Possible contents of a risk-assessment matrix for a grant proposal

There are two classes of risks that are typically considered in grant-writing:

Programmatic risks that the money will be wasted because something doesn't go as you hoped.
Safety and ethics risks based on the specific contents on your research.

The second is generally covered under a checklist of declarations regarding specific topics (e.g., "human subjects research," "dual-use agents of concern," "vertebrate animal research"), rather than general "risks", so I'm going to write my answer addressing the first class.

With regards to programmatic risks, the big issue here is research always involves the unexpected, most often emerging in the form of things not working as well as you thought they would.  Progress might be slow, effects might be small, vital supplies might become unavailable, things just might not work, etc.

What grant reviewers are generally looking for here, then, is evidence of clear thinking about how to handle setbacks of this sort.  You really don't want to give money to somebody with no "plan B", and then 3 months into the project something goes wrong and they end up just frittering away the rest of the money banging their head against the same wall.

How I recommend assessing risks, then, is to sit down with a your project plan and asking yourself the following questions:

For each step in the plan, what materials/people/facilities/information is needed before I can begin the step? What happens if they aren't available as expected?
For each step in the plan, what does "failure" look like? How many different ways can it fail?
Which of these problems are most likely to endanger the overall goals of the proposal?
For all of the "important" problems, what is the plan B for how to ensure money is spent in a worthwhile manner if they are encountered?

Doing this assessment may also cause you to reorganize your plan: sponsors often like to see the most "critical path" or high-risk work up front, so that the most significant and productive problems can be encountered sooner rather than later (and the project terminated if necessary).


Teaching the daughter of a lecturer, while being simultaneously enrolled in his course

I’ve had to teach colleagues children, nephews, and even the son & daughter of the Dean.

Be professional. Treat and grade them the same as any other student. They also think “oh sh*t s/he knows my Dad / Mum so I had better be careful”... :). Don’t call them out in class, but don’t avoid them either. If you do random questions and it’s their turn, then fine.

Don’t worry, they don’t go back to your Dean talking about your teaching performance. They just want to benefit from your wisdom / experience / knowledge same as the other students...


Does it matter how many Nth authors there are on a literature review?

Whether a review has one, two or more authors does not really matter in biochemistry, but being first author is useful, and so is a good quality paper that gets cited. It will be very helpful for your career to build a network and show your skills, and a good way to do so is to collaborate on a review.
Buffy's comment is also correct: authors should contribute intellectually to a paper to earn authorship.
I don't mean to discourage you, but unless you are an exceptionally talented student and scientific writer, you probably need help from someone who has experience writing and publishing reviews to get your work accepted.
Most people would agree that there is a difference between a review written by 1-5 authors and one by 20 authors (if those exist - I do not remember reading one). And of course there are always the rare exceptions of readers who value single author papers more (you did everything yourself), or who may prefer multiple-author papers (you can collaborate).


Should I cite a statement as coming from in journal article or from the related PhD thesis?

Personally, I tend to prefer to cite the most recent work, as it is likely to be the most updated and correct.  There is also a good argument to be made for citing the peer-reviewed version (as long as it isn't too much older).

In general, however, if the two sources are very similar it doesn't matter much which one you cite. There is also no particular need to cite more than one, and I tend to feel it's better to cite only one when the material is basically the same, so that it doesn't look like you're claiming more support than actually exists.


Is there any relation between them like ESCI is less than SCIE and SCIE is less than SCI?

This is what Clarivate Analytics says, "The Science Citation Index (SCI) is a highly selective subset of journals found in the Science Citation Index Expanded. Journals in SCI are typically the most consistently high impact titles in many scientific disciplines."

"Emerging Sources Citation Index provides Web of Science Core Collection users with expanded options to discover new areas of research in evolving disciplines, as well as relevant interdisciplinary scholarly content across rapidly changing research fields... These titles are also being evaluated on a continual basis for inclusion in the SCIE, SSCI, and AHCI."

(http://mjl.clarivate.com/#journal_lists and http://info.clarivate.com/ESCI)

From these excerpts, it seems that with respect to the way they measure impact, Clarivate would probably put SCI journals at the top, SCIE journals that are not also in SCI in the middle, and ESCI journals in third place, although they don't say this directly. My own view based on my field (law) is that some of the journals in the ESCI are much more well-regarded (and more impactful) than some in the SSCI, so I would caution against using these indices as your sole criteria to determine quality. Nothing replaces reading the journals and asking your colleagues and experts in your field about them.


Topics for on-site interview lunch and dinner time

Actually, this advice is quite different from that of Wetenschaap, though I don't disagree with that suggestion.

Instead of talking about yourself, spend the time asking about them. Ask about the students. How motivated are they? Ask whether there are unique aspects of the educational program. Ask about their future goals. Ask about trends, both positive and disturbing that they see on the horizon. Ask about collaboration. Ask about the research of others. Ask about what research seminars are available.

And these are things you want to know before accepting an offer.

Or ask about the local environment. Are there good places to, say, ride a bike or hike. If you have a partner, ask about opportunities for them locally.

Lots of things. But don't make it too focused on yourself or you might seem narcissistic.


Is taking a postdoc for training purposes wise as an industry scientist?

Sorry, this doesn't seem to be a good idea, especially considering some of the more subtle points you've shared. In general taking post-docs after 5-6 years need not be a bad thing, but people would generally shoot for a prestigious fellowship, not something through personal contacts.
I also want to recommend that you take this just because of how unhappy the current role makes you, but considering your situation I can't. You're in that tricky (not uncommon) position where your PhD, current role and future aspirations are in different fields. As such, you should be very wary about letting go of what you have for something that you potentially may get. There is every chance that the grass appears greener on the mass spectrometry side, and after being trained on it (by a grad student!), you may find that there are difficulties and unpleasant challenges that you aren't currently aware of.
You seem to move towards mass spectrometry in the long term, and I get the uneasy feeling that you're jumping onto the bandwagon without enough thought. Primarily because if you really want to make a big switch, getting a nameless (i.e. without a fellowship) postdoc and being trained by a grad student (and neither earning certification nor being under the wing of an experienced academic) doesn't sound wise.
There's every possibility that I'm assuming too much, so please use your discretion and don't be hasty.


How does job security in academic untenured soft money positions compare with job security in industry?

I work at a company with a lot of similarity to soft-money academia: research is PI-driven and mostly funded by external contracts and grants.  In the US, there are actually a lot of companies that either wholly or in part operate this way.

In this type of research organization, in some ways there is more security than an academic organization and in other ways less.  Here are the key points as I see it:

More individual job security: In most academic soft-money posts, you are tied primarily to your grants or the grants of the PI that you work for.  There is very little organizational commitment to you as an investigator.  Thus, if your money dries up, there is little or no bridge funding to keep you going as you try to get more money; you just stop getting paid.  In a permanent corporate post, there is a fallback to being assigned as a performer on other people's projects, even perhaps in other departments, and the company is motivated to find such connections because you are still being paid.
Less institutional job security: On the flip side, universities are extremely durable as organizations, and tend to change much more slowly and less dramatically than companies.  A company might be suddenly acquired or change leadership and suddenly all of its policies change radically.  So despite having a position, you might find yourself not wanting it under a new regime---or research itself might be jettisoned, and you along with it.

The lack of institutional job security, however, is actually less bad than it appears, for anybody with either a healthy research program or who is well-known as a talented contributor.  In practice, what bad institutional change tends to mean is that you end up with a diaspora, in which good people move en masse, either joining other nearby companies with better research cultures or founding their own.  This might happen even if the new "parent company" doesn't have an office in the area---I know of more than one regional branch office that was opened because a group of researchers left Company A and their colleagues at Company B invited them to join, figuring that geography could be worked out one way or another.

In short: from what I see, externally funded research at companies is significantly more stable than soft-money academia, despite the fact that company identity may change over time in various ways.


Re-reviewing a previously rejected article but some authors have changed from the previous submission. Should I mention that to the editor?

It's not particularly unusual for authors to be added during a revision of a paper, but for them to be removed is quite unusual and often linked with something improper going on.

Since this submission is a different publication than the original version that you saw, the editors do not have this history in front of them, and I think that it is indeed a good idea to flag this as a concern to the editors.

Moreover, if the article has not been significantly revised but the set of authors has changed, then that's a major red flag that the authors are doing something improper. If this is the case, then the editors absolutely must know, and should probably investigate wrongdoing.


Is it standard for US-based universities to consider the ethnicity of an applicant during PhD admissions?

If there is one thing that academia is particularly bad at, it is transparency in decision making. Why do some people get admitted and not others? Why are some people hired and not others? Why are some people promoted and not others? From the bottom to the top of academic hierarchy, you'll be hard-pressed to ever get a straight answer, and answers you do get are always suspect because the nature of human decision-making is itself complex and opaque. There are plenty of reasons for this, from self-protection from criticism and gaming of the system, to rapidly changing criteria based on past experience and argument, to the fact that so much of the decision making is based on subjective ratings provided by individuals (often down to individual faculty members deciding if they want to work with a student).

To cut to the heart of your question, while it is not any sort of prescribed standard at the graduate level, you can safely assume race, ethnicity, national origin, and gender will be in some way be "taken into account" by some committees and individual professors. In many states this is actually illegal, explicitly forbidden by law - you can still assume it will sometimes happen anyway. On the other hand, some people will simply ignore demographic factors to the extent they are physically able, regardless of what they are told to do. As Universities have a history of avoiding transparency in admissions, you are extremely unlikely to ever know when it was considered, how much effect it had, whether it was positive or negative, and whether it ended up materially effecting the decision to admit you or not. You cannot know, they will basically never tell you, they will tend to go out of their way to avoid writing it down, and it is common for many people in the process to not even know with any certainty what factors ultimately "mattered".

However, from what I've seen on the inside and the outside of academia and from talking to fellow academics, you can safely assume at the graduate level that other factors matter way, way more. It is simply too high-stakes a decision for most schools to be altruistic, and they tend to steadfastly refuse to intentionally admit people who are utterly unqualified simply because of some demographic fact about them. The vast majority of Universities will only admit you if they think you will do well there, because having a bunch of under-performing students who are radically unqualified to pursue research and teaching is an albatross around the neck that few graduate schools will willingly tolerate. This is even more true at the PhD level, because they aren't cashing in on tuition (which is heavily marked up for international students, because money), so performance is king.

From talking to people working on diversity initiatives, I'll also give you another important insight: the diversity initiatives you hear about are not actually a preoccupation of the majority of faculty and staff, for good or ill. According to people working on actually making these initiatives successful, they report that the vast majority of people mostly want to ignore the issue and focus on other things, and so they work so very hard to make the initiatives public and heavily seen because otherwise they feel they will be unable to make any changes and they will be crushed by the majority weight of indifference mixed in with a heavy dose of active hostility to their efforts. Higher ed can look monolithic from the outside - but on the inside it is highly factious, and what appears as consensus is often a thin facade.

Because of all the above, the only advice I think makes any sense is treat the process as any other student should: apply broadly, see what offers you get, and talk with prospective advisors about what they are interested in. You are welcome to ask them if they were involved in your admission decision and then ask them why they wanted to admit you; I did that, and while it can feel a little awkward at first, a little bit of humor makes it easier and most professors when questioned directly, sincerely, and politely gave very direct answers. Some even said what parts of my profile they thought were a concern, and what other parts they thought would be a strength. Everyone gave wildly different answers, there was no consistency - no two people see the same person the same way.

Once you've got all your offers and finished talking with people, you can make your decision then on what seems like the best opportunity for you.


How do I help minimize interruptions during group meetings as a student?

This sort of thing has roots way beyond academia.  There is a lot about the dynamics of women having difficulty being spoken over in meetings (though I imagine it could apply without respect to gender too, based on differing levels of assertiveness).  Maybe a few things to try:

When someone, even your advisor, talks over her, say "Wait, what were you about to say?" addressed to her, so it's not directly confrontational toward the interrupter.  This is as opposed to something like "Wait, let postdoc A finish" addressed to the interrupter, which is more confrontational.  That is, assuming you want to avoid a confrontation with your advisor.
Mention it casually to her after a meeting.  She might appreciate and/or be emboldened by the support.  Something like "What was it you were going to finish saying before soandso took over?"  This way you show you're both interested in what she had to say and also noticed that she was talked over in the meeting.
Wait until the interrupter finishes, then bring the focus of the meeting back to postdoc A.  "Sorry, what were you about to say earlier?"  or "Hey, postdoc A, what was it you were saying about X a minute ago?"  This is probably the safest thing to try, and if you do it enough the others might even get the point!


Should one avoid using the phrase "note that" in math writings?

"Note that" is a useful rhetorical device in mathematical writing. Its role is to signal to the reader that the statement following it is more noteworthy than other statements, so the reader should, quite literally, take note. While @JeffE sarcastically argues in a comment1 that it must never be used, I disagree; a judicious use of "note that" (in contrast to using it either always as in Jeff's comment, or never) helps to effectively convey nuances of meaning to the reader that are difficult to convey otherwise. This is an example of taking advantage of the English language in mathematical writing. In essence, "note that" punctuates the flow of the text and helps the reader process and make sense of the large amount of information that a typically dense mathematical text often contains, and discern which parts of it are more important and which are less.

Of course, as with any other form of expression, "note that" can be used effectively, or (as JeffE's comment cleverly illustrates) abused horribly.

Now to address your questions:

  some incidents lead me to presume that perhaps those readers who are not that mathematically experienced could take "note that" as an imperative or even a condescending sign?

I really can't say whether "note that" will come across as condescending to those who aren't used to its usage in mathematical writing, but I suppose that's possible (and I'd be curious to hear more about those "incidents"). "Note that" is in fact an imperative, so it makes sense that it will be understood as such by anyone, mathematically experienced or not.

  if I am writing something to someone that is senior than me in academia and that is not that mathematically experienced [...] would it be suggested that I avoid using "note that"?

My recommendation is that when you are writing to someone who is less mathematically experienced, just like you need to be mindful that you must adapt the mathematical terminology you're using to your reader's expectations and knowledge, it probably makes sense to also adapt the style of writing accordingly to take into account cultural differences across different disciplines. It is probably true that mathematicians are more used to the way "note that" sounds and is typically used, so one needs to tread a bit more carefully with this device when speaking to a non-mathematician. I wouldn't say you should never use it however, just maybe pay a bit more attention to when and how much you use it and give some thought to whether each usage makes sense in the context of how it's likely to come across.

1 JeffE's comment I was referring to, which was moved to chat, said: 'Note that “note that” is simply redundant. Note that omitting it entirely does not change the meaning of the sentence. Note that it’s just a bad writing habit. Note that you don’t need it.'


"The file is not eligible for Reference Checking and was not processed"

The applied references within your document might be faulty. This case is something common regarding the MS Word documents. But one could confront with such stuff even within working with LaTeX, where the references to some entry (tables, equations, bibliography etc) are not valid.

Hence, one could assert that you better check the document referencing.

More elaborated illustrations could be found here.


What is the best way to keep your students from getting out of control?

First, realize that the main reason they might misbehave is the same as every one else, whether they are 4, 14, 24 or 94 years old: they will be distracted if they are not interested, bored. Conjectural factors surely also play a role (if it's nap time, for example), but if you get them interested you increase dramatically your chances of having a well-behaved audience.

Now, with regards to exercising your authority on a crow, the principles are again pretty much the same for 4 years old and 20 years old:

Immediately assume a position of authority. You have to be convinced that you naturally assume this authority before you go to the class. It derives from two factors:

    a. By naming you a lecturer, your university gave you authority over the lecture room. Be ready, but not overly eager, to exercise it.

    b. This authority also derives from your skills and knowledge: you are an authority on the topic you are lecturing. To maintain this, you have to be prepared to teach your topic.
Be consistent. Lay out a set of rules, explain them, and enforce them. They have to appear justified and reasonable to the students, so that you can enforce them if need be. Always put things back in perspective: why are we here, and how this justifies what I do.

To give an example: I always start by explaining that “I will not shout, because my voice doesn't allow me to go through the whole lecture shouting. Thus, if the noise level meets the point where I would need to shout, I will simply stop lecturing.” Standing there, silent, is a very effective way to lead the group to self-discipline (“hey, guys, shush!”). If necessary, I will remind them that even if I cover less material, the exam still covers the whole planned curriculum…
Be pragmatic. If things are going bad for some external circumstances, be prepared to make a justified exception to the rules, for the benefit of everyone. For example, if it's Friday afternoon and all students are exhausted from a week of exams, giving them 10 minutes off in the middle of a two-hour lecture might lead to overall improved productivity.

But most importantly, realize that while first impression is important, it is not “do or die”. Even as an experienced teacher, sometime you will underperform a given day (because you're tired, because you're not committed enough to this specific topic, because …), but there is nothing you cannot correct later.


As far as I know, university mathematics departments with any kind of significant research focus do not hire people who have a math ed. degree.  You need a math degree if that's where you want to work.   Even the education option will only hurt your chances of getting a tenure track job in a research-oriented math department.

If you do some searching, you'll find that people with math ed phds are generally employed in education departments rather than math departments.


What is more important for the admission of masters program?

For a purely course-based Masters, in which you do not do research, the research strength of the university obviously won't matter very much.

For a Masters in which you do research and create a thesis, however, the strength of the research group is likely to significantly outweigh the reputation of the school.  This is because the most valuable thing that you can have when applying either for a Ph.D. or an industrial job is a strong recommendation letter from a respected colleague.

If all I know about a student is that they got a Masters from MIT or Berkeley, well, a lot of students get such degrees, and some are excellent while others are worthless outside of the structured environment of the classroom.  On the other hand, if the student comes from Mid-Ranked U with a strong personal recommendation from somebody whose work I know and respect, then they are likely a much better prospect than the unknown from a high-ranked university.


Independent Research and institutional review boards?

This issue actually got some press recently with the case of uBiome, a citizen science startup that raised over $350,000 in crowdfunding.

This startup received a lot of negative attention for not getting IRB approval before raising the money. You can read some of this criticism here, here, and here.

A statement from the founders of uBiome says they were advised that they don't legally require IRB approval if they aren't receiving federal funding, don't plan to publish, and don't plan to apply for FDA (U.S. Food and Drug Administration) approval:

  Before we started our crowdfunding campaign, we consulted with our advisors at QB3, the startup incubator at UCSF, and the lawyers they provided us. We were informed (correctly) that IRBs are only required for federally funded projects, clinical trials, and those who seek publication in peer-reviewed journals. That’s right — projects that don’t want federal money, FDA approval, or to publish in traditional journals require no ethical review at all as far as we know. (No, that doesn’t sound like a great system to us either.)

In the end, they went through a private IRB firm (Wikipedia says it was this one) and got their protocols approved. The founders say:

  This is the same institution that works with academic IRBs that need to coordinate multi-site studies, as well as private firms such as 23andme and pharmaceutical companies doing clinical trials.

This incident raises the question of what you plan to do with your independent research (assuming the kind of research you are doing is generally subject to IRB oversight):

If you plan to publish your research in a traditional peer-reviewed journal, you will usually need an IRB review
If you plan to develop pharmaceuticals that will require FDA approval, you will need IRB review
If you plan to get federal funding for your work, you will need IRB review. If you plan to get other funding for your work, it'll be hard to get without IRB review.
If you plan to create a startup around your research, you may not require IRB review, but not having it can engender quite a bit of criticism (as per uBiome's story)


Remember that research was a lot harder to track down before the Internet Age. We couldn't as easily do literature searches because databases were much more restricted in scope and scale. Therefore, we can guess that keywords might not have found the earlier results.

In chemistry, it's possible that alternate methods could be used to synthesize a molecule, which would certainly justify its republication. In mathematics, an alternate, more elegant route for the proof or justification would also merit "rediscovery."

It's only plagiarism if the same methods and techniques were used after consulting the old material: in other words, only if it's a straight-up reproduction.


I have an issue with one of my teachers and a chance to address it, but they're writing me a letter of rec. Should I address it?

What I wrote is strongly worded but I feel like it gives a fair assessment of what my problem was.

I would reconsider the strongly-worded part. Giving a fair assessment is good, but people rarely react well to sharp criticism, and this can burn bridges. My advice is to state facts, not conclusions. For example, rather than saying that you were "discouraged from intellectual exploration" (a conclusion), you could say that you were "disappointed not to be able to pursue X" (a fact).

  Should I include my assessment or should I hold off until after I apply?

Assuming what you write is not ridiculously far over the line, I would not expect your professor to change their letter of recommendation. Particularly if they've already written it, I doubt they would take the time to go back and make changes.

But, consider the cost-benefit analysis. The (potential) cost is burning a bridge (you can mitigate this by being diplomatic). The potential reward  is that future students might have a better experience, but this is likely only if the professor (a) does not already agree with you, (b) agrees with you after reading your report, and (c) chooses to address your feedback.


How can I tell if an unsolicited offer to publish a book with Springer is legit?

Book editors sometimes send unsolicited e-mails to people who write well on topics that can attract an audience, so this could well be legitimate.  There are a lot of scams, but generally from publishers you've never heard of.  On the other hand, there's no reason to think these signs of initial interest will necessarily lead to an actual contract.  If it interests you, it can't hurt to look into it.  If it doesn't interest you, you can safely send a very brief reply or even ignore the e-mail.

Whether it's a legitimate e-mail shouldn't be too hard to figure out.  If there's a return address from springer.com and someone claiming to be this editor responds to e-mail sent there, then it's probably legitimate (although in principle it could be a rogue employee or a hacker inside Springer's network or yours).  If the e-mail asks you to get in touch in some unconventional way, such as a private e-mail address, then it's probably not legitimate.

Whether it's worth the effort depends on the circumstances.  Springer publishes some truly excellent and important books, as well as others that are mediocre at best.  Whether publishing with them is a good idea depends on your career plans and book ideas, as well as what you think of the contract they offer and their publishing practices.  You should take a look at what else they have published recently in your area, as well as what has been published in series handled by this editor.


How to incorporate a fellowship into a CV

You're generally spot on, but I would tailor this a little more for the benefit of assessors. In evaluating fellowships, I would like to know the following:

Was it a competitive grant?
How long was the award?
How much was the award?
What was the research topic?
What were the outputs?

Modifying your example above:

  Summer Research Fellowship: December 2016-February 2017
  Macquarie University

  The Fellowship is a competitive grant awarded to undergraduate students in the Department of Mathematics. The grant consisted of direct research costs and living expenses worth $20,000. Under the supervision of Professor Geoffrey Killington I worked on a drug trial for patients with metastatic melanoma. The work I did resulted in two conference papers and a manuscript (currently in press).

Good luck!


Global university ranking for graduates, not research

It is not clear what rankings your university uses or what you think is a fairer ranking. The QS World University Rankings ranks on:

Academic reputation (40%)
Employer reputation (10%)
Student-to-faculty ratio (20%)
Citations per faculty (20%)
International faculty ratio (5%)
International student ratio (5%)

I would think that "research output", whatever that is, would impact both academic reputation and citations per faculty. I am not sure if any of the other factors are fairer for judging academic success, but the nice thing about the QS rankings is you can sort based on any of their factors.
If we look at a couple of the IITs
                 Overall     Academic     Employer     SFR     CPF     IFR     ISR
IIT Bombay         222         160          60         400+    301     400+    400+
IIT Delhi          235         199          90         393     329     400+    400+
IIT Kanpur         300         229          229        400+    345     400+    400+

Despite any impact of loss of PhD students to international schools, the "Academic Reputation" is still helping the ranking. The Citations per Faculty are hurting them a little, but they are most hurt by a lack of international draw at the faculty and student levels and a high Student to Faculty ratio.


The exam time was less than the students expected

I would hope this is unusual because it's not very nice to the students.  Students deserve to know in advance how much time will be given for the exam. And in my experience, they usually do know this quite far in advance.

It doesn't make sense to me that the figure mentioned in
the instructor's e-mail would refer to how long the room was booked (which is not something that the students would care about) rather than how much time would be given for the exam.

Another thing that doesn't make sense to me is why, when the instructor realized that the students thought they would have three hours for the exam, he didn't just keep quiet and let them have the three hours.

However, I don't know what you mean by a "protocol how to deal with it." You could certainly let the instructor know that you are unhappy about this aspect of the exam.  But is there something that you think the instructor should do at this point to improve the situation?

Also, what does it mean to say that 90% of the students failed the exam?  It's not necessarily a bad thing if 90% of the students got a numerical score below 60% on the exam, but it would be a very bad thing if 90% of the students got an 'F' grade in the course.


I was published in a journal on Beall's list - how bad is my mistake?

While publishing in a predatory journal doesn't help your CV, I don't see this as anything near a fatal mistake even if you are pursuing a career in academia. The main cost is just the wasted time and effort and the fact that you could have gotten credit for these papers if published elsewhere.

Given that you were at such an early career stage when you wrote these papers, it seems that you can readily be forgiven for falling victim to a predator publisher. Tricking people in this way is, after all, often a component of their business model. When I see a professor publishing repeatedly in these journals, that suggests he or she is trying to pull something over on someone. When I see an undergrad or someone straight out of undergrad doing so, I feel badly for the student and angry at the publisher.

I would simply list these papers on your CV and move on. They're part of your publication record, so you can't really omit them in good faith -- but nor do you need to beat yourself up over it. If someone asks, be forthcoming both about the fact that this journal is questionable and about the way that you ended up publishing there.

You haven't done anything terrible. You've been exploited, and maybe if someone is a harsh judge he will think this makes you look a little silly. But in your situation I don't think most people would hold that against you.


College in high school and math graduate school admissions

You are getting worried about nothing.  You will not be judged negatively for having taken college classes before starting your BA, even a lot of them.  Graduate committees want to have students coming into their program who are going to be successful, and they don't care much whether it took 6 years or 2 years to get that preparation.  They are going to look at what you did with your time, not how long you took.  As long as you're happy and it's not too much of a financial hardship, there's no reason to graduate in 2 or 3 years.  Instead, take the time to concentrate on things that will strengthen your application:

Take the hardest courses available which you can perform well in.
Build relationships with faculty.  Taking graduate courses can help with this, but you can also seek out research opportunities or get involve with things like math club.

Performing well in challenging classes and having stellar letters of recommendation are the basis of a strong application to graduate school.  Issues of timing make absolutely no difference in comparison to them.  Other considerations:

You could do a second major, if there's something else you really want to try.  I think this has probably taken on a totemic significance with students beyond its real import (math grad schools are mostly concerned with how you've done in math; being well-rounded is something like a tertiary consideration), but it sounds like you have the room in your schedule, and certainly no one will think you're lazy.
Find good ways to occupy yourself over the summers. REUs are one good possibility. It sounds like you'll have a decent shot of getting into one after your freshman year. Another is if you can find a counselor position at summer program like PROMYS.
Consider spending a year or semester somewhere else. There are highly regarded study abroad programs specific to mathematics in Budapest and Moscow, and also programs like Penn State's MASS.  There's also Part III in Cambridge, which perhaps you could do after graduating in 3 years (or in 4).


In Google Scholar, is it possible to view the list of papers cited by a specific paper?

As you mentioned, unfortunately, Google Scholar only provides the list of publications that cite a given reference.

However, if you have access to Web of Science, to look up a list of references cited in a given publication, you can use the Cited References tool.

Note that some journals are not indexed by Web of Science, so having several tools to do the job may be the best way to approach this; e.g., in addition to Web of Science, you could also use Research Gate as mentioned in the other answer. For those journals that are indexed by Web of Science, I find the Cited References tool to be very useful.


With regards to undergraduate theses, what level of knowledge should one assume the reader to have?

My rule of thumb -- whether for Bachelor, Master, or PhD theses -- is to assume precisely the level of knowledge the student had when starting to work on this topic. (I.e., "How would you like to have had this explained to you?")


How to deal with and communicate overflow of ideas with a supervisor when working on a thesis?

First an anecdote. A long time ago I was a pretty good photographer. I had a simple manual film camera and two lenses, one fixed, one zoom. I made some nice photos, not just "snaps". Then, when I started to earn more money I bought more equipment. It seems that for every piece of camera gear I bought, I got worse. Just decision overload, I think. Instead of seeing what was revealed in the viewfinder and framing things, I would be indecisive about whether I should use some other lens, or whatever.

Next, a solution, I hope. But it doesn't involve your advisor.

Start a notebook for yourself. Either electronic or on paper. My preferred method is paper. When working on any idea you have another idea that is related, add a page to your notebook, or update an existing page. Just one page (making paper advantageous) so you don't spend too much time and effort on it now. Then, return to your original work.

This notebook is your "future work" resource. The pages are there just to give you a start on an idea that you once had that you now want to develop. In mathematics, it might consist of pages of variations on definitions that you think might be interesting, or potential theorems, or possible relationships between things.

If you can make the interruption of creating a new page in the notebook short enough then it doesn't interfere with your current work, but assures that you have a record of those thoughts so that you don't lose them.

I finished my doctoral dissertation having a fairly large file of these pages, many of them quite interesting. Among other things, the breadth of ideas I'd saved help me gain insight into the general area in which I worked and I don't think I'd have gotten that insight if I'd been too focused on only my dissertation. But I might not have finished the dissertation if I'd immediately followed up each of those ideas.


How to make a transition to a scientific position (from engineering position)?

Since you already have a PhD, and have a strong work experience with one of the top companies with the research-like work, not to mention your published work that you have mentioned, you should be able to get a grant from one of the prominent universities in Russia. If not, then try a country where you can happily continue your research while still supporting your family. As Dexters above has suggested that, with your passion you have nothing to lose, it stands true if you keep trying and not give up just yet. In the meantime you could try to publish your work with the top journals.
Good luck with your endeavours.


Diversifying the academic institutions one attends

While this is generally true, it depends heavily on the field and subfield. Pure math is a little unique compared to many other disciplines, and in my experience has a much higher rate of students staying with the same university/department/advisor from undergrad through PhD--perhaps because if you find a professor working on a given topic you'd like to study, there's a decent chance he or she is the only (or one of very few) person in the country doing it. I know a decent number of people in pure math who did this, and at least two of them are now tenured math professors at research universities--so I don't think it's guaranteed to hurt your job prospects.

I would talk to the professor(s) you're interested in working with and ask for suggestions specific to studying analytic number theory.


World map with academic works graded by relevance?

Perhaps you're thinking of the map below?  It's Figure 1 of the paper Global Multi-Level Analysis of the `Scientific Food Web'.

(source: nature.com)

The caption is "Figure 1: World map of knowledge production and consumption in 6 major geographic areas of the world (North America, South America, Europe, Asia, Australia and Africa)."  An additional note: "Circle size reflects the number of papers $P_i$ produced by the corresponding entities $i$. The inner circle is for 2000–2002, the outer one for 2007–2009. The size of the pies represents (A) the relative proportion of citations $C_i$ that the entities earned in the 6 geographic areas, (B) similar for references $R_i$ recorded in the Thomson Reuters Web of Science database. The number of papers and citations have increased over time in all geographic areas, but their shares of references and citations have changed. For example, Asia reaches higher shares recently, characterizing it as an emergent scientific power, which has become almost comparable to North America or Europe. Note that, in the three leading knowledge producing areas, the majority of references cites papers published in the same geographic area, i.e., proximity matters."


How to deal with scooping when doing open-source tools development?

Having developed academic open source software for 20 years, I have never heard anyone getting "scooped" by putting code out there. And I know lots of people who do all of their development out in the open, often years before they have it all together to make it into a publication.

I believe that the reason why this never happens is that it's difficult to take someone else's code and understand it in sufficient detail without the author's deep familiarity with the subject. Certainly to understand it at a level that would allow that person to write up a publication about it and claim that it's their own invention. (That's in addition to the fact that everyone knows that that would be unethical.) It's so much easier to collaborate with the original author if one had to add something because then one would have the person who understands it all help you with it.

So I wouldn't worry about this. Put stuff out there and see that people use it. You'll build a reputation that way, and that's what you're going for. If you keep things secret, nobody will know it but you also aren't going to gain any reputation points for it.


There is a lot missing information here that makes it difficult to provide an fully informed response. For example, the subject, whether this is a theoretical or application class, the way it is taught, the number of topics, the scope and sequence etc.

At many universities, credit by examination is only possible if the student wants to prove that they already have mastery of the subject. In other words, unless the student is completely lying, they should already be highly familiar with the content of this subject and the simply want to prove that they already know it.

If the current final exam is comprehensive in nature it should be suitably for credit by exam, regardless of one's philosophical position. The reasoning being is that the student needs to demonstrate mastery of the entire subject and not just a portion of it. If the current final exam is not comprehensive, mixing it with the mid-term should help to develop a comprehensive exam.


Yes, it is.  When you omit the citation, you are claiming the text as your own. Any time you use the words or ideas of another you need an in-text citation which points to a reference that has enough detail to allow others to find the source.  If you are using the exact words, you also need quotation marks.


Is it ethical to ask colleagues to write a review of my book?

In the book fields I am familiar with there are two types of reviews. The first is the traditional peer review which is used to help decide if something is publishable. The second type of review, which I think you are asking about here, is a summarizing review.

Finding peer reviewers to judge the if a book should be published should be left up to the editor. If the editor asks for suggested reviewers, you should provide suggestions. In this case, having previously collaborated with the colleague, the editor may see this as a conflict of interest. If you suggest your colleague, you should be upfront about the prior collaboration

For reviews that summarize the work, if you know a publisher that takes unsolicited reviews, and you want a review there, then it is fine to ask people you know if they would be willing to write a review. Knowing, and even being friendly with, someone is not generally considered a conflict of interest. The issue is that the person you want to ask is a former collaborator. This might be seen as a conflict of interest. You can still ask the colleague and mention that you do not see the prior collaboration as a conflict of interest. You might want to suggest the collaboration check with the publisher prior to writing the review.


Is it popular to request TA presence in the classroom for all lectures & is it right?

Yes, attending lectures or other class sessions is a reasonable duty for a TA. Of course, if your contract specifies a maximum number of weekly hours to work, time spent attending the lectures would count toward those hours.

Keep in mind that even though you may be familiar with the basic material, the professor may feel it would be helpful for you to see the same presentation that the students are getting, so that your teaching will be consistent with his.

If you don't agree that this is the best use of your time, and there are more productive ways you could spend that time, then you could certainly suggest to the professor that you try something else. (Be polite about it - I would avoid using the word "force".) But ultimately it is his decision - he is the boss and you are being paid to work under his direction.


How do graduate admissions committees in the US perceive grading systems other than GPA?

A general answer, not just for countries but even for schools in the US we're not familiar with, is that we don't know how to evaluate transcripts/grades.  Different places apply different standards, both within their curriculum, and for assigning grades.  A 77% on its own could be brilliant or horrible (and we mainly just care about grades in relevant classes).  One thing we'll sometimes do is check with other members of our department who might be familiar with the country/school's grading system and standards.

In any case, the main indicator we use for how talented and well prepared the student is are the letters of recommendation.  As long as you're getting letters from some professors who are known abroad for their research and/or are familiar with the system in the US, you should get helpful letters.


How can I get a list of citations for a DoI or PubMed ID?

Quick and dirty version: Google Scholar

Type-in the DOI and read the citation count on the field "Cited by". Google Scholar does not filter for quality, so the citation count will include self-published papers, fake publications, etc. Expect some noise.

Better version: Web of Science

Ask your institution's librarian how you can access the Web of Science database and how to use it to retrieve the data that you need. That might require you to walk in daylight to the physical location of your library. Many survived that journey.


When does "distributing the submissions" process usually start for conferences?

I doubt that the distribution time is important for your actual concern. It probably wouldn't be prior to the deadline, but might be. There are too many conferences with too many policies to be definite.

But you can withdraw your paper and it is unlikely that it would be a problem even after the deadline. But if you want to replace it with a newer version, rather than just withdraw it, you should probably contact the program (or conference) chair and ask for advice.

Many conferences give you a chance to provide a new version after review in any case. If the error isn't such that it would result in rejection, you might be able to just provide the corrections as part of the regular process. But for a serious flaw, contact the chair.


Advisor wants copy of code to give to other student

Should I flat out refuse to share it and make Jen develop the code on her own (given there isn't an immediate paper deadline pending)?

What would be the purpose of this?  You'll upset Jen and your advisor, she'll have to spend time redoing what you've already done, and you'll have substantially decreased the usefulness of your contribution with no corresponding gain to anyone.  The only reason I see is a feeling that Jen is getting away with something and not putting in enough work herself, but I don't think you should be concerned with this.  Your advisor is aware of the situation and should ensure that she does enough work to justify awarding her degree.  Maybe she is doing great things you are unaware of.  It's also possible that she won't end up doing as much as the average student, but that's OK: she'll still deserve the degree, but just won't get strong letters/references.  By contrast, you'll get glowing reports of how you not only completed a substantial project of your own, but also stepped in to make major contributions to an unrelated project and ensure that it met a deadline.  That will put you in a great position.

  Should I question the request?

I don't see a purpose to questioning it unless you might plausibly refuse to share the code.

One option is that you could propose continuing to collaborate on this topic.  However, you'll have to handle it tactfully.  For example, it would be awkward to try to use the code as leverage to force a collaboration (by saying "I'd rather not give you the code, but I'm happy to make further changes if you let me know what you need"), or if it comes across like you are cutting Jen out of the project by offering to play her role and suggesting you would do a better job of it.  If you'd like to collaborate, it's reasonable to say so, but you should be open and collaborative, and make sure to allow everyone an opportunity to contribute.  (And it's best not to let this distract you too much from your primary project, since you'll have more to gain from a project you have greater ownership over.)


Unplanned sequential interviews with different groups

In general you do not have to disclose the exact order or reason for data collection. Most papers are ‘narratives’ written with the available totality of data at this point. Constructs such as ‘because we found xyz we then tested if abc...’ don’t necessarily describe the actual order of events.
The only times where this is truly relevant is when you run statistical tests. For example, if you collected data from the first group and analysis made you collect a larger dataset that now jointly gets analyzed, this has to be stated and included in the statistical analysis.


Can one professor hold more than one endowed chair?

I had personally never heard of anyone occupying two endowed chairs at the same time at the same university. Even if a person had two appointments in separate departments at the same university (for example, History of Science and Psychology), they were usually listed as the:

Dunning-Kruger Professor of Psychology and History of Science

or alternately, if the endowed line (the DK-Professorship) had been bequeathed specifically to Psychology for example:

Dunning-Kruger Professor of Psychology, Professor of History of Science

So the short answer is: no.

But that being said, there are always exceptions. A little digging around at universities that have separate sub-units revealed that, at Harvard there is a person in History who holds two endowed chairs and one regular position:

Annette Gordon-Reed

Charles Warren Professor of American Legal History at Harvard Law School
Carol K. Pforzheimer Professor at the Radcliffe Institute
[Harvard U. FAS] Professor of History

I personally think that this exception proves the rule since the three professorships are at nominally separate entities (HLS, Radcliffe I, and Harvard U FAS) that are under the singular Harvard conglomerate umbrella.


How do I prepare for the UK Research Excellence Framework submission?

Necessary disclaimer: I have not had to be involved in REF. This is what I summarized from my experience of the recent French evaluation system. Reading the REF guidelines, it seems pretty similar in focus (although to be honest, for all their wordiness, I prefer the very detailed REF guidelines over the French way of not explicitly detailing every rule).

So, with that out of the way, I would say there are two ways to “improve” what is essentially one’s societal impact. Both are important.

On paper

This is the short-term way of improving your impact: just present it better. Peruse the guidance documents (and possibly other guidance, including documents your local university might issue in order to help its staff), write down the relevant keywords, list all items that can be counted towards “impact”. Then, brainstorm (possibly with colleagues or friends!) for ways to tie your already existing contributions to these items. Sometimes it is just a matter of remembering stuff you didn't think of (in my case, I remembered that we had some colleagues from an industrial company who showed up at a series of tutorials).

For real

Of course, you can also try to influence your plans to include more activities of clear societal impact. There are unlimited number of things you could come up with, and they depend widely on context (which you did not give). Keeping it short and generic, here are a few good examples that I can think of (some of them more applicable in some fields, obviously):

organize panel discussions on your favorite topic, open to the general public
open lab day
“cultural heritage” research
create visualizations of your research (pictures, movies, whatever), and publish it
interviews or other interventions in the media (even local)
being listed on experts registries: courts, journalism schools
all kinds of work with local artists
workshop or discussion groups involving academic and industrial communities
being a member of a standardization body

It looks like some sort of random list, cause I tried to list diverse activities. I'm sure others will have plenty of ideas to add!


Value of (multiple) master's on the path to the PhD?

You seem (at least in your question) to have skipped over a middle option: as a PHD student in computer science at an American university, it is likely that with no additional paperwork you can enroll in graduate courses in the statistics department.

(As with all things academic, it would be good to run this past your supervisor, but as long as you can explain (i) why you think it will be useful to you and (ii) why it will not significantly impede the progress on whatever else you are supposed to be doing, s/he ought to be supportive of it.  If the statistics coursework is directly relevant to your thesis research, s/he ought to be enthusiastic, even.)

You can then take exactly the courses to develop the knowledge and skills you need.  I don't know your situation, but it seems very unlikely that what you want to learn will coincide precisely with the set of requirements for a master's degree in statistics.  And in terms of your credentials: unless you are looking for a post-PhD position specifically in statistics, given that you already have one master's degree and are going for a PhD, I don't see a second master's degree in statistics as having much value to you.  (Even then, unless your career goal is to be some kind of adjunct lecturer in a statistics department, a second master's degree is not guaranteed to be directly helpful: if you have specific career goals then you should ask around as to what credentials best help you achieve these goals.)

As to the value of the coursework itself versus the time for your CS research: Suresh's comment is the best answer that I can think of to that.  You're right; there are pros and cons to be weighed against each other.  We can't do that for you nearly as well as you can do it for yourself.  Your supervisor is the natural person to go to for some additional insight, but in my opinion the final decision is really yours.


I contacted several ones who have even cited my papers, but they simply replied "they cannot be my reference as they do not know me", meaning that why they bother to recommend someone they do not know.

This is to be expected. The purpose of letters of reference is to provide a personal perspective on a candidate from an eminent figure who knows the candidate well and is able to compare her/him with peers. The simple fact that they cited you means close to nothing. I have probably cited hundreds of researchers, maybe thousands, some of which I don't even remember the name. There is also the question what these references are actually supposed to write in their letters if they don't know you personally - "Mia wrote this pretty good paper in 2012, but I have never met her or talked to her outside of when she asked me for this reference." isn't a great letter of reference.

  This gave me a bad impression that no matter how hard or good you work, career success depends where you are and how many people know/care about you.

It is a bit of a depressing way of putting it, but at the end you are not incorrect. "Knowing people", or more correctly, "making people know you" is indeed very important for a researcher who wants to progress her/his career.

  How to find professional references?

This depends a lot on your level. As a student, you typically want your professors to act as references. As a more advanced researcher, which you seem to be, it is very important that you:

Find and occupy a niche (that is, if people think about subsubfield A in area B, yours should be the first or one of the first names that pop into people's mind). This works only if you repeatedly annoy people about a subject in papers, keynotes, lectures, and tutorials.
Go to conferences, write joint papers, and work on joint proposals related to said niche
Visit other universities, or invite researchers from other universities working in your or a related niche
In this way build a substantial network of collaborators and co-authors
Follow-up on on your network, make sure that people that you once knew are still aware of your recent work
Maintain reasonable standing with the important players in your larger area

If you end up with a reasonable network, which clearly takes time and dedication, you typically want to select the most eminent members of it suitable for a given application to act as references.


How to express about getting informed about a specific position

I don't see any reason to express where you learned about a job advertisement, except if it was emailed personally to from whoever you learned about it, and not widely distributed. However, usually these are mass emails sent to a large number of people (recognizable by several factors). In that sense, I don't see any reason why you would need to state how you learned about the position - unless you want to make a point out of it, i.e. make it clear to Prof. X who advertised the job that their good friend Prof. Y (or maybe the very famous Prof. Z) suggested to you personally that you should apply, which hopefully reflects positively on you in the eyes of Prof. X.


How to get letter of recommendation from current advisor if transferring PhD to another university for family reasons?

If your advisor is generally an emotionally sane person, he should be able to understand your position. If your advisor is not, you're better off finding out as early as possible, and then to run.

That said, the right time to talk to your supervisor is right now, for two primary reasons:

As you're working in a lab, it is quite likely that your supervisor would want to hire a replacement for you, which takes time.
Your supervisor may have contacts to the relevant universities, and be able to help you moving.

When it comes to what to talk about, there are two important aspects besides your wish to be closer to your family:

You'll want to reassure him that you are not leaving unfinished things around. Wrap up your experiments as far as possible before you leave, and be available to work on manuscripts after you're gone, too.
Do you plan to take your thesis topic with you? If so, you probably should discuss intellectual ownership with your advisor. Even if you feel it was your idea, he may disagree.

Finally, is there any risk that your current lab has some "secret techniques" that you'd "hand over" to the competition? If so, try to address potential concerns.


The full understanding of my bachelor's thesis requires the reader to watch a movie, how do I deal with that?

I don't think I see a problem here.

If you were writing a literary analysis of Jane Eyre, you wouldn't include the full text of the novel in your paper, and it'd be entirely reasonable to expect the reader to read the novel in order to understand your paper.  I don't see why a film should be any different.

Your professor can, and should, watch the film, and any others they find necessary in order to make sense of your analysis.  That's not an unreasonable thing to expect, it's just part of their job, like any other background reading they might need to do.  If you can lend them your DVD, or tell them how to otherwise get it, that would be a nice courtesy.

Other readers will have to make out as best they can.  It might be nice to list on your website some ways they could acquire the film (Amazon link, Netflix availability, etc) but again this is more a courtesy than an academic requirement.

But to really cut the knot: Just ask your professor. They are in the best position to advise you, both on the academic standards of your field as to the content of the thesis, and as to what resources would be helpful to them personally in evaluating it.


Is it possible for a conference not to be published?

The important distinction that you want to pay attention to here is whether the proceedings are archival or not.  Fewer and fewer publications (conference or journal) are actually put onto dead trees: it's expensive and heavy and takes up lots of space in your office.

An archival publication is one whose proceedings are in the custody of an institution that guarantees their long-term preservation and availability.  This can be anything from a traditional journal to a large society like IEEE or ACS to a database like arXiv or even a memo collection like the IETF RFCs.  If it's archival, it's a "real" publication because it will be there if somebody goes looking for it in 20 years.  Prestige of the venue is a completely orthogonal question...

Anything that is not archival is transient, and might vanish at any moment.  This happens often with communities that don't have peer reviewed conferences (e.g., many biology communities).  This is fine if the point of what you wrote was to have a ticket to give a presentation or to have a discussion.  If it's not archived somewhere, though, it's not really a publication, because there is no persistent reference that can be followed.


According to the APA guidance on handling interviews, if it is an interview not done by you found in a standard source (book chapter, in your case) then you follow the normal formatting for that source (book chapter if you are summarizing the whole interview; book as a whole if you are taking quotes from the interview with matching citation in-text that denotes speaker of quote).

With regards to the book chapter formatting in this case involving multiple people (interviewer, interviewee, etc.), the APA style blog has all the details on how to capture all of the different authors in the case of a book chapter.  Most of these details apply to the idea of multiple "authors" in the book.  Interviewees wouldn't be classified as authors (i.e., they aren't listed in the front matter of the book as authors), so you don't need to worry about that in this case.

For your specific case, I would do the reference as the whole book, not individual chapters, and not listing the authors as editors as they are credited as writing the whole book in its front matter, and not listing the names of the interviewees in the reference itself (as explained in the APA guidance links):

  Dolphijn, R., & Tuin, I. van der. (2012). New materialism: Interviews & cartographies (1st ed.). Ann Arbor, MI: Open Humanities Press.

Then, I would do the in-text citations in a manner that highlights the speaker of the quotes and the location in the book:

  As stated by Rosi Braidotti, "[insert quote from interview here]" (Dolphijn & Tuin, 2012, Chapter 1, p. [insert single page number of quote]).

When you are quoting the authors of the book, not the interviewee, the in-text citation should just be:

  "[insert quote from authors here]" (Dolphijn & Tuin, 2012, p. [insert single page number of quote]).

In this manner, you keep your reference style consistent with the standard APA book reference style and you clarify the speaker of each quote using the in-text citation, which is the recommended APA method.  You don't want to cite the whole chapter in either case because the result would not specify the specific page where the quote was found.  You would only cite the whole chapter if you were summarizing the chapter's insights as a whole.


Professors are busy people. If you send a random professor with whom you've never had any contact a paper and ask him or her to review it and provide feedback, odds are that you will never hear back from them, because they will ignore the request.

If you want a better response, you will need to cultivate a relationship with the faculty members over a period of time.


Would it be appropriate to mark down a student who selected all the answers in this exercise as "correct"?

I actually think this is a question about mathematics, or more precisely about mathematics education (and in the limited scope in which it is presented it would be a better fit on the Math Educators stack exchange), but there is a larger academic issue which is perhaps what you are “really” asking about.

The point is this: as educators we try very hard to instill in our students the values of precision, logical reasoning, and attention to detail. When they are sloppy in their answers to our carefully phrased exam/HW answers, we mark off points and wag our fingers at them. We go to great lengths to provide them with examples of well-written, thoughtful, precise, polished answers (and other content) that pertain to the topics being discussed, in the hopes that they will pay attention and seek to emulate that style of discourse.

Given all that, and especially in mathematics where that precision is an essential value that goes to the core of the entire discipline, we cannot afford to ask sloppy (and formally incorrect) questions ourselves. It is a terrible example to give students and undermines the very goal we are trying to achieve. A teacher who is sloppy cannot expect to produce students who are any less sloppy than the teacher.

Coming back to your textbook example, it may depend on the age group this textbook is aimed at, but for a university-level audience the problem you cite is indeed unacceptably sloppy. You are not being too pedantic; a student who answers that all answers are correct will have answered the question correctly (to the extent that the question is sufficiently well-posed that it can be said to have a correct answer) and deserves to get full points for the question and to not have anyone be describing their behavior with the word “provocatively”. Such a student will have shown themselves to be more thoughtful (unless they arrived at their answer by pure luck) and to have a better grasp of mathematical precision than the authors of this textbook.


Introduction to how journals and other research publications work?

what does impact factor mean

https://en.wikipedia.org/wiki/Impact_factor

  how important is this metric

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150161/

  who has the right of distributing the
  article considering I want my research to be publicly and freely
  available

The publisher is typically granted sole distribution rights, with exceptions for distribution via personal websites and sites such as arXiv

  what is general process of writing and review

That's been answered elsewhere on this forum.


APIs for titles and abstracts for most or all published articles?

For healthcare, you'll want to check out what the NIH has to offer. NCBI has a bunch of a free APIs, and also allows download of the index data directly. I used to download PubMed Central for local indexing via rsync, but I'm not sure if they still operate that service. In any event, PMC is a key tool that is familiar to health/medical researchers and very popular.


How do I get to know research areas in Physics and Mathematics?

While I agree with Coder's comment that this is probably off-topic here, perhaps I can provide a general answer which would apply to users looking into any new discipline, not just physics or math.

In order to really come to terms with any field, I would recommend the following (in no particular order):

Take relevant classes. As an undergrad, this should be extremely easy.
Talk to people currently performing research in these fields. This can include your professors or perhaps emailing researchers whose work you've seen and been interested in. This is the option I would suggest most, as you're likely to get a wider array of viewpoints.
As Coder mentioned in the comments, go check out some of the recent research papers in your field's top conferences. You'll likely be unable to follow the majority of the work, but you should be able to get a good feel for the general tone of research being done in the field.
Per Carol: Attend the colloquia and seminars that the relevant departments host.


Tracking dissemination of open access publications

I think this is only a concern if you believe that people choose what to read based on how "popular" it is in terms of reads on sites such as ResearchGate. I really hope that this is not the case.... so long as it's citations that you are tracking (which is itself a flawed metric, but less so, and is one that is commonly used), then it doesn't matter where the paper is hosted - what matters is keeping it as accessible as possible.


How to talk to PI about dropping out of graduate school?

One of the points I see in the above message, is that these feelings are so far entirely with yourself. I can of course not know for sure, but it seems to me at the moment that you have not talked to him about this yet.

You say, for example, he points you in 100 directions. I can empathize with that, surely, but do you know if he is doing this on purpose? Is he aware of this? Have you spoken to him about this?

I would say that the best way of opening this discussion is to actually open the discussion by telling him about your feelings. Perhaps he is willing to do things differently, perhaps he is actually afraid to be guiding you too much. All these things are now uncertain.

In any way, if you discuss these things (respectfully, aimed at improving the situation for the both of you), he gets to know you are not quite happy. If you decide to leave he knows you were not happy.

Also, I would like to agree with 101010111100, in that doing something that makes you predictably unhappy is a huge red flag.

Good luck!


Unaddressed ethical violation I know about but have no connection to: Do I report it?

I took action... After carefully reading our honor code and the procedure for reporting misconduct I felt more compelled to act.  Ultimately, I think falsifying data is one of the  worst things you can do as a scientist. I just couldn't stop thinking about the new department he is in, the new advisors he has, and the new cohort he is apart of... all ignorant of this offense.  If I was his new advisor, I would want to know about this.  So out of respect for them and for my institution I knew I would act.  The question was how?

It turns out my university has a protocol for reporting misconduct anonymously, which is great. But rather than go that route, I actually asked the PI if we could meet. PI was taken aback because, although PI knows who I am, we are not at all working together. In our meeting I simply explained that...

"I feel compelled to act in accordance with the honor code given that I am aware of the situation.  But once I report the incident, you will likely be the first person they contact.  So I wanted to come to you instead, out of respect, and explain how I felt regarding the situation and basically find out if you prefer to take care of it or if you prefer for me to move forward acting in my own good conscious."

PI was surprisingly kind about it, empathetic even. PI was very responsive to me explaining that I mostly felt bad for the new people this person was working with, that they were ignorant to his lack of ethical integrity--something the PI had not considered. We discussed how the PI wrote the RA a letter of rec to get into the new program, and I could see a realization on the part of the PI--specifically, that he had a responsibility to let these folks know that he no longer stands by his characterization of this student. In the end, PI assured me that we were in agreement, that taking official action through our university's research office was the appropriate next step. I apologized profusely for meddling but PI assured me I did the right thing and that I would've been equally right to have reported it as well.

So in answer to my own question, I would say that...

First, read your honor code carefully to find out what responsibility you have to report incidents you know about. (This is why S.Diaxo's answer is incorrect; not only is there something I can do about it, I am technically required to do something about it).
Figure out what your options are for reporting misconduct, it may be the case, as at my university, that you can simply report it anonymously and that they will look into it and you do not need to be involved.
If you feel compelled to report something, but you want to be respectful to the people it might involve, consider talking to those people directly (in a respectful and non confrontational manner). That worked for me, and I'm glad I don't need to be the one to report it.

Thanks everyone for your discussion.


Which elsarticle documentclass parameters in LaTeX should I use for different Elsevier journals?

The options not only allow you to chose between three different two-column layouts but also one column modes. The role of the two-column mode is to allow the journal to type-set the article once it should be published. You can therefore use the settings to to see the length of your final article (in terms of journal pages. In other words, you as an author have access to the type-setting mode of the journal paper, this is a side-effect of the versatility of LaTeX class construction in the manuscript handling phase.

The fact that there are no instructions for which to use means you can chose whichever suits the format best. I am, however, sure the journal can take the final manuscript in any of the modes since the only thing they need to do is to switch a comment between two lines if your choice is not optimal. I would send in the manuscript in single-column format and let the journal worry about which of the formats they use in the end.


How your PhD is counted depends a lot on from which country you obtained it. Currently, degrees from Australia, Canada, Japan, Israel, and most doctoral-granting American universities are recognized as fully equivalent to "Dr." Beyond that, however, the PhD is listed as a PhD, so long as it's been granted by an institution accredited to give out doctoral degrees. (It has to be legitimately "earned.") You just would not technically be allowed to call yourself "Herr Dr. Hans Wurst"; you'd be "Herr Hans Wurst, Ph.D." (or whatever the formal name of your degree is).

Unfortunately, the classification of the degree does matter in Germany. Someone who holds a Dr. rer. nat. (sciences), for instance, will have a harder time getting a position in an engineering faculty than someone who holds a Dr.-Ing. (engineering). PhD's may or may not count as being equivalent to either degree, unless the specific regulations of the universities allow for this. (This can make a difference in setting up thesis committees, depending upon the regulations of the faculty in question. Yes, it's really annoying, but that's the way the system is set up.)

Fortunately, as Nate says in his answer, the rest of the world is nowhere near as strict as German law (even the modified version now in effect).

Also, you can apply to the Zentralstelle für ausländisches Bildungswesen (Central Authority for Foreign Education) for recognition of a foreign-obtained degree as equivalent to the corresponding German degree.


Filling in a form before going out of town

Employers generally like to keep track of their employees' whereabouts, both for practical reasons related to things like insurance (as mentioned in the comments) and to prevent abuse in the form of employees using work time for completely personal travel.

Now, in the specific context of your question, it's true that academic faculty enjoy an almost unparalleled freedom to travel whenever and wherever they like during times when they don't have specific duties like teaching. Most faculty are responsible and ethical people who wouldn't abuse this freedom, but in a large department or institution invariably there will be some who aren't. The form that you are describing is a minimal form of oversight that lets the department know when faculty are traveling and for what reasons, and signals to the faculty that they should act responsibly and that ultimately their travel during workdays is subject to scrutiny by their employers. Maybe it is a bit annoying and intrusive, but if you compare this level of scrutiny to what workers in basically all other industries are subject to, I think you will find that academics are incredibly fortunate, and that having to fill a form isn't really a big deal in the grand scheme of things.


One First author paper, what are my prospects in academia?

To be frank, in molecular/cell biology your chances are rather slim. The 'standard' is almost 3-5 papers from your PhD which can be expected to be out by the end of your first postdoc plus some output from your postdoc. Of course, it is stupid to judge people only by their paper metrics, but this is what very many people in academia do. If you are lucky, you find a person who is not that quick with her judgement and searches for the hidden gold, carefully reading your letter and CV and the reference letters or is giving you a chance and invites you for interview. That can happen (happened to me once), but is rather rare.

Chances are even lower if the hiring process involves a committee panel or external reviews (as for grants or scholarships). Competition is often high, so you will usually only have a chance when you get very good/top marks from all reviewers. Because if there are three candidates who get 3 A+'s and then there is you, and even if just one of the three reviewers was only looking at publication output (chances for that will be veery high) and gave you a B or C, then you are already out and the decision will only be between the top-rated candidates.

On the other hand, a combination of a convincing letter AND the luck of being at the right time ready for the right job AND a bit of luck of hitting a person who is not overemphazising your publication output might put you into your 2nd postoc. Your chances are low but not zero.


Does consistency in how my name is presented/abbreviated as author on a publication matter?

If you find yourself publishing under multiple names, e.g., "First Last" in one journal and "F. Last" in another, you might want to consider registering for an ORCiD. ORCiD provides a unique identifier which a researcher can use to unite all the different names she/he has published under.

If you have a more common name, like "John Smith", an ORCiD can help differentiate you from other researchers with similar names. And if you change your name, ORCiD can help you link the older to the newer.


Contacting POI regarding status of my application

The professor's recommendation to the department is not a promise of admission. You can ask the professor about when you might hear from the department one way or the other - particularly if you have other positions you need to decide about. You can't reasonably expect an official letter at this point.


Can a person from arts background with masters in Computational Linguistics do Masters in Applied Mathematics?

You should start by writing to the graduate program directors of the departments where you are considering pursuing an MS in applied math. Explain you background and ask whether you can be considered for admission to their MS programs.

Typically,  master's level courses have one or more undergraduate courses in the same discipline as prerequisites. If you don't have these prerequisites, I am guessing that many universities in the US/Canada would be reluctant to admit you into their graduate programs. However, some departments may have an option where a student without an undergraduate degree in specific field or related fields takes a few essential courses at the undergraduate level (in that specific field) and obtains a minimum specified GPA. The student is then offered admission to the graduate program.


How to rephrase this statement in a paper? "Due to a limited number of pages, ..."

Details are omitted to conserve space.

Terse. Because you don't want your explanation to cause you to go over the page limit.


Should I email a corrected version of my essay to graduate admissions?

You can send it. It probably isn't necessary. It probably won't be considered. But it won't hurt. Just include a note of apology for the bad formatting.

But an error like that should have no effect on your application.


I don't really understand what the motivation here for the professor is. Since you did all of the work for this paper at University B, you should not list your new affiliation (whether it's an internship or another school) as an "active" affiliation for this paper. It can be listed as a "current address," but not as an active address for this paper. In that way, the professor still gets credit for your work, with your affiliation showing as being part of his group. (I suspect that the professor's concern is that, if you are at another institution and list that as your address, he won't get credit for his work.)

Another issue is that if you are not going to present the paper at the conference, he may have felt it was in his interests to list himself as a first author. How appropriate this is I have to leave to the CS community to judge.

In general, however, the first author should be the person who has made the largest contributions to both the research and the writing of the paper. Deviations from this need to have a very good foundation.


Is it advisable to apply to more than one PhD program?

Yes it is common to send multiple PhD applications to multiple schools. I am doing this now, I would RECOMMEND it actually because getting into PhD programs is difficult.


The money will come as a grant to your institution, from which you can take summer salary.

Note that if you are in a position where “summer salary” is relevant, you are probably subject to the NSF limit that you can only have two months a year on your NSF budgets, and also that for many (most?) programs, you are unlikely to get more than one month a year on any single grant.


Exactly, they are tenure-track assistant positions. After 3 years, if you pass a successful evaluation based on your research activity (abilitazione scientifica nazionale), you become an associate professor. The guidelines for this evaluation include an indicative target number of papers and citations, which is field-dependent. This is only indicative, there is a national committee in charge of the evaluation, and they are supposed to always check case-by-case.

The teaching load is quite low: 60-80 hours of frontal teaching per year, plus exams (warning: there is a lot of exams in the Italian system). As far as I know there aren't other obligations, apart from maintaining a good research output to get the abilitazione. Supervising PhD students is not required.

(The teaching load becomes 120 hours after you become an associate professor.)

The system for the final evaluation is still provisional and has to undergo a new reform in the next months. These positions were introduced in 2010, and things are still new and bleeding-edge. But in any case they are worth pursuing, there are not many other chances to get a permanent associate professor position in Italy.

To be eligible, you need at least 3 years of post-doctoral experience (comparable to an Italian "rtd-a" position).


Is it preferable to list the limitations of the presented method in the paper?

Actually, in every field, limitations should be mentioned. Otherwise the paper gives an incomplete account of what is known and what is not.
But that assumes that the author(s) recognize the limitations and that may not be an easy thing to do in some fields. In some situations, however, the limitations may be obvious to the reader, and thus are omitted. Some limitations might be trivial, though I'm having trouble coming up with a quick example of that. And, in statistical studies, the limitations are well known from the methodology used; sample size and such.
But including limitations should not negatively affect the likelihood of acceptance. Quite the opposite, I think. A reviewer, noticing an unstated, but important, limitation would be likely to comment on it and suggest an update.


Submitting a manuscript that is not ready yet just to fulfil a contract

Contracts for scientific research can often be thought of as having two components:

A set of "minimum requirement" fixed deliverables that you must accomplish or else face penalties, and
A set of actual goals, which may or may not be able to be accomplished as anticipated, given the uncertainties of every sort of interesting research.

Typically, the fixed deliverables are things like "write annual reports" and "create a prototype implementation of X" that should be able to be accomplished as long as the research is progressing well.

"Submit a paper on this research," on the other hand, is a foolish requirement to have in a contract, because whether a paper should be submitted at a particular time or not is very dependent on context.  For example, you might have been doing wonderfully, but then be unable to submit as anticipated because of related work that other people have published in the mean time.  It is for this reason that in my contracts I typically propose something more vague like, "communicate with scientific community on results of the research" and put the fixed deliverable as reports to the funder on what we've done.

So something's already rather screwy in your contract, and you need to deal with it.  I think the most important thing to figure out is whether the pressure to fulfill the letter of the contract is coming from a program manager who cares about the research or an accountant who does not.  Talk to the leaders of the project and see if they can figure out, because my recommended path depends on which it is:

If the pressure to publish comes from an accountant or similar "box-ticking" authority who does not actually care about the research, only about fulfilling the ridiculous contract, then I would recommend fulfilling the technicality by asking something like Nature or Science to desk-reject your manuscript.  Confirm the plan with your co-authors and others on the team, and make it clear what you are doing in your cover letter, and I'm certain they will provide you the rejection you desire without doing any significant damage to your career.
If the pressure to publish comes from a program manager who actually cares about the research, then you are in a much more difficult situation, and the desk rejection ploy is unlikely to satisfy them.  At the same time, the program manager could likely grant an exception to the contract to allow you to not submit. In this case, I think that it is important to understand why there is so much pressure to submit (perhaps it signifies that the whole project or program is in trouble?), and for the project leaders to negotiate with the program manager.  If they've already done so and failed... well, you're stuck in a bad situation.

If you're in the second situation, negotiations have failed, and you really must submit, I would recommend not submitting results that you believe should not be published.  That is the sort of thing that can haunt you for your career.  Instead, I would recommend submitting the part that you are comfortable with---the study design---in a paper that clearly and honestly says this is all that is done right now and puts the completion of the new study into future work.  Make sure that anything you submit is something that you would actually be OK with seeing in print if it does get through the peer review process, and make it clear in your cover letter that you are aware that this is preliminary and will be happy to accept a decision by the editors to either proceed or not.

And then never accept a contract with such a horrible clause in the future.


Who should the authors of a corrigendum be?

I can think about a few arguments to include all original authors as authors of the corrigendum.

 They actually work on the corrigendum by reading your manuscript and making comments;
 The corrigendum has no "primary" value without the original paper, it can be considered as an extra chapter. It does not really matter that you worked on this chapter more than they, since they probably contributed to other parts of the paper;
How would it look if you publish corrigendum without them? A little bit like "These senior guys screw it up, but luckily I able to fix it", isn't it? Do you really think this is an impression you want to make considering their contribution?


Funded PhD at low ranked school(s) vs one year funded TA at a top 5 school

There are so many confounding factors in these sorts of decisions, that it really has to come down to you to decide.

That said, my opinion is you always go with the funding.

Not only for the obvious benefits of having money.  The main benefit as I see it is the school's signal of interest in you, and desire to have you in their program.  Irrespective of what you think is the best fit, these schools see a lot of students, and also have their own opinion on what students are good for their program.  Your two offers with full funding looked at you and said "we want this person," and then put money on the table.

By that metric, the first school has a much more luke warm response.  Presumably they fully funded some other students, but decided against extending full funding to you.  The "why" of it is immaterial at this point.

That leaves just your 2nd and 3rd options.  It sounds like number 3 is an excellent fit that you're excited about, from what you've written.  Regardless of what you pick, congratulations on having multiple offers to pick from though!  This is a good problem to be struggling with.


Getting stuck in a rut while writing a thesis

My adviser said to just "Get er done". I found that the biggest hurdle, as you alluded to, was how do I make real progress. Here are some ideas:

Decide on the sections of the thesis. (This may already be predetermined by your department.)
Write an outline of the thesis.
Get a template for the thesis.
Look at how others from your department organized/formatted their thesis.
Write an outline for each section of thesis.
Pour your knowledge into the thesis without worrying about sentence structure, spelling, thought flow, grammar, etc.
Use Mind-mapping tools to get your thoughts in writing.
Set small intermediate goals. (i.e. I am going to write the description of x result in 30 minutes.)
Make a game out of it. (i.e. I got x words written yesterday, today I am going to write x + y words.)
Listen to music that has no lyrics.
Get a good night's rest. (I know this can be hard, but it does help.)
Change your work environment every now and then.
If you don't feel like writing on a certain day:

Refactor what you have already written.
Create a graph of your results.
Take a break. (Many times I was able to clear my head while walking away from the computer.)

Most of all keep in mind that what you write down is probably going to be modified, changed, added to, moved, or removed many times.  Celebrate your successes, and let your failures educate you.

I had the same anxieties that you are having when I was writing my thesis. Many of my peers had the same struggles well. I would say this is a normal part of the process.


how to handle a problematic previous advisor?

Get on with your life. Best way to get revenge would be for you to become successful and renowned in your field despite conflict with previous advisor.


Handling "contraband" tattoos in closed-book exams

"Cover it up" seems the only realistic solution if it appears to be a tattoo.

However, since we're discussing this in the hypothetical, writing a theorem on your arm may serve as a nice reminder of a basis from which to work on problems, but it can't really answer something useful for you. Just as younger students tend to look at their fingers when counting, they still have to put in the work of translating an abstract numerical problem to their fingers, then "read" the information from their hand, and finally write their answer down. We don't restrict their fingers as counting tools. Advanced students make more elaborate associations between concepts they're learning and something concrete -- this is usually encouraged by instructors when we explain things in plain language or metaphors. So, your question makes me think about what questions I'm asking my students. If it's just "Write down this definition from memory", then maybe I'm not going deep enough in the topic. Suppose instead that I said something like "Here's a definition of a key term you can look up anywhere, or tattoo it on your arm if you really like it! Now, which of the following things matches this description?"


Can I reliably determine the quality of a journal by checking citation numbers in Google Scholar?

Even in case you generally accept numerical measures such as citation counts or the h-index as a measure of quality, Google Scholar seems to be rather unreliable in them. In the case of evaluating individual authors, let me cite the Wikipedia article on Google Scholar:

  Vulnerability to spam — Google Scholar is vulnerable to spam.[26] Researchers from the University of California, Berkeley and Otto-von-Guericke University Magdeburg demonstrated that citation counts on Google Scholar can be manipulated and complete non-sense articles created with SCIgen were indexed from Google Scholar.[27] They concluded that citation counts from Google Scholar should only be used with care especially when used to calculate performance metrics such as the h-index or impact factor. Google Scholar started computing an h-index in 2012 with the advent of individual Scholar pages. Several downstream packages like Harzing's Publish or Perish also use its data.[28] The practicality of manipulating h-index calculators by spoofing Google Scholar was demonstrated in 2010 by Cyril Labbe from Joseph Fourier University, who managed to rank "Ike Antkare" ahead of Albert Einstein by means of a large set of SCIgen-produced documents citing each other (effectively an academic link farm).[29]

I'm not aware of a case where this has been exploited by a predatory journal, but if a publisher wants to do that, it doesn't seem to be too difficult.