What can I do to convince my advisor of my ideas?

First step is to have good ideas. :)

But wait, you are starting your phd, by definition, you wouldn't know what a good idea is, you do not have the experience (usually, let's leave the genius outliers aside for now).

When I have a crazy idea, I develop it a bit, to see where it leads. If leads somewhere interesting, I prepare a nice, informative presentation, and schedule a meeting with the boss. Sometimes I get shot down, sometimes the idea is accepted, but "preparing the field" is important. You need to present your ideas properly, in a well prepared manner, to increase the chances he would understand it. And clearly presenting ideas is the bread and butter of research.

With that said, have you tried an honest conversation with him on this aspect? Nothing wrong with an student telling me he is lost and he needs a concrete direction. Even better if that direction has specific, detailed objectives, including some easily attainable ones to keep the morale high.

Be honest, be polite, be patient, and be clear.


From "Review in progress" to "Ready to review"

I had a similar experience. I contacted the Editor, and it turned out that one of the reviewers they contacted backed out of reviewing my paper, so the progress went back to something like "ready to review" (not those exact same words, I can't remember the exact status, but basically is a step back from being reviewed or in progress). I never would have known that if I didn't contact the Editor. A polite email to the editor won't hurt. IMHO.


Listing GPA on undergrad CV when reaching out to professors

Conspicuously missing a CV makes a worse impression.  The most important thing, in my view, is to take some time to properly understand what the professor is doing, and how you could help his/her research efforts.  A thoughtful contact of this type is much more valuable than crafting the correct CV/profile.


How to send your transcript directly from your US university to grad schools without the transcript office knowing which schools

If you're in the US, talk to your registrar about what we call a "Privacy Lock." It is pretty much a set of measures to apply should the students wish to remain private. Things as extreme as taking you off the online directory, conceal all your names and e-mails, etc. can be done. Each school may do it slightly differently so you'd need to talk to them and get a sense of what is covered.

As for the transcript recipient, you can actually try asking them to put a flag in your personal profile. Most school registrars will probably open up your online record should someone call and ask about you, and if they see the flag they will know how to act accordingly. You can discuss with the registrar on what kind of privacy measures are in place by default and see if additional flags is appropriate, such as "do not disclose information unless in a face-to-face meeting with official proof of ID," etc.

And lastly, you may have to learn about the same security measures in your next school as well, perhaps as soon as you're enrolled. A lot of information is put online and I personally think it's exhausting to make sure that your name will not be featured anywhere. For instance, what if you applied for a scholarship and got it, and the funding agency wants to make a press release? What if you wanted to publish a paper and the journal needs to know your name and affiliation, and will print them if your work is accepted? Somewhere somehow they may still be able to find you so you'll need to be prepared.

And whatever that is driving you guys apart, I wish you'll find resolution and peace soon.


Where to search for conferences and workshops in computer science?

A very good site for CS conferences and journals call for papers and their respective deadlines is A Wiki Calls for Papers.


Cite a R function/implementation from a website

If you use a script written by someone else, it is best to acknowledge them in some way. Citations are common, and many R packages define citations explicitly. Some authors will write papers documenting the code and publish them in journals, allowing you to cite the documentation rather than the code directly. However for one-off functions like your example, these options are usually not available. The information can be included in a footnote, or you can create a full citation.

You can cite an online resource in bibtex using the @online record and include the URL and access date. I would recommend the following bibtex record for this resource:

@online{zhoucode,
  author="Mai Zhou",
  title="LogRank1 function",
  url="http://www.ms.uky.edu/~mai/splus/LogRank1.r",
  addendum="Accessed: 26 May 2020"
}

In the latex document, you can cite this using \cite{zhoucode}

This should not be the only method by which a reader can access the source code. For reproducibility, it is best to make your analysis scripts publicly available for review so that future researchers can repeat your calculations exactly, and it is best to include a footnote in your text that links to a stable repository of your code. This can be accomplished in a number of ways.

@louic in another answer recommends publishing the script as supplemental materials (with the script writer's permission) which if available is the best option because the materials will always be available with the paper. This may not always be possible or reasonable depending on journals or the amount of code.
Some scholars use Github to host their materials and analysis scripts. Github is stable, publicly accessible, and maintains a history of changes made to your analysis scripts allowing review of the process and not simply the end point. Other public code repositories such as Bitbucket and sourceforge exist but are less popular in my experience.
If you preregister your experiment and analysis through the Open Science Foundation website, they allow uploads of analysis scripts. Preregistration is useful in its own right, but uploading your analysis scripts makes them available to others in a stable repository linked to your work.
Have the internet archive save the page and link to the archived copy. This solution is far worse than the above recommendations because it doesn't show how the script was used by you, only what the source code of that function was. While other methods should be used, this method is better than nothing.


How should I respond to being addressed as "Dr. [MyName]" when I don't have a PhD?

This is a very common experience, and mostly I think that you should ignore it.  From my experience, the primary reasons that you will get addressed as Dr. (or Prof.) are:

The sender doesn't know who you are and doesn't really care ("Honorable Dr. please send your excellent paper to our predatory journal sir!")
They are using a form or other automated system that is automatically inserting the title.
Somebody who does care but isn't sure of your status "rounds you up," figuring they are less likely to offend by too much honor than by too little.

If the person is somebody you actually want to have a relationship with or are concerned about misleading, then you can correct them, but for the most part just don't worry about it.


Applying to PhD programs whose research topics mismatch my experience

It can be an advantage. Many people are aware of the value of interdisciplinary research. Your different background knowledge can bring new views into their field. That is a good card to play.


Manuscript hasn't been sent to peer-review for two months

There is no general answer to this kind of question. It is field or discipline specific. For Computer Science (or, mainly engineering disciplines), it is very normal. The following would be my interpretation:

  The status of my manuscript has been "editor invited" for one month ...

Let me guess that the manuscript was submitted in May. Probably, for some time, the journal admin (or assistant) was on leave. So, (s)he sent the invitation late and the process got delayed. Moreover, the intended editor was on leave as well to support the delay.

  .. and now a month later, it's still "editor assigned".

It is good that the invited editor has accepted the request to handle the manuscript. And, probably (s)he is searching for reviewers; or, already has sent the review requests to many researchers, but none has answered yet because of the summer leave.

  Should I inquire about the status of the manuscript? The journal stated that it takes 4 months from submission to first decision, but I am unsure what first decision is, and whether it includes desk rejections or not.

I don't focus on these statistics. These hide relevant details. These statistics are usually skewed to two ends 'desk rejection -- 15 days', and 'first peer-review comments received -- 10 months'. It is actually an 'unreliable' mean estimate.


Is it fair for a professor to grade us on the possession of past papers?

If this was not mentioned in the syllabus (or at least announced prior to the papers being returned), this is totally inappropriate.  While it may be foolish for students not to keep their graded work (at least until the end of the term), if it was not established as a requirement before the students got their papers back, it cannot reasonably be made a retroactive requirement.

You should bring this problem to the attention of the instructor.  You do not need to reveal whether you actually have all your past papers when you bring this up, lest the instructor try to wave your concerns away if you say that you actually do have all the papers and are just complaining as a matter of principle.  I would also suggest having multiple students come to her together to make the same objection; that may make it more likely that she will relent.  However, if the instructor does not agree to make a change, you should take this up with someone higher up.  That could mean the department chair (or another departmental official, such as the director of undergraduate or graduate studies) or a student ombudsman, if one is available.


How to explain to letter writers that I want to apply to completely different PhD programs?

TALK. TO. THEM. These are presumably former professors and advisors that you know well. Sit with them, skype with them, or buy them a coffee. You might learn a lot about what you actually want to do from the discussions, and they'll surely be happy to help tailor your letters.


Should I mention in my letter of recommendation that my student has bad handwritting?

I would not mention this no, this should not have any consequence to the students application, it may be a little out of place. It would be worth advising the student to inform any future places of study about his handwriting he may be able to get some alternate support with regard to exams.

I would not see this student as a liability, just maybe needing a little extra support in this area, it is fair for an examiner to not spend ages marking one students paper due to bad handwriting, so long as they give it a fair go and a good effort.


Interviewing for tenure track jobs: When will the committee contact your references?

Can anything be interpreted from the timing (e.g. after the on-campus interview) of the committee's initiation of contact with your references (or their request that letters be sent)?

As the comments on your question suggest, the culture on this issue are highly field/department/institution dependent. Below are some reasons why different time tables may be considered (or not considered) for requesting letters from your references. However, if letters are not requested with the application, then a request for letters at a later time means that your application has made it past one or more rounds of winnowing.

As far as contacting references, it is probably safe to assume that such contacts can occur at all stages of the hiring process at most institutions/departments depending on the candidate. If such a contact occurs, it is probably a good thing. If the hiring committee was not interested, why would they bother to contact your references?

  With the initial application.

This is an equitable way to handle letters of reference if you are not expecting a huge candidate pool or if your department wants to use letters of reference to help eliminate candidates that might not fit with mission and culture. For example, if no letters that accompany an application to a primarily undergraduate institution address the candidate's teaching style and/or efficacy, that may be a flag. A research institution may be on the lookout for individuals who too closely duplicate the niche specialty of existing faculty (ultrahigh vacuum single molecules spectroscopy).

  After the initial application, but before any phone interviews.

This is probably the way to go if you expect a large number of applications (or a large number of applications from candidates who are below the minimum qualifications). In this case, you can apply a first-pass filter to select only the candidates meeting the qualifications (e.g. a Ph.D. in Biochemistry or Molecular Biology preferably with a focus on proteomics) and remove the inappropriate candidates (M.S. in Electrical Engineering).

  After the phone interviews, but before potential onsite interviews.

As mentioned, given the cost of onsite interviews, this is another logical time to check references. Likely, however, letters have already been requested, and at this stage the hiring committee may be contacting the references for further clarification. For example, "Candidate X is ABD with a proposed defense date of July 17, 20XX. We want candidate X to start on August 10. Will Candidate X be ready to defend in that time frame?"

  After the onsite interviews.

There seems to be no good reason to wait this long before asking for letters. Hosting onsite interviews is expensive (the institution or department usually pays for these, perhaps in contrast to industry). Again, references may be contacted to clear up questions. For example, "Candidate Y is completing a postdoc with you on synthetic fuels from biomass. However, Candidate Y's research presentation was on supramolecular tensors. What is Candidate Y's experience in this area?"


What does "archival quality" mean in the context of journal aims and scope?

Generally "archival quality" implies some level of "completeness" and comprehensiveness (to the degree that any work of science and engineering can really be "complete.") In many fields, early work can be published in some conferences, but journal papers that are expected to be "archival quality" are supposed to be more mature.

To quote from this Guidelines for Expanding Conference Papers for Submission to the IEEE Sensors Journal:

  Conference papers are usually short, and deal with very recent research results or new ideas illustrated by preliminary experiments. An archival journal paper, on the contrary, contains an overview of the state-of-the-art (with references to other’s and one’s own past work), a problem statement, the concept of a solution, a discussion of the theoretical
  background, experimental set-up, sound measurement data, an evaluation of the results, discussion and conclusions – a much more complete presentation of the overall project and its results.


Scheduling anything with committee members is a big pain. The way I scheduled my defense and comps was to just send a doodle poll (like you mentioned) and have them select all the dates. Two of my committee members were very nice and checked all the dates going through almost 4 weeks and two of them never responded or even clicked the link. I just used these dates to check the availability for a conference room in the dept. and sent a final set of 4/5 days to the ones who didn't respond. After sending that a few times and reminding one of them in person, I just scheduled it on a day that I thought was OK and went ahead with that. Everything worked out great and even the person who never responded didn't protest when I picked the time and date. Good luck o
n this. I will celebrate the fact that I never have to do this again :)


Is it appropriate to put conference volunteering on a CV?

As a general rule: anything which is clearly academically related can go on your CV.  As you say, there are certain things that are required or nearly required on your CV, but even these vary by discipline and sometimes people in the same discipline have divergent ideas.  (For instance, every once in a while I find a CV which doesn't list the candidate's undergraduate institution, or lists it without indicating the years that they spent there.  I would have thought that was strictly required.  I guess I was wrong.)

What to fight in adding "academically related" information to your CV is clear: if you put in too much routine stuff, you'll get a bloated mess of a CV that few people will actually read.  Drawbacks of a lengthy CV can be mitigated by very careful and clear organization.  Nevertheless, you can compare CVs of two absolutely cognate people -- e.g. who attended undergrad and grad at exactly the same time and arrived at their current institution at the same time and with the same seniority -- and you'll find significant variations, including up to at least 1/3 in the total length.  It's really your choice how much detail to put on your CV, and I would be skeptical of anyone who tells you too stridently what you must and must not do.

Having said that: yes, very early career academics (especially students) really struggle to have a CV that doesn't look unhelpfully skimpy.  Conference work sounds like a great thing to put on a junior person's CV -- and in fact, even on a senior person's, although a more senior person might be more selective about the kind of conference work that goes on your CV.

One tip: "conference volunteering" might be an undersell.  Most conference organizing is unpaid, hence is volunteer work.  "Conference assistant" sounds like your work was really on the level of secretarial work / technical support.  If that is an accurate description of what you did, great.  If you do such things more than once or twice, you should think about asking to be let in on some of the more content-related aspects of the work.  For instance, if you had a say -- however small -- in choosing or recruiting the speakers or attendees, then I would go for something like "co-organizer" rather than "assistant".


Do I need to cite the source every time I paraphrase in this particular project paper?

I can see the use of many references for the review of literature which is to be expected as that is establishing the state of play at the moment.

In the methodology section you describe how your experiment will be carried out, possibly referring to another’s paper or experiment as a “support” or justification. But it is a description of your method, not someone else’s method so it is unlikely to need referencing.

Then, the results should be those from your work, and only your work as any references to the results of others will be in the discussion.

Then in the discussion you would compare your results with subsequent analysis with the results from others so references will be needed.

From what you show and what I understand is that you are referencing all the material for every section from others - where are your results, analysis and conclusions?


Are there examples of more efficient funding systems than grant applications?

Of course. Remember that in many countries, institutions get a lot of money based on solely being. As an example, in the Czech Republic, the Czech Academy of Sciences receives a lot of budget money for its operation, and some of the money is of course used "for research". Just as an example, until recently, almost all employment expenses (salaries, offices, building maintainance, etc.) was covered exclusively by budget money. Similar model exists in other countries, for instance in France with CNRS, but the difference is that most CNRS people are associated to particular universities, just without teaching duties.

It works well because you moreorless know what you get. Financial stability helps in establishing long-lasting projects etc. Of couse, some level of control is necessary so that good people get the money. In the Czech system, this is based on (AFAIK 5-year) audits which evaluate each person separately, and then whole departments, working groups and institutions.


Yes, asking the editor about this seems very reasonable, as not getting any sort of report from the reviewers sounds like an error.
(I have published one paper in J. Algebra, and we did get a reviewer report, just as one would expect).


What is the best job for fresh graduates to improve chance of being admitted to top grad programs?

The best job option is the research assistant or research and development related position because mentors or advisors want to see you are capable of doing independent work and that you are familiar with publish or perish practices in academia.


As far as I'm concerned, if you're using someone else's photograph and you don't have a clear set of rules stating that you can edit it i would avoid doing so, unless it's a very, very basic thing, like cropping it to hide the cars.

You could also use the legend box commonly written below the picture to help explain it, for example: "Recent picture of a church constructed on the XII century."

If the visual aspect of the church is really important to you could try to recreate how it would look when it was recently constructed (maybe pay a designer to do so) and make it your own thing (of course, referencing the original author: "Recreation of what the church of bla bla bla would look like on the XII century. The original picture was taken by XXXXXX and treated using (...)"


How long does it take for an article to get accepted to the arXiv?

From the arXiv help, emphasis mine:

  On Hold

  Your submission was identified by arXiv administrators or moderators as needing further attention.

  Submissions may be put on hold for a variety of reasons, ranging from questions about proper classification, pending moderator approval, presentation issues, copyrighted PDF, etc., to editorial concerns. Most of these do not require any further input from the submitter and will be dealt with in due course. arXiv urges submitters to be patient. Due to the large volume of submissions, it may take several days before a resolution is reached.

  Note that oversize submissions are automatically put on hold, and this is one particular circumstance in which submitters should follow up with arXiv administrators.

  Submissions in this status will not expire. Authors must not create a new submission with the same content when a pending submission is on hold.

  Please be sure to include the submission identifier of the form submit/NNNNNNN when contacting arXiv administrators.

In other words: wait a little while. Especially at busy times of year for academics, like now. After a week or so, if nothing changes, you can contact the arXiv administrators following the instructions above.


Standard way to specify roles in authorship

There is no standard way, not even in the same field or sometimes even the same journal.

But when people put contributions at the end, it typically looks something like this:

  Author Contributions
  AB conceived the project. CD and EF designed the experiments. AB and GH performed the experiments. CD and EF analyzed the data. AB wrote the article with input from all the other authors.


Difference between faculty position at a public university and state university

State universities are public universities. The other main type of university would be private, non-profit (I'm assuming you are not looking at for-profit universities?). Public universities are often controlled by the state legislature, so they are sometimes vulnerable to political decisions, such as cuts in funding, determination if faculty get salaries, the number of courses required to teach, etc. For instance, during the recession, California had a budget crisis and there were constant talks of faculty lay-offs at state universities. The amount of salary offered to faculty vary based on your discipline and the university. Some private universities may offer higher salaries, some may not. You should look at the individual school. In many states, faculty salaries at public institutions are public record and you can see how much faculty earn, if that helps with your decision.

Since state governments control state universities, the university norms differ from state to state. I previously was at a state university in Florida and now I'm at a state university in Alabama. The University of Alabama has a lower research designation than my previous institution (I was at an R1), but there are fewer universities in Alabama and UA is the state's flagship school, so I am provided with a  better salary and more support for my research than I was before. Also consider the cost of living where individual universities are located, versus salary. The cost of living in Alabama is much lower than where my previous institution was, in Miami.

The take away? Find the faculty positions that are related to your work and compare institutions then. Hope this helps. Good luck!


Transactions journal with impact 2.5 or IEEE internet of things journal with 9

I don't know about your specific journals, but Impact Factor is a fake measure and should be ignored. Both the idea of measuring "impact" by number of citations and the methodology itself to collect such data are flawed, hence impact factors constitute meaningless information in most cases.

What is important are the norms in your scientific community. Ask your colleagues what is better. Do not look at "impact factors".


The feeling of inferiority entering a PhD program due to one's undergraduate school rank

(Source: I am a math professor at Stanford, with connections to the CS department and many former students in the CS Master's program, and experience with graduate admissions.)

Nothing about this situation suggests that you are any less intelligent than your classmates. The admissions committee isn't running a charity: if they thought you weren't prepared to excel, they would have admitted another student from MIT instead of you. They invest a lot of effort into determining which students are positioned to be successful; it's not a perfect system by any means, but I think they know better than you do whether you're prepared.

I have never considered undergraduate institution or background when considering who to work with, and I haven't heard of any colleague doing so either. As a grad student you get better and better at learning, so it's easy to patch any holes in your background.

If you are concerned that you haven't had the opportunity to take all the classes that the CS undergrads at Stanford have: well good news, the majority of CS courses are online, including all the lectures, slides, and homeworks. And you have 7 months before you'll start grad school this fall -- that is plenty of time to complete all the courses you're worried you've missed, if you really feel that's the best use of your time.


Does university have any cultural mission?

Almost all universities have a larger mission than simply provision of educational courses.  For example, consider the mission statements of two very different publicly funded American institutions:

The University of Texas System, in addition to education, aims to develop ethics and morals, appreciation of arts and culture, and prepare "educated, productive citizens who can meet the rigorous challenges of an increasingly diverse society and an ever-changing global community"
Bunker Hill Community College is much closer to the "pure skills" model, but still also aims to provide community leadership and to ensure that "no eligible student shall be deprived of [education] because of an inability to pay tuition and fees."

In both cases, the university is explicitly aiming to promote social and cultural change towards a society in which most people would generally prefer to live (even though the particular goals of each are different).

Now, mission statements are one thing, reality is another.  Every university's leadership decides how it wants to interpret and/or modify its mission statement. Universities also generally have some sort of board overseeing it, which will attempt to guide and shape the university's actions.  This is where, especially with public universities, there is often a great deal of fighting about the university mission and policies around it.  For example, conservatives who are uncomfortable with the cultural broadening provided by universities often argue that a university should "just stick to teaching skills."  In general, however, the faculty and leadership of most universities tend to promote some sort of cultural mission, even if some are very different than most.


For undergraduate studies, you do not need to have publishable papers. Hence, exploratory thesis it is fine if you understand and do all the calculations, and perhaps you can also explore implementations in numerical programs.


Considerations for transitioning from a teaching to a pure research position

Some issues that will need to be considered are:

getting up to date with the current developments in your field – this will involve intense and selective reading
finding new topics to work on
justifying in grant applications the gap in publication record and demonstrating potential to produce results
attracting students to work with you – this may be easier if you've been teaching a lot, as you've put yourself in a position where students can see you.

Good luck.


Manuscript transferred from editor to editor

This is probably the result of the journal's structure. I would guess that papers in this journal are handled by:

Author submits paper (say, on the topic of "simulations of the solar system's formation").
Someone (possibly the editor-in-chief, possibly the desk editor, possibly an automated system) assigns the paper to the associate editor with the closest expertise. Odds are the journal only has a few associate editors so at this point it could be quite general, e.g. the associate editor could be an expert in "general relativity" which is not the same as the paper's topic, but is relatively related.
The associate editor then assigns a subject editor. The subject editor is also a member of the editorial board but has a more specialized focus. For example the subject editor could be an expert on "planetary science" which is closer to the paper's topic than "general relativity".
The subject editor assigns reviewers.

So: nothing to worry about; wait for the process to run its course.


In the US, primary education is the first seven or nine years (depending on location), and secondary education is usually considered high school. Primary and secondary education are compulsory and are provided free by the state (of course some go to private school).

"Post-secondary" education refers to anything you do after that, including bachelor's, master's, and doctorate-level degrees, but also things like associate's degrees and vocational training.

From Wikipedia:

  Higher education (also called post-secondary education, third-level or tertiary education) is an optional final stage of formal learning that occurs after completion of secondary education. Often delivered at universities, academies, colleges, seminaries, conservatories, and institutes of technology, higher education is also available through certain college-level institutions, including vocational schools, trade schools, and other career colleges that award academic degrees or professional certifications.

If you wanted to distinguish between college or university education and vocational training, you might call the former "tertiary" or "higher" and the latter "further" or "continuing," but it's not a well-defined distinction and not universal.

A master's or doctorate degree is "postgraduate" education.


CV for PhD application with little relevant professional experience?

It's called a "CV", but it's really the same as a resume at this stage. Moreover, how you format it, and what you put on it, is completely up to you.

Try to be as creative as possible, and really sell yourself -- don't be afraid to brag. What are your strengths? Things that may seem irrelevant could still impress the admissions committee.

Also, without research publications, the best substitute is good performance in advance classes and (more importantly) a good recommendation letter, or two, that can vouch for your research potential.

  "I received a very good grade for my undergraduate dissertation"

That will look great -- put it on. Find or make an appropriate section. Then say "received highest possible grade on dissertation" or whatever; cite statistics on dissertation scores if you can find them and they make you look more impressive.

  I do not yet have any publications and have not spoken at or attended any conferences apart from attending a postgraduate conference at my university last year.

You can put on that you attended the conference. Publications are not necessary in most fields -- if you have them, that's a huge leg up, but most candidates will not have them (at least, at all but the very top-tier universities, and in most fields).


Should an undergraduate claim ownership of their article uploaded on arXiv?

Congratulations on your paper!

You don't have to, but it would be a good idea to make an arXiv account and use it to claim ownership of the paper.  This will make it easier for people to find your work when searching by your name, and vice versa.  It will also establish an account that you can use for any future papers you write.

The fact that you're an undergraduate is irrelevant; arXiv doesn't care.  In fact anybody at all can create an arXiv account.  In order to actually submit an article, there is an endorsement process, but that's not really important here: endorsement isn't needed to claim ownership of a paper submitted by someone else (and presumably your co-author is already endorsed).


Who should I ask for recommendation letter after graduation?

Attempt to contact your previous instructors, wherever they have moved to. At least they know you. Professors and academics move around a lot and their recommendation letters are still valid and respectable. If moving around is a barrier to recommendations and support letters, I think academia will cease to function...
Whatever you are doing now (post-graduation) is likely to be relevant and may be helpful. Any jobs or roles that you have held will support your work especially if they are in the research/writing vein.


Applying to work at an acquaintence's school

How do you go about telling such an acquaintance that I am planning to or have already applied? Is it acceptable for me to simply drop them an email? Is there anything specific I should tell them?

Yes, you should just send them a short email (don't make it too long, or write it in a way so that the recipient is pressured to answer it). I would email them after all of your application materials are in, and tell them that you have applied to their school. If it is among your top choices, I would mention that in the email too.

  Most schools list a designated contact person within the department.
  Would it then be inappropriate for me to ask my acquaintance questions
  about the school or position?

The contact person is most likely the secretary of the department, or the head of the hiring committee. However, every member of the department has some say in the hiring process, and it is generally better to establish contact with your acquaintance. However, I would hold off on asking questions about the school or department until you receive an interview, unless the answer to the question that you are asking decides whether you will apply to the school or not. If there is no chance that you will be hired, then you don't want to annoy your contact and waste both of your time.

  One of these acquaintances works at a school that is far from the
  region I would like to end up living someday, and I believe that they
  are aware of this. How will this impact my chances at that school?
  Would it still be beneficial to make them aware of my application?

This seems like a tricky question. If you are a superstar, they might still try to interview you and convince you that their school is fantastic. However, if they are deciding among several candidates of similar calibers, and if one of the candidates rank the school as their first, that could tip the balance in their favor. Nonetheless, it wouldn't hurt to alert them of your application. However, do not lie and say things like their school is your top choice. In a small world like academia, you do not want to burn any bridges if you can help it.

Finally, I'd like to add one thing out of paranoia. Do not apply to positions that you would not accept. This is especially important at tenure-track level, where there is a lot of work that people have to put in before an offer can be made. At the tenure-track level, once you receive at least one offer, it is expected that you accept one of them, otherwise you may not be taken as seriously when you re-enter the tenure-track market in a later year. These kinds of things get talked about, and as the job market is a sensitive issue for most mathematicians, people tend to have very long memories about these sorts of things.


Should I ask my online PhD interview panel whether my partner can sit in?

I would find this odd and unprofessional. I recommend against this.

Also, I want to be able to talk freely and openly with you in an interview, and have you respond in kind, and I would be worried about how having your girlfriend on the line will affect this dynamic. (For example: I might worry that you would be distracted by thinking about how she is perceiving the interview, or trying to impress her.)

I might also be concerned that needing moral support for an interview this badly does not say much about your ability to handle the stresses of graduate school.


What material should I bring to my first meeting/interview with my prospective advisor?

It looks like you're set with respect to material things. What I would encourage you to prepare is an agenda -- which, in this case, means a set of immediately practical questions you need answers to, and one or two conversation-starters regarding your would-be advisor's research and that of his existing advisees.

Practical questions: what paperwork is involved in formalizing the arrangement, when should you report to start work, that sort of thing.

Conversation starters: "I read your recent 'Mathematical Models of Baskets' in the Journal of Underwater Basketweaving; are you still working on that?" "What are your current students working on, and is there anything you wish somebody would tackle?" and that sort of thing.


The reviewer is probably talking about https://en.m.wikipedia.org/wiki/Significant_figures

If you are reporting numbers like 3.23436, you likely have far too many significant figures: you are reporting precision that just isn't relevant. Report something like 3.2 instead.

In your table you have percentages. Round numbers like 40.6% to 41% throughout. And be consistent either with number of decimals (round to nearest 1%) or sig digits (12% and 3.5% both have 2 significant digits).


Is referencing another PhD dissertation or Master's thesis a reasonable practice in a Master's thesis?

Yes, you are able to reference their work in your text, as long as you make clear in the bibliography what type of document (master thesis, PhD thesis, Institution) it is.

However, i would not consider it to be ideal if your work critically depends on such references in the sense that a central assumption or starting point in your thesis breaks down if the reference provides false or incomplete results. Particularly in the case of master theses / dissertations it is not generally clear whether and to which extent they are peer-reviewed and what their overall trustworthiness is. With (accepted!) PhD theses things are better, as these normally go through a review process. Furthermore, for PhD theses i would expect that their main points have been published somewhere (conference or journal) and then you clearly should prefer these publications.


Is submitting papers based on classwork papers self-plagiarism?

The problem with typical self-plagiarism is that a scientific work or part of it is published twice in a peer-reviewed venue. This inflates the scientific credit obtained for this work and wastes the times of everybody involved in the publication process.

Assuming that your classwork is not scientifically published (if it is, you should know), you should not commit self-plagiarism. To be on the safe side, I suggest to clearly reveal the history of your paper when submitting. This way, the publisher cannot claim that you hid something from them and they can decide themselves whether they have any problems with it.

Some further remarks:

If your work was published non-scientifically (e.g., hosted on the course’s website), this may conflict with the exclusive copyright wanted by some publishers. However, for most publishers, this should not pose a problem. Be sure to read the copyright-transfer agreement or similar thoroughly in this respect.
Your university may impose some restrictions on publishing coursework. You’ll have to check.
Be aware that whoever supervised your classwork (if anybody) may have contributed to it to such an extent that they deserve authorship. Again, this is something you have to check.


Am I allowed to write an essay about a scientific theory without violating the copyright?

Yes.

Scientific principles are never subject to copyright—you cannot copyright a scientific idea, theory, equation, or concept.

That said, you do have to worry about copyright if you extensively quote from copyrighted primary or secondary resources as part of your text. If you are not directly using their language, then you need only cite the works, and no royalty or copyright issues should arise.

(Note that in the particular case of the special theory of relativity, it is more than 95 years old (as it was announced in 1905), and thus is no longer under US copyright protection in any event, so you could in principle reuse or even reprint the entire text of his article.)


What are the chances of getting into a PhD program in math after other pursuits in life?

I don't know where you are, but at least in the US, research experience is not expected before enrolling in a PhD program.  It is also not expected that you have take graduate-level classes, unless you are trying to get into a top program.  However, it is true that admissions committees want to see that you are sufficiently motivated and committed.

My suggestion is that you apply to several masters programs and maybe a few PhD programs you are interested in.  You may or may not get into the PhD programs, but it's easier to get into a master's program first.  Having done a master's in math should be sufficient evidence that you're serious about doing a PhD (if indeed you still are), and this will make it easier to get into a better PhD program.

As you will need letters of recommendation anyway, I also suggest you contact some of your math professors from undergrad and let them know of your intentions.  Then you can also ask about letters of recommendation and see if they have any suggestions for which kind of schools you should apply to.  (By looking at your CV and transcripts, they should have a reasonable sense at what kind of schools you have a good shot at.)

By the way, as a bit of encouragment, many excellent mathematicians have started off in other careers, and your situation of wanting to do a math PhD after trying something else is not uncommon.


Author list mismatch; should I recommend rejection?

Inform the editors as soon as possible. They will decide what to do. This is probably a minor issue that can be resolved in communication with the authors directly.


Is there a pre-print server for building physics papers?

No, there isn't yet a pre-print server for building physics, although some people have successfully smuggled such papers onto arxiv.

Furthermore, there aren't really any heavyweight open-access building-physics journals, and established journals in the field haven't been quick to embrace open-access.

There is the option of producing internal working papers and circulating it without publication, to get some of the benefits of pre-print, without risking a publisher's refusal. However, it's not easy to reach a very broad audience this way, nor a new audience.

Building-physics papers do often span multiple subjects - we often cross-over, for example into health, for example, when we look at condensation and mould, radon, or dust mites; so there might be other pre-print archives that we can use.

And, although it's a completely different thing, there's always the possibility to air early thoughts on the building-physics tags on the Physics and Sustainability Stack Exchanges, which can be a way to get a bit of an airing, and reach a different audience to that reached by circulation of working papers.


How to write side-note reviews on assignments without sounding testy?

I can see you've given some thought to balancing the negative with some positive.  That's good.  Note, you don't need to remark on every single thing they did right.

If you have a rubric, a list of elements you look for in each lab report, you may wish to put a check mark in the margin wherever you see that a required element is present.

Sometimes a student doesn't manage to get much of anything right.  In that case, it can be helpful to notice something positive about what they were trying to do, e.g. "Glad to see you caught this contradiction."
Try expressing things as questions, rather than statements.  Examples:

  Can you also check such-and-so?  How does this fit in with etc.?

One of my professors would write in my proofs, instead of "Does not follow" or "Not relevant,"

  How is this germane?

As a student, with certain graders, I was sometimes unsure whether a particular comment was positive or negative or just food for thought.  So try to avoid those misunderstandings, e.g. "Food for thought: etc." or "Enrichment idea: etc." or "Conclusion is correct; be careful to make clear the connection between…"
Be tactful — meaning, your belief that they are trying hard, and can get better with your guidance, should come through.  Example: "Watch out, need more digits here to avoid rounding error later on."
I suggest you arrange with the professor to visit the class briefly at or near the beginning of the semester, and maybe at the midpoint again, to introduce yourself and show a friendly face.  Convey to them that your job is to give them lots of specific feedback to help them improve their work.  This can help humanize things.


Official abbreviations for CS conferences

I am not aware of any comprehensive list of abbreviations for CS conferences. One way to see many abbreviations is through CS conference listings and ranking. For example, here and here. The most obvious way is googling the name of the conference then checking the conference website.


In which type of schools can I have better research experience in Biology, liberal arts college or large research university?

I went to a small liberal arts college and worked at a large university lab, that had undergraduate interns. From both experiences I agree that it is the lab and not the school that matters. However, there are conditions that you will be more or less likely to find, depending on the type of school. In general liberal arts colleges will give you more personal attention and large universities will have more resources. Funding at liberal arts colleges is focused on undergraduate education and funding at larger universities is focused on research.

Personal Attention:

Liberal arts: A lab is led by a principal investigator or PI. Liberal arts colleges often do not have graduate students or have few graduate programs. So, at a small liberal arts college you will work closely with your PI and get to know them well. I left my college with great letters of rec that helped me overcome a poor GPA (due to a medical problem in my first two years) and get into grad school.

University: The undergrads were trained by PhDs and post docs and had little contact with the faculty. Post docs and PhDs can often be great teachers, though, since they either are students or were students recently and might be able to anticipate the student's perspective. At a university, they will normally write your letters of recommendation and the faculty will sign them.

Independence:

Liberal Arts: All of our grants were training grants, so the emphasis was on teaching, as opposed to producing results. This means you will get to do more independent work. I got first hand experience with the equipment (EEG) and techniques (analysis of FMRI and EEG data) that few undergraduates get to use. Additionally, I know of at least two of my friends who published, as first authors, in major research journals. This is not uncommon in my school.

University: The undergrads had to learn a program that is no longer used by most labs in the field. There was little room for mistakes (all of the labs grants were research grants), so the undergrads were given the task of modifying previous work and really did not develop any understanding of how the program actually works. However, this lab was an older lab. I also believe students at an older lab at my undergraduate school had a similar experience, where the methodology they were taught was not consistent with current standards in the field.

Connections:

They are pretty equal in this area. Liberal arts college professors often collaborate with people at larger institutions and can connect you with other labs. I have friends who got summer jobs at Stanford and CalTech this way. At the large university, one of our undergrads got to go to Oxford for the summer, because of the professor's connections to a lab there.

Equipment and Resouces:

Liberal arts: We did not have access to some of the most expensive equipment (an MRI, for example). However, one of my professors also worked at a local university that had access to an MRI and we got to use it there. Ideally, you should get some lab experience at a major research university, so you are exposed to techniques that require more expensive equipment. You can do this during summer internships. Getting more experience at different labs will look good on your application.

On that note, a liberal arts college is more likely to have grants that will help students study at other institutions. My college had several such grants for student research grants. Additionally, all senior thesis was funded by the department. The senior thesis funding and one of the summer fellowships both require students to focus on their own original ideas. In most fields the first author is the person who had the idea for the project. This is how undergraduate students were able to become first authors.

University: Universities will have the best equipment, but they are less likely to have funding for student research. The institution I worked at had grants for students, but they were only for work at that university. They also had no specific grants that would allow students to propose their own projects, based on their own ideas.


A summer school is usually a way to have a focused series of lectures on a specific topic. The best analogy I can think of is that of a master class for musicians. The audience are students who are usually sufficiently adept that they can handle the intensity and focus of a short program taught at a high level. For example, if you're just starting out in grad school in computer science, a summer school in specialized aspects of (say) deep learning might not be very useful. This at least partially answers your first question.

Summer schools are useful because they can bring a set of experts on a topic together in one location, at a venue where this expertise might not otherwise exist. In computer science, this might also be part of the explanation of why there are so many summer schools in Europe: since many topics in the field are dominated by the US, it makes sense to have summer schools in Europe for the reason above.

The speakers of course get the opportunity to travel and teach a focused group. It's a prestigious thing to be invited to such an event. The organizers make their mark (and benefit their institution) by organizing such an event. The students learn about a topic that they might not otherwise get exposure to, from the experts in the field. And that is an answer to your second question.


How does the government shutdown in the United States affect research projects at universities and national labs?

Has federally funded research at universities and work done at the national labs in the United States been halted due to the government shutdown?

The current shutdown affects federal employees - and even then, not all government departments or agencies are affected. In particular, the Department of Energy, which funds the DOE National Labs, already had an approved spending bill, so DOE is unaffected for now. The NIH and Department of Defense, which fund their own institutes and labs, are in the same situation. However, many other institutions, including NIST, NASA labs, and the Smithsonian have had to cease a lot of their work. Some activities are considered mission critical, and can continue, but that's getting into the specifics. See e.g. this Washington Post article.

University researchers are not directly affected, since they are not federal employees*. Even public universities in the US tend to be on the state level. However, there can be a large indirect effect since e.g. NSF, a large funding agency, has shut down. If this shutdown is anything like the 2013 one, this will not only delay grant applications, but also grant decisions, causing a lot of uncertainty, hiring delays, and lost research productivity.

*The military academies might be an exception, but since the Department of Defense had its spending bill approved they probably wouldn't be affected anyway.

  Do researchers just stay at home and not show up to work? Or do they show up, and do something similar to what you would see at a labor strike, e.g. megaphones, demonstrations, make demands?

Generally the former - at least at the largest of the affected places security would (rather sensibly) be considered a mission critical operation, and security would be instructed to stop people from going to work. There tends to be some protests, e.g. at the White House during the shutdowns, but I doubt these are dominated by researchers. There are many, many others affected - some 800 000 government employees in total, many who'd be hit harder than your average federally employed researcher.


Ways to spend gap year/semester before applying to mathematics PhD

Options I can think of (I bet there are even more than these):

Take some upper level undergrad, or first-year grad, math classes as an unmatriculated student
Audit some classes (this saves you some money -- you don't get credit, but you learn the material)
Apply for a master's, in a program that doesn't require a math GRE (for example, with some quick googling, I found a good program in statistics that doesn't require the math GRE)
Take or audit some non-math classes that you find interesting
Become a K-12 substitute teacher (this only requires a Bachelor's degree)
Be a Vista volunteer
Get a job and build up a bit of savings, to make it easier to get through grad school on a TA stipend
Study abroad for a year but not as part of a PhD program for the reasons you mentioned

Note, if you are working full time, I find that one challenging class at a time is enough.  If you are working 20 hours a week, depending on the type of job, maybe two challenging classes would work comfortably.  I remember taking data structures and linear algebra at the same time while I was working a 40-hour week, and I went a little nuts.  In retrospect, it would have been better to negotiate a reduced number of hours at work.


Citing different papers which use different notation for the same concept,

This probably varies between fields, but in my field, mathematics, what I"d do is to explain the notation that I want to use and then express other people's results in that notation. I'd probably say something like "XXX proved [citation] a theorem that, in the notation explained above, says YYY."


If a research project leads to potential financial benefits, who owns such benefits?

This isn't a full answer, since it depends on the laws and regulations of the place of employment, including university contract rules. However, note the following.
There is a big difference between holding a patent and monetizing it. The latter is a business process, not a research process, and takes lots of inputs. Money doesn't automatically flow from the possession of a patent.
Obtaining a patent in the first place can be expensive since there are (varying) regulations governing it that normally require lawyers (plural perhaps, expensive usually).
Defending a patent against someone who wants to invalidate it can be very expensive. Even defending against someone who wants to exploit it without permission or license can be very expensive.
For university employees, as for employees elsewhere, there are often contract stipulations about patents. A typical contract provision gives the responsibility for obtaining, licensing, and defending a patent to the university itself. This is normally advantageous due to the costs entailed. Large research universities may have patent attorneys on staff or on retainer for this.
The patent may be applied for in the name of the researcher, or (perhaps), jointly in the name of the researcher and the university. Other contract arrangements are possible, and I don't know all of them. The researcher may be entitled to a portion of any profits that derive from the patent, but are normally protected against losses. The last is, potentially, a big deal.
I don't know of funding agencies who get involved in this, but that isn't outside the realm of possibility.
For your own case, if you are in a situation where it matters, start with your own employment contract. Or, consult a patent attorney.
While the patent may remain in your name only, you may be required by contract to assign some of the rights to the university (or company). Search for "Patent assignment" on google or other search engine. An example explanation is here: https://www.legalzoom.com/articles/patent-assignment-how-to-guide


What level would an assistant professor be hired at, if applying to associate professor position at another institution?

Based on what I've heard and seen, most schools fall into the second pattern, with the first and third happening much less frequently. However, I've known all three possibilities to occur. Ultimately, there is no "most likely" or "least likely" option, as it really depends on the rules for tenure promotions at the individual school at which the applicant is being hired.


Re-entering teaching after working in the industry (in Europe)

While it depends on where the possibly foreign university is, I can answer for the UK (...for now, pre Brexit. Post-Brexit will just be some sort of crazy nightmare so who can say). Simply put, yes, if you were applying for a teaching-only position, having a stretch of time in industry and outside of teaching is likely to be seen as negative on balance. With numerous qualified people applying for every position, committees can pick and choose and they usually pick and choose people who have fresh teaching experience rather than someone who has been out of the game for a while. It isn't impossible to come back to teaching from industry, especially if you can show how you working in industry would be an asset to your teaching, but it's hard. Indeed I only know of examples of a move back to teaching from very few fields and it would be unlikely in mine (Social Sciencey and Artsy).


How to give credit for conference presentations on CV?

All official and known conferences will need the authors to present their accepted work in oral or poster manner, and will publish the proceedings of the conference. I am not sure what you mean by undergraduate conference. But a presentation, where no paper has been presented to the research community, is not a big shot to be declared in CV, at least because there is no clear evidence for such accomplishment.

If there were any paper, You would mention the paper in a typical manner in your CV (considering yourself and any other one, who had any contribution) and insert an unpublished assertion in front of it. But in this situation, the better idea could be citing the thing in your CV, as a Given Presentation at blah blah blah Conference. If you do it, you might better explain something about undergraduate conference, because the reader may not be aware of this term, leading to confusion.

Good luck


Why are the German professors addressed as Prof. Dr. XXX?

In Germany, in rare cases also non-doctors can become a professor. Then it's just "Prof. Müller". Regarding Doctors, we don't have a "PhD" title. "Dr." is the official title for a doctor which is traditionally a prefix to the full name.

See also: http://en.wikipedia.org/wiki/Doctor_(title)#Germany


What if the value cannot be accurate to one decimal place?

Thinking about data in terms of decimal places is misleading.  You should really be thinking about data in terms of the precision with which you know the values, also sometimes referred to as significant figures.
How precisely do you actually know those values? It is 12.736% because you actually have enough data to say that it is accurate to one part in 100,000, or is it because of something like Excel defaulting to three decimal places?
You need to figure out the amount of error in your measurements, and once you know that, then the answer to your questions will be clear.


Is it polite to send an email to check if a proposal has been submitted?

Yes, a polite and simple check-in like you write should probably be just fine.


How do STEM professors become so hyper-efficient with their research?

Efficiency tends to rise with demand - the more demand for a resource exceeds supply, the more efficient with it you quickly learn to be. Time in the lab/office tends to follow a similar process. When you have 10 hours to write that abstract, it often takes 10 hours. When it's gotta get done in the next 45 minutes because that's the only time you have, you just write it in 45 minutes and be done with it.

The other main issue is experience - having done this thing before - completely changes how long it takes to get something done. When you are doing something the first few times, everything is new and requires a lot of cognitive load. Nothing is automatic yet - everything is not only deliberate, but you may need to take time thinking out all the options, then going through each of a dozen possibilities trying to explore what you should try next, then wondering what you will do if that doesn't work out quite right, are you really sure that's going to work, etc. Hours (or days, or weeks, or months) of wondering and exploring can be cut down into minutes of doing. But you kind of need learn how to do it in the first place to move on to that point.

It's valuable to look up to highly effective, proficient, efficient people and try to learn from them, but there is the constant danger of discouragement if you compare where they are now - after possibly a decade or more of experience, hundreds of papers, and who knows how many collaborators and mentors they've learned from in this time - to where you are now, comparatively just starting off. And when they were just starting out, they were not so efficient as they are now (don't believe all the legends that tend to grow with time on their own, either).

I don't know how efficient you can become, and the funny thing about human growth and development is you don't really know either. No one really knows the future, or the extent of any individual's potential. It's up to you to decide if you want to find out how efficient you can become, if you can improve your organization skills, if you can cultivate greater creativity - then you can give it you all in finding out what you can accomplish, as a sort of experiment, or you can decide if you'd really rather do something else instead. But you haven't indicated anything that signifies you are doomed from the start, so long as you are willing to accept that it takes much time and sustained effort to achieve such growth in anything that you choose to do.


The short answer is: yes.

Sabbatical is not a vacation but is rather a leave of teaching to focus on research and publication. At many schools it is not automatic but must be applied for and is granted at the provost's discretion.

Some schools will only provide six months of funding, but will release a full year of teaching, making the faculty member responsible for getting grants for the remainder, or effectively working at half salary.


Should I inform the graduate admissions committees (of all the Universities I have applied to) of the acceptance of one of my papers?

Ben Norris' comment is right.  I will elaborate a bit.

As an undergrad, having an accepted paper is much more significant than having a rejected paper (i.e., the net perception is very positive even if they learn about both).  Furthermore, rejection is probably temporary (you'll probably resubmit after improving it and it may get accepted) whereas acceptance is permanent.

Tell them about the acceptance.  If they ask directly, tell them about the rejection.  But there is no reason to feel obligated to broadcast a paper's rejection.  The people reviewing your application certainly don't list their paper rejections when they apply for a job or a grant!


If this is just an internal document that will never be seen outside your own institution, it doesn't really matter.

For a document that will be distributed outside your institution, the abstract should be fully comprehensible even if that's all you see. It's quite common for databases to include only the abstract or for it to be much easier for people to see the abstract than the rest of the document. (For example, on ArXiv, each paper's "home page" includes the abstract but you'd have to download the whole paper to see the references.)  For these reasons, an abstract that says something like

  We build on the statistical analysis of [5].

isn't very useful.  This isn't so bad with a long reference style:

  We build on the statistical analysis of Smith and Jones (2005).

is better, especially if that is a well-known paper in the field but not everything builds on well-known papers and the reference is potentially vague if Smith and Jones wrote multiple papers together that year.

The best way to do this is to give a full citation in the abstract itself:

  We build on the statistical analysis of Smith and Jones (J. Interest. Res., 3(1):41–59, 2005).

Some journals forbid citations of any kind in the abstract but that seems to force people into the suboptimal "Smith and Jones" style.


Is it unwise to get a recommendation for philosophy phd apps from a professor you had relatively early in college?

I don't have experience with philosophy, but I can't imagine this part of admissions is too different.  It's pretty common for students to have one or more letters from faculty they haven't had classes with in the past year, so no that's not a problem.  (In fact, sometimes it happens with all the letters, if the student takes time off--e.g., see: If you want to do a PhD in mathematics, how important is it to start immediately after finishing undergraduate studies? )  What's important is that each letter writer should have something meaningful to say about your preparation, talent, attitude, performance, work ethic, etc.  Also, depending on the circumstances, it may be very natural for you to continue to have plenty of interactions with this professor over the next year or so whether or not you take another class with her.

That said, you should get letters from some people you've taken in your 4th-5th year (particularly master's classes if possible).  The main reason for this is you want recommendations which can discuss your performance in more advanced classes, which is presumably what you'll be taking.


Submit a comment or reply to own research paper?

Don't write a comment on your earlier paper. Write a short article and post it on a pre-print server, or submit it to an open-access journal, depending on your field.


Could trying to prove myself after being accused of academic dishonesty cause me to get a more severe penalty if I don't do well?

It is unlikely that the sanction will be increased if you protest your innocence. But you don't say whether you did actually cheat in some way. If you did, then you should probably accept it and move on.
But if you didn't then, to me, the "evidence" seems a bit circumstantial. If it were me and I was innocent, then I would protest vigorously to whoever would listen.
The "infraction" is likely in your file in case there is a repeat accusation. But, in most places, it won't follow you after graduation - and it would be improper if it did.


Why do past PhD exams appear more difficult than current ones?

(In mathematics:) I'd be willing to believe that pre-college math curricula, and lower-division college (in the U.S.) curricula have become easier to get through, for reasons mentioned in other answers and comments. But I think this becomes less universally so at upper-division level (last two years of undergrad in the U.S.) and even less so with regard to the sort of "prelims" that math grad students typically do/take in the first year or two of their graduate work. This reflects my observations over the last 45 years in math in the U.S.
So then how to account for the phenomenon apparently observed by the questioner? Again in my own direct experience, decades ago there were impulses to ask "interesting/challenging" questions on prelims, that even the other exam-writers might not be able to do. Some contest-like spirit, resembling the old Tripos in the UK? At the same time, again somewhat contest-like, the questions were at a lower mathematical level than nowadays. This, combined with the impulse to ask challenging questions, led to many Baroque, Rube-Goldberg-like questions whose statement alone might be difficult to parse, and whose relation with any known mathematics was unclear. E.g., very complicated questions about iterated operations in point-set topology, with delicate separation assumptions? Difficult questions about proving that a bunch of relations in a group implies another one?
After a decade or so of that kind of thing, it was apparent to me that such exams did not encourage forward-looking study on the part of the students, which was a bad thing. Often, as in prep for contests, some amusing tricks were learned, but basic, standard, useful more-advanced ideas were neglected entirely because they'd never show up on those exams. Thus, around 1989, we deliberately changed the nature of those exams to address less-tricky, higher-level mathematics that would actually be used by people in doing their PhD work. Another attitudinal change has been within the last 10 years, when we have moved completely away from surprise/tricky questions at any level.
At least at my own University, it's not at all the case that basic graduate education is being diminished in favor of supposedly jumping into research immediately. As in some comments above, it's not feasible to really start doing modern mathematics research while not knowing anything... But, yes, we do try to encourage a more active version of engagement than merely "fulfilling requirements" (even while those "requirements" are aimed to be useful).
So, in the end, I'd argue (as in other comments) that the exams are not truly easier, but just "modernized", so that some acclimitization to modern mathematics makes them seem easier in our context.
(And, yes, I recognize that in fact some grad programs in math have "thinned" their prelim requirements, apparently motivated by "getting students into research faster", but it is not clear to me that this can truly accomplish the avowed goals... though I am equally confident that programs would be disinclined to candidly discuss such a thing. The ever-increasing commodification of "research" does provide considerable pressure to degrade things...)


What to answer an author asking me if I reviewed his/her paper?

You could say something like

  "I am not in the habit of telling people whether I did or did not review their papers, sorry"

or

  "I don't feel comfortable answering this question."

Or you could defuse the question with a humorous answer, e.g.

  "I would tell you but then I'd have to kill you"

or

  "I don't remember, I always take an amnesia pill immediately after reviewing a paper"

or some similar kind of obviously nonserious smart-assery. None of these answers provide any useful information to the asker, and all of them convey some level of disapproval on your part at being asked, making it unlikely that the asker would press the case any further.


Is an actual recommendation letter (vs. the name of a reference) standard at the UK Lecturer or US Assistant Professor level?

Having made more that 50 applications for Lecturer posts in the UK, I can share some of my statistics.

Only 3 Universities of 50 asked for LoRs to be communicated through the applicant.
The majority, 47 of 50, asked for a list of references, and contact them asking for LoRs only if a candidate is shortlisted.

In the U.S. the customs may differ.


How does the author's native language impact the likelihood of having his publication accepted in an English-speaking venue?

It's probably more a commentary than an answer. I look forward to others' input on this issue as well.

As an ESL myself, I joined the English academic community knowing that language will be an extra barrier. I wrote (or perhaps still write) many awkward sentences that are grammatically sensible but funny to read from the angle of general English usage. To compensate this shortcoming, I read papers and study their styles, I read books on scientific writing, and I coauthor with native speakers. My English has improved somewhat and now I can even throw a couple trivia about academic writing in front of my native speaker colleagues. But deep down, I know it's a never-ending project, and chance is I will not be as fluent as a native speaker, and should perhaps settle for "good enough."

If I were to talk to your author friends, I'd probably ask if those submissions were anonymous. And if they are anonymous, and in multiple occasions comments like "English needs improvement" were given, I would suggest them to spend some time to work on their English rather than complain about unfairness. Non-native speakers having more difficulty to publish in English speaking channels is logical; to expect a fair ground that would totally ignore linguistic difference is unrealistic.

To formally answer the question, I have not come across with any study similar to what you described. And even there is one, I will study the results very cautiously. Native language cannot be randomized, so it's impossible to have a randomized controlled trial. This means what we will likely to see are observational studies, which are prone to missing important confounding variables: Native language intertwines with too many factors (education system, country of origin, culture, socioeconomic status, writing style and syntax construction, quality of English education, existence of equivalent concepts in English, etc.) that probably cannot be fully adjusted for in the analysis. At the end, we will likely see that non-native speakers are at a disadvantage, but the true cause of such disadvantage may be lurking elsewhere, and the true effect contributed by the linguistic difference alone is next to impossible to be parsed out.

Truth be told, I believe discrimination exists. If a reviewer reads that the data were collected in a non-English-speaking country, he/she may pay more attention to the grammar, or be more likely to suggest comments like "Please consult an editor or a native speaker in order to polish the English." I am fortunate enough to be working in the biomedical field in which most writings tend to follow a framework of being succinct, direct, and optimally simple. Most of the time I could easily parse out the ideas from the writing quality and give comments separately to both. Researchers in other fields may feel differently.


Doing more research and get publication are always good, especially if you want to go for PhD and/or follow academia path. However, as you're working full-time, I wonder if you can do intensive research as it's a very hard work. So, my answer is: Yes, it's worth to do more research but you need to reschedule your time and prioritize which activity you want to do most: work or research.


What is the proper protocol for applying to a postdoc sponsored by an one's undergraduate adviser?

I would suggest that you apply in the normal way, just as anyone else would. There may be rules for how that is done and you have to be attentive to them. Provide all of the required materials and make your best case for your application.

But you can, in addition, send the professor a simple "heads up" email that you are interested in the position and are applying. Don't try to make your case in this email. Do it in the application materials.

If you didn't have a previous relationship with the prof that you have maintained, such a letter would be presumptuous and ignored or treated as an irritant. But in the case at hand it would be a normal thing.

You aren't taking advantage, exactly, since you have no control over the process.


How good is an LoR based on a correspondence on one's paper?

From your description, it sounds like this individual has effectively functioned as your research mentor for this project.  A letter he writes for you could certainly be quite valuable as part of your application.  Graduate schools are looking, more than anything else, for the potential to do cutting-edge research as a Ph.D. student and after.

So I would recommend definitely using his letter.  However, keep in mind that this letter will not be able to cover much beyond the quality of your research output.  Your contacts with him have been much more limited than would be typical if you were working with an on-site research supervisor.  Most letters of recommendation submitted through online application management systems require the recommender to give quantitative evaluations of students' skills, relative to some other population of undergraduates.  This professor is saying that he is going to have to select the "don't know" option in multiple categories when he submits his recommendation.

That is not a big deal, but it's not nothing either.  Moreover, this professor is not going to have any way to comment on your classroom performance.  So if you do get a letter about him that points to the high quality of your research, you should make sure that you have at least one other strongly complementary letter that addresses the matters which the first letter cannot.


Can you post an article on arXiv while under peer review?

It depends on the journal.  If it is not found on their web site, ask them.


Does authorship matter when applying for academic jobs?

While obviously this can be very specific, not just in disciplines of engineering, but also perhaps to individual departments and groups of different institutions with different focuses, I'll try to give a somewhat general answer.

First authorship is definitely important - it generally shows you "did the work". An important consideration for a hiring committee is how well your research direction fits into their focus. Your first author publications show "your" own work, and that you can do research. Generally these would be impressive and in high ranking publications, to show impact and recognition from other researchers.

Your "non first author" papers are either from collaborations with other researchers, or from supervision. Having good collaborations (perhaps with other institutions) shows a good ability to interact with colleagues and others in the field, which means you can likely attract funding. An important part of an academic job is to attract funding. Collaborating with others shows that others were (presumably) prepared to work with you, and there were results.

As a supervisor though, the quality of your students' output is also important. At least in my experience of engineering, the nearer the end your name is, often the more senior you are. For the avoidance of doubt, I am not referring to the addition of senior grant holders who had no input - let's presume we have 3 or 4 authors on a paper. The first one may be a PhD student. The second might be a collaborating PhD student. The third may be a RA or more senior PhD student, who helps the fourth (the supervisor) with supervision and advising students.

To give an anecdotal example (also in engineering), I started off writing papers with only myself and advisor as authors. After a few months, I found myself helping out some new-start students, and helped them get their own first publications. I ended up as second (of a few) authors. This continued and other students would approach for help and advice, and I'd be happy to assist them. As this happened more, I obviously have less active input in the specifics of the work, more helping to plan the research, and helping to confirm findings and challenge their own interpretation of the results. This pushes you down the author list towards the supervisor position.

I suggest that you want a healthy balance of work - good, high impact first-author papers to show your skills and expertise and research ability, combined with collaboration work, showing work with colleagues at other universities, as well as in skillful supervision and mentoring of your (or someone else's) students. All these things are considered in my department, and the potential to obtain research funding (and produce good quality PhD graduates) are both seen as very important. Having no real first author publications has given people problems before, as has having no collaborations or supervisory-capacity publications.

To address sole authorship: In engineering, I find (at least in my field) that sole authorship is uncommon, and have not seen it regarded differently than first authorship on a paper with several authors. As an academic you form part of a group and it is expected you'll work individually as well as part of a team. Therefore sole author doesn't seem to be treated differently to first author.


Typical phases of student experience/motivation in academic education (e.g. PhD)

There is a brilliant book called "How to Get a PhD" by R Murray that I found really useful when I was studying. In the references to that book I found the following:

Hockey, J. (1994) New territory problems of adjusting to the first year of a social science PhD, Studies in Higher Education, 19: 177–90

You may also want to investigate studies in the Journal of Graduate Education but I cannot find any online links to its content.


How to prevent papers from being published in advance by others?

If I upload the paper to arxiv, will others not be able to use the same idea as me?

They absolutely can, but because you have uploaded your paper, you have established precedence: you can claim you had the idea and did the work first. Others can still use your idea (and you should feel flattered they do!) but they would have to cite you.
There are many papers on the arXiv that have accumulated lots of citations but have never been published in journals, e.g. this one. If the authors of that paper ever submit it to a journal, there's a high chance it will be published quickly, simply because it is so impactful.


When did it become commonplace for data set providers to ask users to cite their paper(s)?

I don't see a logical distinction in citing used algorithms vis-a-vis data sets. Both seem perfectly natural to get cited. Both are an integral part in the results you are reporting in a paper and hence should be attributed.

You're probably thinking in terms of machine learning papers, where typically a new method has to be benchmarked on a large variety of data sets. While it may seem like overkill to cite each and every data set that was used, lets not forget that whoever provided that data also put in effort and deserves credit for it. Again, this isn't that much different from citing the competing algorithms you are comparing against.

(Academic) software packages should also get cited, or at least mentioned, when they are used. This isn't really a new thing, for example the old 4-clause BSD license essentially demanded the same thing.


Why are our responsibilities and duties centralized instead of more evenly distributed?

One way to answer this question is to borrow a concept from economics known as the Pareto Principle. This principle, slightly reworded, states that 80% of the work is done by 20% of the people. This concept plays out in many different fields beyond your question in relation to academics. The talented people tend to do produce way more than the average and not so talented.This gives the appearance of centralization when it is really just the 20% producing 80% of the results


Why do we pay to present at conferences?

It costs a lot of money to put conferences on.  Generally, the fees are to help cover this.

In many fields, the majority of people attending are also presenting.  If they didn't charge people to present, they wouldn't be able to generate enough revenue from attendees to make it work.

Note that $50 is very cheap for an academic conference--in my experience, most cost hundreds of dollars. Even then, in many cases the conference fees don't cover the whole cost of the conference, and the difference has to be made up with sponsorship or from other sources.


In physics we deliberately do not prove the series converges, because we are not interested in teaching concepts like convergence.  Physics courses are not intended to be mathematically rigorous.  It just is not one of the goals.


Something similar to MBA, but with support?

I would definitely suggest the Chartered Financial Analyst program (aka, the CFA exam, https://www.cfainstitute.org/pages/index.aspx) for learning the few "hard" skills I would expect a business manager to have -
 such as, accounting, basic finance, elementary quantitative/organizational skills, etc.

Not only is it basically free compared to the cost of an MBA - total cost = $4000 is possible - it is, with regard to the relevant, real, demonstrable skills and knowledge base, far more rigorous and comprehensive than probably any MBA program (explanation below).

While I am not exactly sure what you mean by "a reasonable level of support (teaching assistantships)", if interpreted as "a desire to obtain requisite knowledge", I believe this is the best route available regardless of how much money you have. If that interpretation is incorrect, then hopefully the following will help out a bit.

While the CFA program is considered to be a graduate level program, it is not an actual university "Master's". This may be of concern when considering the culture of management and, more generally, business today.

First of all, you can get an MBA in about 2 years. Furthermore, you can do so while applying very little effort. Of course this all depends on the school, whereas the CFA takes at least 4, if you make it through. (Last I saw, success rates for the level 1 exam were 33% - has there ever been an MBA program that failed 2/3's of their freshmen class in any given year? Levels 2 and 3 have rates slightly higher, somewhere around 45-50%)

Combined with the notion that university education, especially in these related fields, has been transformed almost completely into an instrument for class division and social hierarchy (and away from learning and education), it may be (and I am certain it is) that an MBA is not for training, knowledge, skills, performance, etc, etc. but rather as a prerequisite for acceptance into the management/business class/social structure.

For evidence of this see the growth in the administrative body of universities compared to faculty and combined with absurd growth in the costs of it and ask yourself what this does to the society at large and why it is necessary. Not satisfied? Need a stat?

According to the article by Andy Beckett in a recent Guardian publication, "In 2017, half of recent UK graduates were officially classified as “working in a non-graduate role.”[1]

Combine those tidbits with the fact that evaluating the success, merit or performance of managers, or of the tatics/skills/curriculum generally associated with their education is extremely difficult if not impossible. And the idea that what you are really paying for with an MBA is the acceptance into a social class may at least seem plausible.

Now, it is apparent that I am not a fan of the whole business world and the state of higher education but, I think it is hard to argue that the value in the MBA program is not, at least in some material way, dependent on what it means for one's social status. And this value must be accounted for when accessing the CFA program which is void of such factors.

Another commonly referred to source of business school value is that of "networking". I'd love to trash that idea as it is literally the opposite of what university education purports to be (pursuit of knowledge, anyone?) but, it does in fact hold some value somehow, and that source of value is absent from the CFA.

And, in demonstrating evidence for my claims against b-school and management and to back up the idea that we cant even be sure if any of it or its teachings have any value or truth at all, don't forget that the business/MBA led world recently failed to predict, understand, or even recognize the complete collapse of the system they were suppose to understand and were completely in charge of.

If you can ignore the emotions such a statement and its content may invoke and realize that my goal is to compare the program I suggested as an answer to your question, then it should be evident that while the points I have made may be debatable, hold some amount of truth. Because of this and that I don't think I fully understand what you are looking for, I think these points are relevant when considering alternatives.

Anyways, this got long, point is, if you are seeking to learn management principles you would be fine in buying maybe a couple hundred bucks worth of books. This is essentially the CFA is combined with a difficult exam to validate yourself with. Whatever the case, best of luck.[2]

[1] https://www.theguardian.com/news/2018/jan/19/post-work-the-radical-idea-of-a-world-without-jobs
[2] Full disclosure,I passed the first 2 levels of the exam before focussing on software development. But I can attest the fact that it is pretty difficult but definitely achievable.


We use pure at our university to register publications. Maybe we also use it for other purposes, but I have only been affected by the publication part.

The registration of publications is a necessity, because the university uses this information to distribute money to different research groups (e.g. each year there is a bonus based on the number of published peer-reviewed articles in a recognised journal.

I've occasionally been assigned the task for my group to make sure all our articles were "registered in pure", and I can say that it works reasonably well. The interface is not superb, and I wouldn't like to work with it all day, but it gets the job done. I don't know anything about the alternatives.

It does also generate a fancy and completely useless person graph.


If you are on a trajectory that will let you quickly complete a doctorate, then I'd suggest that you don't redirect at this time. This depends on your country, of course, and the requirements for a doctorate. In the US, having a broad enough knowledge base that you can pass qualifying exams is a necessity and is also an advantage in that you would be able to teach nearly any undergraduate course after completion. But standards differ.
But you can always broaden your view later if a narrow view is indicated at present. And you can then do so without compromising career goals.
I'll note also, that having insight into one area of math doesn't necessarily translate easily into insight into others, even if they seem quite similar in some ways. I (retired now) had great insight into Real Analysis, but very little into Abstract Algebra. I could fight my way through algebra but it wasn't fun. So, broadening may mean a longer path than you need to travel at this instant. But math can also be synergistic, so ignoring other sub-fields, long term, probably isn't optimal.
If you are well supported in what you are doing now and the end point is reasonably in sight, then it is probably best to keep on keep'n on.  But note that this is mostly just opinion, and others will differ.


Is there any systematic approach to select/find a research topic?

I don't know whether it is standard. there may be some standards, but probably not worldwide. I personally had to write a 2-page research proposal on a topic I didn't choose.

IMHO, it's a great opportunity to choose a topic that you can like, if the topic was imposed (or changed after a few years by your supervisor) you would probably hate that, since you have this opportunity, I'd try to make the best use of it.

Systematic approach to select/find a research topic (by trylks):

Make a list of the  areas that interest you
Make a systematic literature review (so the approach is systematic) for those areas
Find research problems in the literature review and at least one that:

has not been researched yet (it's "open")
should be done next. It's in the frontier of the state of the art

a) Without many previous requirements or they will become your thesis

b) it's interesting from a research perspective
not too many people are working on it (best is zero, but that could be for some reason...). The problem if there are too many people (and you are not a part of their team(s)) is that the frontier of the state of the art may keep moving before you are able to reach it.
you have the necessary knowledge and skills to advance the state of the art in that problem
you have the necessary resources to advance the state of the art in that problem (e.g. don't choose something that requires access to the data from LHC if you won't have access to that data)
There is some economic interest in the problem and the results of your thesis (you don't need this for the thesis, but it will make everything much easier, specially after the thesis)

WRT the frontier of the state of the art, it usually looks like:

a) Some limitation in current systems/techniques that has not been addressed (specially in engineering)

b) Some question that remains open (specially in science)

c) Some question that has not been addressed (in some particular way) (specially in philosophy)

But well, research in those areas is more than that and it will be done in different ways depending on the topic. Computer science is sometimes considered an engineering (software engineering), sometimes a science (and can be empirical with benchmarks or formal with proofs) and it can be as well philosophical (specially in AI, IMHO). The kind of problem should arise from the review of the literature.

BTW: don't try to rush, this is systematic, but it will definitively take very long.


Are there any new(er) models of publishing/reviewing and if so how will they address the problems that we have today?

As I see it, the issue is not actually how publishing and reviewing work.  There are lots of alternative models out there, including modifications of blinding (e.g., Frontiers names reviewers when a paper is published), alternative approaches to peer review (e.g., IETF RFCs, math and physics use of arXiv), and decreased need for additional journals by removal of artificial "throttling" of publication rate (e.g., PLOS ONE).

Instead, my belief is that the problems we face lie more in the way in which quantification of publications is used as a proxy for evaluating significance and impact of work.  Peer review is a reasonable system, and many of the tweaks on it look like fine systems as well.  Making peer review high stakes, however, turns it into a system that people need to try to game and distort because it directly impacts their ability to remain employed and to fund their research.

Because of this, I think that any attempt to "fix publishing" will not actually fix the problem: at best, it will simply shift the focus of high-stakes distortion to a different area.  This is something that we see already, with the emergence of this great diversity of different "quality metrics," each of which is gameable in various different ways.

At the end of the day, however, all decisions about scientific funding boil down to some mixture of personal judgement and some sort of metrics.  The more that we have metrics (publication or otherwise), the more that the system can be gamed; the more that we rely on personal judgement, the more subject the system is to bias, prejudice, and cronyism.  I don't have any clear notions on how best to go about improving the balance in order to improve things, but I think it's important to have a clear identification of the actual locus of the problem that needs to be addressed.


Would an online masters degree help me to become a professor?

No.

In the US, permanent university-level teaching positions in computer science, even at small four-year colleges, require a Ph.D.  As I explained in my earlier answer, an online master's degree will not help you get into a PhD program.

For some non-tenure-track positions, a master's degree with a thesis may be enough, but a terminal/professional/course-based master's degree won't be; whether that terminal master's program is online or on-campus is essentially irrelevant.

In short, if you want a permanent teaching position, you need formal research experience.


Doing PhD in math/physics after obtaining a bachelor degree in an unrelated field

You should contact potential advisors who work in the areas in which you are interested.  Introduce yourself, explain any work you've done, and ask if they have specific feedback for moving on in your career.  You should contact several people.  If you live near a university, arranging a time to meet with some current faculty members is also a good way to go about this.