My significant other is a member of a research project that I coordinate. How to allocate funding?

I served for a couple of years on the Conflict of Interest Committee of my institution. During that time I learned many useful and sometimes counterintuitive things about the subject. The principles that should guide you in thinking about what to do to avoid exposing yourself to any accusations of policy or ethics violations are:

You should avoid putting yourself in a conflict of interest with respect to the grant and your significant other, if at all possible.

The point of the “if” qualifier is that, as you seem to believe, it may not in fact be possible to avoid without taking unreasonably drastic measures such as you or your SO resigning your roles.
You should avoid creating the appearance of an unmanaged conflict of interest, period. No exceptions.

The point of “appearance” is that it’s not just the conflict that needs to be avoided but also the appearance of one. You may be the most ethical person on the planet, or you may even know certain facts that not everyone knows that explain away the conflict and make you confident what you are doing is fine, but the appearance of a conflict can invite consequences that are just as bad, and possibly worse (e.g. a headline in the New York Times followed by calls for your resignation, a public lynching or whatnot), than the conflict itself.

The point of “unmanaged” is that if you can’t avoid a conflict - and one of the surprising things I learned is that conflicts can not always be avoided, nor is avoiding all conflicts at any cost even a desirable goal to have - then the next best thing is to find a way to manage the conflict. For example, at many institutions one can set up a conflict management plan, which may involve additional levels of oversight (for example a department chair or dean signing off on your funding allocation decisions pertaining to your significant other, and maybe additional reporting requirements such as you filing a letter of explanation justifying any such decision).
This goes without saying, but you should find out all applicable rules and policies that govern your situation.

The bottom line is, you should ask for guidance from your institution and your funding agency on how to address the situation. Have in writing documents, written (or at least reviewed and approved) by people in authority, which specify how you are expected to handle the situation. Then follow what these documents say.


You're not expressing the question in the most flattering way, but yes: most academic jobs are a mix of research and teaching (and also service / administration), and there is a lot of variation in the importance placed on each from job to job.  Some people are more interested in one than the other, and the faculty at liberal arts colleges have signed up for a job in which more emphasis is placed on teaching and student contact than a, well, a research university.

At a good liberal arts college faculty are still expected to be research active -- it's just that they spend more hours per week on teaching than their colleagues at a more research-oriented institution.  Someone who felt like writing research papers was pressure that they didn't want to face would probably be more comfortable at something like a four-year, junior, or community college, in which in most cases the research expectations are really nominal.


Should I mention that I refereed a paper in my CV/SOP?

Yes, it can be mentioned. I would put a category on your CV titled "service to the profession." In that section, mention the year and the name of the journal that asked you to referee. It's not a major point, but it shows that you're willing to be a team player and help out the journal. That speaks both to your professionalism and to the fact that the editor trusted your judgment.


Using pictures of 16th–18th century paintings in PhD dissertation?

I begin with a ton of quotes from the German copyright law (Urheberrecht, original, English translation):

  § 15 Allgemeines

  (1) Der Urheber hat das ausschließliche Recht, sein Werk in körperlicher Form zu verwerten; das Recht umfaßt insbesondere

  das Vervielfältigungsrecht (§ 16),
  das Verbreitungsrecht (§ 17),
  das Ausstellungsrecht (§ 18).

  (2) Der Urheber hat ferner das ausschließliche Recht, sein Werk in unkörperlicher Form öffentlich wiederzugeben (Recht der öffentlichen Wiedergabe). […]

  Article 15 – General

  (1) The author has the exclusive right to exploit his work in material form; this right shall in particular include

  the right of reproduction (Article 16),
  the right of distribution (Article 17),
  the right of exhibition (Article 18).

  (2) The author further has the exclusive right to communicate his work to the public in non-material form (right of communication to the public). […]

  § 51 Zitate

  Zulässig ist die Vervielfältigung, Verbreitung und öffentliche Wiedergabe eines veröffentlichten Werkes zum Zweck des Zitats, sofern die Nutzung in ihrem Umfang durch den besonderen Zweck gerechtfertigt ist. Zulässig ist dies insbesondere, wenn

  einzelne Werke nach der Veröffentlichung in ein selbständiges wissenschaftliches Werk zur Erläuterung des Inhalts aufgenommen werden,

  […]

  Article 51 – Quotations

  It shall be permissible to reproduce, distribute and communicate to the public a published work for the purpose of quotation so far as such exploitation is justified to that extent by the particular purpose. This shall be permissible in particular where

  subsequent to publication individual works are included in an independent scientific work for the purpose of explaining the contents,

  […]

  § 64 Allgemeines

  Das Urheberrecht erlischt siebzig Jahre nach dem Tode des Urhebers.

  Article 64 – General

  Copyright expires 70 years after the author’s death.

The questions relevant to your situation are:

Do you have to publish your thesis? If yes, copyright applies (§ 15) as you are reproducing and distributing the images or photographs thereof. If not, more lenient laws for private copies apply (§ 53).
Did the creators of the images die more than seventy years ago? If the images are from the 18th century or earlier, this should apply.
Did you take the photo of the image yourself? This is the most tricky question, as the photo may be a copyrightable work on its own.

Last year, a court rejected a lawsuit against Wikimedia Germany which was about using a photo of a public-domain image. The court argued that this would be an invalid prolongation of copyright that surpasses the public domain and also mentioned that a purely technical reproduction is generally not considered to be copyrightable. You can read about this here and here.

However, these links also mention lawsuits with other decisions and there is no general law about this situation.
Does § 51 (quotations) apply? – For the images, this is something that only you can decide. However, if the photograph is considered a work on its own, one may argue that you do not explain the photograph in the sense of § 51.

So, to summarise, there are several laws in your favour if you made the photographs yourself. Otherwise, you run a small risk of a copyright lawsuit, which I would consider rather low.

In general, I suggest asking the owners for their permission to be sure. Also, they may have high-quality photographs, which they can provide for you. After all, museums and similar places generally like if their exhibits are the subject of scientific works.


What should I do about a group project in which I did almost everything?

Proceed with caution. It may be that it will be your behavior that is not acceptable. Group projects are supposed to be done collaboratively. A student who takes over and does everything might actually be graded downward, just for that.

You were focused a lot (too much?) on the product. Perhaps the entire point of the exercise was to focus on process, instead. Perhaps your "team mates" gave you low scores also for taking over too much and cutting them out of the project.

So, before you "rat out" anyone, make sure you understand the requirements and the consequences.

But, if the others just refused to help and/or didn't come to group meetings, etc., then you should make appropriate comments on the peer evaluation that you did.

There are, of course, professors who only care about the product. I don't know if that was the case here, but in my course it would not be. A group project is supposed to support everyone's learning and to give practice in collaboration.


What are appropriate questions for a closed-door (non-public) part of a PhD (or master's) defense?

Generally speaking anything and everything is on the table unless you are told otherwise. There are no limits. It is up to individuals what is asked and up to those and other individuals to evaluate the answers. The candidate may not be able to answer everything.
But it probably isn't required to answer everything. What is required is to say sensible things, including "I never studied that".
But for the foundational knowledge of your field, you'd better be able to give pretty good if not absolutely ideal answers.
The (second) worst story I ever heard, though it may be apocryphal, is one in which the candidate in biology or chemistry gave his dissertation presentation in which he repeatedly mentioned pH. There was an outside member of the English department on the committee who said she didn't have any real questions, not understanding the subject, but would like some layperson's explanation of pH from the candidate. The person, who had long ago studied it formally and was able to use, froze up and gave no answer. He failed.
But maybe that was just a horror story told around grad students to scare them into working harder, something like a campfire ghost story.
In a private oral exam of my own I was asked a question and started to develop an answer (math - algebraic topology) and it went nowhere. I stopped and admitted that I wouldn't be able to finish it, but was able to say exactly what the flaw in my argument was. This actually impressed the examiners more than if I'd given the correct answer immediately, as they told me later.
So, you don't have to be perfect, but you do have to make sense. Do that and you will probably be fine, subject to the vagaries of personality.


Can I publish an algorithm without time complexity?

An algorithm that solves a problem in a new way is interesting, regardless of whether you beat the state-of-the-art, because that new way might start a new line of research that beats the state-of-the-art. But, as it stands, you seem unaware of where your algorithm ranks and establishing that is highly desirable (perhaps even necessary) prior to publication. Thus, although it might be possible to publish now, it seems better to delay publication to establish your algorithm's ranking.


Is it recommended/allowable to get a Master's degree that is not directly related to my bachelor's degree?

It is definitely allowed and even recommended based on your current interests and future ambitions. I did my bachelor's degree in Electronics and Communication. But then I did my Master's degree in Computer science. And I have not regretted my decision on bit.


Should I mention (double-blind) submitted conference paper in CV?

The biggest factor here is the stage of your career. If you're a grad student, for whom a single submitted paper might be a very large fraction of your research output. it's OK to mention it in a CV, provided you're upfront about its submitted status. However, beyond that it's counterproductive, and should be avoided.


Best practices for keeping a campus computer network from getting brought down by inappropriate use?

I see this as a resource allocation problem, not an academic freedom problem. Your network just does not have the resources to support many users with high-bandwidth demand (whether the demand is academic in nature or not), and your school does not want to apportion more money to upgrade network resources.

It sounds like you don't really want to prevent a particular use of the network; if you did, it would be in your Acceptable Use Policy. You just want to prevent a user from hogging network capacity, which degrades the experience for everyone else.

Instituting bandwidth caps (or a similar content-agnostic strategy) to prevent excessive resource use by one individual does not violate academic freedom. For example, Amtrak limits use of WiFi on its trains; streaming music, streaming video, and downloading large files are disabled. This is understood to be a reflection of their unwillingness to spend the money that would be required to support high-bandwidth content, not censorship.

If you want to make sure that students still have access to I Love Lucy and other essential academic content, you can offer uncapped network access in specific areas (e.g., in the library).

Of course, if you plan to implement this, you should announce the change, explain the reason for it, and expect students to be very, very unhappy about it. "Network" is simply one of the resources that students expect from a college; from their point of view, you are failing as a college if you do not provide a reasonable amount of this resource.


This is a really really late answer (5 years late) but a natural solution seems to me to be to use OBS, open broadcast software. I believe it was developed for people who wanted to stream themselves playing video games. So it will certainly grab content from your computer and broadcast it. Personally I have only used it to record in the past.

Note that I have no connection to OBS and it is free!


Would tenured professors who are charged with a crime generally be fired?

Criminal acts are certainly a reason to revoke tenure.  In fact, this is probably one of the most common reasons.  It is possible to terminate the employment of a tenured professor as soon as the university learns that they have been charged with or suspected of a criminal action.  (This happened at my university: it was an extreme case.)  Terminating employment because of a criminal charge is obviously a quite precipitous act to take: I would be surprised if a university did this in any situation except one in which they are sure that the faculty member will/would be found guilty of the charge.  A tenured employee who was fired because of suspicion of criminal acts and was later found innocent of these acts would have, in many cases, a heck of a lawsuit against the university.  (Untenured employees might as well...)

The things that "you heard" sound a little dopey to me, honestly.  Tenure offers some measure of job security.  It does not confer any defense against or immunity from criminal acts.  Getting convicted of domestic violence is "something bad happening to the professor", right?  Not being able to carry out your duties because you are incarcerated is a sufficient reason to fire a tenured faculty member!  In the scenario with the "stalker" it is so unclear what happened or what was reported to whom that I would not be comfortable commenting on it.  Nevertheless, one can certainly imagine circumstances in which a tenured faculty member could be fired for stalking even without a criminal conviction.


How to make a one-year study plan for a difficult exam and remain motivated throughout?

I would recommend you not to rely upon external entities for motivation. Rather then relying upon just some books and software, practice "Self Motivation".

Each day think about the happiness and satisfaction that you will achieve once you got an admission in the targeted postgraduate school.

Furthermore, browse through the list of notable alumni from the same school and make a target that you will also feature in the same list some day.

It will encourage you to put 100% effort each day without losing excitement.


Is there any regulation governing the accessibility of research papers? (to ensure they can accommodate the reading preferences of the users)

To the best of my knowledge, no such law has ever been passed (though I'm no legal expert).

Even if such a law was passed, however, enforcing it would likely be difficult or impossible:

How could one assess the accessibility of a paper that can only even be understood by a tiny community of specialists?
How could one ensure that an obscure or newly-invented notation can be translated to alternative formats?
How could one effectively force scientists to invest time and energy in compliance, when funding agencies can barely even get them to do quick and easy things like pre-registering medical studies?


How much would it cost to remove pay-walls?

Zero. The government of the nation you live in can pass a bill that mandates that all (existing and future) published research papers are made publicly available and redistributable.


How can I get a reference letter if I was never "close" to any professors?

Unfortunately you've left yourself in a tight spot.  This is actually one of the biggest pieces of advice I give to undergrads: if you're thinking of grad school, build relationships with professors.  Even to the point of skipping a class you would prefer more in order to take another (still-relevant) class with a professor you're trying to build a relationship with.

Now that you're here however, I don't think you're in an impossible-to-salvage situation:

First off, see if any of your letters of recommendation can come from non-academic sources.  In my experience it's not uncommon for schools to want, say, two of three to be professors and would take a third one from your current boss (assuming your job is in any way relevant to what you want to study).  That would get you a third of the way there.
Secondly, begin with any professors you took more than one class with - that sort of thing tends to stand out unless they're huge sections with too many students to notice them all.  Seeing your name on papers and grades twice may have cemented you in their mind enough that a gentle reminder will get you there.
Third, turn to any professors you did particularly well with, or had very small classes with.  Did you have a project and presentation that might have made you stand out?
Fourth, look for professors whose classes are particularly relevant to your desired area of study.  It may not help you much with being recognized, but the fact that your program fits their interests so well might inspire them to dig a little deeper.
And finally, if at all possible, go visit your professors in person to ask.  They may be more likely to remember you if they have both your face and name to go with your request.  If you have to do it over email, include some details to help them out; tell them exactly what class you took with them and when, maybe include a link to your Linkedin page or webpage so they can go see your picture if they want, etc.

However you end up doing it, simply explain that you weren't originally planning on grad school and have been in industry for a year, but now you really want to further your studies.  Most professors will be inclined to help you out as much as they can, or at worst they should be willing to tell you if they don't think they can write you a good letter, giving you a chance to ask someone else.


Strategies, approaches, methods for motivating innovation adoption in academia

The best way to illustrate the value of new tools is to effectively use them yourself. If you are an active researcher and you are twice as efficient as your peers, then your peers might ask you how you manage such a torrid pace.

It sounds like you are not an actual user of your own tools. Moreover, it sounds like researchers demonstrated a willingness to try your tools and were not impressed. I would advise concentrating your energies on figuring out why these researchers chose to go back to "business as usual". You are most likely to succeed if you start from the premise that they know how to do their jobs effectively.


I'm thinking about quitting my PhD program and seeking advice

I have a few thoughts. First, since you have completed comps and the dissertation proposal, there should not be any reason that you have to remain in state to finish your degree. At my university, many students finalize their dissertations while living out of state. Perhaps moving back near your fiance and family would alleviate some of the pressure that you are feeling. The downside of moving is that you would have to finance the remainder of your degree. If you do not have a large number of dissertation hours required, this may be feasible. Also, if you tell your chair that you will be moving out of state after the spring semester, he would know that he is going to lose his GA even if you do not graduate.
Dissertations are hard. All of our ideas and work are constantly being judged. It is common to feel loneliness, despair, stress, frustration,and the list goes on... I believe that the current pandemic has heightened all of these emotions making the dissertation burden even greater. I think it is also common to begin to hate the field in which you are completing the dissertation and to question if you will ever be able to use your future degree.
Ultimately whether or not to continue is your decision. Your parents will love you no matter what you decide. Will you be disappointed in yourself if you leave the program? Will you always question how life might have been different if you completed the degree? These are questions that I would ask myself.
Wishing you all the best as you move forward.


What to do if you do not understand a lot coming up with a research interest? PhD admission

At least in the US, I don’t think most research advisors would expect undergraduate students to have the ability to understand everything in their published work. The idea is to be familiar with the general ideas, methods, and “top-level” results. If someone comes in with more than that, it’s a bonus.

In other countries, where the PhD program follows after a master’s degree, the expectations are naturally a bit higher.


Should GitHub repositories be included in a resume or statement of purpose?

I would definitely include the links in your resume. Even if they're not finished, as long as they have clear documentation and everything makes sense, go for it. Before including it, I would go through as thoroughly as you can and try to read it as a third party: what does this mean, what's its purpose, how could this be done differently? Even if you don't actually change anything, it would be good to have comments and notes throughout the code that are understandable to a third party, explaining things like those 'major bugs' you mentioned.

As for where, I have a section in my CV for personal projects: I would suggest you do the same. Alternatively, anywhere where you are describing relevant interests, you can casually drop the link in. However you decide to do it, I think it would be good to give links to specific projects with a little description of what it is and why it exists. The alternative is to just put a link to your GitHub account in your contact, like you said, but I feel that sometimes that can not be very helpful. Sure, it's there for them to look at, but if you can engage them with a description of a project you've worked on and then give them a direct link to the source code, I think that has more impact than them having to look for it themselves.


How can a PhD student defend their correct ideas or claims to their supervisor?

How to defend your correct ideas or claims in front of supervisor?

If your advisor is anything like me, they care much less about right or wrong in these meetings, but they want to hear what your thought process is and which angles you have covered. Suggestions to try something else should not usually be understood as "you did something wrong, do this other thing instead" but more like a probe whether you have also investigated this other angle, and if you have not chosen it, how you justify not doing that.

As such, the central element in "defending" your idea is to, briefly but clearly, outline why you have done what you have done, and not done what you have not done. Proving stuff in front of your advisor should help, as long as you do it correctly and clearly. If it doesn't, you are either not being as clear as you think you are, your advisor isn't competent in your topic, or you have a much deeper problem (e.g., you and your advisor are not on the same page about what problem is to be solved). However, note that even an objectively "correct" approach is not immune to questioning - maybe there are other approaches that are easier, faster, or preferable in some other way? You need to have an argument at the ready for why you have not chosen them.

If looked at in that light, situations where they suggest approach A in the first meeting and then probe you on your usage of A in the second start making more sense - they have not suggested A because of some secret advisor-tech that makes them know the right answer in advance, and telling in the second meeting that they suggested the idea is not a convincing enough reason to go forward with it by itself. Even if they suggested it, you still need to explain why A was better than other approaches.

  Too many times, I have to defend my ideas or claims in front of my supervisor.

Frankly, I can hardly imagine a supervisor who questions your ideas "too much". As long as they are respectful and helpful, questioning your work and suggesting alternatives is pretty much all that good advisors do. It's kind of the job description.


Should I change PhD programs based on available recreational activities?

Go for it!  Many east coast academics, or people in general even, are not going to understand how you feel.  In my experience, for many academics on the east coat, outdoor recreation is not a priority (yeah, yeah, it's a generalization...).

You say:

  "either of those places offer me a refuge to break the work-sleep
  cycle (I am obsessed with backpacking and climbing). At my current
  institution, I feel very "trapped", like there is nothing here except
  working, sleeping, and drinking"

100% agree.  You can find a way to make grad school and your outdoor passions work together.  Just don't expect many of your (east coast) colleagues to understand this.  I have found that many academics in the west are very understanding of the outdoor lifestyle.  I've worked with researchers who live out here because of the outdoor opportunities.  The point is that sharing your honest reasons for wanting to transfer may actually help build connections.

I need to be near, or on, mountains.  This is a huge factor in what makes me happy.  I grew up in the West, but my undergrad and graduate pursuits were on the East coast because I chose to go to schools with name recognition over location.  For undergrad it was okay, but I couldn't stand it in grad school.  I turned down some great opportunities on the East coast to move back to the West.  Most of my advisors could not understand why.  Only one who loves to ski actually supported me.

As for how this will play out in industry, this is hard to say.  I am currently in industry in an area with tons of biking, climbing, skiing...  Part of the company culture is being outdoorsy, fit, and adventurous.  While the name of my school played some role in getting an interview, I think what really made me appealing was that I could connect with my future boss about all the awesome things we do.  Now I have a beard, long hair, and go on road trips all summer.  Wouldn't be doing any of that out east.


What should I do if a group project member is not contributing anything but is also depressed?

I have been in your shoes in a similar situation when I was in undergrad. Our group member was also going through some hard times and did not contribute much to any of the project reports that were supposed to be written by all of us.

What we did was notify the professor but in a way that showed we were concerned for the student. I think it makes a big difference how the professor is notified, since you definitely don’t want to put the group member who claims to be going through a hard time in a though spot (it is good to give the person the benefit of the doubt). What happened in our case was that our professor has scheduled a meeting with all of us (in your case would be a zoom meeting, I suppose) and we discussed all together what happened so far and what must happen for the group member to successfully complete the class. That worked for the person in my group, although he felt really embarrassed by this situation, he actually contributed more to the project and kind of put himself back together- not only in our project but in all of his other classes.

Additionally to this, I have contacted the person and offered to be there for him if he needed someone to talk to. At the time we were not friends and maybe this looked a bit awkward, but in the end we became really good friends and he actually became a great student for the rest of the undergrad.

So, in short, I know you must be frustrated, as well as your group members, but realize that you have to bury this frustration deep and try to address the problem while being helpful. You guys are still undergrad and have a long way to go ahead of you. You don’t want to discourage your fellow because of a small thing like a group project.

And believe me, you could help change his life by being supportive and understanding in this period.


Which letter of reference would be better: from a teacher who knows me well or from one in the same institution I am applying for who doesn't know me?

Generally speaking, the LOR that recites a lot of detail and describes a long relationship is more helpful.  When I write an LOR, I assume the reader has no idea who I am or what my standards are.  So, that's why I try to give a lot of objective information about my relationship with the student, so the reader can decide for themselves whether they agree the evidence supports my recommendation.  I'm sometimes asked for LORs from students I don't know very well.  Perhaps they're sophomore and they were in my section of a large intro CS class.  I try my best but realistically those LORs will never be as helpful as the ones I write about a student I've known for several years, was in a small class where I really got to know their work, has been in my office a lot, worked for me as instructional aide for a class I taught, etc.


Change a graph of an accepted conference paper (before submitting the camera-ready version)

Unlike with a journal, the short review and revision timeline of an IEEE conference (or other EE/CS-style conference) means that it is unusual for there to be any opportunity for additional review.  As a result, there is somewhat more trust placed in authors for making "reasonable changes" for the camera-ready, and it is typically not just permitted but even expected that authors will improve their papers for the camera-ready version.  If nothing else, they are expected to do their best to address the issues raised by the reviewers; fixing problems that they themselves have found is entirely desirable as well.

In short: if your correction does not significantly undermine the basis on which your paper was accepted, you should simply make the change, and everyone will be the better for it.


Submitting paper to IEEE journal using the standard `article`/`proc` LaTeX class

I disagree with Bill Barth's answer: I strongly believe that you should use the LaTeX classes that IEEE has provided you with.  The reasons are two-fold:

The reviewers will be used to almost always seeing IEEE submissions in IEEE standard formats.  If you submit in another format, it will likely prejudice the reviewers against you, as it will appear "amateurish."  Whether or not this is fair, it is a risk you are taking with your paper that there is no need to take.
Many IEEE journals have length constraints, and some are quite adamant about them.  If you submit in a non-standard format, it will be difficult to tell whether you are actually complying with the length constraints or not.  This may annoy the editor, again unnecessarily.

IEEE formats are pretty easy to use, and have really good instructions.  Since that is the case, I simply see no up-side to avoiding the standard formatting, and plenty of down-side.


I have been using a very simple system and am very happy with it:

have one projects directory
have one private directory
have one life directory

Inside these directories, I create one new directory per year, for example projects.2015.
Inside this directory, each new sub project gets its own folder that starts with the date at which I begun this new project, for example 20150902 rendering performance analysis. Everything related to this project will be placed inside this directory, no matter when it is done.

When your projects get too complex, you can always add a text file describing the content of your files in more detail, and place this file inside the projects.2015 folder. However, do not place anything else in this folder! Only folders starting with a date and maybe one file giving more information.

This system has worked for me for about ten years and I see the following advantages:

very easy to implement
does not depend on software that may or may not be available in 5 or 10 years
works on Mac, windows, Linux, etc
can be backed up easily, for example by placing your files on your cloud storage folder
future ready: when I started online backup, for example, did not exist yet and we do not know what will exist in the future; but system will probably be compatible.
very comprehensive: chances are you will remember what year and maybe what month you did a specific project, so it will be very quick to find your stuff.

Finally, if many projects contain a similar structure, stick to an identical organization of your data. Whatever your structure, sticking to a system will make it easier to retrieve your files later. For example, inside your folder 20150817 afm study 1055nm grating and any other measurement folder, you could have the following sub folders

00 notes
01 code
02 raw data
03 processed data
04 plots

Personally, I often use numbers because this orders the list of items in my desired way and because in Unix, Mac, etc, I can just type cd 03[tab] and the system auto completes.

Whatever you end up choosing as a system, my recommendation is that you look for something trivial to implement that does not slow you down. The more trivial the logic, the more likely you will stick to it over the years and benefit from the ordering you have.

Have fun


What does "post-secondary academic work" mean?

In your question, you say they ask for the transcript of all work.  They don't want all work, as no one has that kind of time to read it all, they just want to know your performance in each course/module/etc.

The reason they stress the transcripts of all work, is that sometimes someone may have, as in your case, completed one program but not another and they would like to see the performance from that incomplete program (or perhaps you did two programs —in full— but one was in an unrelated field, they still want to see how you did in both).

Transcripts, thankfully, generally aren't very expensive to have translated.


Can I hire someone to write code for my dissertation (if I've designed the algorithm)?

Misrepresenting the hired work as your own would be inappropriate, but the following strike me as safe conditions for academic subcontracting:

Have your advisor's consent (thanks mdiener)
Find a suitable programmer and get them to understand the algorithm
Verify and document that the program operates correctly
Disclose everything in both thesis and defense


Should a professor require students to attend classes well past their listed times?

The usual advice is to first try to work things out with the professor. In more extreme cases, if you can't work it out with the professor, you should move to their immediate supervisor, which is often the department head / department chair.

Different universities have different cultures about professors extending class. At some, it would be viewed as normal, while at others it is unheard of. So you should make sure to take into account the culture of your school in that regard.

With that being said, I think you indicated the professor is adding an extra 150-240 minutes per week (if I read the question correctly). That seems unreasonable, in my opinion, and I do think it is reasonable for you to ask for a better way of handling the presentations.  Even if the professor mentioned this in the first week, it is such a large amount to time that it could seem like an unfair imposition.

One option would be to simply email the department chair. Be very brief in your statement: one or two sentences on what is happening, and one or two more explaining how you have tried to discuss the situation with the professor. Phrasing the email to the chair as a request for advice is one polite way to raise a concern: "Here is what the professor is doing, do you have any advice for handling the situation?" That gives the chair a lot of flexibility in responding.


Recently published paper does not cite my very relevant work

That happens. Maybe they didn't do a thorough literature study before they published, or they did but before your work was available. This is more frequent than we would like to think. Note that it's generally expected from authors to have done a reasonable effort in searching for previous work, but it's not unethical per se not to reference every previous publication that could be relevant (it's also practically very hard).

  Is there anything I can do regarding that already-published paper?

No, missing a previous related work is not a valid motivation to complain to the authors or editors. Just forget about it and move on.

  Is there anything I can do to prevent this from happening in the future?

Yes, become so influential in your field that reviewers will know your work enough to spot when someone else submit a related work without citing yours.

Side note:

  I am keen on improving my h-index and citations count.

Without going into how this might not be what you should focus on (while very good researchers tend to have a high citation count, the inverse relation is not always true), the best way to do that is to produce high-quality research, preferably on a hot research topic.


How can I put my publications into Scopus?

Scopus uses its own sources for publications in the form of publisher provided content. Their selection procedure is explained here: https://www.elsevier.com/solutions/scopus/content/content-policy-and-selection

There is no procedure to add individual documents to Scopus that I could find on their help pages. You should also be aware that it can take several weeks for a published paper to end up in Scopus. Some publishers (smaller publishers typically or new open-access publishers), conferences, technical reports might never make it to Scopus though.

On a related note, the citation count will probably lag behind Google Scholar.


How to enhance my use of Google Scholar?

No, you cannot follow specific papers or journal-level keywords on Google Scholar; you can only follow researcher profiles.
However, there are other databases that support such a functionality.
Alert for specific keyword-searches in journals
For instance, on Web of Science, you can set an e-mail alert for your search keywords. Using their Advanced Search Options, you can design your keywords such that you only search in specific journals and only in their Abstracts and Titles. After you have done your search, click on Create an alert in the left menu.

The same applies to Scopus where the option is named Set alert:

Alert for specific papers
On Web of Science, click on a search result or publication. On the right-hand side, under the heading 'Citation Network' you can click on Create Citation Alert:

In Scopus, the same function can be found as Set citation alert.

Or on ResearchGate, you can get alerts for citations to specific papers by clicking Follow:


How can I best edit a paper to help get it published?

You've already talked about reading up journal articles in the field, so I'll skip that. On top of that, there are a few ways.

Follow the journal's format guide

Ask your friend which journal is the next target. Go to visit the journal website and look for the "instruction to authors." You can find format-related instruction there. A format compliant article is less likely to trigger an instant rejection/return.

Read about scientific writing

There are a few guides that I consider pretty useful:

The Craft of Scientific Writing by Alley is perhaps a classic for engineer-type of writing. It also provide a good collection of tips and gems for different sections.
Essentials of Writing Biomedical Research Paper by Zeiger is a wonderful desktop reference for biochemical type of writing. It also provides a lot of good vs. bad examples.
Writing Science: How to Write Papers That Get Cited and Proposals That Get Funded by Schimel is a bit of a black sheep. It does not teach you how to write, but it gives an excellent account on how to chain up or arrange ideas for maximal impact, done in the levels of the whole paper, to section, paragraph, sentence, and syntax. It also draws heavily from techniques used in fiction writing, which is quite intuitive.
The Craft of Research by Booth et. al. does not purely focus on writing, but also discusses how to set up arguments, present concepts. It may be a bit more hands on for you, probably more suitable for your friend who is doing the writing.
A Manual for Writers of Research Papers, Theses, and Dissertations, Eighth Edition: Chicago Style for Students and Researchers (Chicago Guides to Writing, Editing, and Publishing) by Turabian is an overall very useful desktop reference. It complements the Craft of Research.

Talk to the specialists

If the paper is really that controversial, I think you should talk to some people who have a good command in that particular field and get a gist of how to present or package the ideas with maximal chance of being considered.

Hire a professional editor

It's also prudent to know your limit. If you feel this is too much, then you should ask your friend to get help from the institute's English language support or hire a professional scientific editor. Editors can come with different specialties, some are experienced in medical writing, some are in science. Check their portfolio and try to match the article type as best as you can.

I said this because there is a problem in your question, if you feel that you're not capable of editing a scientific paper, how come you feel confident to evaluate his work with certainly such as: "My friend wrote a fantastic paper in their scientific field. I believe it is truly ground-breaking but it calls a lot of existing theory into question. If he's correct it will force many accepted articles to have to be rewritten?"

I don't mean to be insulting, just wish to point out that professional works sometimes are best left to professionals, especially when we don't have time to become one.

Best of luck, and I wish your friend a successful publishing process.

Disclaimer for everyone:

When reading/evaluating my answer, please be mindful that in no way I am agreeing that the paper is ground-breaking or fantastic. I merely provide resources to the questioner to improve his/her ability to comprehend and edit a scientific paper.

Whether someone with limited experience or capability can do ground-breaking work is not in the scope of this answer, and I have no comment either way. I just want to point out that I have not read the paper so I can't comment.


Is it a good idea to write a larger than expected project report?

If I say "3 or 4 pages" and get 5, not problem. If I get 12, my first reaction is to give minimal grade, for not following simple guidelines. If I'm in good mood, I'd read it (unlikely, term's end isn't a time for jollyness ;-), and if it really dazzles me (no rambling, no unending tables that could have been summarized in a graph or two, does the work asked, and goes far beyond it in useful direction) I might even give some extra credit (and bookmark you for later). If just longwinded explanation that could be summarized in 3 pages, again fail.


Getting peer review for research without submitting to conference or journal

The way most people do this is to call one of their "peers" and ask them to review the paper. This could be a co-worker or someone from a different department or university. If you do not know anyone, talk to someone who does.


Students using the same flawed online solution sheet as the grading TA

If the online sheet is incorrect and you suffered because of it, and if you have proof that the TA used that sheet, then you should point out to the professor of the course what has happened.

But, ask for a a comparison between your answers and those that the TA suggests. This will make it clear. The other students may suffer or not, but that is up to others. You have a right to a correct evaluation of your work and the professor should be made aware of online solutions - especially if they are incorrect and misleading students.

One set of students getting credit when they've broken rules and other students suffering when they have done the correct thing is the worst outcome possible.

You don't need to accuse anyone. Point out the online sheet. Point out the (matching) solution rubric. Show your own work and ask for a fair evaluation.


After working 10 years in the non-profit sector, will getting a PhD open new doors?

The issue isn't your age but what you want to get out of a PhD.

A PhD teaches you how to do research. If you want a job doing research or teaching at the university level, then yes, it might be for you!

For any other type of job, it will probably result in slowing down your career without opening many other doors. In the US, a PhD can take 4-7 years of full-time work with very little pay.

The other possibility is that if you really just love the subject and don't care that it won't increase your salary potential, then it might also be for you.


This happens with source files. For the .tex file that is OK: in fact, the .tex file should not appear in the proof. For the pictures, it probably means that ScholarOne doesn't process .png files: convert them to a supported file format, e.g. .pdf or .tiff.
In my experience, the above is usually enough to make the proof work, and if it's OK, submit, even if you still get that message for the .tex file.


How not to come off as boasting or arrogant, if you are one of the few active students in a class?

One good heuristic that you might use is to discriminate between two types of questions:

Questions with a clear "right answer"
Questions encouraging discussion

Questions with a clear answer are typically more about polling for whether people are tracking, and answering deprives somebody else of a chance to answer.  For a question encouraging discussion, however, your answer instead may break the ice and make it easier for other students to join in with answers of their own.  Answering discussion questions also benefits you more, since they are where your answers can demonstrate deeper understanding, if you have acquired it.

If you and your instructor both know you are doing well, then why not "step back" and leave most of the "right answer" questions for other students?  Especially if you let the instructor know that you have realized you are talking a lot and want to give space for others, it should not reflect badly on you in any way.


Was there ever a time in American history when humanities PhDs were more sought after than STEM PhDs?

While there may have been a time when the number of humanities doctorates outnumbered those in STEM, it was before 1957, at least in the US, according to this article

The number of non STEM doctorates has been pretty constant while the number of STEM doctorate has grown since the 60s. Given the difference in growth rate, it is possible, even likely, that at some time before 1957 there were fewer STEM doctorates.


In PhD admission is research internship or a job in a research lab better?

To expand a bit on my comments:

  In PhD admission is research internship or a job [at a research lab] better?

Whatever you think gives you a better research profile at the end.

If you get a job at a strong research lab like Microsoft Research (MSR), you will typically also write strong papers, collaborate tightly with academics, and go to conferences. Hence, many of the advantages you would hope for from a research internship you would also get with a job at a good research lab. That being said, you may also get swamped with tasks more focused on "transfer" or productisation tasks, which are likely still valuable for PhD admissions, but arguably less so than actual research papers.

That being said, I am wondering whether you are (without a PhD) actually competitive for a job at a good research lab. As far as I know, these labs typically hire primarily at postdoc level and beyond.


Is it bad to apply to the same PhD program two years in a row?

You are absolutely allowed to reapply to schools in successive years. However, unless you have had a substantial updated in your profile, such as through improved grades, or additional work or research experience, I would not necessarily expect a better result.

However, it is definitely possible, and if there has been a substantial improvement, the results can be very different. (I've seen firsthand examples of this in students for whom I've written letters of recommendation!)


I have an opportunity to do internship at the cost of a gap in my academic year. Should I accept it?

You will have to weigh the pros/cons for yourself. There is no right answer to this and will vary for everyone.

Potential benefits:

More time to build your CV to apply to better universities
Real-world experience
Far higher income than graduate assistantships (at least in STEM in the US)
May provide you insights into your future research directions
Possibility of publications and patents if the organization does research
Networking that you may not normally be able to do (and letters of rec)

Potential downsides:

Delays grad school which probably delays graduation and getting a full-time position
If you have already been accepted to grad programs, they may not let you postpone them
Could potentially be a distraction from your long-term goals

Note, I did 5 internships during grad school so I obviously value internships. I do suggest to be strategical about internships to see if they are taking you closer to your goals. If so, go for it!


Can I share my notes of copyrighted materials on my blog?

Needless to say, this is not legal advice about your specific situation, and if you're really concerned about this, you should consult a lawyer.

However, here are the general rules.  (Law professor here.)

Copyright protects expression, not content.  So if I read a textbook in order to learn something, and then summarize it in my own words to share that knowledge with the world, I own the copyright to the summary, the textbook author does not.
Not all text is copyrightable.  In particular, text that just represents information that can only be expressed one way isn't copyrightable.  The classic example of this is a telephone book (see Feist v. Rural Telephone Services).  But there are academic examples that would fall in the same category.  Off the top of my head, an obvious example would something like the information in a table of mathematical results (although if the table is in a novel structure, the information as laid out in that structure might be copyrightable).
Not all information that is copyrightable is in copyright.  For example, the formulas in a math textbook for a subject that's been around for a while may not be in copyright because whoever first wrote them in that form did so a very long time ago, and copyright is time-limited.
Finally, there's fair use.  That's a super-complicated subject, but broadly speaking, noncommercial uses of small amounts of copyrighted work tend to be ok for purposes like teaching and critique.  But for that, it's best to do lots more reading and tread carefully.  More information.


Data exchange between academic institutions

In France, the network RENATER, which connect many universities, publish some statistics showing the live load of links:

(the French phrase "charge des liens" in the legend means link load)

Paris area:

Metropolitan France:


How do I find researchers to collaborate with online?

First, you need to clearly identify your field of interest (for instance, Bayesian meta-analysis of clinical trials).

After that, it is up to you and your time and resources. These are some suggestions:

Look at other SE websites and visit the profile of leading
contributors (eg CV);
Check recent and impactful scholarly papers, retrieve
the email of the corresponding authors, and write to them (eg Chatterjee et al, JAMA Neurology 2013);
Look at
leading academic institutions in your field, and write emails to
selected contact people (eg David Spiegelhalter at the University of Cambridge);
Ask a local or nearby opinion leader for key selected contacts.

You need to clearly state your goals, your expertise, and your commitment, and then see if these fit. Try multiple times and multiple venues, eventually I am sure you will be able to create a fruitful collaboration.


As a new faculty, I lack the knowledge of fundamentals in my field. What should be the course of action under my special circumstance?

You indeed need to master the topic that you will teach. So before each lecture, you need to make sure that you master the content to be able to teach it and to answer potential questions from students.
Having said that, you still have some control over the content that you teach during each lecture and how you teach it. Thus, you can sometimes select some parts that you prefer to teach over others. If you use some good textbook, then your job will be much easier.  So looking for a good textbook or teaching content online can help. And you only need to master the parts that you will teach.
Normally, you should be able to prepare 2 hours of lecture in 1 day or less, even if you are not very familiar with the topic. But if you have a good textbook it can be easier. So if you have one month, you have a lot of time in front of you.
Having said that, the life of a new faculty member is generally hard the first one or two years because of all the new courses that we usually have to teach. But then it gets easier as you teach the same courses again.
When I started to teach, I had to teach three new courses on a 1 week notice, including one that I was not familiar about computer networks. That semester, I worked hard everyday from morning to evening and took a one month online course at the same time to master the topic that I would teach the next semester. Then, after the first year, things got easier, and I focused more on research again.


Progress tracking tool for managing PhD students

Like @Orion suggested, trello is great for organizing work. It is a kanban board where you express tasks as cards and you pile those cards in different decks; usual decks are TO-DO, DOING and DONE, but this is up to you. You can have different boards, one per student. It is collaborative and allows to grant access to a board to specific users (e.g. each student's board would be accessed by the student and you). you can open a card and write comments on it.

If you prefer not to depend on an external service, you can self-host a trello clone, like wekan.

Update: for Gantt charts within the kanban board approach, I see 2 options:

Pay for the Trello extension called elegantt.
Use the open source kanban board called kanboard. It is less visually appealing, but comes with a Gantt view out of the box. You can either host it yourself or subscribe to the hosted version.


How to encourage students to answers questions from other students posted in Q&A online places dedicated to the classroom (e.g. Piazza)

I used Piazza in my undergraduate business and society course last year. Students were required to participate, but I found that if I myself commented on some of their posts and then brought up some of their arguments in class that this encouraged more active posts. In particular I made a point of highlighting debates between students during subsequent class periods.


Sometimes when doing course work for university, I'd like to write
  about it on my website, or publish it in its entirety, because I think
  that other people might be interested in it.

This re-enforces your learning BUT will current students have access to it.

Once, a student from my University did this, and someone else copied from her. There was a big mess about this. Fortunately the student got a passing grade for the class.

  and most courses reuse homework questions and paper topics over
  multiple years.

and

  So my question is if it would be ethical for me to do so, and under
  which circumstances.

Instead of using exact question answer, can you create similar question and give solution. This way you are tutoring other people and making them think (and making yourself think), rather than giving the answers to students who just want to pass the class and forget what they "learned".


How to address email to professor your advisor knows

Probably "Dear Professor [name], I am a student of Professor [your advisor's surname], and (s)he suggested that I write to you about ..."

At worst, a bit of excess formality may seem silly, but it will not seem disrespectful or rude, in any case.


should I present solution ideas in a cover letter?

The big danger here would be drawing disproportionate focus on your suggestion, which you are likely giving without an intimate understanding of the research and problems that the people in the research group are privy to.

Because of this lack of knowledge of the fine details of the work, it can be dangerous to start giving suggestions as it can very easily come off as uninformed (especially to them, as they've been working on it for a while), arrogant/delusional ("does this person really think they've solved the problem after reading a few papers?"), insulting ("of course we tried technique X, does this person think we are morons?"), or woefully misinformed ("that technique is completely inappropriate to our topic - this person doesn't have any idea what we are doing but is trying to pretend they do"), etc.

It could also be a really brilliant insight, and they'll be impressed. Wouldn't that be great?

But realistically, this is like trying to throw a dart across a room at a tiny bull's eye target that happens to be surrounded by people...what's the chance of you hitting the target, vs landing a dart right in someone's backside?

So while this is not something you strictly absolutely must not do, I would urge you to be extremely cautious as it is so very easy to do this wrong. You are interested in their research and have read papers - that's great! Have interesting questions about how certain potential methods might suit their research? Great! Tell them they should just use technique X? Whether you are right or wrong, you run a very real risk of being perceived negatively.


Sole data analyst in an academic lab, is authorship viable?

With that description, especially if you write up the technique used for the paper and any conclusions drawn, you should be a coauthor. Anything else is ethically suspect in my mind. You should talk about authorship with the primary author, the lab director, or the PI about this now rather than waiting for the analysis to start or the paper to start coming together. There's no better way for resentment to start than to wait for the thing to be nearly done for you to start the conversation about authorship.


Can you add nouns/adjectives/articles in a direct quotation in Chicago MoS keeping the message intact?

You are allowed to add parenthetic words to a quote, so long as your additions are consistent with what the original author was trying to say.  The standard method is to use square parentheses to show an addition or replacement you have made to the quote.  Thus, you can write your altered quote like this:

  "... during an economic downturn, it is no easier to find a job in a region with [a] lower prevailing unemployment [rate] than in one with a higher [prevailing] unemployment rate."

By putting the additional words in square parentheses you indicate that you have added them to the original quote.  The reader will see that the original author only referred to "unemployment" rather than the "unemployment rate" in the first instance, you have added the additional word.

I tend to agree with other commentators here that this addition is probably unnecessary.  If you particularly want to frame things differently than the quotation, I would recommend paraphrasing here, instead of quotation.  In any case, the above is how you make additions/alterations to a quote if you want to do that.


Is it bad to teach high school science for a few years before attending graduate school?

Teaching experience is a good thing.  If you want to teach again after completing your PhD, the teaching experience will help you get a job.

However, I have doubts about your financial strategy.  In most STEM fields, you can expect to get paid more if you have a PhD.  The sooner you complete your PhD, the sooner you get the extra pay, and the more years you will keep the extra pay for.  I am not knowledgeable about teacher pay, but I suspect that the best American PhD programs pay students only slightly less than typical entry level high school teaching jobs in America.


Electronic supplementary materials for scientific journals

I cannot tell for Springer or Elsevier, but a couple of years ago I published a paper in an IOP journal which contained a table with several diagrams.

I submitted the diagrams separately and included them in the table's cells with \includegraphics, as I did it preparing the manuscript. It worked.

Each journal has its own idiosyncrasies when it comes to LaTeX practices. When the guidelines do not provide enough information, my strategy is to first try submitting the files as they are, following my workflow, and if it doesn't work I resort to other solutions.


Claiming that the model is the first model of its kind

In 1988, in their paper Quantum Hall effect devices as circuit elements, Ricketts and Kemeny presented a first circuit model for quantum Hall effect devices [1].

Here is how the model is presented in the abstract:

  The electrical behaviour of a quantum Hall effect device is described
  in terms of an equivalent circuit. This circuit is able to model the
  principal electrical characteristics of an ungated Hall bridge device.

In the Introduction:

  In this paper we describe the behaviour of a QHE
  device in terms of an equivalent circuit.

And in the Conclusions:

  An equivalent circuit has been presented that can represent the DC
  electrical behaviour of a Hall bridge device under QHE conditions.

This is just a random example, but I think that it aptly shows the right way to present a first model: review what is known about that device and its behaviour, so that it becomes evident that, to your knowledge, there isn't any model of that kind currently available; tell the reader what kind of model you are going to describe and what phenomena it can model.

Then, let the reader decide if it's really a first one.

[1] B. W. Ricketts and P. C. Kemeny, J. Phys. D: Appl. Phys., 21, 483, 1988.


Having worked in sales and academia, I have often come across the "how often do I contact this person" question. The answer heavily depends on the situation and the person whom you wish to contact.

You have contacted him twice thus far, and he encouraged your being persistent. I would think he would have no problem in you checking back with him every two weeks. Going to his office may even be suggested after several attempts had been made.

Try to approach the professor in your emails with courtesy, but also with urgency. Always thank him for his time, but also stress that you would like to get your research plans finalized, so if he could respond by such and such date it would be helpful.


What is the most logical course of action if your P.I does not write you a letter of recommendation in time even though s/he said that s/he would?

I'd say your best course of action is to notify the institution that you are applying to that there has been a delay, and to find someone else who can write you a recommendation within a week's time. The admissions department is likely to have a little bit of grace period for you to work with, but probably not more than a few working days. That said, they may not accept the late recommendation, but it is worth trying.


As a PhD student, I want to limit myself to 40 hrs/week. How to maintain this boundary?

First of all, I know many PhD students (also myself) who did exactly that and finished their phd:
They worked 40 hours a week (or less), had a "normal life" , knew they would go to industry afterwards and wanted to learn/do research before (and stay connected to the system "university") because they loved uni/studying. It helps that in my country, studying and also titles are traditionally seen as something valuable (so there is no feeling of "only study if this aids you in your future job" in my country).
Some students also saw it as a fun experience to live abroad before returning home.
For me, it was similar: I didn't want to become a researcher because for me the postdoc life seems horrible -- but one can do a phd realtively risk-free. (Now I teach at university).
It is certainly not possible to work only 40h with all profs/in all subjects. Maybe also not in all countries (in which one do you want to study?) Probably it is also not possible with the most famous universities/professors.
I do recommend you to do good research on your prof what kind of person they are. Is it possible to do this kind of work with them or not?
I do think your attitude "I am not dead set on completing" is great. If the prof makes unreasonable demands (or other things like misconduct), just go. When they suggest longer working hours, tell them you don't want to do this unless absolutely necessary, if they keep insisting, just go.
Do keep your eyes open while doing the phd for skills you need in industry.
Note that there are even (incredible) people who finish a  PhD and have little kids (and some of them, no partner!)
(Of course, you might have two fewer papers afterwards for a good university career, but as this doesn't seem to be your goal..)


Transferring PhD programs due to parent's sickness

Advisors are humans too (at least most of them). Most would be willing to think with you to find creative solutions. Maybe you can stay with your old institution, but arrange for you to visit the new institution. I my old institution a couple of months in another institution was mandatory. So you can keep the progress you have made and still spent some time closer to your family. Maybe, you and your current advisor can arrange for someone from the other institution to become your co-advisor. This might enable you to regularly travel back and forth as part of your normal work, and combine that with family visits.

If people are willing a lot is possible, and in situations like yours a lot of people are willing. So my advise is talk to your advisor. Don't limit yourself to that new institution. Your primary aim is to spent time with your family, and the new institution was one possible way of achieving that. Maybe your advisor has other ideas on how to achieve your aim that work out better.


Running title: "the title or abbreviated title of a volume printed at the top of left-hand text pages or sometimes of all text pages"

It allows readers to determine which paper they're looking at just by glancing at the top of the page.

If your actual title is already very short, use your actual title. If your actual title is not very short, use an abbreviated version of it as the running title. (The maximum length is often set by the publisher; for example, APA style sets the maximum length of the running head to 50 characters, APS style allows 55 characters, etc.)


Are papers published as a result of winning a competition considered worth more / less than regularly published papers? (same journal)

In my experience as reader and contributor to biomedical journals, if the journal is impactful and the prize is provided by an established entity, than a manuscript published in a given journal and awarded in some way is most always been given more recognition and dissemination than a standard manuscript.


Is the order of authors' names important?

The answer depends on the field of research. For example, in most areas of mathematics and some of theoretical physics, authors are listed alphabetically. In other fields this is different, and there typically the first author is the one that did most of the work. In such fields the first author position is the most prestigious one. The last author typically has a role more on the background, for example by posing the research project and/or playing an advising role.

I have never heard of any convetion where the supervisor is the first author if they didn't do the majority of the work.


Not Quite an Outsider has given the definitive answer in a comment. But answers belong as answers, not as comments, so I'll reproduce it here:

  "No, not really." Consult your librarian for details.

There is no single definitive store. There are several authoritative stores, and then a few that are broader but contain a lot of junk too, like Google Scholar. Part of being a post-graduate researcher is acquiring (if you haven't already), these skills & knowledge of the whens, wheres, whats, whys, and hows of search.

Work with your supervisors and fellow students to develop your own search skills.

And talk to your librarians. Seriously.


As a postdoc, how to harmonize increasing independence with relation with your supervisor

As I and others have said many times in this forum, the appropriate method to resolve such problems is communication.

It doesn't help anyone if everyone just interprets each others words and behavior without any factual knowledge what they really mean. Write B an email with content such as

Dear B,
I've given the issue of how we try to hire our graduate students for
project X some thought, and I think we're pulling in slightly different
directions. I think it would be good if we could exchange a few
ideas to make sure we're on the same page with this.

Would you be available for lunch on Thursday to talk this over?

Point being that you make implicit assumptions on why B behaves the way he does. Your assumptions may make sense, or they may not -- I suspect the latter, given that you call his actions "erratic", "feeling threatened", "wants to undermine" you. This is not how most people behave. Most people have very rational reasons to behave the way they do, but you may simply not know what these reasons are, and you will not find out if you don't talk it over in a frank conversation between colleagues.

I would suspect that ultimately both of you have the same goal, namely making this research collaboration a success, because that is in the interest of both of your careers. On the other hand, "putting someone in their place" is not in either of your interest (in particular, not in the interest of B either if it jeopardizes the collaboration). That would imply that you ascribe B's actions to the wrong motivations, and it is on both of you to clear things up.


How to quote a definition from a paper which cites another paper for the definition

In general, citing the original source is the way to go. As long as you cite correctly there is no need to worry about plagiarism.

Consequently, you should cite paper2. Since you cannot find the exact wording of the quote in paper1, I would suggest you paraphrase the quote and cite the original source with your own words.

This would be much better than citing the already referenced quote in paper1.


Should I be 100% truthful while writing my Personal Statement for Graduate application?

Yes, the Bob version of your paragraph is a good start.  But if you want to make an impact on the admissions committee, you're going to have to find out a lot more about your topic, so that you can speak about it in more detail.


Why would a European-style professor want a Ph.D student instead of a research staff? What are the advantages and disadvantages?

Well, I'm a German professor in CS - my answer is biased by those facts. Some might be generalized, though. Some answers are based on German employment rules in the public sector and those will most likely be specific to Germany.

Usually, contracts in the public sector are either permanent (horray!) or temporary positions. We have a law stating (simplified version) that you are not allowed to be employed more then 12 years in temporary contracts (if you want to know more look for the "Wissenschaftszeitvertragsgesetz" - we love those words!)

An other rule is, that for "permanent tasks" you should have a permanent position whilst for temporary / project style jobs you can hire people in temporary positions.

To make things even more complicated: A university / department usually has both types of positions and can distribute them among researchers and central administration.

If the university does not have enough positions availabe, you have to acquire thrid party fuinding. This is by definition project related and therefore temporary.

This brings me to the following:

In general, I would love to have research staff - but ressources are limited and usually you are not having too many available.
If I acquire third party funding, it is just available during the project duration - in good cases this is long enough for a PhD candidate to finish a PhD thesis (in the field of the project).
If the projects ends without the PhD candidate beeing finished, I usually try to apply for a follow-up project which helps funding the candidate. Since I want successfull PhDs afterwars, this is a top priority - and induces some stress on professors.
Yes, I could hire someone without intention to do a PhD or even a postdoc, but at least in CS industry is paying that much better, that the possible PhD is the only chance to motivate highly skilled people for this salary (which is ok, but less than in industry).
This brings me to the last point: Motivation! A PhD candidate is not only interested in the project but in his/her PhD as well. So they are usually quite motivated and it is more fun to work with motivated people.

Things are a bit different if you are in a graduate program, but most of what I wrote above still applies.

To add a few words on the comment of Monika:

At least in Germany you cannot fire a PhD student at any time since you are usually having a labour contract.
I agree that there might be strong tensions when a permanent position becomes available and it is open who might get it. But permanent positions in research are quitre rare nowadays in Germany so it does not happen that often.

Added after OPs remark:

In fact the situation for postdocs is or less the same: Usually you don't have the funding to support a postdoc for a longer period of time. With this, it is questionable why a postdoc would like to work in such an environment. Doning a habilitation / postdoc-phase and preparing for a full professorship could be a very good motivation as well. The tasks for a postdoc are usully different from the ones for PhD candidates: As postdoc, you want to demonstrate that you are capable of running a group - which involves writing grants, guiding PhD candicates, involvement in teaching, etc. Depending on your field it allows you to do original independent research for the first time (e.g. in medicine in Germany). So if you are looking for such a person in your group, a postdoc is great, but usually most funding schemes are more hands on and so it is difficult to get funding for a postdoc, unless you are having very large funding schemes.


What are the best questions to ask a PI upon the first meeting to join some of his projects?

Ask the prof to tell you about his work. Then ask what expertise/skill set is most important to him among his lab team. Listen closely and then look for opportunities to describe how your skill set fits what he needs in his lab.


It is unlikely that a single bad semester will be decisive, given everything else, especially good letters. You aren't alone in stalling for the final semester, of course. If it is burn-out, then you need to deal with that explicitly as the overhang can be pretty bad as you start a new program. You need to start with a fresh and eager perspective.
But "top 20" is an incredibly narrow range of schools to apply to. I'd suggest, instead that you cover yourself by taking a broader attack against the full range of research (R1) institutions. There is a lot of competition as you note yourself.
And, other than the small effect on your GPA a failing grade in art history is unlikely to be a block for a mathematician. You do have to fulfill all graduation requirements, of course.

From your description, I've assumed this is the US.


Is age a factor when applying for federally-funded pre-doctoral fellowships (such as NIH's F-31 grant)?

The NIH offers a bunch of comparison data of NRSA recipients.  I think you should  pay considerable attention to figure 2.9

Only about 55% of fellows receive Ph.D.'s by 30.

There is more data to be mined from the entire report -- and it shows that about 10% of NRSA recipients received their degrees at 36 or older.  Given what I think the applicant pool must be, I suggest that age is likely not a bias.

Also, the mission statement for Kirchstein states that:

  The overall goal of the NIH Ruth L. Kirschstein National Research
  Service Award (NRSA) program is to help ensure that a diverse pool of
  highly trained scientists is available in appropriate scientific
  disciplines to address the Nation's biomedical, behavioral, and
  clinical research needs. NRSA fellowships support the training of
  pre-and postdoctoral scientists, dual-degree investigators, and senior
  researchers.  More information about NRSA programs may be found at the
  Ruth L. Kirschstein National Research Service Award (NRSA) website.

  The purpose of the Ruth L. Kirschstein National Research Service Award
  (NRSA) Individual Predoctoral Fellowship (Parent F31) is to enable
  promising predoctoral students to obtain individualized, mentored
  research training from outstanding faculty sponsors while conducting
  dissertation research. Applicants for this F31 program are expected to
  propose a dissertation research project and training plan in
  scientific health-related fields relevant to the mission of the
  participating Institutes and Centers. This training plan should
  reflect the applicant’s dissertation research project, and facilitate
  and clearly enhance the individual’s potential to develop into a
  productive, independent research scientist.  The training plan should
  document the need for, and the anticipated value of, the proposed
  mentored research and training in relationship to the individual’s
  research career goals.  The training plan should also facilitate the
  fellow’s transition to the next stage of his/her research career.

As with any grant, you should ask yourself whether your situation matches the institutional aims.  I would think the more "atypical" your application package is, the more you need to consider this.

Age is a balancing act.  The older you are, the more mature you are, and the better you should be able to describe your aspirations and career goals.  If you look like you're putting off hard decisions, your application will suffer.  This is true regardless of age, but probably especially true for older applicants.


Academic CVs vary quite a bit from a traditional CV in ways that will help you illuminate your research experience. While there are plenty of (conflicting) guidelines about how to structure or format an academic CV, the following sections are generally included (if you are at the stage of your career that they are relevant), not necessarily in the order below:

Basic demographic information (name, contact address, possibly birthdate and marital status and photograph, depending on the country)
Brief statement of your research area/interests/objectives
Degrees obtained/in-progress (institution, supervisor, thesis title, GPA)
Academia-relevant jobs (e.g., research assistantships, teaching assistantships, tenure-track appointments)
Publications (especially in the case of junior researchers, also papers that are under review/in submission)
Awards or honors or grants
Teaching experience (including in labs, if you are a junior researcher)
Supervisory experience (if you have helped co-supervise other students)
Service (reviewing duties, committees on which you've served, organization of workshops/conferences, editorial work)
Research project experience (where you can outline work that you have done in a research lab)
Presentations and seminars (especially if you have been to any conferences or workshops)
International network (if it is important to show that you have international collaborators)
References (presumably your previous supervisors)

In your case, specifically, the fact that you will have submitted the paper is quite important, because at that stage you can list it as a paper (under review) on your CV.

Regarding your masters thesis, you can indicate a working title for your thesis when you list your Masters under your education. This implies research experience and the area in which the experience has been acquired. You can furthermore describe under your research project experience what skills/roles you have had in the lab in which you have conducted your Masters research. (You can also indicate here your summer internship, since it sounds like it was research-focused.)

Furthermore, you can highlight the especially salient points again in your cover letter, especially if there are elements of your Masters experience that relate to the specific PhD programme to which you are applying.


Presenting skills in a presentation for a PhD position

Perhaps you should organize it around things you have done and then mention the skills it took to accomplish that. Projects undertaken, research done, ...
Some things are more nebulous. Do you read a lot in the field, and take (and organize) notes, for example. What have you written? What sorts of organizational skills were required for that?


Which edition/version should I use for citations with page numbers

Things can occasionally get tricky, but most situations are handled by these guidelines:

Cite what you've seen.  If you have one edition, don't assume that another has the same numbering (for pages, chapters, sections, equations, or whatever) without checking.  It's always better to cite an out of date edition correctly than to risk giving an incorrect reference to another edition.
If you've seen several editions, try to cite the one that will be most useful to readers.  Recent editions are generally preferable, both because they are easier to find and because they may be more up to date in other ways.  (But if a book is out of copyright and reprinted by many publishers, then recency may not be salient.)  If you know that a recent edition is not useful (for example, because material was cut), then you should say so.  Translations may be preferable for readers who do not speak the original language.
If you can't tell which edition would be most useful, then the decision probably doesn't really matter.  The most recent edition is generally a safe choice, if you can get your hands on it to check the reference.
More detailed references can help disambiguate.  A quick numerical reference is efficient, but it becomes near useless if the numbering has changed, while adding more context can make it easier to figure out where it might have moved in another edition.


"We" when I mean "I" or should I say "the author"?

"We" is correct, even if you are the only author, by "we" you express "me and you, my dear reader". Therefore it's completely fine to use it in your thesis.


Applying for NSF (Math Fellowship) before being accepted to a university. How to find a Sponsor?

You're looking at the NSF Mathematical Sciences Postdoctoral Research Fellowships, which is for funding postdocs, not graduate study.

You probably want the NSF Graduate Research Fellowship, which is the main NSF fellowship program for PhD studies in math and science.  This program doesn't have a "sponsoring scientist" requirement.


How can I choose ahead of time where my research should be published?

Format and style should rarely, if ever, be your first concern in writing a paper. Your top objective should be describing good research to your readers. You need not worry about how to cite a paper or if you should use British or American English spellings at first. (Or at least not until you complete Rule 9!)
Instead, what this is rule is advising you to do are tasks such as organizing your thoughts, collect references, write up your methodologies, and think about the graphics you will want to use to help illustrate your points. This is more or less the same advice given by people like George Whitesides in talks and as a "editorial column."

Knowing where to publish is not that difficult. Look for where the work you're drawing from is currently being published. If many of the papers you are citing are from journals X and Y, one of those will likely be a good home for your paper. Which one to select might be a matter of which audience you're trying to reach: for instance, The Journal of Physical Chemistry and The Journal of Chemical Physics cover very similar sets of areas. However, the former journal is mainly a chemistry journal, and the latter is primarily for physicists. (There is, as you might imagine, a lot of crossover.)


Does being a poorly-performing undergraduate researcher mean that I have little chance of being successful in graduate school?

To address the titular question, no, being a "poor undergraduate researcher" does not mean you are not cut out for graduate school.  First, many people who go to grad school in math have no research experience in advance.  Second, having one bad research experience does not mean you are a poor researcher--you're not even in your third year yet.

Having bad research experiences is pretty common, and I know several professional mathematicians who've had bad experiences.  I was part of a summer program and a workshop where I felt I was in over my head and everyone else seemed to know the topic much more than me.  Fortunately they weren't my first research experiences, and they didn't last as long as an REU, so they weren't too discouraging as a result.  These experiences also provided no gauge as to whether or not I could be a successful researcher.

Research takes a lot of time, usually more than you expect (even when you expect it's more than you expect), as well as adequate preparation.  It's also hard to find good problems that are suitable for undergraduates to do in 6-10 weeks.  Part of the problem is, before you work on a project, you don't know how hard it will be or exactly what it will involve.  Therefore lots of REU projects don't amount what was hoped for.  It sounds a least like this project wasn't appropriate for you at that time.  Whether that was due to the supervisor being too ambitious or you not having the expected background, I can't say.  (There could be other reasons for your admission besides your "minority status.")  What I can say is that is easy to get the impression that everyone around you understands or knows more than you just because they're more vocal or they know different things from you.

To address what seems to be your principal concern now, the primary reason to go to grad school in math should be because you want to learn and do more math.  Getting a master's or a PhD in math does not mean you will be a math researcher, and you often don't even need to do any research to get a master's.  It's unfortunate if this experience turned you off from math, but I suggest you wait a little while to see how you feel about math.  Maybe after this experience fades from your memory, you'll get more excited about math again.  Or maybe you'll find something else that excites you, which is good too.

By the way, if you've already taken all the math classes offered at your school by your second year, then possibly your school doesn't have an environment as conducive to developing mathematical maturity as other schools.  If you do want to pursue math further, you might look into transferring, a semester abroad, or taking classes at other nearby schools.


When to include degree classifications on a CV

I would mention it and leave it on your CV going forward. It is recognized and awarded by your university. Some people might discount it and others might not.
It is a minor thing, however, as it is normally simply a reflection of your GPA. And in applications that contain the GPA, that is a more precise indicator of where you wound up.
But it is an accomplishment, nevertheless and it is valid to be proud of it.


Job advertisement: "Liaise professionally"

This one is pretty easy. The requirement that you've mentioned simply asks for some proof, at least, informal one, that a person is capable to successfully facilitate professional interactions by communicating with people from various subject domains and convert ideas and information between domain "languages". In other words, successfully act as a subject domain translator.

The simplest example of such role from the industry would be a business analyst, which most often requires to translate requirements and other project information between business-focused groups and IT-focused ones. Roles of project / product / program manager are related, though different.

Therefore, to meet such requirement, which is very typical for both academia and industry due to their collaborative nature of work, I would say that listing successful projects (with specifying roles and relevant tasks & achievements of facilitating interdisciplinary cooperation) in a CV is enough.


How to answer the diversity question during faculty interview

It's not "delivering a winning answer", any more than "delivering a winning answer" would make sense when talking about teaching and/or research and/or mentoring.

That is, the question should be about what you have thought about, or acted upon, to move forward in social issues in the U.S.  Yes, in some regards, it is U.S.-centric, though I am sure analogous issues exist everywhere.

In the U.S., the bias against women and non-white ethnicities in STEM (Science, Tech, Engr, Math) fields has existed for decades, and continues to be a problem. Meanwhile, the undergrad student population, and, in happy circumstances, the grad student population, has shifted to be significantly more representative of the actual population of the U.S. This does matter at least for the state universities (even while, ok, the state funding is rapidly declining...)

So, apart from truly being willing to think about and deal with a more diverse student population, at least in math there is interest in knowing what you may have already done to work for this... and, as a milder condition, how open you are to spending some energy on this.

Yes, traditionally, in the U.S. as in many places, such stuff was irrelevant (supposedly). Now, belatedly, and, formally, rather abruptly, "we" are trying to catch up to decent behavior.


How do you become a referee for a math journal?

Generally, you would publish in Journals, and the Section Editors will descend on you like vampires in search of fresh blood asking you to do reviews.
If you have trouble breaking in, talk to a mentor, and ask them if they can recommend you to the section editors (in place of themselves) for any refereeing jobs that are really up your alley.


This appears to be the algorithm:

Order publications by decreasing number of citations
Assign a weight to each publication as the inverse of the number of authors (e.g., 1 author paper = 1; 2 author paper = 0.5; 3 author paper = 0.33, etc.)
Take the cumulative sum of weights while this cumulative sum remains less than or equal to the number of citations for a given paper. This is the hm-index.

So, in R code, it might look like this:
hmindex <- function(citations, authors) {
    dat <- data.frame(citations = citations, authors = authors)
    dat <- dat[order(dat$citations, decreasing = TRUE), ]
    dat$weights <- 1/dat$authors
    dat$cweights <- cumsum(dat$weights)
    list(
        citetab = dat,
        hmindex =  dat[sum(dat$cweights <= dat$citations), "cweights"])
}

And here's an example using the data from the paper of an academic with 8 papers each with a certain number of citations and a certain number of authors.
citetab <- data.frame(
    citations = c(16,15,14,12, 10, 3,3,2),
    authors = c(2,2,3,3,2,2,3,1))

hmindex(citetab$citations, citetab$authors)

It produces the following output:
> hmindex(citetab$citations, citetab$authors)
$citetab
  citations authors   weights cweights
1        16       2 0.5000000 0.500000
2        15       2 0.5000000 1.000000
3        14       3 0.3333333 1.333333
4        12       3 0.3333333 1.666667
5        10       2 0.5000000 2.166667
6         3       2 0.5000000 2.666667
7         3       3 0.3333333 3.000000
8         2       1 1.0000000 4.000000

$hmindex
[1] 3

I.e., the researcher's h-index is 5 (because they have 5 papers with at least 5 citations. But their hm-index is 3 (i.e., largest cumulative weight that is greater than or equal to paper citation count).
Some comments:

So it does not distinguish between different author positions (i.e., 1st or last author and weighted more in some metrics).
If a researcher only publishes sole author papers, h-index equals hm-index. In all other cases hm-index will be less than h-index.


How can I maximize my chances of a professor of another university accepting to be my undergraduate research advisor?

For reasons completely unrelated to your own skills and background, I think your chances  here are slim. The professor has little external incentive to take you on and doing so will complicate his/her already too busy academic life. There might even be rules forbidding it, though the chance of that is small.

But, you ask how you can maximize your chances, so I'll give some hints.

This is the sort of thing you want to do in person, not by mail/email. You certainly won't get a positive answer via an email exchange. You might get an invitation to visit, but that puts you face-to-face in any case.

This is the sort of thing you want to do in conjunction with an advocate/intermediary. If you were already established in "your" college, one of your professors would be good for doing that. Especially since the prof once studied there. But if you have a current teacher who knows this person (or is known) they might be willing to intervene on your behalf, perhaps even accompanying you on a visit to the other university.

I'm not sure that waiting until you are established at university is a good thing or not. You won't have a lot of time to become recognized before you need to make the contact. But it would give you the potential for finding an intermediary.

You will need to convince the prof that you have unique skills and that it would be a missed opportunity not to work with you. That is a pretty steep climb. It would help if some of your research interests align. So you need to demonstrate that you know something of the research of the prof and how you might fit in.

But I also have a small wonder about why you chose the university you did, rather than the other one. You would maximize your chance by going there instead.

Don't worry about being/seeming awkward. Lots of people in academia are likewise.


Grad Application: Does a bad exchange semester matter?

It does totally depend on the inherent nature of your overall program. Exchanges are often considered within the main path of the program. If so, you have no way to camouflage that poor performance. But if you can, legally and reasonably, skip that part, such that your program would not be under effect of any gap, you better leave it and try to augment the rest of your academic trace.

You need to prepare official certified copy from the university, which did issue that transcript. Take that copies into account for the apply.

Best


Can I write the language specific summary of my thesis in dialect?

Not asking your university because there are no guidelines makes no sense. Since there are no guidelines, you should ask your university. Not random strangers online. They are the only ones who can answer. Ask your advisor too. If both tell you they don't care, do what you want. If one of them has some requirement, do what they say.


What is the difference between cumulative dissertation and regular dissertation?

Cumulative dissertation is probably a literal translation of the German Kumulative Dissertation, which denotes a thesis by publication, compilation thesis or article thesis, i.e., a thesis which typically consists of some peer-reviewed publications, an introduction, and a conclusion.
The alternative to this is a monograph thesis, which is written separately as a coherent monolithic work and whose individual chapters are not intended for being read on their own.

The requirements on such a cumulative dissertation differ between universities and even faculties, so you have to look into their rules for those.


Writing Thesis: Copying from published papers

A general answer for this problem can not be given here with 100%. Here some hints:

The problem you might be running in is called self plagiarism and
   different institutions allow/forbid different approaches here.
If you are planning to write the thesis like this (which is absolutely your right) then:

It is essential for you to get the guidelines of your university before starting to write (and save them somewhere where you will still be able to find them even years later)
Check the policy of the journals that you have    published in - most    journals allow to re-use published material in    your
thesis but make    sure to also print out these guidelines and keep
them.

Checking with the university and the journals (and to have written proof of it!) might save you many troubles later. Because if someone later claims that you commited self plagiarism then you can always cite the official guidelines that were in place at the time when you wrote your thesis.

You should also check with your supervisor but just having his/her oral Ok might not be enough many years later.