Is it polite to ask my mentor to recommend me to Professors she knows in the graduate school?

Yes it is polite and it is actually proper to ask a mentor for this in most cultures, I suspect. Some professors might be reluctant to do this, but I think not very many.
But what it actually gets you depends on the admissions system at the universities you apply to. In some, say in the US, it might have little effect on admissions but it places (and fields) in which professors hire their own students it would be much more valuable.
But in any case, having been introduced will be a small (at least) advantage if you wind up at one of these schools and it is a good idea to go meet the people you were introduced to. You might even be able to pick up a new mentor at the new place.


Phd Application follow up contact the lecturer or the school

I have been involved in multiple PhD student searchers. Things tend to be rather informal. If I were you I would send him an email inquiring about the status of the application. Keep in mind tho that sometimes things are slow in Academia.


Where does the money earned by universities in the USA from sports activities go?

Revised answer:  At my university, where football is big, the athletics department supports itself, and that some of the money goes back to the university, but the only specific instances I know of are donations to the art museum and history of science collection.
That said, I am sure most of revenue generated stays within athletics.

For instance, this article talks about the most profitable football programs, and out of Alabama's $110 million revenue in 2013, $6.5 million (5.9%) went back to "academic programming."  However, the details of how that money got used, and how much actually went back athletics (via athletic scholarships) is unclear.  In any case, this is a small amount of the university operating budget.  Florida that year gave the most back to academic programming $7.2 million, but the general and educational expenses were $524 million.

However, most universities lose money on athletics (see, e.g., this and this).  These universities make up for this by doing things like charging students fees for the athletics program and cutting funds to other programs/units.  Even some of the ones which are termed profitable get large subsidies (e.g., student fees)--only 7/230 Division I athletics programs did not take subsidies last year .  These articles say that even the donations athletics help generate goes back to athletics and that a relatively small amount of the athletics costs (about 16%) goes to student aid.


The work should be credited to the institute at which it was done - this is important for citation and publication metrics, and will be pulled out of the metadata of the publication by several services. The author is a separate entity to the institute which employed or supported the author. A subsequent change in affiliation - for contact details, e.g. - should be taken care of in a footnote in the front matter.


Is it acceptable to ask my professor for help for another class during her office hours?

This might depend on local custom, but I don't think there is any reason that you shouldn't ask for help. You may be sent to the other professor or just told that the one you ask hasn't the time for you. But asking is fine.

Of course it is also appropriate to say why you ask the one and not the other. But having a relationship with a professor makes it easier to discuss things with than with someone more distant.

The professor will set boundaries if necessary. You don't need to be overly concerned with whether you are interfering with other students.


"Very Similar" vs "Based On" for purpose of paper "narrative"

In an ordinary scientific paper, nobody expects to get a narrative of your investigation, but rather a clear explanation of how the ideas fit together.  In fact, it has been argued that success in science is precisely defined by the separation of statements from the circumstances of their creation.

I would thus argue that you should no more feel obligated to tell a reader that you invented an idea independently than that you invented it while riding a bicycle.  You may not have started by basing your method on the other method, but now that you know it exists, you can skip all sorts of argumentation and verification by changing the way you think about your method in order to base it on the prior method and the work that has been done to establish it.

Thus, I would recommend using something like your statement 1a/1b.  That is not the history of events, but based on what you report, it appears to me to be a true and more accurate characterization of the current relationship between the concepts.  Since you discovered this prior method, you are no longer proposing a new method: instead, you are applying a slight variation on an existing method, as adapted to your circumstances, and should report that fact accordingly.


How could publishers, in particular disreputable ones, prove that you “signed” a copyright agreement?

First, I would like to clear up a little misconception. A signature is never proof of anything. There is very little difference among a hand written signature, pressing the I agree button, and writing an 'X' on the signature line. They all carry the exact same legal weight provided they were done in a proper fashion. The only time a signature is ever really sufficient proof is when it has been notarized (which is much more than just the notary's signature). So, signing a paper and faxing it over, for instance, doesn't have much more value then pressing your "I agree" button. Without being notarized, signatures in any form are simply evidence.

Third parties, in this case, can effectively act as notaries to a certain extent. There tend to be very strict guidelines when dealing with electronic signatures. Depending on the field and the government involved, how the signatures are stored is often very important. Other than the legal requirements, the person or court would need to ask the question "Why would the third party forge the signature" and "Was the signer who they say they were". Usually these are emailed and involve a unique token, so identity is based on the security of email and the token is stored and hopefully not accessed. Periodic backups (using non-re-writable media) that are stored securely can often be used to ensure data hadn't been added or modified.

It is nearly impossible for a party of the deal to serve as the sole witness to the authenticity of any signature as they generally have reason to lie. Instead, they need to show that you agreed to transfer copyright as evidence that the signature is authentic. If they don't have you agreeing to the publication somewhere, then they are just waving around a piece of paper with an 'X' on it.


Is it true that articles cited in Wikipedia get more citations?

There appears to be some literature comparing citations on Wikipedia to citations in academic journals, but I have not been able to find any randomised controlled trial (RCT) on the matter.  For example, in a comparison of Wikipedia citations to journal metrics, Nielsen (2018) found that "[t]he Wikipedia citation numbers showed high correlation with the [Journal Citation Report's] numbers for the total number of citations to a journal" (p. 4).  If go broader than Wikipedia, Lawrence (2011) finds that free online availability is positively correlated with citation rate.  Both of these studies use observational data and show correlation between the outcomes, but they do not rule out other causal relations that would lead to correlation (e.g., if papers are more likely to be made available online, or added as citations in Wikipedia, if they become more cited).

If there are any enterprising researchers reading this post, this sounds like a good research question for a randomised controlled trial (RCT).  Since Wikipedia can be edited with a free account, it should be possible to set up an RCT where you add a randomised set of presently uncited academic articles to Wikipedia and track their citation progress in academic journals against a control group.  First find a set of articles relevant to a subject that are not presently cited on Wikpedia; then randomise them into a control group and treatment group, and add the articles in the treatment group into Wikipedia articles; then watch changes in the citation count in the academic journals over time, and then test for a difference in the groups.


Can someone ever be accused of self-plagiarism after the course is over?

In theory, you could get in trouble for this, but the risk is very low.  Universities generally retain the authority to change grades and revoke degrees forever, at least when matters of academic dishonesty are involved.

However, nobody is likely to be looking over your old work to find this.  It probably doesn't even exist in recorded form any more.  So I see little cause to concern yourself, especially if this was a product of a misunderstanding.


How conceivable is it to research independently while working in a non-research role in industry, to improve my profile for graduate admissions?

It is hard to do both research and industry work especially something that is not related to your main research topic. I work as a database administrator and software developer. After I finished my undergraduate degree, I started working in industry in 2003. Fast forward to 2016. I used 3 years to finish a master and used about 9 years for a PhD. I am about to finish my PHD, but it was hard to do so.

I offer following advices. Note that these points are mostly useful for PhD. You can and most people do finish your master degree while working.

Try to find a company which do R&D, and try to align your thesis subject in your company's vision. This way even when you work for your company related work at least you learn something about your research.
Try to find a company which allows about academy work leave in its employee guide. Even you talk about your academy leave when you interview about your job, another manager may not allow it. But if company has a clearly defined policy about this, they have to allow it.
Be prepared to spend more time than others. Think about it. A normal PhD student in my country spend 4-6 years for PHD. In some countries, PHD does not require course work and qualification exam; thus it may took only 3 years. But this is their only job. If they spend 20 hours (reasonable for 45 hours) every week for their PHD. This means that they spend 3120( 3 years), 4160(4 years) , 5200 (5 years), 6240 (6 Years) to finish their PHD. You will not able to put 45 work hours + 20 PHD hours. You may be able to put 10 hours at best. This means that if you do not put extra effort in holidays and your leaves, you will need two times more time to finish PHD.
If your institution require Qualification Examination, be prepared to take leave from your job. It will be near impossible to be successful in this exam with full time work. I changed my job to part time (2 days) for 6 months for this examination.
Be prepared to fail. If you need industry work for your livelihood, sometimes you have to put your work ahead of your PhD. This is especially hard for normal academia people to understand.
Similar to above point, try to find an advisor who understands your situation that sometimes you need to put your job ahead of your PhD. My advisor is similar to me that he changed his career from industry to academy. But I saw very different attitude from others in my university. And this is from a university where I pay tuition with my own money. I had an argument with department head about this subject. He told me that I need to put my PhD first, I told him that if I could afford that I would already have done that.  I know that I would have host of other difficulties with other universities. Some universities in my country does not accept working PhD student.
Be prepared to give up a lot of your social time for your PhD.


When emailing a potential supervisor, should I offer to send them my researched material?

As stated in comments, you should make the papers available to the potential supervisor online:

Create yourself a basic webpage with a sensible address.
List the papers, with full details and references.
Link to the pages of the places they are published.
If the copyright agreement allows, link also to a copy of the paper.
Given the option, make this copy on the arXiv (get the supervisor from the paper to endorse you, assuming it's in their field).
If you cannot use the arXiv, store the copies on the same website.
Alternatively, your current institution may have an eprint system you can use.
Make sure your co-authors are happy with this.
Include the web address when you contact potential supervisors (if it is long, perhaps use a tinyurl with preview).


Bibliometrics analyses with Pubmed metadata

Publication metadata does not have license restrictions. I work for the European partner of Pubmed - Europe PMC, and you can get metadata for every article available in Pubmed via the open API (https://europepmc.org/RestfulWebService).

In some countries publication abstract may be under copyright. For UK and USA it is possible to reproduce abstracts if your use of this data falls under "fair dealing claim" (see https://www.copyrightservice.co.uk/ukcs/docs/edupack.pdf).


Mathematicians frequently come up with questionable names drawn from a variety of questionable sources. And then at some point there will be the inevitable MathOverflow thread about why such-and-such is named what it is. I personally rather like "meromero," but in the context you're describing, I don't see how it's an improvement over saying "unique 'good' solution," where you define what exactly you mean by "good."


An invitation from a not-so-famous journal called "world biomedical frontiers" to feature my paper on their website

No; this isn't how reputable venues approach authors. This will have at best zero value (possibly negative value if someone notices, which is unlikely given how little visibility they apparently have), and will cost you $38.

(Its funny that they advertise that they get 8000 website hits per month. This strikes me as an exceedingly low count, given that they probably get a hit from many people they send this spam email to)


Being accepted then rejected to an academic conference

I'm inclined to think the simplest answer is human error. Someone overbooked a set time slot and your acceptance was taken back.
You'd be hard-pressed to get anyone to admit that, though. ;)


Is it bad to use the same interview instruments?

You need to give credit where credit is due. So if you use their instrument, be open about that and cite them.

Just another reason for reusing existing instruments: You probably want to compare your findings with the findings of the original author. In that case using the same instrument is very beneficial.


Etiquette with regard to email read reciepts

Am I obligated to accept this parent's request to send a read receipt for their email? Would it be considered rude to decline it?

No, there is no obligation on anyone's part to send a read receipt for emails.

It may be considered rude to the email sender if they, upon encountering those who choose not to comply with the read receipt request, assume that the lack of compliance is a giant "middle finger": it certainly is possible that some portion of email senders fall into this category (but/and there are those who think it is rude, annoying, etc. to inundate email recipients with this additional hurdle, so it works both ways).

  is there a certain expectation around read receipts for internal email?

Expectations are not always set in stone. In this case I suggest that, if you do not typically comply with read receipt requests, that you get into the habit early on of not doing that. Over time, people will know that "Oh, yeah, AegisCruiser never bothers with that when I send emails to them!"; some will respect that, and others will get annoyed. Having said that, if you come across some, for instance, powerful administrator at your institution, and you know that they want you to utilize the read receipt, then it's probably better to comply, or, if you cannot tolerate that, stand your ground and see what happens, possibly having in mind some other opportunities should the need arise.

Since you mentioned that you are working in the US:

As a side comment, I suggest that you do not contact the parent of your student directly, since this may violate FERPA rules: it is my understanding that, if a student has FERPA-ed their details, then we instructors are not allowed to confirm with anyone that an individual is a student in our course/enrolled at our institution. In this case, I suggest discussing with your department head how best to proceed.


How to deal with potential data falsification?

In science, a lack of reproducibility leaves you all on the hook. But, I would probably recommend getting a third expert in Monte Carlo to review the code. I'll assume this is you.
First, it can be the case that a small change in code makes big differences, permutation testing for instance can do this. But, you can run the simulation lots of times, look at the results, and find what quintile the original results are in. This corresponds to a p value for falsification, or as I will call it: a possible mistake.
Nonetheless, Monte Carlo is not very complicated, and in the paper regardless you will have to explain how the answers were obtained. If you cannot do this, you cannot push paper into community. So, inspect, conclude, rework.
For their sake, I hope falsification is not the case. That's a very very ugly way to go about research, and it will crop up.


Do I publish a paper independently or ask a professor to mentor me?

First, you should assure yourself, and then again, that the work is correct by the standards of your field. It is this point that requires insight into your topic. You know best by yourself whether you need a mentor or not.

Second, you need to 'sell' your work. This point does not require expertise in your particular niche, but it can benefit from knowledge of people in your discipline. This includes aspects such as Academic English, Writing an Abstract, Writing an Introduction, and so on. Maybe there are some trustworthy (!) persons in your discipline that could proofread it for you?


How does one choose which articles to cite for a very broad sentence?

Either none at all if you can assume that the most likely audience of your publication is aware of that as if it was a basic fact of life.
Or recent reviews that provide a wide overview of Gaussians used in mathematics and/or statistics.
I searched for TITLE: (Gaussian) AND DOCUMENT TYPES: (Review) AND YEAR PUBLISHED: (2015-2021) in Web of Science. The query led to 56 results, many of which have accrued considerable citations and thematize mathematical or statistical issues. Perhaps you could do a similar search and pick some suitable papers to cite.


Can I ask potential advisor what topics he is currently most interested in?

You could ask, but it would be much better to arm yourself with knowledge to facilitate asking a better question.  Do your homework and search for his recent publication record, and find and read the recent results.

So yes, asking "what are you doing now" will reflect somewhat badly on you.  Saying "I'm aware of all your published work, and wonder if you are looking into any new directions that aren't published yet" sounds (and is!) much better


Data sets of academic conference budgets

Based on my experience as a conference organizer, there are only two sets of organizations likely to have this information:

Professional societies, such as IEEE and ACM, which require their sponsored conferences to make budget reports as a condition of sponsorship.
Funding agencies, such as the US National Science Foundation (NSF), which have explicit programs for sponsoring meetings, and which therefore require reporting on how those funds are expended.

No other organization is in a position to compel systematic reporting (not even universities, unless they are managing the conference accounts), and thus conference organizers will not in general report it anywhere else.

Neither funding agencies nor professional societies are likely to give this financial information out willingly, since it is financial---though you never know what you might get if you ask the right people nicely enough.  Government agencies like the NSF, however, have public reporting requirements and may be susceptible to data gathering via requests for records release, under FOIA in the US or its equivalents in certain other countries.


I was a full member of both IEEE and ACM in the past year (2014). I tend to like ACM. The CACM seems to have better quality articles and they are more CS-ish compared to IEEE which I felt are more CompEng-ish. I also prefer ACM because they send more meaningful mails and less spam compared to IEEE. For instance, ACM will send you a customized list of articles based on your interests.


Unless your journal, advisor or institution insist against this (which we cannot know), yes, you can.

I have done this myself in publications and nobody complained.


Should I mention the mutual acquaintance who recommended me to a professor in an email?

It's a good idea to remind the prospective advisor of who you are (namely "prospective student that colleague X recommended"), but doing so in the subject line might be overdoing it. I'd suggest writing that reminder in the first line of your email, since most people seem to read emails using applications that will display the first line, even if they don't open the email. Also consider cc'ing your referring professor on the email.


How to properly include research papers that are still not published in a curriculum vitae?

Work in Progress is good and it  is good to have such a section.
You can also annotate each paper title with the expected time to (or of) submission. "Submission expected in December 2020", for example.


Is it common for PhD programs to require students to have a minimum number of papers to be eligible for the defense?

Publishing papers is not a requirement in many places, but it usually depends on the specific university and graduate program. In the U.S. these things tend to vary from school to school. Sometimes research projects funded by industry prohibit the people involved from directly publishing results.

As for a world record, I'm pretty sure nobody keeps track of that. It is pretty subjective. How would you determine whether or not the paper is from your thesis rather than just being in the same field? There shouldn't be that much value in the number of papers either.


Writing sample requirement for PhD application - submit something you assisted in writing?

Would it be okay to submit a portion of this as a writing sample for my phd applications?

Yes. (Personally, I'd submit the whole paper.)

Or is this not allowed since I'm just a research assistant and not a
co-author?

You should make the circumstances clear, e.g., the seed idea was the professor's, the literature review is yours, your literature review influenced the concept of the paper, you wrote 80% of the material, and anything else that's relevant.

Also, the paper is meant to be submitted to a journal for publication so will it be illegal for me to submit a portion of it as a writing sample?

Sharing preprints is fine.

I will definitely not send the results sections.

You can send the results section. If there's concern over IP theft, just make the entire paper available as a technical report.


How to find past editors and editorial board members of scientific journals?

Check the journal's past issues, which will usually come with a page that says who the editorial board members are. If you can't find it online, get it from a print copy.


Leaving a Master's Degree Early for a Doctorate Degree?

If you're in your last semester, the best path forward is to finish your MA thesis. Your dissertation does not need to follow directly from it, particularly if you're studying in the social sciences.

Finish the thesis for a few reasons. First, finish it for the MA degree. You've (presumably) paid for 3 semesters of coursework. Failing to finish would mean that, essentially, you've wasted the past three semesters. Second, finish the thesis for yourself. In 20 years, you won't care a whit about your strained relationship with your mentor, but you will care that you saw the program through, even when the going got tough. Third, finish the thesis so that you don't have to explain it in the future. People will wonder why you failed to finish your thesis, and it might cast doubt on your ability to stick through tough/challenging projects. Academia is a small place, and you don't want to be known as the guy who didn't finish his master's degree.


Doing Math Research in a "non-mathematical" environment

The proximity of a large university can be a big plus.  Here are some things you might find helpful:

Get in touch with the people in your field there, telling them you are in the area and are interested in keeping up with mathematical activities in their department.  Ask to be added to their mailing list for seminar announcements, etc.
Try to arrange your teaching schedule so as to be able to attend seminars at the big university at least occasionally; regularly, if possible.  If there is dinner after the seminar, try to go.  Talk with the faculty (and the visiting speaker) and look for shared interests, that might lead to things you could collaborate on.
See what kind of access you can get to their library.  At minimum, you should be able to walk into their library and use MathSciNet, read books, download papers from their journal subscriptions, etc.  You can probably also arrange borrowing privileges, and possibly remote access, either as a member of the general public (maybe for a fee) or as a professional courtesy based on your affiliation with your own institution.  The university's faculty in your area might be able to help if you run into bureaucratic hurdles with this.

Also, don't discount your own institution's library.  Even if they don't have much in the way of books and subscriptions, it is very likely that you can get almost anything you want via inter-library loan, albeit with some delay.  Get to know your professional librarians.

And a note regarding funding: it's not unusual for conferences to have some travel funding available for participants.  (This is more common for smaller specialized conferences than for big general events like the Joint Math Meetings.)  Fresh PhDs like you usually get first priority for this, so try to take advantage while you can.


Can co-authors disagree in their own paper?

It is rather unusual, but it has occurred before. In the paper

  Piccione, Michele, and Ariel Rubinstein. "Equilibrium in the Jungle." The Economic Journal 117.522 (2007): 883-896.

each of the authors has their own conclusions, marked "4.1. Concluding Comments by MP" and "4.2. Concluding Comments by AR." It should be noted though that the writing in economics tends to be less structured (no such thing as a "method section") and this is a somewhat unconventional paper to begin with.


Postdoc project with poor scientific content and unlikely to lead to publications

I think that the more you stay in the position the more you’ll be trapped into it. I see in the comments that you are at a national laboratory, so I understand that the salary might be tempting and that’s not easy to give it up. However, from a long term perspective, you could lose an opportunity to flourish and to get known. Plus, how long is your contract, 2-3 years? None or few publications could harm your chances to stay in the field, particularly if you want or have to move to another lab or university. It comes down to choosing between being well paid today or increasing your chances to be successful in the future, unless you think you can change your situation without leaving.


Is there a reason a TA and a professor may have to travel together?

In most cases, a teaching assistant would not have any reason to travel with their professor, since their responsibilities are around teaching. Perhaps if the class was an expedition for field work in an archaeological department or something (I think I have heard of a department doing this), but then it would have all of the students as well.

A research assistant, on the other hand, will often travel to a conference with their advisor, if they have a paper or poster to present. Thus, to me, the most likely case for a teaching assistant traveling with a professor is if they are also supervised in research by that same professor.


How to be more interesting to prospective PhD advisors

You probably don't need to do much if they have already expressed interest. However, if you want to do more, read a few of their papers so that you are thoroughly familiar with what interests them. That should suggest at least a question or two. I think that questions are more useful to you than statements.

You can ask about funding, but the easiest question to ask is for who you should speak to about funding if not themselves. This lets them know you need it and also lets you contact whoever is responsible.


Talk to people. Here, elsewhere on the internet, but most importantly in real life, whether it's with people from your program (if you feel like opening to them) or at a local discussion group or whatever. Don't isolate yourself.
Recognize what you are experiencing: describe its symptoms, put a name (or names) on it, identify it. Recognize that it is quite common, and that there are solutions.
Make some time, even if it's not much, to do something else (vacation, volunteer work, some time with family, …) to put things in perspective. This should help you evaluate your overall goals, and decide what you are willing to do to achieve them.
Talk to key people involved (advisor, your boss at the company), and let them know in a professional way that you have hit a bump in the road.

From you post, it sounds to me that you've made a great deal of progress on that path already! You'll get through that hard time, believe us.

I'll maybe add something more personal, regarding the “if I quit, I wouldn't get promotion” part: advancement in your work is not the ultimate goal, it is only worth pursuing if it makes you (and the people around you) happier, directly or by achieving other goals. If it makes you miserable, you have to realize (and accept) that failing is an option.


Part time industrial work during a mathematics PhD

I think it would be very challenging and unusual to work part-time at a job and be taking graduate classes or doing thesis research.

But it's quite common for graduate students to work full-time (as interns) at government laboratories or in industry during the summer (or at another time of year) for perhaps 3 months.  Mathematics students I have known have worked at

Google
Microsoft
US Dept. of Energy labs (Sandia, Los Alamos, Livermore, Oak Ridge, Argonne, etc.)
Oil companies (Schlumberger, Total)
US NSA contractors (cryptography)
US Geological Survey
NOAA

and many other places that I've forgotten.  Talk to your advisor and to other faculty in the program.  Your university may also have someone who coordinates these things.


Should I report I might have been snubbed from a paper even if I don't have means to substantiate it?

Unless you outright had years of valuable work stolen out from under you that imperils your future career in your field, and you have strong proof of what occurred that would establish to an outsider that clearly something very seriously wrong was committed (way, way past a snub), I'd "count your blessings". From the sounds of it, you have made a clean break from the field, the lab, and most (or all) of the people. There's no huge ethical issues with the paper itself (no fraud, abuse, etc), so you don't have to worry about guilt by association.

You don't need letters from them, you don't need to collaborate in the future, you don't need to even see them passing down the hall. It really sounds like an amazingly good outcome, with the worst-case scenario being you didn't get co-authorship on a paper no one particularly cares that much about. And demanding to be removed from the acknowledgements would make you look like a bit of weirdo, from an outsiders perspective - "give me authorship or don't acknowledge me at all", honestly, will not give anyone a good impression of you to anyone. No upside to be had.

As of right now, from an outsiders perspective, it sounds like did reasonable work as an undergrad, and moved on. You were a bit unresponsive (not checking email for a month tends to be uncommon), but quite understandable given the big changes - though it would not have been cool to be aware of pending collaboration and not even tell your collaborators you are not going to be "online" or reachable for weeks on end. People in the lab may have been disappointed that you weren't more interested in continuing the project to publication, so it sounds like there was some miscommunication, misaligned expectations, and you weren't all on the same page as to where you stood on the project now that you graduated and moved on to something not strictly related. I don't know what conversations you had together, so we can't determine if someone was just being demanding or if you had indicated interest in continual involvement but then effectively didn't follow through. Not our business, but something you might consider for yourself.

Given the lack of major downside, it would be a great opportunity to learn how you might avoid a situation like this in the future, because you'll of course eventually move on from your current position and most people don't perfectly have all work tidied up and permanently finished when they leave. Reflect on how to set clear boundaries, avoid making promises (expressed or implied) you aren't dedicated to following through on, set clear limits to what you are agreeing to, communicate your availability to collaborators, have direct conversations with people to ensure everyone has matching expectations, etc. These skills will be invaluable to your future career, so no time like the present to improve on them, learn from past experience, and build up to a more happy and productive future.


Best aspect ratio for conference presentations?

In the following, when talking about displaying a presentation with a certain aspect ratio on a projector with a certain aspect ratio, I always assume that the presentation’s aspect ratio is preserved and black bars are added at the appropriate sides. Never have the projector digitally warp your presentation: It destroys hinting¹ and may make fine lines invisible.

The best aspect ratio is the one of the very projector you are presenting on, as you can make best use of the space. In particular with projectors, you do not want any content to be unnecessarily downscaled as their resolution is very low to begin with and the projection area may be rather small (and thus difficult to see for the audience). An okay 16:9 presentation may be rendered unreadably small, if displayed on a 4:3 projector.

Now, depending on your presentation and how dynamical you program it, adapting to a different solution may be a rather simple thing with Beamer (apparently in contrast to Powerpoint, going by the article you linked). I once changed a presentation of mine from 4:3 to 16:9 in about half an hour, and this included recompiling complex animations and a lot of perfectionism – a “normal” presentation could be adapted much faster.

If you do not want to adapt, the choice essentially depends on the average age and purpose of projectors in your conference venues (I would guess that newer projectors or projectors mainly used for movies are rather 16:9). Thus it depends on your field and probably also your continent. Anyway, most projectors I have encountered so far had a 4:3 resolution and most of those who hadn’t had a resolution very close to it. I’ve only encountered a single 16:9 projector. I thus use 4:3 as the default.

¹ To give you an idea, the following shows this sentence as natively rendered by my computer (with hinting) and the same text digitally stretched or squeezed:


Submission of survey paper and graduation thesis almost in same time

This is ultimately up to the journal to decide - so you should contact them/consult their guidelines. I cannot imagine any scientific journal treating a thesis (PhD or MSc) as a prior publication, but this might be field dependent. In any case, you should explicitly write in your paper "This chapter is based on the author's PhD thesis to be defended (...)" or something to this effect, and I would think that this will be enough for the journal.


Providing additional material for a paper in external source

Short answer: it depends on the publisher/conference organiser.
Unless there is a strong reason not to, ask them.

It is quite common to host additional material on a website.  Generally speaking, though, the paper should stand on its own, and any background reading and data visualisation should not be necessary to follow the narrative. Imagine an interested reader would want to see some more material after reading the paper, but not need it to understand everything.

On the other hand, if there is no need for it at all, then it is best to not even refer to it - by referencing an online resource you commit to maintaining this, keeping the same URL and so on, and a strong, self-contained paper is always nicer.


How to write a recommendation letter if you are not sure about its appropriateness

Decline on the grounds that, indeed, you've worked too little together.

However (and actually adding to Peter K.'s answer), a discussion in order to understand why they chose you might be useful -- meaning that usually one asks for recommendation from people with whom they've worked longer. If their background and intentions don't seem suitable, maybe also tip them that another career path would be better?


What does it mean when someone says a discussion section is not "well-developed"?

If the reviewer says the Discussion section is not well developed, it suggests you either need to cover more of the elements that go there or go into greater depth on the things you do say there.

Carnegie Mellon has a nice handout about what different traditional elements of a paper should contain.

  Discussion sections contain the following moves:

  They summarize the main findings of the study.  This allows readers to skip to the beginning of the
  discussion section and understand the main “news” in the report.
  They connect these findings to other research
  They discuss flaws in the current study.
  They use these flaws as reasons to suggest additional, future research.
  (If needed) They state the implications of their findings for future policy or practice.

Further, if the Results section does not comment on the results, such as attempting to explain them and evaluating whether the results support the hypothesis, then that should be part of the Discussion.

Finally, as henning recommends, let a trusted colleague read the paper and ask for their suggestions for improving the discussion section.


Are racist/xenophobic opinions sufficient to revoke tenure?

There are four common reasons for tenured professors to be fired:

Incompetence. Used here in the more general sense of the word, it means that if the tenured professor is no longer able to carry out his or her duties - for example if he or she becomes vegetative after an accident - then they can be fired.
Negligence. If the professor is able to do the work, but does not do it, then it could qualify as negligence. For example if the professor decides to go on vacation during semester, thereby leaving the students without instruction, he/she could be fired.
Immoral conduct. If the professor sexually harasses a student, commits a (serious) crime like robbery, or violates academic norms (e.g. plagiarism), he/she could be fired.
Financial exigency. If the university runs out of money for whatever reason, it can fire professors.

Holding unpopular opinions don't come under any of these four reasons. The most one could argue is that it's immoral, but that would be hard to defend since not everyone agrees that racist/xenophobic behavior is wrong. After all it was pretty common to have racist/xenophobic behavior in the past or even today.

But: it has happened in the past. Professor Edward Ross of Stanford University was effectively fired by Jane Stanford, one of Stanford's founders, back in 1900. Ross expressed some violently racist opinions of Asians. His firing was controversial, and he was defended by many academics who viewed the dismissal as arising from political reasons and therefore a violation of academic freedom. You can read more about it in articles like this one. I would venture that if Ross lived today he'd be less likely to be forced out, but it'd be within the realm of possibility, and regardless of whether he's fired or not it would still be controversial.


Grad school in science that takes non-scientific applicants?

Speaking for the US and as someone with undergrad degrees in the humanities who is now doing a PhD in the sciences, it is hard, but not impossible to make the transition.

First of all, your best bet is Masters programs. Unless you're somehow exceptional (or maybe just very well connected), you'd be hard pressed to find a PhD program to take you when you're completely unproven in an area. However, to start out, there are transitional programs out there (Boston University's LEAP program for engineering is one) to help students move into a science field. Ask around and search online; I'm sure there are at least a few others.

You can also take non-degree courses at local universities to build up coursework in your desired field. For those, most schools don't much care about your background as long as you're paying them. Once you've built up enough background/understanding in your field, you may have some luck applying to Masters programs. I've seen other questions on this site where folks have posted schools that accept students to Masters programs in the sciences despite non-science backgrounds. I'll edit this answer if I can find some examples.

Additionally, once you've built some classroom credentials, you may have some luck trying to work with a professor in his/her lab. Even if you're not a matriculated student, I know of at least 2 faculty who have taken on lab assistants from outside the university. It's not common, but it is possible.

In summary, it's possible, but it will take time, probably some money, and some dedication to make the change. You'd probably have trouble getting in anywhere with zero background, but with some patience you can build that background and get your foot in the door. Once you have that, it just depends on how far you want to go with it.


How to avoid thinking about research in free time?

I agree with @PeterJanson's answer, but I'd like to add my 2 cents on it:

Often, I find myself "constantly" thinking about a problem when I'm stuck or I'm not sure how to approach it.  Often, it's because I've got tunnel vision on the problem.  That is, I'm only thinking about it from a limited number of perspectives and can't think of other possible approaches to the problem.  I used to spend long hours thinking about a problem (even outside of normal work hours) without ever really getting anywhere on it.

When that happens, I find it's good to pursue other activities that stimulate my brain to think outside of the box.  That could be anything from reading semi-related research papers to playing video games to engaging in stand up comedy!  When I challenge my brain to approach other problems from new perspectives, I find those same skills help loosen my brain to engage in research in new ways as well.

While I never really stop thinking about research, I find these other activities help me engage in research with fresh eyes and renewed energy.  And ultimately, that has lead me to better research results and liberates me from "overthinking" the problem during my leisure time.


Is it appropriate to contact professors after application submission?

After reading some of the other reponses to your questions, I feel I need to give you fair warning that we receive tons of these emails, many of them obviously scripted (e.g., my name is in different font, the area described is irrelevant to me, for female faculty the email starts with "Dear Sir," etc.) My default reaction is to delete. Mind you, this is not to say your email would be like this, I'm just letting you know what you're up against.

The only emails that I try to pay attention to are of two types:

1) There's something obviously strong about you by just quickly scanning your email: You are an undergraduate student from a top school, or your grades are super-strong, or you've done some interesting research, or it's obvious that you've read some paper of mine and have legitimate comments about it.

2) Your subject line reads: "Undeterred prospective student." This is actually at the bottom of my info page for prospective students, which is linked to prominently on my home page. The vast majority of email requests I receive is from students that didn't bother to read it, so when I get an email with that subject I make a point of looking at it.

This is irrespective of when I receive your email; in fact, one could argue that the closer to the review period, the better.


Should remote teaching sessions be shorter than classroom sessions?

If you search using Google or another search engine for something like "research on maximum effective lecture time" you will get some ideas. In general, long lectures are less effective than short ones because of the student's attention span. Video lectures should be very short, say 10-15 minutes for effectiveness. And with required activities at the end of each short session. So, a long "lecture" can be presented as a sequence of short but complete segments. Real time is a bit different, but keep all of that in mind in course design.
But it really depends on what you and the students are doing in the given time period, rather than the length itself in any absolute sense. A talking head writing on a board or (worse) showing a bunch of slides gets old and boring very fast. If the students have a chance to break it up with questions or some problem solving activities it is better and the class-period can be longer and still effective. Class discussion sessions is another way to break the monotony, but harder online and nearly impossible with video unless there is an effective communication channel shared by every student.
I used to teach a couple of courses that lasted all day and only met once a month. But the face time was usually broken up into small segments and we used very effective, but simple, communication tools so that students could "engage" with the course and the instructors (two of us) at any time through the period between face-time sessions.
The key is to keep the students active and engaged. Once they lapse into passivity you are lost. Some students have the skills and background to keep themselves engaged in sub-optimal environments, but not all do. Perhaps not even the majority.


Is it appropriate for a PhD candidate to publish a book?

I think it's a very good idea to develop files/manuscript collecting important standard results in one place. To go to the additional trouble (which is much more than one might imagine) of publishing a book with that content, apart from vanity presses, would not be worthwhile for a young academic. Indeed, unless you can do a for-some-reason amazing job of organizing things, since you're not an established expert, have (presumably) no name-recognition, etc., good publishers would not see much reason to publish your book.

But you can assemble a PDF document and put it on-line. And you can revise it as you mature into your subject. Revision is much harder with physical books, or even official "e-books", because many publishers (especially better ones with an established base and style) re-typeset everything into their house style... so correcting typos is not a matter of correcting them in the TeX source, re-typesetting, and re-posting online. :)

EDIT: to clarify the last sentence: Yes, TeX is the current professional standard for mathematicians composing technical documents. It's a mark-up language created by Don Knuth, and donated to the community, in the late 1980s. (There are also WYSISWYG editors.) The older process of typesetting from TeX source documents created a "DVI file", device-independent file, from which postscript files were usually created, although there were DVI readers also. Nowadays, the usual output is PDFs. Further, although years ago it would take several minutes to re-run the typesetting after making changes in the TeX source, nowadays re-typesetting a 30-page document takes an imperceptible time, perhaps a second or two at most. And there are of course various ways of packaging the re-typesetting (as well as creating the TeX source file) in IDEs and so on.


Should you cite a summary in the introduction that's based on information to come?

I think this depends on the technology you are writing about. For some cases, the advantages might be well known (Example: computers make it easier to do calculate complicated things) and would not have to be explicitly "proven".

If the benefits are not as perfectly clear in your field, you should definitely include a source on them. If you cannot find one which includes all of them, try to verify them indivually by providing a source or explaining why you consider them advantages (list reasons).

In case you show them to be benefits later in the paper, mention that you will do so later on. This clearly isolates them to be part of your work rather than a prerequisite.


I have an unfinished translation of a speciality book. Should I write this down on my CV/SOP?

Unfortunately, most hiring committees would at best ignore this contribution and at worst wonder if you allocate your time wisely.

The work of translators is (unfortunately) given little value in academic communities with the exception of the field of literature and even there it is deprecated. The rationale is that the work is not the result of independent research nor does it add any intellectual value -- it is inherently wholly derivative.

There might be some association of value if your translation had been finished, published by a reputable scientific publisher in your country, and you had been given awards or otherwise acknowledged for providing an important service to your community.  But even then, there is a perception of someone as being "just a translator" that is hard to shake off.

Note that Famous People® are allowed to do translations and be recognized for it, but Famous People® have latitude in their work that non-famous people don't.

At the very worst, a committee might worry that the fact that the translation is unfinished and that you have put effort into doing something with little recognized value means that you don't allocate your energy and time wisely, and that you are not capable of independent research.

The same also applies for authoring textbooks. Textbooks are also seen as inherently derivative and while they make the publisher and author money, are not indications of original scholarship.

At this point in your career, you want to be seen as the generator of original scholarship.


To what extent do monetary incentives encourages researchers to publish in ISI Journals?

What is the status in your institutes and to what extent do you think payment for publication encourage researchers to work more seriously?

I've never worked in an environment with payment for publication, so my impressions are based on observing it from the outside.  I'm sure it encourages publishing more papers, but publishing more papers is different from working more seriously:

Publication payments encourage mediocre submissions, since success is defined by having a paper in a certain type of journal, regardless of how good or bad the paper is.  In many cases the optimal strategy is not to work hard on writing a few excellent papers, but rather to write as many mediocre papers as possible and then submit them repeatedly in a search for lenient editors and reviewers.
In addition to the quality issue, payments per paper create an incentive to break work up into least publishable units.
Publication payments complicate coauthorship decisions, based on how the money is awarded.  If every coauthor receives a fixed amount, then it creates a financial incentive to add honorary authors.  On the other hand, if a fixed amount of money is divided among all the authors, then it creates an incentive to remove less important but legitimate authors.  (And if it's just the "first author," then that magnifies the importance of who that author is.)  Either way, authorship is being decided based partly on financial pressure, rather than intellectual contributions.

Of course, all these issues are already serious problems in academia, with or without publication payments, but adding direct financial incentives just makes them worse.  In addition, using a fixed formula heightens the tension by removing ambiguity.  With hiring, one might worry that hiring committees will count papers instead of judging their quality, but at least some of them will prefer two great papers to five mediocre ones.  By contrast, the incentives with publication payments are unambiguous, which strengthens their effects.


What are the major ethical concerns with private tutoring?

You seem to have a pretty good ethical sense based on your question, so I think you won't go far wrong following your instincts.

But if you have the opportunity, it is a good idea to go visit the prof teaching the course for which you are tutoring and ask for any additional general guidance.

It is usually a good idea to answer "trivial" questions with other questions. "What do you think the answer is? Why? Explain your reasoning." That sort of thing. Often the student will get a flash of insight. But if you can point to a flaw in reasoning you help the student without giving direct answers.

Good professors when asked questions by students seldom give out complete answers unless it is in the context of a continuing conversation. Instead, a "minimal" hint is given to get the student over a block and which lets them proceed. If a student repeatedly has problems with the same issue or block, an additional exercise will be given that tries to give the student practice with the reasoning.

But the technique of asking for an analysis of any issue that leads to a block is a good way to diagnose the student's thinking and help them get over it.

Giving students general problem solving strategies is also good, but probably less useful, as it doesn't usually have a diagnostic element. But even "Where did you look for an answer?" can help. Especially if followed by "Where else could you look?". You could then suggest other sources if appropriate.

I'll note for completeness that some students are misled by the resources that they use. Some of those resources are wrong and some may be written poorly leading to ambiguity. I've had students get in terrible jams by using perfectly rational thought processes applied to bad input data. That is rare, but it can occur.


Is it self-plagiarism to summarise a topic in the introduction of two of your papers using similar references and examples?

As you have stated, your papers have similarities and that the text is written separately and not copied, then no, this is not plagiarism (and is unlikely to be seen as such).  Using the same references is fine and necessary for similar concepts.

It also sounds like the context between the two papers are distinct, this should ensure that the two papers are written differently.

Make sure you re-read and compare them to ensure that they are sufficiently different, which you sound like you have already done (and possibly ask a colleague to compare them). If possible and relevant, you could have one of your papers cite the other.

There are many guides about plagiarism and what to check for online, for example, this one from the University of Western Australia.


Developing both Applied and Theoretical Interests

Short answer is yes you can. Now, how/why do researchers change directions? Many reasons;

Chasing different funding/proposals venues.
Being part of a school or department where interaction of professors and available lab equipment can lead (with time) to you redirecting your research.
When advising students for MS/PhD or being a part of search/research committees, one tend to think outside the box (outside of his research area) and incorporate different methods/ideas
You learn more new stuff with time! Remember that a PhD in subject X does not mean that you get to work in X for the rest of your life. It simply means that you know X (in details) much more than other people (or professors).


Academic pipeline: How many papers should you have under review?

You're simply asking the wrong question.  Your goal should be to do the best work you can, not the most — quality, not quantity.  One revolutionary paper is worth far more than dozens of incremental papers that nobody reads.

To put it another way, if you find yourself submitting so many papers that you're worried about being overwhelmed, you're doing something wrong.  Aim higher.  Publish fewer, bigger chunks of work.  Spend less time writing and more time thinking and digging.  Stop just writing papers and develop a research program.  The CV bullets will take care of themselves.


Is the journal indexing by SCOPUS meaningless?

Scopus is quality-curated, i.e. getting indexed by it is not meaningless.

However, it is not as selective as the Science Citation Index, which remains the gold standard.

Therefore you are better off publishing in a SCI-indexed journal if you can. Arguing with your professor is unlikely to be a good idea in any case - they have much more experience than you and will have a better idea where to send your manuscript.


Which license should be chosen in arXiv for reports and preprints to be published in Elsevier?

Is the "preprint" considered a derivative work of the "report"? Is the "postprint" considered a derivative work of the "preprint"?

This probably needs a lawyer to answer definitively. Needless to say, I am not one and cannot give an authoritative answer to this question.

My experience suggests that academics and publishers often treat the preprint and "postprint" - or, in general, different versions of the manuscript - as effectively the same work for copyright purposes (e.g. copyright transfer agreements make a point of addressing what the authors are allowed to do with preprints), even though, strictly speaking, I don't believe this is supported by US copyright law.

If one is to consider the preprint and postprint and other versions as separate works, it seems much more plausible that the postprint would be considered a derivative work of the preprint, rather than the other way around. The argument that a derivative work could be created before the work it is derived from is questionable, although I suppose some odd things of this sort are legally valid, so I can't say for sure.

  Do the authors of the "report" and "preprint" still hold copyright on each of them (despite the copyrights of the postprint have been transfered to Elsevier)?

I suppose this depends on the legal interpretation of the copyright transfer agreement.

The passage you quote, which answers the question "Are you asserting copyright over preprints?" with "No....", suggests that, as Elsevier sees it, the authors retain ownership of copyright in the report and preprint.

  In case of yes, does it means that ANY creative commons (CC) license (CC:BY/4.0, CC:BY-SA/4.0 or CC:BY-NC-SA/4.0) can be applied to the "report" and the "preprint"?

Well, at the time the report and preprint are uploaded to arXiv, the authors are indisputably the copyright owners and there are no other legal conditions that might interfere with applying a CC license to the preprint. So of course the authors can choose to apply a CC license. If they do, in principle, Elsevier could refuse to accept the manuscript for publication; or, if they do accept the manuscript and later find out that a preprint had been uploaded to arXiv, they could argue that the author executed a copyright transfer agreement under false pretenses and the agreement should be voided, or something of that nature. I can't say whether they would actually do this in practice.

Elsevier's sharing policy says

  Authors can share their preprint anywhere at any time.

That means that authors can upload their preprints to a server, and one would hope it implies authors can also grant the server operator the rights to further share the preprint with readers. It's not clear whether Elsevier's policy allows the author to grant others the right to prepare derivative works, which would be (legally) required to upload it to a site like arXiv which distributes preprints under a Creative Commons license.


Ok, lets look at the core issue here (in your and my mind at least): publications and future paths; and then your question.

Lectureship in the Horizon?: This is a touchy subject, and I'm sure academics get divided on this one. However this is a fact: how many postdoc students did you witness with a weak publications who could get a good lectureship position. So the conclusion here is you need good publications to survive and progress as an academic.

Postdoc Isn't the Holly Grail!: This is another one of those time wasting adventures of people who did not think right about their abilities. What environment are your looking for? If you are looking for a perfect environment so you can keep publishing new articles every couple of months; let me tell you it does not exist. Rather, your ability on writing your ideas and contributions are only in your hands. Now if for some very good reason you couldn't publish much during Ph.D. then your new postdoc position could be another story; however if you did your Ph.D the best you could and you still struggled to publish 3 good papers; then let me tell you do not waste your time and energy on doing a postdoc.

Conclusion on the first two points: If you know why you want to continue research after doing a Ph.D., you better understand the importance of publications. If not, you are just wasting your time.

Visiting a Group: Of course you can visit a professor and his/her research group; however two things here:

1.Who Do You Know?: If you know the professor then send him/her an email and request a visit. If not who your supervisor know, so you can go and visit? Other than that, unfortunately people simply ignore those emails.

2.What Will You Provide?: What will you provide to the group you want to visit. Are you going to a group lets say in Glasgow, just to see Glasgow or you want to go there to collaborate? What you want to provide to them? Will you create an unfriendly environment for them and moan about your Ph.D. thesis or you go there for research? You see what I'm trying to say here? This again goes back to the first point that people usually can visit another group, when the professor knows the person first hand or second hand but from the very good source.


What's the proper order for multiple educational degrees/certificates?

Questions over titling are almost always a matter of local convention and personal preference. You can read more than you wanted to know over at Wikipedia:

https://en.wikipedia.org/wiki/Post-nominal_letters

A few rules of thumb:

If you're naming someone in a friendly context then your biggest concern is usually etiquette rather than technical correctness. If someone insists on being called "Jane Doe, PhD, MD" rather than "Jane Doe, MD, PhD" then it would be incredibly rude to object to them. Most people would not care, but if in doubt you should ask.
If you're establishing the credibility of someone, such as in a piece of journalism, then you list only relevant degrees starting with the highest degree. Even if multiple degrees are relevant it's likely that one degree will be most relevant.
If you follow the cite note for US degrees in the Wikipedia link above, you'll eventually get to this page, in which a protocol expert says that this is the appropriate order, with ties within each category being broken alphabetically:

1) Religious orders
2) Theological degrees
3) Academic degrees
4) Honorary degrees, honors, decorations
5) Professional licenses, certifications & affiliations

Don't list degrees that have been superseded by another degree. That is, don't say "John Doe, PhD, MS, BS" because the MS and BS degrees have been eclipsed by the PhD.


How do advisors typically apply pressure on PhD students to get work done?

I am interested in starting a PhD, but nervous that there will be long stretches where I will not have to submit progress or there might not be much pressure for me to get work done.

Congratulations for having identified one of the major differences between research projects on the PhD level and earlier levels even before starting a PhD! In my opinion, dealing with problems on your own and without real pressure for weeks ore maybe even months is really a characteristic feature of PhD research. One of the competences which you should acquire before the PhD degree is to go through such phases successfully.

That said, there's of course different types of support (or pressure, if you prefer to call it so) from your supervisor and your fellow researchers, mostly your supervisor's group or collaboration partners.

Your supervisor may ask you or suggest to submit a paper to a specific conference, which has a submission deadline.
You may be involved in a collaboration project, where regular meetings with project partners take place, and a presentation of the latest results will be expected.
A third-party funded project may require regular reports on research results, which you may be asked to provide if you work on that project or a related topic.
Many groups have regular meetings where people discuss their latest research results. You'll be expected to contribute some results of yours from time to time.

But of course, how much pressure is built up by such expectations varies from place to place.
Also, a difference to undergraduate research or coursework is that consequences usually do not come immediately if you fail to "deliver", but will only be visible on the long run, over the course of one or two years maybe.

Generally, I'd say that a young supervisor with a growing group will put more pressure on you to deliver research results than a more established researcher with a large group, because the young supervisor depends more on your results for his own progress, and should have more time to work with you closely.

Also, the group you're involved in matters a lot, because discussion with colleagues stimulates research ideas, and also puts you into a mode of "having to deliver something". Check a potential group for jointly authored publications (not only PhD student + supervisor) to get a feeling for how active it is in terms of collaboration. The latter point is especially important for a large group with an established senior supervisor.


Could a teacher or the university be legally liable in this situation? In which countries?

The questions seems purely hypothetical and a bit recursive. If a country has repressive laws, as some do, then it could well be that discussions of breaking the laws, even unjust ones, could lead to legal jeopardy.
A strange story recently came out of Thailand, where a person was threatened with jail for leaving bad reviews online about a resort. Saying bad things about Royalty there is very dangerous and so, I would guess, would be discussions of breaking such laws. Not to single out a single country, though. And, while the story is "strange" to me, as a US person, it might seem totally normal to someone else.
When laws are unjust, who can say where it ends. You can't depend on free-speech guarantees unless there is at least a strong societal norm protecting them. And even then, some people are willing to break norms, as I'm sure you can notice all around you.
Was it once true in the US that discussions of ending slavery were forbidden in some jurisdictions? I seem to recall that it was.
In any case, if a jurisdiction has unjust laws, making discussion of breaking them illegal might well be an additional unjust law. Unjust laws all the way down.


Is it wise to choose a better journal with lesser number of similar papers?

Ask colleagues more experienced than you, ideally colleagues with experience of submitting to those journals, what they think of your chances.

If there is a question of whether your article fits in the scope of a journal, you could also ask an editor whether they would welcome a submission such as yours.

Usually, though, it will end up being a judgement call. You could, of course, submit to your top choice, and then go with the other one if your paper gets rejected. This is quite commonly done, even if the top journal is a long shot. However, this takes a lot of time and effort, and in my opinion it is often not as good a use of your time as getting something punished quickly and moving on to new work.


Details to include on the cover letter for sourcing part-time tutoring/marking positions

Key things to include are

Relevant experience - such as tutoring, teaching, marking,
Educational achievement - you have a PhD, presumably this is in a field related to the field in which you will be marking/tutoring,
Other experience relevant to the role, e.g. working with students in any role such as mentoring, personal development, group work, and
Some evidence-based statement relevant to the proposed work.

For number four, this is an opportunity to show that, for instance, you are able to work alone or as part of a team, that you are able to work to deadlines (important for returning marked scripts), and that you have excellent written and oral communication skills (important for feedback). Your comments in this statement must be backed up with evidence drawn from your past experience, work or training.


What format should sources be cited in a thesis Literature Review?

I think you want the link, with as much information as the link text can provide. So

Dumbledore [D1] contains spells X, Y and Z.

rather than

[3] contains spells X, Y and Z.

If you can find a document like yours (same level, same discipline) you can copy its style.
In any case, make a choice. If you use LaTeX properly you can change that globally with a macro change without having to edit the text.


Which authority establishes the equivalence of degrees from different European countries?

Each country should have a government office (or equivalent organization) that makes such determinations. You should ask the university to which you're applying for the appropriate office to consult in their country. If you want one from the country where you obtained your undergraduate degree, ask their registrar (or equivalent officer) who is responsible for such certifications.


Why would the review system status go from "awaiting recommendation" back to "awaiting referee assignment"?

What could also have happened is that the initially assigned reviewer first accepted to review the paper, only to then forget to do so. At the end of the time that he/she had for the review, the journal editor might have sent a reminder only to then receive an apologetic note stating that the reviewer does not have the time to do so - then the editor would have to find a different reviewer. All these things have happened. If you want to make sure what is going on, you can always send a friendly note to the journal editor and ask about it. They are human after all.


Will one 'C' grade due to health issues ruin my chances of admission into a top grad school?

You have shown that you have overcome great adversity and still achieved great results - this says a lot of positives about your character - of resilience and perseverance - two attributes that are critical for any graduate studies.  You had a cancer scare and still passed the subject despite the medical tests and the very justified anxiety.

Maybe, it is not an "ugly spot", but that C, and subsequent successes are a reminder of how much strength and tenacity you have shown.


Is it normal for PIs to change projects to unrelated research

I would say, no, it is not normal for a PI to shift focus so radically.

In the normal run of things, when hiring at the PostDoctoral level (and lower), the PI will have:

Submitted a funding request with a detailed outline of the research plan.
Have received acceptance of that plan and a budget.
Advertised open positions accordingly to the budget looking for people with the necessary skills.
Hire people with the necessary skills for the duration/budget allowed by the funds.
Supervise execution of the research according to the initial plan.

... pretty much in that order.

Topic shifts would normally occur where funding for a project has run out (which should correspond with the end of the PostDoc contract) and the PI wishes to find funds from other projects to keep the PostDoc employed and to extend the contract.

Shifts might also happen if the PI is pooling sources of funding together, which can sometimes happen: they might decide to juggle resources between different projects on the fly. This, however, is far from an ideal situation, esp. for managing researchers on temporary contracts.

The questions I would ask in your situation are: in which of the PI's projects you are working on, has it changed recently, where the funding for that project came from, and what the original proposal was.

If you have moved project, you should ask why.
If you are in the same project, you should ask why the topic changed so radically all of a sudden.


Where and how are Computer Science researchers publishing datasets?

Zenodo is a EU-funded dataset storage site ran by CERN that seems to be slowly gaining traction. Each dataset gets a DOI immediately when you publish it, so you can refer to the dataset in your manuscript. You can also update your dataset later, which gives a new DOI to the newer version and still keeps the older version there for reference.

A workflow could look something like: (1) Publish dataset in Zenodo, you get DOI for v1. (2) Refer to v1 in your manuscript, submit it. (3) Referee wants to have more stuff in the dataset and you agree. (4) Update your dataset, get a new DOI for v2. Everyone who uses the link to v1 also will be notified that there's a new version available. (5) Submit your edited manuscript, refer to v2 there. (6) Paper gets published, readers see a reference to v2.


While @user18244 suggested a viable option, I would argue that switching fields may not be worth the effort, as the poster may run into similar issues regardless of which field s/he studies.

Problems that I can glean from the post:

1. Amateur with lack of direction wasting an expert's time: OP is coming at a PhD level into an unfamiliar subject area. I can see how this might seem annoying to a highly known scientist who is serious about his work and his students, expecting them to be as focused and dedicated to the field as he is. This may contribute to the resentment i.e., "Why don't you quit, that way you would stop wasting my time and yours?"

2. Staying in the country as the main and only reason for pursuing PhD: Despite being "passionate about everything", lack of coherent reason for pursuing advanced study in this particular area, except for unrelated practical reasons such as visa status and desire to remain in a particular geographic area. This alone does not usually cut it as valid rationale for pursuing advanced study for most academics.

3. Personality/cultural issues: As OP suggests, "I...have strong personality. I like to make changes about me and on my surroundings." As a student, you are naturally in an inferior position in relation to the faculty. A student's first and foremost role is to be a humble, dedicated, agreeable, adaptable and quick learner who causes minimum problems for the faculty (read: takes the least amount of time to advise and direct, and in return performs the highest quality work s/he is capable of). When a student's assertive personality causes them to fail to meet this expectation, this may earn the student a 'reputation' for being a "loose cannon" who is out of control and creates more problems than s/he solves. This is not a position you want to find yourself in.

Given the above assumptions, I would recommend the following strategy:

1. Carefully consider how your personality may be causing some of the issues you are describing. Try to find the problem with yourself first, and only then turn to others (better yet, stop with yourself, for now). If you feel that you could possibly express your strong personality a little less strongly when this does not seem helpful in your interactions, try to think objectively about such situations and see how you can change your attitudes, responses, opinions, etc. in ways that would eliminate this as a possible cause of disagreement and discomfort on the part of your supervisor.

2. Fix the communication. Focus on developing the following qualities: humility, respect, patience, and politeness. This will go far with communication with any professional colleagues, and academic faculty are no exception. This is difficult, but one place to start may be to have a conversation with your advisor with the main goal of asking questions and listening, not talking. Be honest and say that you are struggling, but are passionate about this field and give specific examples of topics or theories that interest you (hint: there should be some alignment there with your professor's interests!). Ask for feedback on what strategies you could apply to be more successful in your studies. Ask for guidance, direction, and advice on how to communicate better, study better, and work better so that you could succeed and catch up to your peers. Do NOT argue with anything you hear, but thank the advisor for their time and effort in giving you their feedback. If they say "I think your best strategy is not to waste my time and quit your studies ASAP", ask "I appreciate this, but IF there was just 1% or 5% chance that I could succeed against the odds, what do you think I should start doing immediately to make this happen?" You want to turn the conversation from a diagnosis of current situation to a prescription for how to remedy the situation toward a better future state. Good Luck!

3. Prioritize your studies above all else. This is difficult, but necessary if you truly want to catch up to your peers and "grow" in the eyes of your professor. Study hard and study all the time. A favorite show on TV? Nope, you have a paper to write or book to read. Great weather outside for a picnic? Walk for 30 min, then go back to your homework. A friend's birthday party? Show up for 1 hr, then head to computer lab to do more data analysis or whatever you need do there for your professor. During the first 3 years of grad school I have often sat in the office late (very late!) getting home after midnight, only to return back to work next morning at 8am. My reward was a reputation of a very hard working and reliable member of the research team, who could finish the tasks that were given to him with quality and on time. Achieve THIS, and it is 100% guarantee that your advisor's opinion of you will change for the positive. Good luck!


Is it weird to have a one-year, master's level "general studies" program?

Unless you have some weakness in your undergraduate record, I doubt that this program or another masters will "strengthen up" your PhD application. Most US students apply for doctoral studies immediately after the BS.
And doing it now, rather than later, will give you experience at the doctoral institution with faculty contacts, etc, that can build up your reputation there.
And most doctoral programs will have coursework first, though not "random" courses. Do it now.
I'll guess that most of the students in such a program are not in preparation for a doctorate, but seeking a terminal MS for some purpose.

Note that outside the US, the situation is often very different with an MS required for doctoral study in some situations. Not so the US, however.


How much would an outside second Ph.D. supervisor get paid in the U.S.?

As far as I know nothing.

I've never heard of outside supervisors (in industry or academia) ever getting paid anything.

You should talk to your employer, if he is willing to donate some of your time for this supervision. (Depending on the research being done, there may also be some benefit for him.)


Am I stuck with the topic/advisor that recommended my admission?

This is ultimately dependent on the policies of your department. The basic issue would be that if you switch to another advisor, the other advisor would presumably be responsible for covering the remainder of your stipend. The big question is if you are free to choose both advisor and topic, or if it's expected you'd stick with your advisor, but have freedom to choose the PhD topic.

The right point of contact is the graduate advisor, who will be well versed in the procedures of your specific department.


How to escalate a complaint about errors produced by a journal from the Nature publishing group when Editor doesn't respond

As authors we are very frustrated to see our work being distorted online (in front of the readership)

Release a technical report which doesn't contain these mistakes and explain in the report that the errors were made by the publishing team.

  we don't know how to...get the errors fixed.

It seems you have exhausted the usual, informal routes. Perhaps you can escalate with your university's legal team, since there's surely a breach of contract which reflects badly upon the university. A strongly worded legal letter will hopefully prompt action.


Why don't graduate math texts have solutions to their exercises?

For graduate-level math books, the answer is typically not a value but a complete proof---typically of a related but relatively uninteresting topic.  For example, one of the first exercises in the Neukirch book you reference is:

  Show that the ring Z[i] cannot be ordered.

For such problems, the proof itself is typically much less educational than the process of struggling with the concepts in order to produce said proof.

By the time that students are taking graduate-level mathematical courses, they are expected to have already mastered the general skills of constructing proofs.  Seeing how somebody else has proved a point is thus not expected to be particularly educational, whereas struggling to prove something oneself forces a student to engage deeply with the material at hand.

Finally, examples of working with the concepts in the exercises are typically already given in the chapter, in the proofs of the main results, so adding extra examples by working proofs for the exercises would typically be of only incremental benefit, but undermine the value of students having to work through the proofs themselves.


Can I get a Master's in Economics with a Bachelor's in Mathematics?

Mathematics is a good undergraduate major for a prospective economics grad student. And I suspect that you could gain admission to (and succeed in) a master's program somewhere with the background you already have. But graduate programs in economics do generally expect that you've taken at least some upper-division economics courses, so you would be a much stronger candidate for a master's program (or even a PhD program) with a bit more preparation.

For example, here's what UConn (where I earned my MA) has to say about application to graduate programs in economics http://econ.uconn.edu/grad/apply/faqs/:

  Do I need to be an economics major to apply?
  No, though some economics background is preferred. Students with little or no economics training, however, will usually only be considered for admission to the master’s program and, if admitted, will generally be required to take some undergraduate economics courses before beginning graduate study.

So, I think the answer to your question is "yes" for at least some values of "master's in economics". Completing intermediate level microeconomics and macroeconomics (or, if you can only take one, micro) would probably improve your chances of acceptance, though, not to mention giving you a better idea whether this is something you want to spend a year or two on.

From your description of your interests, though, it sounds to me as though a MPH is a better fit for you.


Will doing a chargeback on tuition hurt my chances at getting into the same university for grad school?

Would this hurt my chances at getting into the grad school later on?

Practices vary, but probably not.

  Will it hurt me later on?

Very likely.  You probably will not be able to complete a graduate degree if the university thinks you owe money.

  I should just let myself be robbed?

No, you should insist on a refund.  Ask the instructor and their department to help you get a refund.  Ask the registration department again.  Ask to speak to the head of that department.

HR is probably the wrong department to contact.


Should I make my code and data avaiable online when the article is not accepted yet?

Ultimately, it's up to you. I do not really see a reason to keep your data and code private, but you may very well have a valid reason to do so. Hence, I cannot answer the question what you should do.

If I were in your position, I would do the following. I would include a link in the manuscript to the data and code, and write that at this link you make the data and code available for reviewing purposes. The reviewers can then access it all so that they can fairly review your paper, code, and data, but if they behave responsibly, none of it should leak to the wider world. I would add a footnote specifying that the code and data will be made available to the public upon paper acceptance.


Is the invited author of an editorial always the first author, even if their co-author wrote the whole thing?

Authorship practices vary quite a bit from field to field, but except in those fields where all publications are in alphabetical order, it is expected that the first author should generally be the one who contributed most to the work.  Thus, if you wrote the bulk of the document, then normal academic practice would be for you to be the first author (I assume you are not in an "always alphabetical" field).

An invited editorial is a bit different, since the people soliciting the editorial were probably wanting to get the opinion of the person they invited.  As such, putting you as the first author may cause embarrassment to your colleague and might annoy the journal.  Your colleague should probably have checked with the journal before asking you to write the editorial, rather than trying to conceal their lack of work by claiming first authorship.

To put a person who hasn't done much work as first author, however, is dishonest and will reflect badly on you as well as your colleague.


The GRE vocabulary is infrequent to meet in academic life. What is the purpose of learning them?

I think it helps a lot here to understand the American cultural context, and in particular the liberal arts model of education that is quite common in the US.

The GRE, and the departments and universities that care most about them, thinks of graduate training as pointing towards a career as a professor, not as a researcher.  In the US, the majority of jobs as professors have teaching (at the university level) as a valued component, and in the US, students at university are supposed to take a broad range of courses rather than courses focused on a single area of study.  This means that professors are also teaching an audience that isn't solely focused on their subject but rather students with a wide range of interests (at least in the ideal case - in non-ideal cases, they may be teaching students with no interests).

Even though I'm a mathematician and teach only mathematics courses, I think I am a better teacher (and academic advisor) because I know a fair amount about philosophy, religion, history, literature, economics, sociology, computer science, and so on.  I'm not an expert in any of these things, and I make this clear, but I can make analogies to a broad range of ideas and use them in conversation with students.

For an American, the vocabulary section of the GRE is meant to test, not whether you can memorize the meaning of a large number of words for the GRE, but rather whether you are a widely read person who has already encountered many of these words in the course of their life and studies.

Certainly the verbal GRE scores are generally taken into account much less seriously (or not at all) when making graduate admissions decisions for non-American students, particularly when the student has no plans to remain in the US after their studies.


Paper Rejection on Molecular Biology, What should I do?

Congratulations on submitting a paper as an undergraduate that one referee found to be publishable with corrections.  That's impressive.

Are you really the sole author on a biology paper as an undergraduate?  Biology is not my field (I'm a mathematician), but that sounds unusual to me.  Even if you are, you must be doing the research under the supervision of some faculty member, right?  If so: ask them for guidance.

From where I'm standing, I would think that what one referee at a reputable journal finds publishable with corrections should be publishable by another journal, and perhaps even one of roughly equal quality. But you should not take the word of someone from a different field who doesn't know your work or your manuscript.  Again: ask for guidance from a faculty member.

P.S.: The fact that the referee with a more balanced recommendation looks like they did more work and understood the paper better is unfortunately a familiar phenomenon to me.  The refereeing process in academia is far from perfect: it works well when the referees decide to be conscientious and fair...but there is almost nothing inherent in the process which forces referees to be conscientious and fair or even allows one to discern with anything approaching certainty whether any given referee has been conscientious and fair.  It is a bit frustrating.  All I can think to do is to try to apply the golden rule and hope for karmic benefits to accrue eventually (if I may mix metaphors slightly).


How to most effectively get good at a new topic?

The simple answer is: Review Lectures, then read the referenced books / papers (in this order).

There are a variety of good lectures on free course websites out there. (For example on youtube or coursera.) It'll give you a good introduction and - more importantly - will tell you what is relevant to know about in this field.

If you can't find a lecture or at least slides, try to find a few (recent) PhD dissertations in the field and read their introductions / related work / background chapters. These are usually available for free and they will give you a good overview of what is considered relevant.

You could then move on to study recent research papers, but - depending on your prior knowledge - you may not know half the methods that have been used here.

In any case, find out which are the most relevant conferences in this field and see which Professors publish there a regularly. (The Prof. is usually last on the author list). From there you'll hopefully find the most key people in the field and check out their websites and latest publications to see what they are working on.

I'll have to stretch that the right approach will largely depend on how well you are familiar with the basics of the field already. You may have to study a few books or some additional mathematics course work relevant to this new field you are interested in.

Since you appear to be going to university - maybe it's also a good idea to just ask the Prof. most relevant to this field on campus for references and guidance. They will most likely know who's book and publications to read. Maybe this should actually be the first thing you want to do ...


Accepting an Assistant Professor position at a low ranked university

The chances of successfully "moving on to bigger and better things" depend on one's discipline, and also what topic one studies within that discipline. Some topics look much more attractive than others to departments/faculties seeking to boost their standing; note that this is, erm, less than perfectly correlated with the actual depth/worth of those topics.

  Would it be wise to take this position in the hopes that several years of faculty experience will allow me to jump to a different college/university that is a better fit for my professional goals (i.e., more research, higher caliber students, more resources for faculty)?

This strikes me as risky, if you feel those professional goals are essential to your job satisfaction within the next 4–7 years. It's also the case, at least in my discipline, that people hiring in smaller places are not keen on applicants who give the impression — rightly or wrongly — that they are using such places as stepping stones.

Moreover, it may not be as easy for you to move on to "better things" as you might hope; you'll be up against younger people applying for similar jobs, and your rate of publication — if that is important in your discipline — will almost certainly be lower than those people, especially if you start work somewhere that has fewer resources than the place you did your PhD.

  Does this happen often, where someone takes a "starter" appointment and moves to a more fitting situation when it arises, somewhat like a Visiting Assistant Professor position?

I'm afraid I don't have anything more than anecdotes and a very partial sample based on my own discipline.

My own experience, which may differ from yours, is that permanent positions in my sub-discipline were hard to come by in my home country. Consequently, I ended up taking a job in North America which, although not in a liberal arts college, was not too far from the situation you describe as

  somewhat of a good fit for me personally in terms of the teaching I would do and the research interests of the other faculty, but lacks the prestige and resources of larger/more research intensive schools.

At the time I did not do so with the intention of moving on, but it was always a possibility I kept in mind, and subsequently I did indeed quit that job to take up a new one elsewhere, which unexpectedly arose. So I guess you could view this story as some evidence to support your initial idea — start somewhere and then move on — but I'd also counsel caution.


Changing research field as PhD applicant

Would my unrelated previous research papers add any positive thing to
  my application [...]?

Your past research will certainly strengthen your application, even if it's not in the subfield you aspire to study in graduate school. Grad schools look for students interested in and able to carry out research, and a lot of those skills are transferable across disciplines and certainly subfields. It's also perfectly normal to change your research interests during undergrad (or be constrained in topic choice by what faculty in your department are working on or any other number of factors).

  [...] would it just be better to apply to a PhD that relates to my my
  published papers?

With the caveat that you should feel sufficiently committed to your new field to not lose interest in grad school, you should definitely want to apply for the PhD that you want to do rather than the PhD you think your CV makes you look like the best candidate for. You'll be in a program that better matches your interests and you'll do work that's more meaningful to you (and hence often much better).


sharing preprint using the journal's template?

If a journal allows authors to post their pre-prints, the general rule—although it is by no means absolute—is that you may use the manuscript in the form in which it was submitted to the journal, but you cannot use the version created by the journal's production staff.

However, you should consult the specific policies of the journal to see exactly what is or is not allowed, as not all journals allow preprints.


How can I convey my knowledge about a field without publications in a PhD application?

Given that you're a sophomore at a fairly selective liberal arts college [*], you still have plenty of time. Indeed, in two years time the work you're doing now might seem rather simplistic and quaint to you, due to your likely much greater "maturity" in relevant subject-matter knowledge by then.

[*] You mentioned this in a comment. You should probably include this information in your question, but perhaps omit the name of the college.

I recommend considering doing a more advanced independent study course with an appropriate faculty member, impress the faculty member, and ask this faculty member be one of those who will write a letter of recommendation for you when you apply to graduate programs. And also do what @Dan Romik suggests.