Should I insert a colour bar if arbitrary units are used?

I would definitely include the color bar.  It just makes things easier to read, since you can compare the displayed values directly with your eyes, rather than having to refer back to a written explanation.  The bar also lets you see how the colors shade into each other as you move along the scale.

If it seems awkward to have the color bar in arbitrary units, you can explain exactly how you came by the arbitrary units (such as "data scaled by the maximum deviation from zero").  Then you can give the bar scale a more quantitative meaning.  Or, you might go the other direction and just labels the ends "low" and "high."


What guidelines exist for volume of evidence in an undergraduate business assignment?

Context: my Bachelors degree was in Management and Electrical Engineering (double major).  Though it was several decades ago, I think I understand your field and setting.  My current PhD field is Computational Social Science and it includes some Organization Science.

I agree with your general intuitions, and the 80/20 ratio seems reasonable but I would definitely not be presenting that as a rule or even as a guideline. Instead, I would say that the nature of the paper and the arguments should dictate the use of evidence and citations.

Papers that analyze foundational ideas might only have one or two citations -- the original seminal papers.  But there might be so many ideas in those papers that the student should devote considerable space to examining them.

In contrast, papers that summarize or survey a sub-field will have a very high number of citations and quotes from the research literature.  The students task is to present the survey as a cohesive whole (if it is one) and to show how the various lines of research tie together or diverge.

Rather than focus on citations, I think its better to focus students on the principles of argumentation -- with analogies to legal arguments and formal debates.  Too often students will believe that their points are "obvious" and "common sense", or maybe "best practice", and thus requires no justification or support from evidence.  Disabuse them of those notions through Socratic questioning: "How do you know that?  Why do you believe that?  How would you persuade someone who holds the opposite view?" and so on.

Once their argument has a structure, they can begin assembling evidence to support it and defend it from criticisms. That evidence might come from published research or other sources.  But they shouldn't include any citations where they do not need support.  They also need to consider the credibility and relevance of the evidence.  No matter how authoritative a citation might be, it shouldn't be included if it is not highly relevant to the student's argument.

Here's a test that students can apply after they have written their paper, in a final edit pass:

For each citation or piece of evidence, ask:

Would my argument be weakened if I removed this?
Can I replace this with stronger evidence?

For each point in the argument or assertion, ask:

Is this adequately supported with evidence or citations from the literature?
Is the evidence and support both credible and relevant?

Have I, as author, fulfilled my role in this paper, given the nature and goals of the assignment?

Hope this helps!


Is it common and acceptable for a postdoc to leave before contract ends?

Usually, a postdoc is a normal contract between an employer and an employee, and as such, terminating it earlier than its date depends on the contract and/or the country. It should be normally specified on the contract, otherwise the laws of the country should apply. For instance, in the UK, I have had a notice of 1 month, in Italy, it was 3 months.

It is normally acceptable for a postdoc to leave before the end of the contract, although it depends on the situation. If the employer does not provide any guarantee for further employment, and if the postdoc has found another offer, starting earlier than the end of the current contract, then that's the rule of the game. If the postdoc has found a much better offer (for instance, a permanent position), then that's also the rule of the game. If personal reasons are involved (going with a partner, going back to home country, etc), that's quite fair.

By acceptable, I mean that the employer should normally not make any problem (assuming the legal obligations are fulfilled), and might even be supportive in the end of the contract. A case that might not be acceptable is to leave in the middle of a contract, breaking some work commitment (e.g., an experiment to run) for a reason that might not appear very strong. But in the end, it depends a lot on the relationship between the postdoc and the employer. The point to remember is that Academia is a small world, and that in general, it is worth keeping good relationship with former employers. In doubt, talk with your current employer, or with a mentor at the place you're working at to know what the rule normally is.


Why are positions in math so hard to come by nowadays?

The number of tenured/tenure track faculty positions in the US has been on the decline in recent years, partly because of a substantial increase in the amount of teaching done by contingent faculty (adjuncts, full time instructors who aren't on a tenure track, and graduate student TA's.)

The number of PhD graduates in mathematics has been fairly steady at around 1200 per year.  Most of these new graduates want to ultimately obtain a tenured faculty position, but there are only about 700-800 such positions available every year.

There's a clear inbalance here between the supply of new PhD's in mathematics and the number of desirable faculty positions that they can chase.

A good source of statistics on this is the annual survey done by the American Mathematical Society.

http://www.ams.org/profession/data/annual-survey/survey-reports


What's the best way to present regression results in a conference?

I'd avoid presenting tables but would focus on (margin)plots that tell a story (which, of course, is based on your hypothesis/es). Here are a few links/references that might get you started:

Using Graphs Instead of Tables in Political Science
Interpreting and Visualizing Regression Models Using Stata
Graphische Darstellung regressionsanalytischer Ergebnisse (if you speak German) or Graphical Display of Regression Results


How to Quote an ICD 10 Chapter in Vancouver style?

ICD-10 Classifications of Mental and Behavioural Disorder: Clinical Descriptions and Disgnostic Guidelines. Geneva. World Health Organisation. 1992.

This is my reference:
http://www.who.int/medicines/areas/quality_safety/ReferenceListEnsBal.pdf


How much time is usually left for authors to return page proofs? What happens if I am late?

With Wiley, the journal I edit has a one-week period for returning proofs. This is set by Wiley and not by the journal. If proofs are not sent in, at some point within another week, the typesetter will typically ask for the proofs through a production editor. This is because the typesetter has the manuscript along with, I would guess, hundreds of other proofs lined up in a production line and at some point they do not want things lying around for very long. So in this case, not much happens if proofs are late and I have never seen any serious repercussions from the publisher's side affecting authors. In the worst case a paper that has been assigned to a specific issue may be moved to a later issue since the production of issues (physical printing) is not possible to adjust other than under exceptional conditions. In the end, it will the author's loss if the paper is not published as early as it could. Since for most papers, electronic publication occurs before printing, the delay just means the paper appears online later by the same amount of time or more; it can be bumped in the production line of the typesetter in favour of those that come in on time.

In my experience, it is not possible to get corrections done after returning the proof corrections. One can always try but if the paper has been corrected and published online, there is no other option than to live with the problem or if it is in some way critical, go through the journal editors to possibly publish an errata.


Should I self-impose a word limit for a journal article abstract

Yes, you should limit yourself because the goal of the abstract is to be short.
Now, where to put the limit?

A good idea would be to look at recently published articles in this journal and note their length.


In the US and UK, at least, PhD students in he sciences and engineering generally receive funding that covers both tuition and a modest stipend to for living expenses. The exact details of the funding (e.g., taxable or non-taxable, benefits, and whether funding is given for tuition or tuition is waived) vary widely. The funding can come from a number of sources.

The easiest to understand are external grants directly to a student. The grant has a budget and the student is expected to keep the research costs within the budget. Additional costs, potentially including space charges and other overhead type fees, need to either be covered by the student or negotiated directly with the supervisor/department/university.

Grants (both internal and external, and start up funds) to the advisor generally cover a project bigger than a single student. It is the advisor's responsibility to make sure each sub project is appropriately budgeted for and negotiate with the department/university for additional money. While some students will be given an "official" budget by the supervisor, most are required to have the supervisor sign off on all expenses. Budget issues often come up during the design stages of a project.

Departments and universities also fund PhD students. This type of funding is sometimes in the form of Research Assistantships, but more often is for Teaching Assistantships where the student needs to teach in order to get the funding. Research costs can be, but are not always, covered by this type of internal funding. It is left to the student to either cover the research costs themselves or negotiate with supervisor/department/university to make sure the costs are covered.

My experimental research is relatively cheap, but I think in the vast majority of fields, the big cost is staff. Apart from possibly the most expensive types of experimental research, a supervisor with reasonable funding, will likely be able to find the money to cover experimental costs for a PhD student. It might require some limits to be placed on the project (e.g., including some modeling or theoretical work to reduce the costs).


If you work at a university and take courses, is the degree the same?

Many master's degrees have other components besides required coursework, e.g. "comprehensive" exams, projects, a thesis.  Certainly to get a master's degree you need to fulfill all the requirements.

Someone who is taking master's level courses piecemeal should check to see whether and in what way they can fulfill these additional requirements.  This may depend on the details of the enrollment.  However, in most cases that I know about, the department and the faculty won't care much about the administrative fine print, so long as the student is doing well in the courses and shows herself capable of doing whatever extra work is required.

If you do fulfill all the requirements of a master's degree, then you get a master's degree.  Whether you were employed by the university at the time has nothing to do with the degree and probably would not show up on the transcript.  By the way, in many academic fields most or all graduate students are employed by the university in one manner or another -- e.g. as a PhD student, I taught every other semester, and every semester that I was teaching I received a separate ID card listing me as an officer of the university.  I had quite a few of these cards by the time I graduated.

Added: In order to get a degree, you need to be enrolled in the program. There is such a thing as a "non-degree student"; you might want to look that up. What I and Bill Barth are saying is that, in practice, a non-degree student who is doing well in the coursework and shows herself able to complete all the requirements of the degree has a good shot at getting enrolled in the degree program.


How to deal with inconsistent advice from my advisor?

When we work on a big project that requires precise thinking and language, it's easy to get into a mindset of wanting the same kind of precision from the people around us.

But sometimes people with sloppy self-expression do have a surprising amount of helpful feedback to offer.

The less defensive you can get the better.  Try to let go of peeves about contradictions and inconsistencies, and try to leverage her comments so as to keep progressing and improving your results and your writing.


When is an academic a -sensei and when is he/she a -hakase?

I've lived in Japan for two years and can speak the language to some extent.
Keigo is complicated, and any rule you learn about seems to have lots of exceptions. After two years, I felt that I had some idea, but I felt that I had far from mastered the intricacies. In particular, older people often addressed me using keigo for reasons I didn't quite understand.
"Sensei" is a general respectful term for a teacher. Since he is interested in an academic collaboration specifically, perhaps he regards you as "senior" because you have an academic position and he does not.
"Sensei" is a general and common form of address, used for academics and other teachers. I have not heard "hakase" used as a form of address.
In any case, he has certainly addressed you with respect. If you're unsure of what Japanese title to use, and your correspondence is in English, I'd encourage addressing him in English as "Mr. X" or (if he has a doctorate) "Dr. X".


Writing a thesis: Is it a good practice to use personalized lists?

The advantage of using a simple round bullet is that it's such a familiar device that people don't notice the symbol itself. The brain recognises that it's a list structure, and immediately starts reading the items.

If, on the other hand, you use a less-common symbol, the reader will notice it, and possibly be distracted by your icon choice. That's not what you want.

There are some cases where it could be useful to distinguish the items on the list in some way. For example, you might have a list of features, and use checkmarks and Xs to indicate which are supported. But even then, I would use better icons. Most of the ones you've shown look ugly and old-fashioned, in my opinion.


Does engineering undergrad performance matter for masters in management admission?

I'll speak from my own experience.

I had only a 2.9 GPA in my major, Economics. But I had a 3.5 overall.

What may have helped me was my GMAT score (over 750). In any event, I got into several top level MBA programs, including the one of my choice.

It helps to work a year or two before applying to an MBA program. A "gap year" (or more) is probably more valuable for this degree than for other graduate degrees.


"Topics in" usually means that the content is

not meant to be introductory (i.e., the reader is assumed to already have some prior familiarity with the subject), and

not meant to cover "all the important things", but can focus on a selection of (well) topics the author is interested in.

For example, a "Topics in Representation Theory" course can afford to skip both the basic properties of finite group representations (as it is not introductory) and focus (e.g.) on quiver and Hopf algebras. Often, books will have more precise titles than "Topics in...", but lecture notes often take their titles from those of the classes, which are often intentionally vague so they don't have to be changed every year depending on the lecturer. For a department, calling a class "Topics in Algebra" is an easy way to offer a course that will be on something different each year without the trouble of having to rename it every year.


How to know whether a journal accepts concurrent submission to the journal and arXiv?

The answer is field dependent, in particular some fields in the humanities tend to consider "already published" what appeared even on a web page. Also, Glam magazines such as Nature and Science want to be able to keep the papers secret until they release them, possibly with communication toward the press. In mathematics, the most theoretical parts of computer science, and some of physics you can definitely put a preprint on the arXiv before submitting to a journal (there might be journals who don't enable this, but they would be a small minority). There is an excellent resource to determine the policy of a journal or publisher.

All of this could be gathered from previous comments. Now, the reason why I write this answer is to stress that for Elsevier, the default policy is that you can put your preprint on the arXiv and later update it according to referee's comment ("postprint" version), but you do not have the right to put the postprint on the arXiv between acceptance and 12 months after publication if the preprint was not there before. To avoid trouble you should thus put your preprint on the arXiv before acceptance (before submission being the easiest way).


How to focus on a single area during PhD?

The main point of a PhD is to learn how to be a scientist. Involved in this is to focus on the work that needs to be done but also to pick up the necessary skill to solve the problem. As an advisor, I would get nervous if a student kept moving into new areas without a plan as to what these would be useful for. So from that perspective, if a student made good progress on the research, diversions would not be a concern; without progress, it would be a problem. Where you stand in this is not for anyone to say except based on a discussion between you and your advisor.

During my own PhD, I spent a fair amount learning tools that were only of marginal use in my own work. I am now very happy I did because as now a long-time faculty member, I have come to realize that the time I had as a PhD student to immerse in topics, is hard if not impossible to recreate after the PhD. I therefore advise PhD students to use their time wisely since the tools they learn during their PhD make up the core of their future toolbox. Contacts with other researchers and research directions is a similar issue in my mind. BUT, I always had in my mind that I needed to show progress and stay with my own research tasks as a priority. Balancing between the core work and forays into other areas is a necessity.

From your question, it does not sound as if you have a good balance and I therefore think you need to discuss the thesis work more with your advisor to make sure it is clear and structured to you. Only then will you be able to see your won progress and judge when you are on track.


Can I conduct independent research and publish a paper on a H4 visa?

If by independent research, you mean that you are not being paid by anyone and are doing it on your time, then in principle it should be allowed regardless of your visa type. Whatever "hobby" you do in your personal free time is your own prerogative.


What do I do as a depressed and incompetent TA?

I utterly disagree with Mad Jack. You do not need to resign and by resigning, you set yourself up for a future where you will think of resigning every time you have a task that you do not think you will be able to complete to the high standards you set for yourself.

Try to disaggregate the two things -- the depression and the incompetence. If you are merely incompetent (or not as competent as you would like to be), read the rest of this answer. If your depression is putting you at risk to yourself or others (and will not be alleviated by acceptance that one cannot be competent at all things all the time), then perhaps Mad Jack's advice is warranted.

Now, about incompetence.

The reality is that you cannot be good at everything you do. Not all classes go well - even with the best of intentions. Sometimes, a class just fails. Sometimes it's your fault, sometimes it's the students, sometimes it's a combination. There are many classes that I've wished that I could have quit teaching halfway through.1

Sure, after you finish this semester your TA evals might be bad, they might be scorchingly bad. But that's ok. You fulfilled your obligation -- poorly, perhaps -- but you fulfilled them. The students themselves will recover. It's terrible that we can't all be always be stellar teachers, but we're human beings. You're just a blip -- one section of one of the 32 classes they take at the university.

You've found out that teaching does not come naturally and that teaching is hard. This is a good life lesson. It's part of your graduate education.  You will get better at teaching the more you do it -- or at least figure out how to work around your incompetencies. We all do.

1. In the interest of full disclosure, I also struggle from depression and so this is written to you from the position of a peer. This advice is of course null and void if you at risk of entirely melting down. Your first duty is to yourself. But only you can know how close you are to endangering your own health for the sake of the class -- not anonymous internet peers.

Anecdote: I was forced to TA a class on a topic that I knew nothing about when I was a grad student. It quickly became clear that the even the most basic students knew infinitely more than I did about the subject. I was a terrible, terrible TA but my professor worked around me, the students learned to never come to my sections or office hours, and somehow we made it work. Now every time I get assigned a terrible TA, I believe it to be karmic retribution for my past sins. So talk to your professor. S/he may have also been a terrible TA and may be more than willing to work with you on this.

Finally, mood disorders like depression and bipolar disorder are not incompatible with academia. There are many successful academics with tenure (Kay Redfield Jamison and Emily Martin have both written books on their own experiences with bipolar disorder). Yes, during our trough periods things can be hard to do, but when the fog lifts we tend to be more productive. I've used that successfully to write two books, publish numerous articles, blah blah. Fortunately I'm at a university that allows for some umm ... eccentrism in the faculty body. I am three sigmas on that scale. :-)


Should I explain my grades in my cover letter?

You only have one year of grades.  That is not many grades at all.  You said most of the grades are not from classes related to the internship.
We do not know what exactly the labs are looking for or who else is applying, so we cannot predict if you will get an internship.  But if you do not get what you want, it will probably be due to lack of experience rather than low grades.  Try again next year.
It is fine to say something like "My grades have improved because of..." and give a brief reason that implies the problem you had before is unlikely to occur again.  In your case, your reason might be "a traumatic event during my first semester."


You wouldn't be the first mathematician with schizophrenia, of course. But you also don't really say whether you want to just do mathematics in a satisfying way, or to be known publicly for doing mathematics.

And, don't be concerned about making stupid errors. We all do that. I've made some real boners that I've luckily caught in a second or third proof reading of my work. Hopefully I catch them all before publication.

While you can learn mathematics from books (and even wikipedia), doing it is vastly simplified if you have someone to give you feedback on your work. It needn't be in person and it needn't be especially frequent.

Let's assume that you keep the medical condition within bounds via professional help, and let's also assume that you aren't dangerous to the public.

What would help you advance in math is to have a mentor of some kind who is aware of your medical condition and who treats you like a human being. If you live near a university, preferably a large one, but a small college might do, see if you can visit the place and introduce yourself to a few people. Universities often have seminars that are more or less open to the public. You can also just write to a department head, introducing yourself, without details, and asking for a meeting. Go with a friend if necessary. Take some of your work. See if you can't wrangle an introduction to someone who works in an area you are interested in. A high powered researcher with little time for distraction probably isn't the right mentor for you, but if your work is "interesting" some professors might be willing to look at it.

It is also possible to make a link from a distance by simply writing to such a professor, stating your interest, showing some of your work, and stating initially that a medical condition prevents your formal participation in most activities. You don't need to say more at the beginning, and can decide later whether revealing more is a good thing or not.

If you can make a link then you have a feedback mechanism for your work. You might even have a conduit for joint publications if the work is promising.

Once a link is made, you needn't necessarily interact in person with your mentor if that is difficult in any way. There are many collaborations that go on internationally simply using email, so distance is no longer a problem after initial contact.

Many mathematicians have worked long and hard in obscurity and done fine work. Sometimes their work is superior to the general run of it since they have their own way of looking at problems. It isn't impossible that the wiring of your brain gives you an advantage in mathematics if you can learn how to exploit it.


How do I convince my professor to keep me as his student?

It's possible that you really aren't capable of doing the work, and that your advisor thought about this for a long time and decided that the kindest thing to do would be to drop you now, before you waste more time.

It's also possible that you weren't really applying your advisor's criticism - for example, you weren't taking him seriously when he told you not to get distracted by new ideas, but to focus on making progress on your original research. Your advisor felt that he was wasting his time because you weren't listening to his advice.

You should really talk to this professor's other students, and find out how they experience him as an advisor. If the other students get along just fine with him, and only you have this problem, then it's possible he just can't work with you.

However, in that case, he should really have spoken to you about the possibility of dropping you before he did it.  (Not just making comments about your work, but explicitly telling you, "I can't keep working with you if this continues; this is what you need to do to show me you are making enough progress to continue.")

In any event, I'm going to answer this question as if you are a capable student, and your advisor is just unwilling to let you learn and work at a reasonable pace. (Obviously, I don't know you, so I don't know if this is true.)

In that case,

If your advisor isn't prepared to deal with a student who is capable, and clearly eager to learn and improve, then you should really reconsider wanting to work with him.

There is a professor like this in my department - brilliant, great to talk to, and there is a lot one can learn from him. But he is under a lot of pressure to produce results (he's new, like your advisor). He is constantly making "threats" to get his students to produce work (e.g., telling them their funding the next semester depends on whether their next conference paper is accepted - although he doesn't follow through on these threats). He isn't willing to let students grow and develop as researchers - he expects them to work up to his standards, immediately.

This professor's students are leaving him in droves. They are either leaving school with an M.S. (instead of sticking it out for the PhD), or switching to another advisor. As a result, he's only published one paper in the last two years (which is far, far below standard in his field).

So, you should think about whether you really want to work with this professor, and consider asking the grad coordinator for another advisor. If this advisor is not a capable advisor, you will not be successful with him, no matter how brilliant he is.

If you decide you really want to work with this professor, do not approach this meeting as a student who is begging an advisor to keep them on.

Rather, come as a student who is willing to stay with this advisor, but understands that both of you need to change for this to work. He will have to give you a reasonable chance to learn from, and apply, his constructive criticism. In return, you will agree to take his advice seriously, work hard, and do your best to improve and succeed.

Talk about how highly you value this professor's experience, and how much you want to learn from him. Explain that you take his concerns (about getting stuck with simple things and getting distracted with new ideas) seriously, and want to work on fixing those things - but that growth takes some time.

And of course, if you are able to work things out, and you continue with this advisor, make sure to talk to him often about what he expects from you, and how you are living up to his expectations. Work hard to apply his advice and improve your research skills, and make him aware of these efforts so that he doesn't think you are ignoring his advice.


If I start in an area I don't feel too excited about, is it possible for me to eventually return to what I truly like?

Let's see if your department can get its act together to do right by you.  Here's what I would suggest:

Write up your specific efforts to start working with a professor on a research project in your area.  Keep it all very factual and neutral in tone, and keep it to one page maximum.  Then make a cheat sheet (outline) that will help you present your information in a conversation.  Make an appointment to speak with some department administrator, maybe you have a dean of graduate studies, for the purposes of asking for advice.  Explain your problem, glancing at your cheat sheet as needed, and then leave the long version with him or her to refer to after you leave.  Ask the dean when would be a good time to meet again for follow-up.
If s/he gives you specific suggestions, try not to let your frustrations show at the beginning, and even if you know the suggestions are a waste of time, do make a good faith attempt to follow them; then report back.

If, after this, your department doesn't solve the problem, then you'll need to take some initiative.

(a) Apply elsewhere.  Apply to at least one "stretch" school.  Even a school that is not top of the line should handle this better than your current program has been doing.  Make sure that the departments you apply to have at least three people who do the right kind of work.

(b) Look for a mentor to work with from a distance.  Here's how you find one: read some papers, write to an author with a question about a paper you read.  When you get a friendly, encouraging response from someone, then you can explain the quandary you are in and hopefully start getting some guidance.

I suggest you send some applications right away just in case.  In other words, it would be wise to start with 2a because we're already in January.  Then comes 1.  While you are waiting for things to percolate, you can start working on #2b.
I studied math programming at UW-Madison (a long time ago).  You should not have to switch streams just because your department can't get its act together.


Applying to theoretical physics Masters in Europe while not having a physics undergraduate degree

This is a tough case. In many European universities, the expectation for master's study in a given discipline is a bachelor's degree in that discipline. Whether or not it is possible to petition for admission with another degree is up to the regulations of the particular university. However, if you do not have formal coursework available demonstrating that you have the requisite background, it is unlikely that you will be able to get approval.

Your best bet might be to look for programs that are interdisciplinary in nature, as they tend not to have such stringent requirements.


Is attending conferences while teaching considered an absence?

While I have never experienced a department that defined "absent days", if your department regulates these things, you need to ask you department chair what the policy is.

Departments that I am familiar with expect you to either teach when you are supposed to, arrange someone to cover the teaching, or rearrange the session. In some situations an out of class activity wold be acceptable and in rare cases outright canceling of the class. One should try and keep these to a minimum, but to the extent that the students are not complaining, you can probably get away with it.

I have never seen a department which limits the number of conferences, but if you are rarely around, it will probably come back to bite you. In general, if you are worried about these things, you should ask a senior colleague.


Should I request a letter of recommendation from current employers that don't want me to leave?

Without further information, I would assume the department head and dean will behave ethically and ignore the conflict of interest.  They should understand you want to hedge against losing the competition for the tenure track position. Therefore you could use them as references.


Since the course overview note is credited to Professor Z, that's who I'd cite. But you could include all the authors in the citation itself if you liked, for example:

Professor Z (2013) Title of the Course Notes. Distributed as part of the course materials for DEPT304 Course Title in Fall 2013, a course developed by Professors X and Y at the University of Hishouse. Available online at http://example.org/.

Of course, it would be ideal if you could find a more widely available source for this information; it might be hard for your readers to track down this one course overview note, but if you could find the same information in a textbook or a review article and cite that instead, I think that would make their job a lot easier!


How do I give credit to some image I included in my paper?

First of all,

  permission which could take a while

Is not entirely correct. Most major publishers have an automated "permission request" system that in many cases automatically grants you permission to reuse a figure from a published paper. It takes about 5 minutes and usually you can find it in the journal's home page.

  Now the reviewer asked us to give credit to the original paper. How do I do that?

This isn't too hard. One way, for instance, would be to add to the figure caption: "Redrawn after Smith et al. (2005)". I think it also depends on what the figure is about. Is it a graph with data points that you used? Is it some schematic drawing? If you edit your question to better describe the figure we can give you a better answer.


Colleague blames me for not spotting typos when I only reviewed the structure and content

"The only real critique I had on my thesis was that the chapter I sent you had typos. I went through this chapter again and found quite a few. In the future when someone asks you to review a chapter you need to carefully check and find typos because it's embarrassing to send a final thesis with a chapter filled with typos. Its disappointing when you rely on someone and they screw you I hope in the future you do a better job."

This is unfair. What happened was, at best, a miscommunication on their part. They somehow thought you would check thoroughly for typos, which you did not have time to do. Unless you told them "this chapter is perfect and doesn't need more editing", I have trouble imagining why they would assume the chapter was camera-ready.

Let me start off by admitting that I am able to see my fault in this. I could've (should've) done a more thorough job in editing.

I don't see that as a flaw. If anything, perhaps you could have communicated more clearly about what you were able to do, as well as what you did not do (thoroughly check for typos).

I feel ultimately it is their graduate thesis and their responsibility for its contents.

Exactly right, and this is truly the "bottom line" here. No one else is responsible for the content of your thesis but yourself. Getting help does not absolve you of the responsibility to proofread your own document and when you defend, you are supposed take full ownership over what is written.

what I do care about are the things they are telling other people about me (ie I screwed them, I'm lazy, etc).

The word for this is "bullying". This behavior is not acceptable and should not be tolerated by you or anyone else.


Should I use the book that is recommended by the professor?

You would probably just be making additional work for yourself by using a different book, even if it is superior. That doesn't mean that you shouldn't do one thing or another, just be prepared for the extra work that might be implied. This might be especially true for exam preparation.

Some professors will ask students to read a section of the text before a lecture so that they are prepared for what will be said. Usually this would be by chapter/section rather than by named topic.

But, if you have the option to speak to the professor you could ask him this question, mentioning the other proposed book(s) and getting his advice. Perhaps he will tell you why it is ok or not ok. Perhaps there is some feature of the suggest book that he will be especially dependent on for the course.


How can I motivate the teaching assistants to grade more strictly?

You have a bigger problem than encouraging stricter grading. You need to provide consistent grading. Otherwise your scheme is fundamentally unfair.
For starters you don't have an option to fail to provide a proper rubric. If you aren't doing that, then you are failing the students. If it is a lot of work to do it, then you have a large task, but a required one.
You can make the rubric as strict as you like (though I don't really like the concept of narrow interpretations), but it has to be clear to your TAs and it has to be reasonable to your students.
One way to assure some consistency is to have more than one TA involved with each student's work. They need to agree with each other or appeal to you for a judgement. If they enter student grades into a spreadsheet you can easily see the differences and can also use it for further TA training as needed, such as, for example when one TA is consistently "too" lenient.
For an exercise with lots of parts, it might be possible to have each TA responsible for only one part. This tends to work for final exams where students answer questions, but less well for programming assignments.
Another way to achieve a good rubric is to have yourself or a small team of advanced TAs scan the student work without grading it and use what they learn to refine the rubric to assure consistency. It is probably a mistake to use this trick to create the rubric in the first place, but it gives you an idea of where the students are going wrong and need correction. An overall view. Once that is in place, the actual grading can occur.
Another trick, though not very easily done in pandemic times or with a large pool of graders, is to bring everyone together in real time to grade all the papers. This could possibly be done online (zoom) and you could be present to answer questions and make decisions.
But, again, consistency is a requirement. The rubric needs to be complete to assure that. The "strictness" is a secondary concern, but could be improved (your idea, not mine) with a proper rubric that everyone finds clear.

Moreover, if you try to grade things on a fixed scale that are fundamentally "fuzzy" then you have an impossible task. If you can define "efficiency" in your example, then fine. But if it is a fuzzy concept then almost every rubric is likely to leave the grading to intuition. Give precise grades on the things that are precise. But for other things, judgement and a bit of compassion are probably needed.
In CS, some things are clear, of course. If a student uses bubble sort on a large array it is clearly inefficient. But selection sort is more efficient than quick sort at a certain scale, which is why library versions of quick sort normally drop back to selection sort for small sections of the initial set.
But judgments about "proper factoring" of code are judgmental. If your feeling is "I can't define it, but I know it when I see it." then it is nearly impossible to provide a rubric that will be used consistently by a group of TAs.


Career Advice (Math Major): Industry or Academia

That sounds like a tough decision but I see no reason why your long terms plans need to be decided now. Keep your options open by enrolling in the graduate level classes that will help you academic applications AND find a summer internship in industry.

Make your decision only after you have applied to grad school (see where you are accepted) and have a better feeling about what you might want to do in the private sector (go on lots of informational interviews).  It is easier to change paths (and leave a PhD program early for industry) than the other way around.

I say act as if you are planning on going to grad school but have a backup plan in case you find an industry job you really like or are not accepted at the grad school of your choice.

Good luck!


Citing a previously unpublished master’s thesis, can I simply use part of my thesis to apply to a conference?

It sounds like you're rewriting your previous research into a publishable form. That's completely above board and very common. You wouldn't have to cite your masters thesis because the thesis is effectively an earlier draft of this paper.

See this related question, except the OP wants to turn a published paper into a thesis.

See also this related question, where I asked about self-plagiarism in conference talks.


How can we find who owns an old book's copyright?

Columbia University Libraries has a helpful document that provides guidance on determining the copyright status of books published in the United States. The guide provides links to online resources to allow you to determine the copyright holder.

  Researching the Copyright Status of a Book: Protected or Public
  Domain?

  A project of the Copyright Advisory Office Columbia University Libraries
  Kenneth D. Crews, Director

  www.copyright.columbia.edu


How to proceed when one peer reviewer gives a much lower score than the others but provides no negative feedback?

My suggestion would be to ignore the scores and focus on the comments. For any comments from anyone that are positive, thank them. For any comments that are negative say how you intend to address them to make the project better.

Fighting over the scores is a matter of interpretation. Ignoring C's positive comments leaves out an opportunity.

Don't think of it as a "rebuttal" but as a "response". Focus on the positive aspects whenever possible and on how you can address any others. Leave the interpretation for others as they will do their own interpretation in any case.

Perhaps C is just known for this.


Is it possible to have a PhD advisor from another university?

Extrapolating from the very few cases that I've seen, I think you'll need an official adviser at the school where you're actually enrolled.  If it's OK with that adviser, then you could also have a "real" adviser elsewhere, on an unofficial basis.  Your school may have some paperwork to be completed if your real adviser is to serve as a member of your official thesis committee.


What would be considered a "competitive" application for mathematics postdocs in the US?

There's no simple answer.  In particular, there are no quantitative standards for how many papers you need.  For postdoctoral research positions in mathematics at top departments in the U.S., it works roughly like this.  (For those from other fields, note that these positions are filled by departmental search committees, not individual professors, and they often involve some light teaching but are focused on research.  The postdocs are independent researchers, not under the direction of any professor.)

Teaching experience and the teaching statement don't matter much for these jobs.  The department will want to know that you aren't a truly terrible teacher, so you won't raise tons of complaints or create a serious problem if you teach a class, but they won't really care whether you are an excellent teacher or just minimally adequate.  (At best that would serve as a tie breaker between otherwise equally impressive candidates.)  Just write something sensible and uncontroversial for your teaching statement and don't worry about it much.
Quality matters much more than quantity for research papers, and trying to write more papers at the cost of writing worse papers is generally a bad trade-off.  In practice, the typical number of papers varies a little by subfield.  In some cases (such as theoretical CS), it would be very unusual to have only one paper, and it had better be amazing if you want to get a job that way; in some other subfields, having half a dozen papers might make people suspicious regarding their quality.  To gauge how your application compares, you can try looking at the CVs of people in your area who have recently started the sort of job you'd like, but keep in mind that counting papers won't reveal their quality.
Strong recommendation letters are absolutely crucial, and getting good letters is worth a lot of time and thought as well as preparation in advance, for example by talking with potential letter writers so they are familiar with you and your work long before you apply for jobs.  Choose your recommenders carefully, and don't limit yourself only to people at your university.


In a CV, how do I list my status of a PhD if I completed the oral exam, but not awarded officialy?

I was advised by my supervisor that on completion of the viva, I would be informed immediately (orally) of the outcome, and from that point I would 'officially' hold the PhD qualification.

The corrections/amendments and the committee/Senate meetings are effectively rubber stamps, providing you actually submit the corrected version.

And so in your position I would state that I have achieved my PhD on the date of the viva within my CV.


How to select which conferences I should attend?

There are many different types of conferences and many different reasons to go to a particular conference.  The most relevant that I would say for your situation are:

Flagship conferences that everybody in a field goes to because that's where everybody goes, and where research presented will get the greatest audience.
Niche conferences and workshops that serve some particular smaller interest group.  They are less prestigious, but are where the communities they serve have a lot of key interactions and get a lot of actual intellectual work done.
Crap conferences that would like to fool you into believing that they are one of the first two.

Some good tactics for judging the quality of a conference:

Where do the people whose work you respect (particularly your advisor) publish and attend?
Where are the organizers and program committee members from?  Are many of them from high-profile research institutions?
Google Scholar metrics

Given your early stage and breadth of interests, I would recommend going to one of the broad flagship conferences, where you can hear about lots of things from lots of different types of researchers and organizations.  Those conferences often have a lot of industry attendance as well.  I don't know your specific field too well, but even from outside I know that USENIX is a large conference with a strong reputation.  Still, use the heuristics I suggest and see if it's really the one you want...


How to find the right balance between a challenging and an enjoyable mathematics exercise session?

As a grad student now who took undergrad linear algebra with a professor I really liked, I will attempt to generalize what I saw that worked.

The best way for students to learn something that is as potentially abstract as linear algebra is to relate it to something concrete. My professor always liked to point out that once you leave R2 and R3, everyone visualizes geometry differently. As a result, he often tried to keep his visual explanations in that space.

However, for higher dimensional vectors, you can still relate the material to multi-dimensional concepts without drawing a picture. A great example (and pretty interesting exercise) is Markov chains. When we went over eigenvalues and eigenvectors, we motivated all of the math by walking through Markov chains. He used Markov chain gambling schemes (e.g. holding a bet steady when you win, doubling when you lose) to illustrate eigen-decomposition in a practical way. In that way you can help students develop intuition by talking about something that makes sense outside of the math-sphere.

In terms of practical exercises, I've found that progressive problems tend  to work best. That is, where each problem is working towards one ultimate problem solution. Generally, each step is a little more complex as well. For example, maybe the first step is finding the Eigenvalues and Eigenvectors, the second is diagonalization, the third is something tangential like inverting the matrix, and the last is applying what you've calculated to some practical problem like a Markov Chain.

In other words, ease students into the harder material by showing them the simpler ways to do it first. Once you can intuitively understand the general concept at basic level, it's easier to move on to more advanced views of the same and similar concepts. Plus, when students see complex material from the viewpoint of something simpler to understand (like maximizing gambling winnings), it provides a reference point for them to start from.


What would be the best way to find foreign professors for a PhD defense panel?

Given that you've written a thesis on the topic, you should know who the experts are.  They are the authors of the papers you read and cited.  Hopefully you have also met them at conferences.  Of course, your advisor should also know these people.


Send introductory email to foreign university professor ahead of classes

My advice is: Do not do this if you just want to introduce yourself or establish a line of communication. For those purposes, just talk to the professor in or after class or leave it all together -- just like the professor wants.

If you have more practical reasons (like if you need to review someth.), do this before and per email. (I'm assuming here that you read all inform. about the courses and do not ask about information posted e.g online.)

If you think there is a chance the courses could not be in English, I would also advice you to ask beforehand. (If the program is advertisted as being in English, I think you should not ask.)

If you send something, I would advice to speak with your classmates and send it together with them (in all their names, after they agree). This advoids you to be seen as a social weirdo who secretly wants to get advantages - after all, the information is important for everyone and you want everyone to have a great experience.


If you're paying nobody cares. Being rejected from a self funded masters program if you have demonstrated a degree of competency is pretty low.


What should I write in a personal history statement (diversity statement) if I am not at all diverse?

Concisely and honestly.

You'll look like an idiot if you cite your love of [insert minority] or your [questionable claim] heritage or your vast experience with [sympathetic cause].

Instead, just write a brief statement that explains how you'll bring "diversity" to the program through your interests and experiences. You can also briefly mention your cultural background. The key thing is to keep this concise and not to say things that you wouldn't feel comfortable saying to a professor in person over a conversation. The common trap is to "pour your guts out" or to pander by making tenuous claims.

If this is an optional statement, you can skip it (particularly in STEM fields), but most people use this as an opportunity to "humanize" themselves by telling non-work-related stories.


Academic career start: Postdoctoral or AP

Well, probably about the "long term carreer" it depends on the laws of the country you are working in. Moreover it is related to the type of studies in which you are involved in the "world leading university" compared to the "average university".

In my humble opinion you should decide first of all with the feeling that you have with your future working group. In fact the rank of the university is just an index but you should love the research you are involved and give everything to be one of the best in your field.


Why did my professor criticize my performance indirectly?

Your advisor said, in the context of a conversation on a new student picking up some of the workload in the lab,

  xslittlegrass is not productive as before

and you seem to have interpreted this as a personal criticism, i.e.,

  xslittlegrass is not working hard enough. I'm disappointed with xslittlegrass's performance

I question this interpretation. Your advisor is eager for the new student to arrive because she recognizes that there is a lot of work to be done on the current projects in the lab, and that your attention is on other things right now - hence your low productivity. That's not necessarily a bad thing. You simply can't "produce" a lot on "your" project right now.  You have been splitting your time and efforts between multiple things: your exam, the collaborative project, and "your" project.

Next year you'll be even less "productive" - you'll be writing your thesis, devoting time and effort to your job search, making sure ongoing projects transition smoothly when you graduate. That's a good thing :)

I also question your characterization of the situation as "under the obvious condition that I can hear it" - your advisor probably did not expect you to hear this conversation. As you said "usually I will close my office door when there is a meeting outside" - so usually you do not hear meetings going on outside. I don't think your advisor noticed your door was open, thought "xslittlegrass can hear this meeting," and decided to use it as an opportunity to give you some indirect criticism in middle of an unrelated conversation.

If you are really concerned about this comment, it's often helpful to have a "checkup" with your advisor. You can ask her directly: "Are you satisfied with my current work? Do you think I am allocating my time and efforts in a useful way?"


How can I convince my postdoc advisor to end my contract early?

Just explain your situation to your advisor.

Say that you are sorry to leave and explain why the new opportunity is great for you.

You do not need to come up with reasons why you leaving early is great for your advisor. (It isn't, but they will understand.)

Advisors worry about your future.


How to argue with postdoc hired for a project, to work on tasks from another project

You can switch her to another project if you have the funding for it. What you cannot do is to have her work paid by one H2020 project to carry out work for some other separate project. If that's what your postdoc says, she is right.
However, even in your existing project, there should be sufficient leeway to do work on good publications, research etc. and improve the work that you have carried out on the core project. Research never stops.
Alternatively, if you have funding for another project, then you can ask for the budgets to be reassigned (Edit: if she agrees) so that she is paid through the budget of the other project. That's perfectly acceptable, albeit you may have to return some of the budget of the original project she was hired for if that is not used in its entirety.
What you cannot do is to have the original project budget pay for work carried out on another project.


my article has been evaluated since 17 months. what do you think about this situation?

If they're not answering emails, that is a very worrying sign. I would suggest sending an email to the editor (cc'ing the editor-in-chief and any other relevant people at the journal) saying that you are very concerned that they are not answering your emails, and that if they don't answer this email, you intend to withdraw the paper.

Then, if they don't answer the email within a reasonable time, send them another email withdrawing the paper.


Is it bad style if a section has exactly one subsection?

Having a section with a single subsection is usually considered bad style: most style guides, academic or not, advise against it. In particular, the Chicago Manual of Style advises against it.

Regarding the reasons why this is considered bad practice, I'll quote Wikipedia:

  Single Subsections
  Just as your English teacher told you, if section 2 has a subsection 2.1, there'd better be a section 2.2 as well. If you see a section with a single subsection, you have three choices:

  If there's a lot of text in the section, followed by the subsection, you ought to be able to carve out a good subsection from the initial material, or even two, to create multiple subsections.
  If most of the section's material is in the subsection, you may not need a subsection. Just combine the two.
  If the content of at the top of the section is short and substantially different from what's in the subsection, you might be able to promote the subsection (for example, change the heading from level 3 to level 2). On other hand, if the subsection covers something relatively unimportant, then don't promote it to a level 2 (top-level) heading.

Other sources, both style guides and writing advice, say the same thing: 1, 2, …


How to efficiently print the image of a whiteboard?

For this I use TurboScan on my iPhone.  It's designed for scanning and there are many similar apps.

It takes 3 photos and combines them to get one with good contrast and resolution.  It optimizes for readability.  It automatically detects the edge of the whiteboard and crops there; you can easily adjust the crop to be smaller if desired.  You can easily adjust contrast.

Here is a photo of what's on my whiteboard right now.  This was taken in extremely poor lighting conditions (dim, with lots of glare).  Also, TurboScan outputs a PDF, so you can zoom nicely without it becoming pixelated, but SE would only allow me to upload a JPEG, so what's below is lower quality.  Right-click and open in a new window to see it better.


What is the basic structure of American higher education?

This flow chart, from the National Center for Education Statistics, summarizes it better than any explanation I can think of.

https://nces.ed.gov/programs/digest/d01/fig1.asp

Everywhere you see an arrow represents a potential change of institutions, or (above the black line) a natural place to exit formal education if desired.  In particular, most people who pursue graduate or professional study do so at a different institution than their undergraduate institution.  (They are usually eligible to apply for a graduate program at their undergraduate institution, if it's offered, but don't receive any special preference over applicants from other institutions.)

I'd also note that in many fields, one can go from an undergraduate program directly into a PhD program, without having to get a masters first.  In that case the PhD program normally takes more time (say about 5 years), and may or may not award a masters degree "en passant".


Can't attend conference but would like to get copy of papers presented

If the conference publishes a conference proceedings volume than you can buy a copy or get it through your library.  You might also request copies directly from the authors.

Other conferences don't publish conference proceedings and there may be no paper corresponding to a particular conference presentation.  You can contact the authors but don't be surprised if they tell you there is no paper.


Awkward situation with editor several month after submission: advice

No, agreeing to peer review a paper for an editor would never cause the editor to have a conflict of interest.  A conflict of interest would only occur if the author somehow incentivized the editor to make a decision on a paper.  B providing (or failing to provide) a peer review is not an incentive to an editor, and it is unrelated to the decision on the paper written by A and B.

If C declines to handle the paper, some other editor will handle it.  This likely has no effect on you.  Probably it is best to do nothing for now.  I suggest that you not request C as handling editor in the future since they seem unprofessional.

If C were to directly violate the journal's policies, you might complain to the editor in chief, but it does not appear that has happened.  Don't complain now.

If C said "I will not handle your paper because you did not complete your peer review" then no, you are not being paranoid.  If C said "You should not complain that your paper has not been handled because you did not complete your peer review" then you are being paranoid.


Independent publishing of paper resulting from a project

You should definitely contact your former supervisor. If you do not have his contact information yourself, then you could try asking colleagues at your institution - such as a professor in the same research group.

While authorship norms do vary by field, the supervisor's contribution (having the original idea, defining the project, helping you in general) is surely enough that he should at least be asked. My impression is that even in those fields where supervisors might not be authors, it would still be very bad to try to publish a paper without talking to the supervisor about it. For all you know, he is planning to publish, and would be justifiably angry if you pre-emptively submitted your own version - and even had it accepted. Even if did not expect to be a co-author, he may still be upset if he does not have the chance to help make the paper the best it could be.1

If the supervisor would like to be a co-author, then he should certainly be able to help with venue selection, and adapting the document from a thesis to a paper. Generally, it's not just a matter of changing the formatting - each kind of document has its own requirements, which aren't exactly the same. For example, in a dissertation you will probably spend more time on general background material than in a paper. The work you have done might not be substantive or original enough for all journals. Receiving advice at an early stage may well make a huge difference in the quality of the submitted paper. (You can still seek advice from others, if the original supervisor can't help.)

As far as whether you should submit a paper at all: I think you are thinking along the correct lines. It may help your career - it certainly shouldn't harm it - and you will be contributing to the general advancement of human knowledge. On the other hand, it will take some amount of work. Again, someone who is more familiar with your research area can take a look at your thesis and give advice about just how much work that might be.

1. Example: A colleague of mine is a mathematician. His student submitted a paper, based on the student's own work. The professor did not expect to be an author, especially since he didn't contribute to the mathematical content. But he was upset that the student hadn't asked him for advice about preparing and submitting the paper. He was also embarrassed that he found out about the paper's existence from a third party.


How should I state my MS degree in my CV when it was in practice a joint-program?

I would strongly recommend listing your degrees the same way they were awarded and (probably) printed on your diploma. You can add, of course, that your specialization was in the subfield of machine learning. This clearly separates the official title from your more specific description.

You wouldn't want someone who needed to check items on your CV to find that you are claiming something that you didn't "earn" and the university doesn't even "award".

This is true for nearly everyone, in fact. My degree is in Mathematics but my field was actually Real Analysis, so I can say PhD Mathematics (Real Analysis) honestly enough.


Professor told me to organize a lecture course

Main thing here is that you provide work that is not paid.

(Assumption: studying and working in academia is not volunteering or philanthropy. Not quite clear what culture would have to do here. If you feel wrong about the situation, seems that you agree with this assumption, and you're not confusing exploitative situations for real opportunities.)

If that's an opportunity that's offered to you, the local unit/department/centre/faculty ought to offer remuneration for the work you provide, either for preparation work only, or for both preparation and delivery. In other words, the staff member should (have) arrange(d) the practical and financial details for the opportunity.

A 'research ethic committee' has little to nothing to do with the situation you describe, as the situation does not relate to your doctoral research activity. The situation is not about research ethics, it's about professional ethics.

Have you talked to your local administrators/support staff to enquire informally about the affluence of the local unit? Simply, is there money somewhere to cover for the work you contribute? Can they afford to provide you a remuneration that is a fair reflection of the work you provide?

Have you talked to your head of department about the situation? Colleagues might not be aware of the situation, and might disapprove, and help you out, of it.

Last but not least, are there union reps on your campus that you could approach for informed advice?


How to read a research paper with too many references to previous works?

What you are describing is pretty normal in academia. People take on old and existing work, and build upon it.

There are typically several reasons for citing prior studies, thus the impact of each individual citation might (and usually does) vary as well. I reckon this is all quite new to you. In your case if you can understand the work presented in the paper without diving into the citations, then just do that and ignore the references for the time being. You can always trace back to specific (read: not all) references later on to fill in any potential gaps in your understanding.

If you cannot grasp the why or the how, then my suggestion is to pay more attention to the introduction section, checking out the important (often recurring) references, and then re-reading the introduction. You should get a fairly good idea of what the paper is really about this way.

Another approach could be to try to discuss the paper with your supervisor or someone else who might be able to judge it better (any grad students or TAs?)


What does the term "highest qualification" mean?

Highest qualification means the most advanced (i.e., highest) academic award (e.g., high school, bachelor's degree, master's degree) that you've been granted (i.e., completed).

So,

  if I am a current undergraduate student, does that mean my highest qualification is "undergraduate degree" or should it be my high school (12th grade)?

A current undergraduate student has not yet been granted that undergraduate degree, so the student's highest degree is from high school (assuming no other relevant qualifications).


Is there prestige to be had by posting to arXiv?

I suppose some senior people may publish exclusively on arXiv but they are a minority and I can't think of any examples right now. Publishing in mathematics takes a long time. Journal backlogs of multiple years are common enough that if you wait for your paper to appear in print it is already old. This is less of a problem in the other subjects that arXiv covers but still...

So what does publishing on arXiv get the author? Primarily it gives the paper a time stamp and makes it publicly available. Putting up a paper is fast, it only takes a few minutes and it gives a reference number so that you can cite it in a talk or in a paper. Normally you would have to wait until you get page numbers from a journal. And if you are giving a talk on your paper when you have just finished the work that might still be years in the future.

One interesting feature of publishing on arXiv is that you can write small notes and put those up. You can write the "user's guide" version of a paper. You can post a supplement to a paper that wouldn't be publishable on its own.

Ultimately what it all boils down to is that people post documents to arXiv that they want other people to see and hopefully read.

As for prestige, no. There really isn't any as far as I know.


While applying to masters programs, how important is GPA of unrelated under-graduation?

This can really only be answered by the faculty of the university you apply to. However, I would guess that your old grades will have a negative impact. The reason is that they were earned in a course of study and you are attempting to join that world again, not the world of work.

The impact of your work experience will differ (greatly) from institution to institution, with some weighing it very heavily, but others less so.

However, your record is what it is and people will see and judge it. You won't know what that judgement might be, however, until you make application and state your case for admission. People will want to know what is different now about your aptitude for and commitment to study and learning. You need to convince them that you will do better in the future than your record of the past indicates.


Co-authors request that others do not use "he" as a pronoun - is this reasonable?

This is an entirely reasonable request and you should honour it. It is very easy to write English in a manner that avoids the unfortunate use of 'he' as a placeholder for either gender, and doing so avoids needless sexism in your writing.


How can I create a DOI for a paper that was uploaded to arXiv but not published somewhere else?

Ultimately, no, you can't. There's no infrastructure to say "I want to get a single DOI for XYZ arbitrary url".

DOIs for most scholarly publications are issued through CrossRef. CrossRef do not assign DOIs directly, but delegate this to members or their agents. Members, who are usually publishers, pay a fee to the central consortium, and agree to issue DOIs based on a fixed set of rules.

As you can see from these rules, the general sense of membership is "organisations issuing DOIs for stuff they control". While there isn't an explicit prohibition against assigning DOIs to third-party material (which surprised me!), point 4 comes pretty close:

  Members have an obligation to maintain the metadata and URLs associated with all registered DOIs.

There is also a general prohibition of 'duplicative' works including preprints:

  Crossref only registers DOIs for Definitive Works (or Versions of Record, if not formally published) but not for Duplicative Works, as defined in the Crossref Glossary. This means that only original scholarly material, for which there is no actual DOI at the time of submission, and no expected duplication in future, is admissible for Crossref DOI registration. Crossref does not permit multiple DOIs to be assigned to certain closely related versions of a work, and hence does not support assignment of DOIs to Pre-prints or Post-prints of Definitive Works or to the Personal Version or a Self-archived Copy of a Definitive Work. For the same reasons, materials for which DOI duplication can be reasonably anticipated, such as an Authors Original Draft of a work being prepared for publication, are not admissible for Crossref DOI registration.

Putting those together, it seems likely that CrossRef's terms would prevent a member agreeing to issue a DOI for a (potentially duplicative) work hosted somewhere out of their control.

So, could you get a DOI from someone else, outside of CrossRef? Probably not. DOIs are only issued through a number of central registration authorities (eg CrossRef, DataCite). These have fairly well-defined areas of activity (eg DataCite won't issue DOIs for publications) and, to the best of my knowledge, none offer a "DOI for an arbitrary URL" service.


Re-applying to Math PhD programs while in first semester of current program. How viable?

There is really no answer to the "viability" question. The only thing to do is to apply and make your best effort to be accepted.
But, as you probably already know, getting accepted to a single institution, considering no others, has a pretty low probability of success generally, due to the competition.
But there is really no reason that you should't apply. If you are turned down you are no worse off than now. Most people will, I hope, understand your reasons.
But there may be another path open, if your partner is in a place with several universities in reasonable distance. You might apply to several universities within, say a 50 mile radius. In some places that is a pretty large set of universities. Not everywhere, obviously.
Your partner can take similar action. Maybe you'll get lucky.


Should we reply to the editor after a paper has been rejected and we don't plan to revise/resubmit?

I don't recall ever having received such an e-mail as an editor, so it's not standard (let alone mandatory), but I wouldn't be unhappy to receive one.  I doubt anyone would care enough to make it worth the effort, but it could be a nice gesture if you feel inclined.


In my experience with academics, many of us will do things by the absolutely last moment. No person that knows what they are doing would set a deadline of "by January 11th" and expect everything to be done at January 11th 00:01.
When it comes to "deadlines" for submitting revised versions of journal articles (non special issue) are there predominately to avoid the case where authors just always prioritize something else and never get it done. The editorial systems I have worked with from the editor perspective would just auto-fill those in a few months time. But there is no real point for the editor to enforce those - it means that the work they've put in the refereeing process is for naught.


Is translating my own work to use it in my PhD thesis plagiarism?

This will depend on your institution's rules and your situation, but here are some general points

You can usually use any (and only) work you have performed as part of your PhD studies* to satisfy your thesis requirements (previous work you've done, other than as part of your PhD, is typically included as if you were referring to the literature). Non-standard programmes, such as professional doctorates and DSc qualifications, may have different rules on this.
You will need to be mindful of whether you're allowed to copy word-for-word. In the UK, for instance, you can use results from your publications in your thesis, but you have to restructure the text.** In other countries, thesis-by-publication is more common, and a direct translation may be permissible.
I strongly recommend appropriate references to/mentions of your existing publications - this could take the form of a page at the front entitled "publications arising from this work".
You will need to be aware that direct reuse could create copyright issues, if you intend to put your thesis online or republish it. You will need to investigate the copyright status of your publications if you intend to do this. This answer explains how to acquire rights, if needed. This answer covers some copyright considerations in more detail.

*The meaning of this is a bit of a grey area. But this usually means performed during your time of registration, towards your registered project, at or under the auspices of the institution(s) you are registered with/official project sponsors.

**This is a consequence of both academic regulations often precluding thesis by publication and the different requirements of a thesis and a few independent papers - in particular, the requirement that a thesis forms a coherent whole, and a typical need for more context and detail in a thesis, vs conciseness in a paper.


No one is going to care about your CLEP credits for general education courses.  Your grades in major courses, your standardized test scores, letters of recommendation, and any research experience that you might have are for more important.


How to stay organized while conducting research?

For me, it is difficult to give a fit-for-all answer. The best method is the method that you are most comfortable with. Different people use different tools. My M.Sc. thesis supervisor was a believer in taking notes in paper notebooks. I prefer to construct a set of structured folders in my PC and and use them for managing different aspects of a project (codes, texts, papers, notes, media, etc.).
Of course, there are software tools that can be helpful too. As Elad Den has answered, reference tools are very helpful (I have personally used Zotero but couldn't like it much and ultimately used plain BibTex files).

On the other hand, there are project management tools that some people are very comfortable with (after all, a thesis is a big project). Trello is a popular and free tool that is very simple to use (I have used it for non-research projects and was very comfortable with it and I believe that it has potentials for managing research projects). Evernote is also another tool that is great for taking notes and has some project management features.

Generally, and based on my personal observations, it mostly depends on your personal preferences and I believe that it is a good investment to spend some time on trying different methods and finding (and/or fine-tuning) your approach. Also, it is not a bad idea to have a talk with your supervisor and have his/her opinion.


Should one mention outside influences that negatively impacted grades on their PhD applications?

In the graduate school I manage (UK Russell Group), you will need to meet specific requirements to even be considered for a place in the PhD programme. If your grades (or English proficiency or industry experience or any other prerequisite you choose to identify) do not meet this threshold, no amount of explanation in your personal statement will be satisfactory. This is the first hurdle.

If you are able to surmount this first hurdle, then no specific explanation is necessary to include in your personal statement about the reason you feel your grades were negatively impacted. You are only required to state that there were personal circumstances of a limited nature that were the cause of the dip in your performance. There are three reasons for this:

Your grades have already been determined. An explanation will not change them. We will use your grades plus other evidence to rank you against all other applicants. Your reason will not be relevant in this ranking process. You will fall into one of three categories. If you are in the "clear accept" category or in the "clear reject" category, then your explanation is irrelevant to us. If you are in the "more information" category, when we will seek further information from you in the form of an interview, for example.
We have no way of confirming that the explanation you provided in your personal statement is accurate.
Your reasons may be highly private. If so, they will be difficult for you to write and difficult for us to read.

Please be clear about what I am saying. I am not saying that the reason is immaterial. Quite the contrary, in fact. What I am saying is that the reasons you declare will be considered in due course and we will invite you to respond and provide evidence if and when we require it. We will also specify the nature that evidence is to take.

Thus, in response to your question, I would advise the following:

DO mention that your performance over a specific number of semesters was atypical and impacted your overall GPA negatively.
DO mention that the reason for this atypical performance was of a significant personal nature.
DO mention that this issue has since resolved.
DO mention that you will be able to provide evidence should we require it.
DO NOT provide us specific details.

An example of such a statement is

  During two trimesters in academic year 2016/17, my academic performance was affected by a serious personal issue that has since resolved. This has negatively affected my overall GPA. The academic performance improved in the next academic year. I will be able to provide relevant evidence for your review upon request.

Finally, it is quite common for us to issue offers conditional on the receipt of further evidence. Not knowing your specific circumstances beyond the information you've already provided, it is likely that this will be the result that you will receive.

I wish you the best of luck.


I find it efficient to make several passes through the all papers. Although it would involve reading each paper more than once, I find I am able to give them better focus and achieve better results, which I will explain.

In the first pass I check for very basic things, such a rubric, have they been labelled correctly in the correct basic format; I check for typos, spelling, citations, bibliography and note anything messy and distracting. Having got those out of the way I find I can now focus on content without being constantly distracted by flagging the visual aspects. I read (scan) through all the papers only handling the trivial aspects. Once done I start again on the next pass.

In the next pass I focus on the reading and ensure the sentences and paragraphs make sense. I can pick up missed words, malapropisms, homophones, punctuation and such like this way. Once I am happy that the words make sense on a micro scale (in all the papers), I can start to look at the bigger picture.

On the third pass I can look at overall structure; is the material introduced in a sensible order, is the focus on the right area and finally did I enjoy reading it and did overall make sense.

It might seem long winded, but I find that my performance (scripts per hour) can be faster and more detailed than myself or compared to colleagues that note everything in one script before moving to another.

This may not work for others, but I offer it as an example methodology.


How can an undergraduate TA ask to give a lecture if they have given one in the past?

My first reaction, if a TA or GTA asked to give a lecture, would be to worry about the time.  Almost every undergrad math class is in a rush to cover the material.  At the end of almost every course, almost every math lecturer is wishing for another day or two.  And you want one of my precious, precious days?  Even if you do a really swell job, you might leave some loose ends, which I have to spend 5 or 10 minutes the next class polishing up. Then I have to cram that day's 50 minutes into 40 minutes.   I say this so you know what you might be asking.

The second thing is that, depending on your location and school, there may be rules about who can teach at what level.  In Texas, there are laws (from the state legislature) which say that a master's degree can teach math classes only up to a certain level.  And that a grad student can teach classes only up to a certain level.  And some schools advertise things like, "All classes are taught by professors."  So you might run into a rule or law that simply prevents you from lecturing in a non-emergency situation.

Having said that, I don't see any problem with you approaching the professor and saying that you would like more experience lecturing.  You understand there are hurdles, but if possible, you'd like to do another lecture.


Getting career advice from different people

It's perfectly fine (and indeed sensible) to ask for career advice from more than one person. Different people can contribute different perspectives. It's also entirely ok to approach people for advice and tell them that you are approaching others too - rather than being weird it shows that you are curious and trying to get as much information and feedback as possible.


How to present in lecture a paper that students have read (or should I not have them read it)?

I recommend the discussion format. The two downsides of it you list can be overcome by using a guided discussion. When you assign the paper, also include a list of questions that you expect the students to be able to answer after having read the paper. When the class meets:

Select students at random (or through a random permutation).
Have the student answer an assigned question as a discussion seed.
Open up the floor to other students to make comments and pitch in their ideas (thus starting a discussion).
When the topic dies down, move to the next question on the assigned list and repeat from step 1.

This format has several advantages:

It ensures that the students have read the paper (since they might get randomly selected)
It encourages them to think of their own answers and participate in discussions.
It eliminates the intimidating factor of the professor having tight control of the discussion (since you only moderate who speaks)
It lets you address the key points of the paper (through your initial selection of questions) without having to go over the whole paper in class.

I have experienced this format in upper level undergrad/grad courses during my undergrad and enjoyed it greatly. It really encouraged me to read papers and reflect on them carefully.


Is there a website for rating and reviewing journals openly?

I know just one site where you can review the manuscript submission process. It is called SciRev.org:

  The idea for this website was born from our own experience with the scientific review process. This experience is similar to that of many colleagues: endlessly waiting for an uncertain outcome. Through SciRev.sc we aimed to improve this situation by offering researchers the opportunity to share their experiences and select an efficient journal to submit their work.

I don't know if this website is well-known by the scientific community, but I consulted it because I had some problems with a particular journal and I found comments from researchers that had the same issues as me. I think that it is pretty useful.


How to establish a global authority to deal with academic plagiarism?

I'll try to shed light on how a Russian group of this kind, Dissernet, works. They run full texts of the theses through their own homebrew plagiarism detection system and employ volunteers to examine possible cases of plagiarism and check the proper attribution of quotes. As their call for action describes, checking a single thesis requires:

obtaining a digital full-text version or OCR'ing a paper copy
running a plagiarism match
searching the Internet for possible sources of misappropriation
preparing a report on the results, filing it in the database and giving context to the results

Apart from that, running a society of volunteers requires:

running a server for reports and databases
paying for full-text theses access
paying for OCRs and paper copies
paying for commercial plagiarism detection software to complement your own software
paying for legal professionals, mailing expenses, logistics and running the office

In three years from 2013 to 2016, they have produced around 1300 reports, making a living on community donations. At any given moment of time, they had 10 to 20 volunteers active. This might give you an idea for the scope of effort in these kinds of projects.


Is it OK to re-use data from a previously publication in a new publication?

Looking for guidance in journal instructions, I find that at least one journal-running society says

  In the event that the authors' previously published figures and/or data are included in a submitted manuscript, it is incumbent upon the corresponding author to (i) identify the duplicated material and acknowledge the source on the submission form, (ii) obtain permission from the original publisher (i.e., copyright owner), (iii) acknowledge the duplication in the figure legend, and (iv) cite the original article.

That makes it clear that some data re-use is acceptable so long as it's clearly indicated as such.  The journal also says

  It is incumbent upon the author to acknowledge any prior publication, including his/her own articles, of the data contained in a manuscript submitted to an ASM journal. A copy of the relevant work should be submitted with the paper as supplemental material not for publication. Whether the material constitutes the substance of a paper and therefore renders the manuscript unacceptable for publication is an editorial decision.

which makes it clear that it's not a blanket okay, and the editor will use their judgement as to how much is acceptable.


My paper is still with editor for about two months. Should I email the journal about that?

The same thing happened to me. The status had not changed since the submission date. After about two months, I wrote to the editor and asked him politely to tell me if there is something wrong with my paper. Then, he responded. But, the response was nothing but just "I apologise for the delay to your paper. I have sent a reminder to the Editor to progress your paper." After three days, the paper was rejected.

So, I think: it is better to send an email to the editor and ask him to tell you the status of the manuscript. Otherwise, the status will not change (at least in the near future). Be prepared to see what I saw.


How to manage the relations between supervisor and institution?

You don't say what country you are in, and what instutional checks and balances exist is going to dependent on that.

In the US, you will have a thesis committee that is (at least supposedly) indepedent of your supervisor, and, at least in theory, pulls rank on your supervisor when it comes to matters of your studies. In the UK there often isn't a committee, but almost all universities have a system of "second supervisors" or "academic advisors".

In both cases there will be almost always be a head of graduate school, or directory of graduate studies for the department, school or faculty, as well as a chair of the department/school/faulty. The head of studies nomianally out-ranks the supervisor, although politics can come into play here, but the chair of the department/head of school/vice-chancellor of the faculty genuinely does outrank the supervisor.

Failure to progress (i.e. not doing well enough to continue your studies) is a disciplinary matter, and would be dealt with in a quasi-judical manner according the instututions rules and regulation. You will be able to find these online.

In the UK there will be Student's Union, and perhaps even a Graduate Students Union who can represent you if you feel you have not been fairly treated by either your supervisor, your department or the university. I don't know how many US institutions have similar. In the UK you can ultimate complain to the government ombusdsman, the office for students.


Waiting to hear back from a professor—how long should I wait?

This is business, send a nice and polite email to your professor to ask him if he has news since you don't.

Don't wait 3 weeks on a job application.

Obviously, maybe he'll say 'it's summer everyone is on vacation', maybe he forgot, maybe his colleague forgot. Show that you're willing to work with them, just don't spam their mailbox every couple days.


Is it acceptable to add results to an arXiv publication?

If the change from the conference version to the journal version is relatively minor (so the new results are unimportant), it's fine to add the new results to the arXiv.

If the change from the conference version to the journal version is substantial, post the conference version on the arXiv paper unchanged, and later post the journal version to the arXiv when you finish it. If you don't change the title from the conference paper to the journal paper, it might be a good idea to indicate in the arXiv paper titles that one is the conference version and the other is the journal version, so that people don't get confused.

This way, the papers on the arXiv reflect the published papers, so people who are trying to track things down in the literature won't get confused. You're shouldn't feel guilty about wasting resources, because you're not—the cost of hosting one more paper on the arXiv is tiny.

And you should consider whether the results you're adding to the conference paper are significant enough to deserve their own paper. Each paper should tell one "story". If the new results don't fit in the "story" of the paper, in my experience nobody will notice them, so you're better off writing a new paper containing them.


GRE Score advice: Should I retake the GRE?

This seems to be a common question, and I think the primary question you should ask yourself is: will retaking the test significantly improve my score? If the answer is no, then I would not bother. Generally speaking, if you didn't have some extenuating circumstance during or before testing, such as a serious illness, I would not expect the change to be quite so significant.

Competitive applicants have good GREs perhaps as a consequence of the ability of the applicant, and are not necessarily competitive because of their scores itself. There are some other relevant answers regarding GRE scores. see: 1, 2, 3


Taking into account courses from another university

The best answer to this question is Chris Gregg's comment.

You need to check with each individual school or even each individual program.

The schools you already checked with will allow it. Chris's program allowed a maximum of two courses. My graduate program accepted transfer credits infrequently. Some programs may not accept any.


You almost certainly need permission. Check the publishing agreement you signed for each of the articles. They're probably all the same, but you might double check the copies you saved if they were in different years.


Messed up my PhD. Hope for academia lost. Not attractive for industry. Hoping for some advice

First, you didn't really "mess up your PhD" if you get your diploma at the end, something which seems very likely in your case. The main goal of doing a PhD is to get a PhD diploma, so you should evaluate success by this criterion even if it's not everything you had initially hoped for.

What you're going through is a period of low self-esteem/regrets/depression, a very common symptom of finishing a PhD (see for instance here). It's normal but be aware that currently you are not completely rational in your self-evaluation, and don't hesitate to seek professional help if you feel like you need it.

  I really messed up, I don't know what should I do. Academia seems closed. Industry a far fetched dream. I am in the US and I am an international student. Sorry for the rant. I really can use an advise. Is it possible to come back from such a disastrous profile?

These interpretations are the result of your low self-esteem at the moment. For example you will know if academia is closed to you only if you apply for academic jobs. Sure you might not get a position in a prestigious institution, but there's a lot of postdoc opportunities everywhere and if that's what you really want you should definitely apply. A year or two of postdoc in a different place, on a different topic and with different people could completely change your perspective and your academic profile.


How to cite a paragraph in project report?

When you use someone else's words verbatim, you must either

put it in quotation marks, or
indent the paragraph (make it a block quote)

to indicate that those words are not your own. (Most style guides recommend block quotes for long quotations.)

You must also indicate somewhere near the paragraph (e.g. in a footnote, parenthetical reference, or other kind of inline citation depending on what citation style you use) which source in your reference list it comes from. (You must do this - indicate what source it comes from - any time you use someone else's ideas or material you found in a reference, even if you summarize or paraphrase it in your own words.)

In general, a rule of thumb for avoiding plagiarism:

For any idea or information that isn't your own work, clearly indicate where it comes from. (Excluding facts that are "common knowledge".)
Additionally, make it clear any time you use words or images that you didn't write/create yourself. (For example, with quotation marks, block quote formatting, or image credits in the caption.)


How do PhD admissions committees view double majors?

Would, say, a MechE/CS student maintain a leg up applying to a CS program related to robotics? A Math/CS applying to theory-based CS? Does it vary between fields?

All else being equal, YES.  Speaking specifically for theoretical computer science, I am much more likely to recommend a PhD applicant for admission if they have a strong mathematics background.  A second major is not the more important thing, though; majors are just administrative hurdles.  I look for which advanced math classes the applicant has taken, how the recommendation letters describe their mathematical ability/maturity, and how fluently they use mathematics in their research statement.

Yes, the effect varies significantly between fields.  For example, my robotics colleagues are much more likely to recommend applicants with strong mathematics backgrounds, and my software engineering colleagues are much more likely to recommend applicants with software industry experience.

Of course, as Daniel points out, ceteris is never paribus.