.

There isn't any secret code to deciphering the submission tracker. Things just always take much longer than we think they would.


How can a graduate student most efficiently become an expert at his research topic?

For most disciplines, advanced textbooks still provide, albeit necessary, foundations. Conferences allows you to hear what is new and is as such a good way to know where fields are going. I am not sure what you mean by seminars but discussing new papers and topics is always a good way to advance knowledge. But, the major point is to read up on published papers and to focus on the topic of your thesis. The point of research is to advance knowledge and this means you will, or at least have a chance to, be an expert on the field you are researching. So in my view none of the activities 1-3, or combinations, make you an expert, only your own sweat over publications and own work will do so.


Cite Repository in manuscript: GitHub link "https://github.com/User/Code" VS zenodo link

GitHub can change in the future. You could push new stuff that changes the results you got and published. At the very least you should package a release and link that instead. I really hate methods sections that are just "this is my github repo no I've never heard of comments why do you ask".

Zenodo doesn't change. That's the point. It's locked in.


How to integrate a paper where I am third author, but did a lot of work, into my master's thesis?

This situation does not sound problematic to me.  Many people write theses that incorporate papers written under these circumstances.

However, you need to get official permission, rather than relying on what random people on the internet say.  Specifically, you need to check three things:

What does your thesis advisor say?
What are your university's regulations regarding reusing text from published papers, particularly with coauthors where it is difficult to identify who contributed to a given passage?
Does the publication or copyright agreement with the journal permit reusing this text in your thesis?

If any one of these has a negative answer, then you cannot copy the text.  If they are all positive, then all you need to do is attribute the text properly.  For example, you could clearly state at the beginning of a chapter "This chapter is an edited version of the paper BLAH."  Your advisor, university, and publisher will have suggestions or requirements for how this attribution should be done.


Is it a good idea to apply to the same professor again after having been rejected the year before?

It very much depends on why you were rejected.

For example, a year ago, it's possible the professor couldn't fund a student. Or there were limited spots, and someone else urgently needed a student. Or they were just getting a project going, and didn't want to add another person into their lab.

All of those are circumstances where it might be possible to revisit your application.

If you don't know the reason, you might still try. After all, if you don't apply functionally the answer is "No".


Second try for PhD after failing comprehensive exam

It certainly is possible; I too have anecdotal experience.
There's really two main items at question here.

Why did you fail your qualifying exams the first time?
What will you get out of completing a PhD?

My experiences are as follows -
First, I failed because I took them too early and was not professional about my studies as I should have been, plain and simple. At that point, I was locked into a rigid timeline for a retake which I attempted to negotiate with the department. They pushed back and I passed 2/3 retakes, but that was not enough. I did great research, my advisor totally had my back (and is still incredibly disappointed with the department and the handling of my situation), the only reason I didn't continue was because I did not pass the qualifiers.
Based on the fact that you are at a 'Big 4' consulting firm, you probably  have a good career ahead of you. I was in industry for a while before returning to academia after undergrad, so I totally understand that academia provides truly unique opportunities. For me, it allowed me to re-orient myself from a management career track to a technical career track. And in the process, I fell in love with the process of finding research problems and having the freedom to really dig in and become an expert. Academia is really the only way for me to pursue the topic that I want to pursue, and to continue to develop myself as an independent researcher.
You really need to think hard about both of these questions. I did, and I knew that I wanted to continue. I worked hard to develop a relationship with another PI. And honestly, I'm working on problems which are more interesting to me in a niche field that is on the cusp of some very interesting results at the intersection of theoretical results and application.
There was another member of my cohort who didn't pass the qualifiers in the same round. They already had a master's, and decided that getting a PhD just wasn't in the cards for them.

On the practical side of things, you're giving up 3-5 years of, I am guessing, a 6-figure salary with good retirement package. That's a LOT of money, not to mention bonuses, raises, etc.. On the other hand, the golden handcuffs are likely not too tight on you yet, so now would be the time to take them off without too much pain.
In the end, this all really falls on you and how much you want to get the PhD - at this point, I would say it's not just want, it's how much you need to get it, for personal or professional reasons. There's plenty of ways to work on interesting projects doing what you want to do without a PhD. My biggest recommendation: exhaust those options before jumping back in.


Difference between university/departmental service and extracurricular university service on CV

Extracurricular service is things you do completely outside the university setting. Volunteering at a food bank or such like these days. Tutoring disadvantaged kids.
The other is service given to the university and its students and staff in some way. Being chair of an admissions or hiring committee. Writing a report, or serving on a committee that is trying to make plans for the future.
There is also an overlap area. If you lead an informal campus Judo club or Chess club, just because you want to, you can probably list it either place, but "extracurricular" is more literally true.
They should probably be separated if the instructions separate them. But if they just ask for service without qualification, you could probably combine them.
And the required activities under Teaching and Research are separate, as you suggest.


Could a journal reject an article due to the style or quality of accompanying code?

You will not have a paper rejected for poor coding style. Particularly not in bioinformatics. Unless the paper is a tool development paper, the chance that a reviewer even looks at the code is not that high, and if they do, it will just be to check that its reasonable. In the outside case a reviewer might spot a bug, or poor assumption that actaully makes the result wrong, but they will not reject you for poor style.
However, having the code associated with the paper massively increases the chances that it will be useful to someone else.


Why should (or should not) a university have a policy of not hiring its own PhDs?

I have not come far in my career but I have a family of academics, this question certainly came up a number of times over the years.

I guess the main point of having a formal requirement of foreign exchange/post-doc period is two-folds:

to avoid the drawbacks of academic inbreeding. Academia is partially built on a strong tutor-pupil, or rather mentor-protégé, relationship. While this is a great way to pass on the experience and good skills, it can also be the cause of conservatism in the form of sticking to what you know only. Likewise it's truly important for young academics to experience different cultures, and I don't mean it like a charter trip to a warm place, only to hang out with friends/family. To learn, adapt and eventually appreciate a foreign culture is beneficial for any person, let alone for those who are supposed to keep an open mind to the unknown.
going to a new lab somewhere else is also a fantastic way to improve on your professional skills. It's another reason why young academics are often expected to go somewhere else, learn something new and overall improve intellectually. In the corporate world this is encouraged in terms of changing jobs, those prodigies who are groomed for high level executive positions usually end up switching jobs every 3-5 years, often taking on a new but not completely unfamiliar role.

I should also note that our department has a similar issue, in the form of internal recruiting. A significant portion of the PhDs are recruited from those who have taken the course our department gives for undergrads in a particular program. What that leads to then is that the department becomes more or less an alumni hangout. While it may be nice for those new recruits to feel more "at home", for anyone else who does not have the same background it creates a BIG barrier to overcome in order to get familiar with the people in the department.

That was my two cents, I hope it helps.


How and what do I present at my PhD coursework

I'm going to be a bit more harsh than the current answers, and ask whether you knew what you were getting yourself into when you signed up for a multidisciplinary graduate program. What you describe is very common in such programs; you enter with significant knowledge in one field (e.g., comp sci), almost no knowledge in another (e.g., biology), and your task is to familiarize yourself with both to the extent that you can perform academic-level research that straddles both fields. Anecdotally, I went through a biomedical engineering PhD program, and every single student who went through the program experienced some degree of what you are describing. Without knowing specifics, your advisor is likely not responding because they take it for granted that you will learn to cope the same way that all his other students do.

The solution is simply to start at the beginning and take it from there. Clearly, you won't find help from your advisor, but there are many other resources. Find other students in a similar situation and create a study group. Talk to the TA. Use online materials and forums. If the course is simply too advanced, drop it for now and take (audit?) a lower-level (undergraduate?) course first. I know many students who did this. They ended up fine.

You will likely encounter a similar situation many times, where you need to familiarize yourself with a brand-new field, and this is a fine time to figure out how to do it.


Citing a Hollywood movie in a scientific paper

I'm coming from a humanities background so there may be some differences in actual citation styles but I think the following would be used by most styles.

Name of movie
Director
Distributor
Year of release
Medium consulted (DVD, VHS etc)
Sometimes the main performers(depending on citation format)

In text styles of course depend on whatever citation style you are using.
I know for example MLA is (Director, Movie Name) and APA is (Director, Year).

For your example of Highlander in the APA style it would be (Mulcahy, 1986) for a inline citation and your reference entry (assumed DVD) would be  - Mulcahy, R. (Director). (1986). Highlander [Motion picture on DVD]. Thorn EMI.

This Link has a pdf showing examples in MLA, APA and Chicago style.


How do I deal with an old reference letter from an advisor for job applications?

Not exactly an answer, but a couple things to note.

Letters on MathJobs expire eventually; I think you can see the expiration date on the "cover sheet" page. It will be very awkward if it expires partway through the application process.

Also, note that your advisor will be able to remove or update the letter at any time, which could be a problem if he is really vindictive - he could replace the letter with something unfavorable.

So in short, regardless of how an old letter looks to the committee, it may not be wise to use the letter against your advisor's wishes.


How to list both journals and conferences on your CV when you have worked in two fields with different publication cultures?

I work with this situation myself right now, as I am active simultaneously in two fields with these opposing publication cultures.  This is further complicated by the fact that some of the publications I am most proud of are not peer reviewed in any fashion (e.g., standards documents).

I thus simply organize all of my publications according to categories and try to include enough information that people from different fields may at least understand that there is a culture gap.  The current categories in my CV are:

Journal Articles
Book Chapters & Theses
Peer-Reviewed Conference Articles
Peer-Reviewed Conference Abstracts
Workshops, Symposia, and Seminars
Published Whitepapers and Technical Reports

This allows me to distinguish between conferences that people should take seriously ("Peer-Reviewed Conference Articles") and those which they should view as "light weight" ("Peer-Reviewed Conference Abstracts").  Conference poster presentations that haven't even received meaningful peer review I don't even list at this point, though at an earlier stage I would have put them down as another category.


How many minutes per day do most professors spend reading and replying to emails?

I'm not sure what the exact percentiles are, but I'd estimate that most faculty members who handle their own emails (more on this below) probably spend on the order of an hour a day or more dealing with emails.

I think that emails don't necessarily increase when one is teaching as opposed to other times of the year—unless there are no TA's for the course. In that case, since the professor is the only contact point, emails will rise, although this depends on the course enrollment.

Other determining factors are more or less obvious: the more active and senior a professor is, the more emails they will get:

Professors with larger research groups will have more email traffic associated with group management.
Professors in larger departments will have more email originating at the department and committee level.
As professors move up the ladder, they are asked to participate in more reviews and external programs, which increases the burden still further.

On the other hand, one advantage that many senior faculty have is that they may have dedicated administrative assistants, whose responsibilities can include filtering out the unimportant messages for them.


What is this "mixed" citation style that includes both numbered references and author-date formats?

Speaking about major citation styles that I've seen, I think that it could be the IEEE Citation Style, as your example matches the IEEE Style for electronic references (for non-electronic references, the in-text citation is the same, with the only difference, being related to reference list, is that the year is located at the end of the reference entry).

Alternatively, if it is not the IEEE Style, it might be either a publication-specific style, adopted by a particular journal or other publication outlet, or a hybrid style, manually developed by some authors.

Naturally, speaking about using LaTeX for biblographies, there are a couple of aspects that I'd like to mention. Firstly, according to Mori (2009), the citation style that you are curious about resembles the default reference formatting style for LaTeX. Secondly, if you use (or plan to use) LaTeX for producing your publications, the following sources, in addition to the paper by Mori, might be quite helpful for customizing bibliographic features to required or desired style: this guide by Patrick Daly (note that it describes a quite old version of natbib package - try to find a more up-to-date version or a similar detailed guide), this brief guide by Ki-Joo Kim and this excellent answer by Alan Munn.

References

Mori, L. F. (2009). Managing bibliographies with LaTeX. TUGboat, 30(1). Retrieved from https://www.tug.org/TUGboat/tb30-1/tb94mori.pdf


Change of affiliation in manuscript under preparation

If you are doing the revision work at the new place you can just add the new affiliation as a second one (e.g. with 1,2).

Yes, I would update the email as there is no point in a dead old one for anybody.


Whether to tell my PhD advisor about transfer

Since you've already reapplied, you're best off waiting until you've heard from the other university. There's no point in poisoning your existing relationship, which would have been the net result of telling your advisor you've applied somewhere else, and then not gotten in.

However, have you had an open discussion with your advisor about why you want to transfer? Perhaps there's something that can be done to improve the situation—maybe a co-advising situation, or a transfer to another group at your current institution?


Is it a bad idea to change/remove a co-author from a manuscript which is revision?

You need documentation that this person doesn't believe that their contributions merit co-authorship (or that they didn't contribute at all). I would write them an email like this (adjust as necessary for specifics and to not upset them further):

  Dear Charles,

  Last Monday you mentioned that you do not want to be listed as author
  on our paper "The missing link between dinos and birds" since you believe your contributions to be too minor. I just want
  to make sure that we are on the same page: Can you confirm that you
  would like me to remove your name from the author list?

  Thank you,

  A. G. Install Happyness

If they confirm, you are free to tell the editor that the co-author was included by mistake and agrees to be removed from the manuscript. If they don't confirm you need to clarify what outcome they desire and then discuss this with them and the other co-authors.


Relative Advantages/Disadvantages of Interdisciplinary Degree vs Discipline-Specific Degree

The main reasons are pretty obvious, I think.
A narrow field of study will (probably) make you more suitable for employment in that field and less in others.
A wider field of study will (probably) give you more options, but those who have specialized in something will have the upper hand (again, probably) over you it their specialty.
None of that is necessarily true and you can always either broaden your outlook later or specialize further as necessary. So, I suspect that any effect is most important only for your first job.
But it also depends on the individual program. I can imagine one in which the mathematical techniques are pretty generally useful, but also one in which they are not. This might be worth exploring with you proposed advisor.
On a different dimension, an interdisciplinary program might leave you more grounded in applications, where a straight applied math program might (not necessarily) leave you wondering how to actually use what you have learned.


Balancing between students who do homework and those who do not

If 40% of the students aren't doing their homework, and you rely upon students doing homework for your pedagogy style to work, then something is seriously wrong.

You have two options:

(1) Make homework dramatically more appealing.

Put much more effort into the homework--make it fun!  E.g. calculate strain on an iPhone screen instead of a aluminum sheet; don't have someone read a novel but rather ask key questions about it such as to list all the times some character/historical figure expressed defiance against the state.
Institute quizzes that are drawn directly from the homework.  Do them practically every day.  Staring at a blank sheet of paper and not knowing what to do is a lot more uncomfortable than hearing you babble about something incomprehensible.
Change the grading scheme so homework is most of the grade (if you're allowed).

(2) Make homework dramatically less necessary.  (Note: usually not an option for mathematics.)

Do the key problems on the board in class instead of assigning them as homework.  (Assign a similar problem as homework, possibly after you've done it in class.)  Not possible for literature review, of course.
Rely upon in-class participation instead (if you have the personality to make it work, and the homework is of the right type).
Don't make the learning environment one which requires the students to do the homework in order to understand most of the next lecture.  Lecture on the important points, review at the end of one lecture and the beginning of the next, and go on.  They might not develop their skills at doing problems, but at least they'll have some hope of following for a while.  Probably won't work with literature, but almost everything else can be quite successful.


Are there any undergraduate research/internship opportunities in math/science education/history?

Find some people doing your dream job.  Write to them and request an opportunity to do a shadow as part of your career exploration process.  Include a copy of your unofficial transcript and CV.  Make it clear that you would be grateful for any advice they may have about where to study, and any additional degree, coursework or job experience that would help you achieve your goal, but make the advice part optional.  Let them know how to contact you if they would find phone easier than email.

Please also consider applying for science outreach jobs.  These might be available at a research institute that is part of a large university.

Sometimes people create such a job organically, starting by doing this and that while employed doing something else (possibly related).  For example, enrichment classes taught after school at elementary schools.  Being a community advisor for a science club at a middle or high school.


How PhD classes are different from undergraduate?

Graduate-level classes are not necessarily any different than undergraduate classes, just more intense and more specialized.  Some graduate-level classes are just exactly the way that you describe.  Others have more of a "seminar" format, in which there is more reading and discussion, and in which students are expected to do part of the teaching---but at many institutions, there are also undergraduate classes like this.

The real heart of a Ph.D. program, however, is not the classes, but the research that students are involved with and should ultimately learn to initiate themselves.  Typically, Ph.D. programs start with a couple of years of intense classes, but then, once students have "qualified" (often by passing an oral or written examination), then classes become largely optional and you are expected to focus on research instead.


Who to contact when handling editor is anonymous and manuscript is delayed?

Is it an appropriate approach for associate/handling editor to hide the identity
  from an author?

This question has been discussed extensively in the question you linked. Whether it's "appropriate" is a difficult question, but it's not entirely uncommon and I am not sure why it would be an ethical problem. Personally, I prefer transparency over information hiding, but there are definitely arguments in both directions (and most of the time it probably simply does not matter).

  Is it appropriate if I write email directly to Editor in Chief?

Sure, why not? 5 months is a fairly long time for a minor revision, and sending an email to a person concerning an official role that (s)he voluntarily took over seems almost always ok. Whether this will change much is a different question, but it's worth a try.

  if yes, then how should I compose my email?

Short and respectfully. Avoid being combative, avoid assigning blame, and don't ask who the handling editor is so that you can bug her or him yourself. Briefly state that you have submitted a minor revision for the manuscript XXX on date YYY, that you are wondering what the cause of the delay is, and want to inquire whether a notification date can already be foreseen.


What exactly does it mean to say that a conference is "peer reviewed"?

Things vary a bit, depending on the field you are in.
Some fields only review and publish abstracts (e.g., medicine), in some fields conferences are more important than journal publications (e.g., computer science).

But as a rule of thumb: a conference is only considered to be peer-reviewed when the full paper is reviewed, and not an (extended) abstract.

Personally, I think that there are great conferences out there, where only an extended abstract is reviewed (e.g., SPIE), but many working in academia do not consider them to be peer-reviewed.

Be aware! There are also scam (or near-scam) conferences that pretend to have a peer-review process, but actually hardly perform any review at all (and have accepted computer generated nonsense papers in the past). Try to avoid these! They only cost (a lot of) money, and will actually degrade your CV.


Undergraduate school affecting acceptance to a prestigious graduate school

Getting into a good grad school has more to do with demonstrating your potential for being a researcher than the quality of the school you attended as an undergraduate. If you don’t have any evidence of research, it’s unlikely that you’re going to get into a top-10 school. If you have an extensive body of solid research as an undergraduate, it can compensate for weak(ish) grades.


Am I entitled to any benefit by implementing an idea from my professor's published paper?

This is a perfect situation for you to suggest that if possible you would like to get started on a career that includes publication of scholarly articles, either alone or in collaboration with the prof. Ask him if this project is a good vehicle for this. It assumes either the implementation or an extension of the original paper is valid for publication, of course. You might wind up a big winner. He will, in any case, likely consider you for a future project if this one doesn't seem right to him. There is little to lose.

Don't ask him for a gimme. Ask for collaboration and help in learning how to develop and write for publication.

There are two additional thoughts. Maybe he just didn't think of it, so your approach might wake him up to the possibility. And also, he may put your name around to other faculty who might be willing also. Just expressing your interest can start a lot of wheels turning.


Is it legal to download textbooks from academia.edu?

Someone who downloaded a textbook from there could make the argument that they had good-faith belief that the content on the website is available for public use, and was not aware of any legislation barring them from such download.

Thus, even if somewhere in the world it is illegal (which I doubt), the person downloading the book is extremely unlikely to get prosecuted or sued, and were they to be prosecuted - extremely unlikely of being convicted.

This, as opposed to textbooks you somehow got (without being able to make any assumptions about the source of the file.


Should I list talks I invited myself to give on my CV?

Yes.

If you discover that a friend in a distant city is having a birthday party, and you ask "Hey, can I come?" and they say "Sure!", you've been invited to the party.

Same thing goes for talks. When the host institution agreed to let you talk, that was your invitation, which makes it an invited talk.

That said, you may want to distinguish plenary talks at conferences and formally organized departmental colloquia from random seminars run by individual faculty.


Who should create contacts with other universities/departments/researchers during a PhD study? The supervisor or the student?

Both:

The supervisor will already know plenty of people and help the student establish contact when it is on topic.
The student should just as well try to get in touch with other researchers who might provide opportunities for collaboration, depending on the context the student is in. For instance, the student has particularly good chances for that when being funded from a project that involves researchers from different institutions, or when attending conferences in fields where conferences are commonly held and visited.

  How these contacts may affect the continuing of the academic carrer of the student?

They provide opportunities of getting in touch with different fields, possibly exchanging some data that can be used in the other's research, and learning how to autonomously organize little "projects" (by this, I mean e.g. studies and ensuing papers).

  May be possible that a specific contact during the PhD will evolve in a post-doc position later on?

This is one of many theoretical possibilities, though probably not one you would normally strive for in most cases.

  Should contacts always be made?

This is somewhat vague, but as a general rule of thumb: If there is an opportunity to get in touch with another researcher, at least have a brief conversation to check whether the two of you are "compatible" to start with.


How to start abstract of previous research activities for a PhD position

Don't overthink things here. I recommend something like the following:

  I began my research in this field by investigating bla bla bla (refs).  discovered that bla bla bla (refs), leading to our research on bla bla bla (refs). At this point, I was awarded a research grant with Dr. Bob to investigate bla bla bla  (grant ref), and we discovered that bla bla bla (refs).

Concise and full of as many refs as you can cram in. If you won any grant awards, mention it, unless you're out of space, in which case get rid of some of the other text and mention it. Short and sweet is key here.