How does the US National Science Foundation (NSF) research funding system work?

I'm most familiar with the NSF mathematical sciences research postdoctoral fellowship, which I was lucky enough to get 15 years ago.  The application process is described in detail in NSF's formal solicitation, but here's an executive summary:

Unlike most other NSF funding, this program is limited to US citizens and permanent residents.  (NSF's regular research grants formally fund the institution, not the PI, so non-American PIs can win grants; on the other hand, NSF's graduate research fellowship has a similar citizenship requirement.)  There was a parallel program for international postdocs for several years, but it seems to have been retired.
Applicants must be within two years of their PhD and must have no previous US federal grant funding.  In practice, this means each applicant can apply at most three times: once just before graduating and twice after.  Applicants do not need an academic affiliation when they apply.  (Again, the fellowship funds the applicant, not the institution.)
The application itself requires a bunch of NSF boilerplate, but the main content is an abbreviated (3-5 page) research proposal, a one-page project summary, and four recommendation letters (submitted separately by their authors).  As usual for NSF, the proposal absolutely must contain a paragraph explicitly labeled Intellectual Merit and another paragraph explicitly labeled Broader Impact.
Applicants also need an agreement from a sponsoring scientist/mentor/advisor.  The sponsor separately submits a statement describing their proposed mentorship role, research opportunities available in the hosting department, and promised infrastructure (office, computer support, libraries, specialized equipment, etc.).  The sponsor cannot also write a recommendation letter.
All applications are submitted electronically through NSF's FastLane web site.  Considering how much FastLane has to handle (basically everything NSF does), it works amazingly well.
The applications are reviewed by a panel of mathematical scientists (or more likely by multiple panels, given the number of applications).  Panelists are invited by the program director, but in my experience, NSF program directors are happy to hear from volunteers!
Each panel recommends and ranks a subset of the applications they review.  Standard NSF practice is to fund all applications strongly recommended by the panel, and some applications with weaker recommendations, depending on available funds and other criteria.  (NSF is deliberately vague about these other criteria, but gender, ethnic, and geographic diversity are likely guesses.)
Applications for fellowships to begin in Fall 2013 are due October 19, 2012.  Yes, this is really early.  Winners are usually notified in February and announced on the NSF web site soon thereafter.  All applicants receive a summary of their panel reviews.
The total award amount is $150,000, distributed over a two-year period.  Most of that is salary, but about $30,000 is set aside for stuff like equipment, travel, and benefits from the host institution.  Frustratingly, fellows are neither employees of the hosting institution, employees of NSF, nor formally self-employed; the US Treasury Department simply injects $5000 into your bank account every month.  So good luck with taxes!
Fellows need to submit progress reports once per year and a final report when the fellowship ends.


Am I allowed to share a final copy of my published paper privately?

I believe that it is a moral obligation of scientists to make their work available to colleagues, except when larger considerations such as safety intervene.  Most publication agreements allow for some form of sharing, even if only a preprint---you might or might not be able to post it for free online, but you can at least share via email.  There's a decent fair use argument for it as well, which is likely to cover ambiguous agreements.

I also believe that if you discover that a publication agreement explicitly prohibits sharing a pre-print via email, then it is appropriate and ethical to commit civil disobedience and share a pre-print of the article.  I believe this because I think that a publication agreement that prohibits individual exchange of pre-print scientific documents is itself unethical.  Don't share the final version, though: the moral obligation of scientific openness is served well enough by a pre-print, and the final version does often clearly incorporate real work and value added by the publisher, which you have no moral right to.

Do note, however, that if you choose to share when you are prohibited from doing so, that you should realize that you are committing civil disobedience and that there is a chance (however unlikely) that you may have to take the legal consequences for doing so.


Linking to ancillary material formatted as Jupyter nb?

I think you're asking the wrong question here.

For the sake of persistent archiving you should put all ancillary material at a sustainably archived website specifically designed to preserve scholarly communications material e.g. Zenodo https://zenodo.org/ or Dryad  http://datadryad.org/ or Figshare https://figshare.com/

Refer-to or cite the ancillary material archived on Zenodo with the Zenodo DOI that is generated upon archival of the material. From within that ancillary material which is archived, you can link to an nbviewer prettified instance of your Jupyter nb.

Direct-linking to nbviewer from within your article is a really bad idea. In five or ten years time it's very likely that the link will be broken. Always refer to ancillary material with persistent identifiers e.g. DOIs.


Is it better to repeat a caption or reference an identical caption?

It depends on several factors:

Can you expect readers to read this part of the caption only once and remember everything important for the rest of the reading? Or do you expect that readers need to constantly consult the caption to understand your figure?
Do you expect figures to be read in order? Or is it likely that a reader will look at a later figure in the series first?
How much information does the caption contain? This is not the same as the first point, as not all of this information needs to be important. Also, this is not exactly about length; a short caption with a lot of numbers is worse than a long caption describing straightforward concepts.
Do you need the space used by the repeated captions?

Positive answers to the respective first questions are in favour of referencing.

But why reference at all, unless you need the space? Because redudancy, in particular in technical aspects is annoying and time-consuming for the reader. If a caption references another caption the reader still remembers, this is the quickest way of communicating it. Otherwise the reader has to read the same (usually boring) text again. Moreover, if there is an unneeded redundancy, I would expect that there is a reason for this, e.g., that you changed some details of what is described in the caption. This would usually make me frantically compare the two caption (and thus flipping back and forth).

If you have the space, I suggest a third way that takes the best of both worlds:

  Fig 7. 2×167 in 10–200 mM KCl: (a)–(c) as labeled in Fig. 6, namely: (a) shows the reduced intensity for the varied sample conditions with the inset showing a key region. (b) shows how the scale applied to each data as a function of the concentration. (c) shows the time dependence.

This way, all the information is available for the reader who does not remember or has never read the earlier figure’s caption. But the reader who did, knows that the rest of the caption is redundant.


Is it appropriate to speak to the reader in scientific paper (but without using "you")?

It is not frowned upon and is mostly seen as a stylistic choice. It might be annoying if the same phrase is repeated many times ("Note, note, note, note"). If you prefer an alternative, here are some.
"The reader should note..."
"Readers familiar with XXXX will realise..."
"For those unfamiliar with... an explanation is provided in footnote/ appendix/ section"
"Notably,..."
"It must be stressed that..."
"We emphasise/highlight/note that..."
"It is important to note..."
"Let us note that" - from @user151413
Or simply do not refer to the reader but to the fact.


How can I tactfully ask a professor to bring requests to me earlier?

Channeling JeffE, just ask him directly, as if he were human.

  I was glad to be able to help with the grant proposal.  But if something like this comes up again in the future, would it be possible for you to give me a few weeks of advance notice?  That will help me arrange my schedule to make space for the work and avoid conflicts with my own teaching / research / dissertation / etc.

However, my guess is that prior to asking you, he thought that he could handle it all by himself and wouldn't need any help from you.  He probably found at the last minute that he couldn't, and had to scramble to look for help from anyone who could give it.  So if this is how he tends to operate, such a request may not help too much.  But at least it will be a nudge in the right direction.


What to write in first mail to a role-model researcher for PhD position?

This is a wrong approach and attitude. The whole thing will result in disappointment 99% of a time, because:

Your Work Should Impresses People Not Your Emails: If you think there is golden secret rule, that make your email irresistible to those people you want to impress then you be wrong. All you need is a good set of achievements.

Finding a Role-Model Without Knowledge: Whatever key points you might think that highlight a good researcher might be wrong because you did not achieved a good sense of research yourself. You might think, well he/she done this or that, and he/she might even rightfully impresses you; however, without knowledge of a field, finding a role-model to collaborate with is wrong.

High Maintenance Supervisors are Worst For PhD Students: Good or bad, you need to make your PhD an impressive achievement, and not your supervisor(s). Now, lets assume that your assumption is right and he/she is the God in that field. These people are mostly are worst supervisors, because they have no time to spend on you. While you might ask him/her about a topic, you think he/she has the mental power and will to answer you? He/she is running around to that class/conference/journal or book deadline/new faculty member interviews and on and on.

Conclusion

Don't waste your time chasing "role-models" while looking for PhD position. Find a supervisor that has time to spend on you. Someone that is always around to help his/her students. If you go with a "rock star" supervisor, then you most likely will be disappointed as he/she has no time to guide you through your PhD.


Dealing with competition from inside the lab

Science is a collective endeavour to build and spread knowledge, improving our understanding of nature. Collaborating and building on each other's expertise with proper recognition is a must.

You collaborated with a colleague of yours, and not only did this joint effort  produce a better result, but it also produced a further result, unforeseen at the beginning (and which, for you, came almost for free).

Celebrate the successful moment, hope that all your future collaboration will work out smoothly and productive as this one, and if necessary rethink carefully at your motivation in doing science, to avoid being stressed by something that should be the normality (and that too frequently, alas, is not). That is, be competitive against yourself to improve yours and everyone's knowledge and not against someone else.


Should I normalize inconsistent proceedings titles?

The Conference on Precision Electromagnetic Measurements (CPEM) is one conference in my field that suffers from the same problem, complicated by the fact that the proceedings are called conference digest, instead (digest is put sometimes at the beginning, sometimes at the end). I have never seen works from this conference cited in the same way, and given that this conference started in 1962, if there were serious problems in finding the proceedings in the libraries, probably some form of standardization would have come out along the years.

In general, I try to be consistent, at least within a paper. Your example, composed of both the full and the abbreviated titles, seems fine to me: in any case it gives the reader, even one not familiar with your field, all the possible search keys to identify the volume (and one familiar with the conference would probably not care anyway).


Skipping MEng to go straight to EngD or PhD from BEng

I'm not in UK, and it isn't my field, but the only real barrier is getting accepted into a program. You may be missing some technical background without an MS, but if you are accepted there will presumably be a way for you to fill in what you need.

Some places the rules may make it impossible for you to even apply, specifying a given degree, but otherwise, the only way to know is to make application and make it as positive as you can. Let the review committee know why you are a great candidate with a high likelihood of success. Of course that is the situation no matter what your formal background.

If an institution doesn't have a path from where you are, it is very likely to be obvious from their online materials.


Are academic indicators (h-index, impact factor, etc) really adopted by institutions? Currently used? And how?

On the European research market, various opinions have been offered on the use of h-index by ERC grant evaluation committees, and the broader relationship between h-index and ERC funding success. People who provide such opinion can be classified in three categories:

affiliated with the ERC
consultants whose business is to offer advice to (potential) candidates
individuals involved in another way, whose advice is most probably only anecdotal

So, what do the first two categories have to say? The official word from the guidelines is, well… absent. But it is politically correct to assert that h-index is not a good indicator of scientific quality and, as such, not used. This gives quotes like:

  Quality in science is not proved by accumulating quantitative points. The role of commercial impact factor and h-index is limited. Overemphasizing of publish or perish policy leads to a gradual perishing of all.

On the other hand, practical advice might be a bit more nuanced:

  There will also be a new h-index study the successful 2011 awardees in the PE and LS domains. The h-index is regarded as a background indicator rather than a determining factor and the study on the 2010 Advanced Grant awardees showed that each panel made awards across a considerable range and that there were significant differences across the different ERC panels. There was a big variation between different disciplines within the main domains.

and this:

  Every applicant had to choose his 10 best publications published in the recent decade and add how many times each of these papers were cited in the literature. The total number L of these citations describes well how the scientific community perceives their recent achievements. These numbers were provided by the ERC in the dossier of every applicant. However, during the evaluation process the panel did not put much emphasis on any bibliometric data. It was the opinions of the experts which did matter, not the bare numbers. Only after completing the evaluation process, I realised a correlation between these data and the final outcome.

To give another perspective: in France, a new evaluation system for higher education and research was put in place 5 years ago (the newly created agency performing the evaluation is called AERES). AERES evaluates each research group every 4 to 5 years, in order to give it an overall rating, which could be A+, A, B or C. This had at least two very practical consequences that I know of:

For yearly financial negotiations between each university and the Ministry for research, the ministry started to require a spreadsheet with the number of university teams rated A+, and the number of A team (B and C didn't seem to count). Financial support was then dependent on that number, at least as a starting point for the negotiations.
It became customary to include this grade in your French grant applications, because a A+ rating was considered a serious advantage. This was written in the “rules”, however…

So, all in all, are bibliometric and, speaking more broadly, academic indicators really adopted by institutions? Hell yeah! They make deciders’ job easier: quantification of research quality makes it easier to make decisions. Smart decision makers do realize, however, that a single indicator does not make for good decisions.


How do I cite an image from wikicommons in my thesis?

Even if its in the public domain its always good to cite where you get your information from, be that data, images, or whatever, even if its public domain
When I use images that are governed by a license (including public domain, and "fair use") I identify

the source,
the original author/photographer/painter/etc, and
the specific license that governs its reuse.

Using thorough and accurate citations ensures that you've done everything that needed to give proper credit where credit is due.
It also allows the reader to verify that what you cite is really at the source you give, and is licensed for the use to which you put it.
It doesn't hurt to include in the source, links to the actual source, and to the license (say as defined by Wikipedia, or the specific source you used.


Research approach for PhD thesis in Taoism: top down vs. bottom up

In general, I agree with JeffE. Both top down and bottom up.

In the case of Taoism, there is more - how proficient is your Chinese?

You said pursue lifetime in Taoist research. I am not sure you can do that without knowledge in Chinese language equivalent to at least masters degree in Chinese.

Taoism is rooted from Laozi's original text Daodejing. Reference Taoism. Most native Chinese speakers do not understand that text. If you want to conduct life time research in Taoism, that book is a must read and must understand. Without fully understanding that text, you are at best a second class researcher in Taoism.

I am a native Chinese speaker. How much do I understand the text? Less than 5%. If I spend 20 years or more on it, I might be able to understand 80% of it. Actually, I am bluffing. Some people contribute his whole life in it and then claimed that he only understood less than half.


How to ask for code from authors who have proposed algorithms in computer science?

Tell them what you told us. You are working on a different algorithm and implementation for the same problem and you'd like to compare to the state of the art. You've read their papers (cite them), and you'd like to see if their code is available for cross-comparison.

If they don't make theirs available, you may have to reimplement their algorithm in your code as well. This latter case is pretty common. There's a chance you might not do this as well as them, so there's some incentive for them to give you their code to get a proper comparison done.


Should I say "few literature" or "little literature"?

Little literature is common. You could also say "there is a paucity of literature on this problem"; "the literature on this problem is
scarce,
sparse, or
still in its infancy!"; or as @AliJamali and @paulgarret suggested, limited or scant literature.


Would getting a faster MSc instead of just BSc affect admission chances for PhD?

(I'm on the admissions committee of a top-10 US computer science department; my advice may be way off base for mathematics PhD programs.)

All else being equal, getting a master's degree in one year would probably count against you.  You're far better off taking some graduate-level courses, and possibly getting some research experience, while staying in the BSc progam.

At least in my department, PhD applicants who already have master's degrees are held to a significantly higher standard than applicants who only have bachelor's degrees.  While having formal research experience is an advantage for undergraduate applicants, it's a de facto requirement for applicants with an master's degree.  One year is not a lot of time to get some real (meaning publishable) research experience, especially since most one-year master's programs have heavy coursework requirements.  And you'll be competing with other MS applicants who've already spent two years in graduate school.

My department steers PhD-oriented undergraduates away from our 5-year BS/MS program for this precise reason.


Should I show mark boundaries on academic CV?

If the exams are listed in your transcript, then you do not need to repeat them in your CV. The reason is that they'll be better (and officially) explained on your transcript.


What happens if someone publishes a paper on your current PhD thesis topic

A lot of it depends on how far along you are, your institution, your career goals, and to some extent whether its your fault or not. That is, you DEFINITELY need to search the literature to see if your topic was already studied. But sometimes, someone might just have the same idea because they are thinking about the same issues and reading the same existing literature as you are.

If someone scoops you, it's likely a lot of your work won't be publishable anymore. In some fields it might be possible to publish as a replication (with low impact) or it may be that if you look carefully there is some areas of non-overlap that you can run with. The issue of publication will matter a lot more if you want a career in academia: you need a strong publication record to move on to the next phase of your career. In that circumstance, it might actually be better to delay your PhD just to get some publications, unless you expect you can get a good post doc regardless.

If you are early in your work, even halfway, it may be possible to switch topics. It's also possible all you need is a minor shift. I got scooped. Twice. Both times it hurt, but both times I also realized that there wasn't anywhere near 100% overlap, and my work was still publishable, it just took some extra time to rework things, reemphasize novelty, etc.

Overall, though, your PhD should be awarded for the work you do, not necessarily whether the work pans out. Your institution shouldn't prevent you from getting a PhD if you have been scooped. Negotiating all these issues should be the role of your thesis committee. The thesis committee should be comprised of at least some relatively unbiased professors who can judge whether or not your work is acceptable. The point of the PhD should be to train to be a researcher. Sometimes being scooped is part of the learning experience.

(note: I am answering this mostly from the perspective of biological sciences in the US - of course there may be differences by field and location)


There is very little regulation with regards to online teachers, so you probably wouldn't need to get a certification.
False! Not all online classes are on BlackBoard or Moodle. There's Khan Academy, Lynda, and a bunch of other spots online that are similar. Your skype teaching experience is also not irrelevant at all. A lot of these courses do "workshop" style classes, which are essentially group skyping.

A few things about teaching online:

don't expect to be paid a whole lot
if you're looking for something lucrative, it can be way easier to join some sort of tutoring program than to teach traditional classes in an online setting with multiple students
most online teaching is now happening in a pre-recorded video format. Production values seem to keep getting better and better. Have you checked out MinutePhysics?
there are so many ways to teach online. If you're looking for a more standard university experience, plenty of universities have online programs. Occasionally these programs get outsourced, so I would look into the companies that they outsource to. The ones that don't outsource, of course, tend to hire in-house, but I feel like they would be open to a new application. Perhaps that's something to consider?

Anyway, I know this is maybe a less clear answer, but hopefully it will give you some ideas with regards to what your options may be.


This sounds like a case of your supervisor being too busy and pushing work they consider less essential to the background. I'd suggest that, since you have alternate sources of feedback here, that you explore those and just push on toward the end.

I think it would be harder to avoid something you represent as a "complete" draft or a "final" draft. At that point I hope the supervisor moves your work up to the first level of importance.

Even feedback from a third party might be valuable if you can find a way to get it.

But there is no reason for you to stall your own progress. But trying to force someone to do something they don't see as essential in the moment doesn't sound like a plan for success. Especially when they have the power.


Alternatives to relying solely on student evaluations of teaching to help administrators more accurately assess teaching effectiveness

I am a recent part-time faculty at community college level. In our campus students as well as peers evaluate faculty teaching.
We have only one student/peer evaluation per year. In my case, I got feedback from a professor who taught that course for more than 25 years. His recommendations were not that different from what student's suggested in their evaluation.

Another option would be to test students understanding by assessing Student Learning Objectives (SLOs). For example, I give my class a questionnaire assessing their knowledge in SLOs on the very first day of the class and plans to give the same SLO questionnaire at the end of the course.

Hope this helps!


Transition from PhD to postdoc with an intent to change field

As one of my advisors once told me,

  The best dissertation is one that is written.

Tounge-and-cheek as it may be, I would strongly advise finishing up your PhD first, especially if you can do it in three months.  If you have doubts about whether your committee will approve your work, then you should be having that conversation very frequently (at least once a week, if not more) with the committee members that you think will have an issue with the work.

If you are indeed "certain [you] want to pursue an academic career," choice (2) may be the hardest path.  I've known a number of people who were certain they wanted to move back into academia after working in industry, but they didn't publish enough once they had a full-time non-academic job, and they weren't competitive for future academic positions.

Choice (3) would be a soul-killer if I were in that position.  To see the finish line three months away and then scrap it for 2-3 more years of work?  Not for me.

Choice (4) would probably be the worst decision -- every day you stay unemployed lessens the chance someone would eventually hire you (although maybe there are a ton of post-docs in your field).  Proving that you've learned these things on your own is difficult, although you would have more time to publish (but will you have a university association still?).

Tough choices all around, but I suggest finishing up the PhD at least.


Does APA style require a cover page for short student papers?

General points: APA style is principally designed for submitting manuscripts to academic journals.

When it is used as a style guide for student assessments at universities, it is common for the requirements to be adapted. So for example, many people completing honours, masters, or PhD theses in the behavioural sciences will use APA style for referencing. But their university may have other requirements for the formatting of title pages, heading formats, line spacing, paragraph indentation and so on. Or these details may be left up to the student.

If you are setting the assignment, you are free to pick and choose which aspects of APA style you want students to follow.

Your specific question: Note that APA style calls it a "Title Page" rather than a "Cover Page". Any manuscript submitted to a journal using APA style requires a title page (i.e., with title, author names, affiliations, author note, etc.). Those who create a university assignment based on APA style are free to adopt or not adopt aspects of APA style when it pertains to APA style. In some respects it doesn't even make sense to fully adopt APA style for Title pages on student assignments. For example, you wouldn't require them to provide a "corresponding author address" (a key requirement of APA style title pages), but you would require them to include their student number.


Notetaking with Latex and collapsing text for research papers

You could use Emacs/org-mode. Advantage: It is a simple yet powerful (and in principle infitely extendable) plain-text outliner with all the features that you require. Disadvantage: It requires some familiarity with the Emacs-editor, which has a relatively steep learning-curve.


Number of slides for 45 minute defense presentation

Why are you fixated on the number of slides? What matters is the story you tell, the important messages that people who listen to you will be able to take home after the presentation. Sure, you'd like to say more, but that's not how it works. Don't plan to talk faster, to run through your talk at lighting speed. If the content doesn't fit the time frame, drop some things. You may not want to hear it, but you have to.

Another hint, maybe too late for you, but which I find useful: there are two things which are very interesting to know about yourself as a speaker:

How fast do I usually go? I.e., for a typical presentation, how many slides per minute do I do? This allows you to get a rough idea of timing, for future presentations, even before rehearsing (or allow you to skip rehearsing at all, once you become good at it!).
In real circumstances, am I faster or slower than during rehearsal? This depends somewhat on circumstances (being tired, being excited, etc.) but it is still interesting info. For example, I know that I tend to digress more during real talks than rehearsals, which means when I time myself I know I have to leave some margin. On the other hand, some people talk faster on the stage.

When my students preparer for their first conference talk, I usually ask them to think of the above, and write down their timing. It is useful to prepare later talks, and also their PhD defense!


Statement of purpose: One-for-all or one-to-one?

I assume you are talking about a document that is part of your application to universities (e.g. for a PhD), which would be called a research statement here in the UK. Then the answer is simple: you want to maximise your chances of each application. So invest the extra effort and make individual documents to maximise your chances.

Different departments have different priorities, so you want to emphasise how your plans fit to the research agenda of each place you are applying to. While it may be convenient to send the same SOP to each place, you can show that you have researched the place you are applying to and at least modify the SOP to fit to the place you are applying to.


I have 3 months to submit my PhD thesis. What should be my strategy be like?

Make an output schedule that will let you finish.  By "output" I mean completed material, e.g. a page a day.  For each day, work at least as long as necessary to stay with the schedule.

If you can do that, you'll finish on time.


PhD programme dilemma: Doing it in a good faculty with strong supervisor or weaker supervisor but more interesting project?

Here are some good things to think about.

Research topics look very different when you dig deep into them.
Right now A's work might look sexy, but you can get 3 months in and
realize details that make you understand why it's not "hight impact". The reverse can happen with B: when you
actually start doing it you may find it more interesting than you
thought (this is quite common!). The fact that B's research
generates so much buzz means I think it's likely that when you learn
more you'd find it more interesting, or you might not.
Your Ph.D is a long hard process where you will have plenty of doubts. I personally believe the only way to keep your sanity is to be working on a project you truly love. I am saying that as a current student where right now things are tough but I'd never leave because this is the only thing I want to be doing, while I hear others who are almost ready to quit because it's a lot of work and the reward is quite far away. I know I'd be reconsidering what I am doing if I didn't love my projects.
You will do much better work and put more time into what you find interesting.
When you say the research centre is tough/challenging, did you get any bad vibes from the students? Trust your gut instincts. They won't say anything bad about their boss when he's around. The only thing you'd hear on a visit is little sour notes dropped around. Pick them up and understand them. Look at the professor's CV. Are his/her students doing well after graduation? If they aren't, that's a big warning sign.
Have you asked B to explain to you why his/her work is interesting? Sounds silly, but that's probably the most common thing B has to do. It may totally change your perspective.


Would a journal paying money for reviews, with open access and ad-based revenue, work?

Your idea has no chance of success. I'll ignore the part about reviewers being PhD students and postdocs and just look at the publishing model, because that alone is enough to sink the concept.

Ad revenue is not enough to sustain a journal. Just consider: who is willing to pay to advertise in a journal?

You might be able to get some ad revenue in a print journal, but as a whole, print is declining (maybe ~20% of the journal market at this point and dropping), plus with the most lucrative markets (developed countries) almost fully using electronic articles, you're not going to reach much of an audience that advertisers will be interested in.
Plus, if you do print your journal, you have printing costs to pay for.
Even if you go fully electronic, academic journals don't have nearly enough readership to attract advertisers. Just compare how many subscribers you need on a YouTube channel to monetize content (I use YouTube because this is also an advertisement-driven service). YouTube wants one thousand subscribers. Academic articles don't come close to 1,000 readers on average.
And to top it off, not only are you generating no revenue (diamond open access), you want to pay your reviewers. Where are you going to get the money from? You can beg your editorial board members work for free, you can use a free editorial-management system, you can outsource copyediting and typesetting to the authors, you can ignore marketing your journal, you can strongarm your institution to host your journal's webpage for free ... but paying reviewers involves cold hard cash.

The only way this can work is if you manage to secure renewable, external funding. Depending on how much you're willing to skimp on a journal's operating costs, as well as on how many articles your journal gets, you might not need more than a couple of thousand dollars every year. However even this level of funding is not easy to get. There's a reason why diamond open access journals are rare.

tl; dr: you can try, but expect to fail.


I have had people I know who are senior mathematicians tell me in private conversation that they believe it is right and proper to discriminate in favor of females in mathematics in things like graduate admissions and job hiring. In some cases they essentially admitted (in a circumspect, plausibly-deniable sort of way) to practicing this kind of discrimination themselves.

Based on these anecdotal experiences, I believe it is indeed quite possible that you were discriminated against. It’s also possible that you weren’t; there is simply no way to know for sure. It’s not even clear that there is an objective underlying truth to this question, since the notion of what it means to be discriminated against isn’t scientifically defined.

The people I mentioned are people I respect and believe to be quite sensible, well-intentioned people. Their views seem to be widely held among professional mathematicians in (US, and other countries) academia today, including many people whom I would characterize as very reasonable and moral. On the other hand, many other members of the academic math community disagree and believe that gender based discrimination in math and science is unethical and unfair regardless of which direction it takes place in. So no, you are not the only one, far from it.

I don’t think there is a legal remedy for this issue. Who will you sue? How will you prove that a specific program or person discriminated against you? Besides, the societal debate about affirmative action has been going on for several decades and doesn’t seem about to end. There have been numerous lawsuits with results going both ways. The battle lines move a little, then move the other way. Laws are passed, then get ignored or worked around. At the end of the day, there is simply a wide chasm in our society over the belief in the morality of such actions, and no law or court can change that.

For math specifically, the issue will likely subside in importance over time as the number of successful women mathematicians grows closer to (or reaches parity with) that of men in the profession and a younger generation takes over that doesn’t carry the baggage of the older generation and is baffled by the very notion that it was once believed women could not succeed in mathematics.

I understand that all of this big-picture stuff might offer only small consolation for you in your personal situation. It is reasonable to be upset, but keep in mind that most women also have plenty of things to be upset about, and while two wrongs don’t make a right, statistically speaking, you will probably end up getting just as much of a chance as your girlfriend to prove your worth as a budding mathematician, and you will probably be at least a little bit advantaged over her in other ways that you may not realize.

Life isn’t completely fair for anyone. Go out there and succeed anyway! Good luck!


Choosing PhD advisor in a field different from your undergrad research?

You are talking about what you did as an undergraduate. When talking to a potential supervisor, you have to remember that you are still going to be a student. You will be learning things. A supervisor will see your previous research and your potential for additional research.

As an undergraduate, I'm pretty sure that you did not become a world expert in astrophysics. So it's not like that you will have "wasted" knowledge, now that you will switch to a different topic.

Also, it's not like you're changing from biology to physics. You are staying within the realm of physics, and any skills that you gained doing your ("unrelated") undergraduate research will only benefit you when doing your graduate research.


Preparing a presentation for interview regarding a PhD position

I would focus on the research "questions" that you will attempt to answer. What hypotheses you have about the subject in question. Something about how you will begin to attack the questions (methodology), even if not too detailed. If time permits, something about where you think the research would lead you in the future.
If you already have approval for the research, then I suspect that all of this is readily available to you.


Optimal project stage (ripeness) for conference presentation

For me, the best stage of presenting work at a conference is when you feel submission is imminent, and then you stop presenting it once it's been published. The rationale here is that you are using conferences to basically sell your work, and that timeframe is when you have the most to sell and when you actually also need to sell it, either to get it published or to start new collaborations.


How to find new advisor after being let go

The way to find a new advisor is to ask. Whether they say yes depends on many things, including the known behavior of your current advisor. Are they reasonable or not? Is it you or is it the advisor who is the problem here?
You should also look at why you are having difficulties. Is the problem you are working on just too hard. This can happen in mathematics, for example, and it may take years to get partial results. Or the problem may even be unsolvable at the current state of knowledge, or even unresolvable in theory. If your have an impossible problem then a new advisor with a new problem would possibly work.
When you apply make the best case that you can be a success and get the best letters available to you. Your current advisor might write a good letter or not, but that depends on circumstances. Are you being let go because you aren't up to it, or because the demands of the research program of the advisor demand faster results. That might be the case in some lab sciences.
But in the end, all you can do is ask and apply and make the best case you can. Stress successes you have had, not failures.
It may well be that working harder to meet the deadline is a possibility. That would probably be the shortest path to success if you can manage it.
But any other path will take time. Be prepared for that and examine and evaluate all of your options.


Double degree in mathematics and computer science for PhD admissions

A PhD is a first and foremost a research degree. Having some research experience will be much better than a whole bunch more bachelor's level classes. Instead of doing a double bachelor's, spend that time doing research during your MS degree. Having a published journal or conference paper will probably go a lot further in an application than a double BS


How to describe teaching experience on an Industry Resume

Academics do a poor job of appropriately accounting for their time as teachers in a way that industry will understand. The point of industry resumes is to emphasize what you've done meaning the skills you bring to the table. CVs do not have the same intent, serving more like a 'Table of Contents' for your career. The assumption with a CV is that people will then go to your scholarly writings and read them, but you need to present as much as possible in that 1-2 pages of a resume, and know that they are not going to read more than that.

You want to:

play up numbers or other quantifiable achievements as much as possible. The more concrete the better.
explain how what you have done has created outcomes.
use terms that are accessible to an audience that may not be familiar with your field.
bridge any gaps between the way that things are done as an academic with how they are done in industry.
give context to the environment you were working in (i.e. Harvard is qualitatively different than working at a national lab. One is not necessarily better than the other, but identify where you were working right up front.)

Avoid:

jargon, either from industry or academia, especially if you are unsure of its use.
list of accomplishments.
assumptions about how much the audience will know about the things you are talking about.
lies.

Things that teaching demonstrates, which are highly valued, include but are not limited to:

presentation skills
organization and planning
leadership
ability to train others
knowledge of the subject matter
management of budget (sometimes)
cross cultural awareness

Try to include examples of all of these things in your resume.

In general, the standard seems to be as follows

  Organization (flush left) Position (center, or to the right of Organization)  Date(s) (flush right)

  verb number in order to create outcome
  verb number in order to create outcome
  verb number in order to create outcome

So it would look like this:

  University of Fredonia, Instructor,  2010-2012

  Developed 5+ curricula including 40 biweekly helping others to master underwater basketry
  Counseled 100+ students on composition, research, career and professional development
  Integrated Blackboard, git and multimedia allowing students with different learning style maximum opportunities
  Taught underwater basketry, Pig Latin textual analysis and yarn theory

Finally:

try to fill the line (I find LaTeX is helpful for that) and don't go over one line per point if possible
no periods at the end of the lines
don't repeat verbs or outcomes if you can at all avoid it
If you taught multiple topics, and instruction makes up the majority of your resume have different entries for each topic so that the first line would read "University ..., Subject Instructor, etc."
Unless the subjects you taught are directly related to the job you are applying for, and if you need to make space, there is no need to list the topics you taught, in other words you could drop the last bullet point in the example above. (e.g. it might be worth knowing that you taught accounting if you are applying for a position that involves accounting, but the odds of any position involving "Medieval German Literature" are very low, so you can leave it out.) What you demonstrate as a teacher usually matters to businesses much more than the topic you taught.


To what extent is the students' perspective on the lecturer credible?

Student feedback can sometime be a difficult thing for a teacher, and it is sometimes  inappropriate that teaching quality is measured in terms of student feedback.
Let me explain this by means of anecdotes. Imagine a colleague who is a good performer, much as a stand-up comedy act. They give good jokes, tell stories, show interesting films. How would many students rate them? Quite a few students might give them a good rating on the basis that they had a good time. However ask them in five or ten years time what they got  out of that class, and they might remember one of the jokes or stories.
Now imagine a colleague who works their class. Makes them do test and examples. Makes them go places that makes them think, makes their brains ache from the thinking they had to do. It is possible that quite a few students might really give some negative feedback that this was a class they did  not enjoy and might have liked to be changed. However, ask some of these students in five or ten years what they got out of that class and it might surprise you. It might be that they remember what they were taught and use it in their profession.
Good teaching can be preparation for the future and sometimes students can only discover that when they reach their own futures. I started to find this out when I would get unexpected emails saying "remember me". "I didn't believe you when you taught me that thing, and now I see that lesson playing out in front of my eyes every day. Thank You."
We have to balance those two aspects of teaching. We have to give them something for their now and something for their future. In fact something for our future and our grand-children's future, because that is what we build by good teaching.
As has been said by others: if you care, you will find ways to improve. You are doing the right things. Keep going. Best of luck.


Referee report ignored and not sent to authors

I agree with Patrick that you should let things go with the journal and not take things personally--what happened was probably just a result of everyone being too busy.  I doubt your relationship with the journal or editor will improve by pushing more.

To address your last question, yes I think it's worth contacting the authors.  You have a chance to fix some mistakes in a paper before it gets published, so I would probably contact the authors, and just say that you were asked to review but couldn't finish on time so the journal didn't accept your report.  (You also don't have to send them the exact report, but could just point out the mistakes.)  Edit: To be clear, I am suggesting your explanation of this situation is short, and matter-of-fact, in a way that doesn't blame anyone or anything except your tardiness.

I think this is okay, because you did not end up being a referee for the paper, you don't need to maintain anonymity.  There should certainly be no problem if their preprint is publicly available, in which case you don't even need to tell them you were supposed to be a referee.  However, if their paper is not public, you may want to first check any secrecy agreements you may have made when you agreed to referee the paper.


Can co-authoring a paper as a new grad harm my reputation/career?

I somewhat disagree with the previous answers. I think it is largely improbable that publishing a paper would harm your career, but it could if, for example, it is really poor and someone happens to read it.

Eykanal in a comment to Dave Clarke said that "no one would consider holding you accountable for the content of the paper"; I recall that there is a important trend to insist that all authors of a paper should be accountable for its content.

The fact that you do not want to pursue in the direction of the paper is completely harmless, though. There is really no problem working in different areas, the only thing to be careful about is not to spread oneself efforts too much, but this does not apply here.

So the main issue is (a); here I would say that it can be difficult to judge the quality of a result, especially for an undergraduate, and I would advise to trust your advisor. So it is really, really unlikely that co-authoring this paper could do any kind of harm to your career; in fact it could do more harm to decline this opportunity, since your advisor would probably not understand and you will probably need his or her recommendation.

At the end, I do not disagree that much with other answerers; but I would be less general in my statements.


Contacting prospective advisors before graduate school applications - courtesy or annoyance?

Actually, it can be either a courtesy or an annoyance, depending on a number of things. A cold email from a student in an unrelated field that looks like a mass mailing is clearly annoying and will be discarded without an answer. But an initial contact from one of your professors with a recommendation to look at you, especially if they are colleagues, will meet with success. Most contacts are somewhere between these extremes.

I think you were lucky to get responses from both. The fact that neither was dismissive suggests you had a good approach.

The prof who refused you, I suggest, was being honest. Others were in the pipeline already and there was little time, as you say, to make a good and fair analysis.

I don't recommend sending out resumes blindly to a bunch of folks. It is unlikely to result in any success. But when you are stuck and in a time bind yourself, you do what you must. But having a faculty advocate initiate a conversation in your case might have been an even better way to proceed.

And, as always, do your homework. If your background and interest are aligned with those of the recipient you stand a better chance. Even better if you can indicate that you know something about their work. Blind praise of their work, not knowing what it really is, is easy to detect and such letter easily slide into the trash.


Is including references of journals with low or no reputation considered bad practice?

If you use insights from a publication, you must cite that publication, no matter how low the regard in which you or others hold the venue.
If you're nervous that there's a high risk the insights will be wrong, there are things you can do to reduce that risk:

seek out an independent corroborating source for the same insight (and cite it in addition to the "low quality" source);
check the chain of logic from evidence to conclusions in the "low quality" source step-by-step for yourself (and still cite the source);
if it can be done ethically and affordably, repeat a few of the experiments (if any) reported in the "low quality" source to see if the results are reproducible (and still cite the source).


Is having a co-adviser a good idea in a PhD program

I wonder why it is necessary to formalize an advising relationship at this time. If you are getting good advice from a second person, you are fine. If something happens to remove your principle advisor from the picture, you have a backup.

I also wonder what you mean by "advanced age". Many grad students think that 55 or so is old. I passed that milestone 20 years ago and am still kicking mentally (though you can judge that from my writings here).

But if you do think a formal relationship is advisable, you might tell your principle advisor (a) that you have been getting good advice from the other person and (b) s/he has suggested a formal relationship. Ask what they recommend. But don't bring up age - please. Such a formal relationship can be good for the other person, of course, and may be the principle reason why it was suggested.

It doesn't need to be a "touchy subject".


Department member forwarded complaint about professor to that professor

While I can understand why the advisor reacted this way, why would a department member forward an email explaining a problem between a professor and student to the professor?

Is it the senior professor's formal task to handle complaints about or escalations from the advisor?

If yes, the senior professor indeed acted fairly unprofessionally, although it is a reality that in most cases the person that you complained about will learn about who complained about them as a matter of practicality (see some other answers for why this is).

If no, then, well, I am not sure what you thought would happen. Then you sent a random (presumably busy) senior person a mail about an issue that is in no way relevant to their tasks, and they did the only thing that makes sense from their perspective: glance the mail and forward to the person who is actually in charge for the request.

Look, I get that the first instinct when you get an unsatisfying decision is that you "would like to talk to the manager", but this is not how academia (or, really, any business) works. Department administrators delegate specific types of decisions to individual faculty members so that they don't have to deal with them one-by-one anymore. This is arguably not helped by the fact that faculty in academia tend to be very wary to step onto each other's toes. Hence, you will need to work with the undergrad advisor on these issues, even if you don't care for him much.


How to review a major revision of a paper?

When a major review has been requested, I think you really do need to go through the whole paper, for exactly the reasons you cite—the changes you've requested may conflict with the changes another reviewer has requested, and therefore the authors may have had to exercise significant discretion on which one to formally include in their revisions. Similarly, there may have been other changes that arose from your comments or those of your fellow reviewers.

Minor reviews require a lower level of commitment, unless the authors have indicated more substantial changes have been made.


How to deal with a professor who grades assignments and exams incorrectly

Not a definitive answer, since I’m a postdoc with comparatively limited experience of such conflict situations, but I do have a few suggestions.  They aim to:

maximise the chance of getting better grading without ruffling too many feathers;
give you solid documentation if you do end up escalating the complaint;
minimise the embarrassment in case it turns out that you’re misunderstanding something and your lecturer’s grading is defensible after all.

If you confront the teacher again, do so by email rather than in person.  This has several advantages.  Firstly, it allows you to look over what you’ve written and make sure you’re phrasing everything as tactfully as possible.  Secondly, it gives her time to (hopefully) get over any initial anger/embarrassment and give a considered response.  Confronted on a sensitive topic in person, it’s easy to get flustered and defensive, and entrenched in a position it’s difficult to climb down from later.  Finally, if she doesn’t respond constructively, you have the exchange in writing, so are on firmer ground for escalating the issue to the department head.

If possible, phrase the question/request so that your desired outcome is also palatable for her.  If you argue that she’s fundamentally misunderstanding the course material, she’s pretty unlikely to accept that — admitting that one’s wrong about something is already difficult, admitting one’s incompetent is a whole lot harder again. Instead, you could say that (e.g.) you have learned some of the material previously, and so know it with a different viewpoint from hers (and maybe give a couple of examples here, ideally with sources in well-established literature) and you would like to check that this angle will also be acceptable for work on the course.  I’m not saying you should say exactly that — but look for something that allows her to concede that your understanding is correct, without having to admit (to you or herself) that hers is wrong; and down the line this makes it easier for her to improve her understanding of the subject, rather than remaining antagonistic towards your suggestions.  On the other hand, if she does defend her current approach, this gives her a chance to lay out her case more clearly and carefully.

If you do this and she still doesn’t engage constructively, you’re now on very solid ground to escalate the complaint.  You have a written record of your good-faith effort to sort this out tactfully.  You have specific examples where she has doubled down on her misunderstanding of the material.  (I’d suggest double-checking these with your advisor or another faculty member to be absolutely sure you’re right about them.)  Even if the head of department supports this teacher in general, it will be comparatively difficult for them to dismiss the complaint or paint you as a troublemaker.


Mentioning possible PhD principal investigators in graduate application w/o being asked to do so?

I believe in this situation you have to decide on a proper ordinal scale for schools, faculty and the program. Since you mention that you have done the legwork and identified 4 labs, it would make sense at this point to possibly write to them and ask if they might have openings in your projects of interest.

Additionally, I don't believe faculty will disregard you for listing their colleagues, unless they have a personal feud. Younger faculty especially, will consider students who might have listed more senior faculty, if they themselves have not made it clear that they are looking for students. i.e, if a new assistant professor has not set up a group website, but sees a student has applied to a senior colleague in the same field, he will most definitely consider you favorably.

The point to remember is that you are looking out to do research you find interesting and in a field where you feel you will be able to make a meaningful difference. It is not a good idea to be vague in hopes of acceptance if you are not sure of working with the PI in question anyway.


Scientific output of researchers in industry and academia

Disclaimer: this answer applies to computer science. I suspect things are dramatically different in the natural sciences.

It's hard to measure these things, and a bit unfair. If you work as a professor, publications are the base unit (along with funding) for measuring your performance as a researcher. You also are encouraged to grow research groups that in turn will produce more and more papers.

If you work in industry (even industrial research labs) (and I've done both), you are evaluated not just in terms of paper output, but in terms of internal metrics relating to how you help the company.

So the incentive structure in industry is different.

Bottom line, since I haven't really answered the question: I expect that the average number of publications/researcher will be slightly less in industry than in academia, but the average will get closer as the lab characteristics become more "university-like": think MSR vs (say) Walmart Labs.


What are the pros and cons in sending a research paper to well-known author, before publishing?

I've worked on a few method development projects and I'm of the opinion that it is a good idea particularly if the author is well-known and well-liked (if they are a dick or you don't like them, that's a different story).

The obvious reason why is because when they happened to see your paper going out for review which claims a "massive improvement" over previous methods, they aren't going to get upset at you and pull strings to make your life miserable. Furthermore, they might have insight whether or not the new method is useful or merely enhancing a particular error which makes it look good.

The only instance where sharing the paper might be a bad idea is if they happened to be working on a similar improvement. Receiving the paper may motivate them to scoop you.


Mention two-body-problem in PhD applications? If so, where?

I would not do this. For faculty applications there is an argument to be made that alerting the search committee about the two-body problem gives them time to come up with solutions. A faculty candidate is a large enough investment on the part of a department/university that spousal hires/accommodations are a reasonable thing. I have never seen a PhD student, however, who is so good that the admissions committee would give the idea of offering a place to the trailing spouse a second of consideration. They might, however, decide you are not worth the effort if they know a partner is involved.


Do US universities publish an official definition of what constitutes a particular race/ethnicity in the context of scholarships or admissions?

The short answer is no. There is no definition. Our history is very complicated around race and after several hundred years we are still grappling with it. There may be a bit of abuse of the system, but not enough to cause people to try to start defining one another with rigid rules that we would not accept in any case. We have enough problems without that.

In places where such definitions have been used, some of them lead to atrocities. There are current examples in the world now, actually.


How closely is Electronics and communication engineering related to computer science?

This depends very much on your electronics degree. Most universities will ask for a certain amount of credits of certain subject (e.g. programming, data bases etc).

With electronics you will most likely have the basis and low level parts (math, architecture of cpus etc) well covered but you might have a gap in the more computer related areas.

The best way is possibly to informally ask where you want to apply to (attaching a syllabus of the courses you have taken). Some universities might also offer additional courses in order to catch up if you are short on some prerequisites.


I get no advice or guidance from my supervisor

Several things come to mind:

First, know that this is frustrating for many PhD students and it is normal for people to feel anxious if they aren't on a set course for their dissertation at the end of year 1.

Second, is it possible that your advisor is not a great match for you? My dissertation chair was not an expert at all in my dissertation topic (no one in my program was), but he was an accomplished scholar who could help me develop skills in identifying appropriate literature and narrowing down a topic. You may want to consider if someone else in your program is a better fit and switch advisors. This happens sometimes. It's normal.

Third, this is why PhD programs have students assemble dissertation committees, rather than just work with one person. If switching advisors is not an option, find someone else in the area you want to research and meet with him or her. Invite him or her to coffee or lunch. If they are at a distance, ask them to talk on the phone. Many researchers would be flattered that you are interested in their area and want to pick their brain. This may help.

Finally, does the literature indicate that there are specific topics in this larger area that need to be explored? Maybe you are not consulting with the right literature or there is a lot more out there to consult with.

Hope this helps! Good luck!


Big switch of field (from synthetic biology to cosmology) of research from PhD to postdoc?

I think it's going to depend a lot on the specifics of the field that you are switching to.  You're actually doing a bit of a surprising direction of shift---I've known a number of people who made radical shifts in the opposite direction, from highly unrelated fields into synthetic biology, which works pretty well because it's a young and rapidly expanding field, both inside and outside of academia.  Cosmology, on the other hand, is much older, not particularly growing (to the best of my knowledge), and without a large non-academia research sector, so it may be significantly harder to transfer into that field.

That said, if you're going to transfer, postdoc is the right time for "retraining."  The key question is to look at the skills you have, and try to figure out how they can be remapped into something "close enough" that it will give you a chance to shift.  You might want to consider looking at ESA or NASA, who have both cosmology and biology and where they may be close enough to help move from one to the other.  If you do the shift, you should also expect a fairly long period of postdoc, probably multiple postdocs, while you retrain and build credibility for your new field.

Finally, speaking as a synthetic biologist, I might urge you to consider that your view of the field may currently be quite limited.  Synthetic biology is an extremely wild frontier with a lot of things you might be interested in.  Are you sure you are tired of the field and the wetlab, or are you just tired of your particular lab and how it uses its wetlab people?  There is a wide variety of labs and cultures out there, along with a lot of non-lab companies with good positions for people with prior lab experience. Unfortunately some academic labs have rather toxic cultures and treat their graduate students like underpaid lab techs, rather than investigators in training: if this has been your experience and what's driving you out of the field, consider that it may be much better elsewhere.


I think that the criticisms which you describe are within the scope of constructive criticism. While you should not ignore them, they are not in themselves indicating any kind of "failure".

Depending on your discipline, and on the particular supervisor(s), feedback on progress reports of this nature can vary greatly. Some supervisors only write comments if they have serious concerns; others, who are basically satisfied, may still wish to give detailed suggestions for improvement. So it is difficult for strangers on this site to offer conclusive advice; you should probably approach your supervisor or some kind of departmental "Postgraduate Tutor" if you are worried about this report.


What is the etiquette for using empty desks in a communal grad student office?

Think of it like visiting somebody else's house.  Your friend is your host, but also shares her "house" with a bunch of roommates.  She is the one who will know best what sort of etiquette is followed in her community.

Why not ask her, "Where would be a good place for me to study around here?"  You might get sent to one of the desks, or to an empty meeting room, or the student lounge, or the coffee shop down the street.  There's no way to know without knowing the lab culture, and your friend is the one in the best position to judge.


How do I approach professors for reading courses?

I think the best approach would be to find out when the professor will be in his office and approach him and ask (or wait outside his class until class ends). I think he would appreciate having someone be interested in his work and maybe agree - after all, a university is meant for knowledge sharing right?

You're right, if he is on sabbatical then there's nothing you can do. You will probably have to show that you are really interested and aren't there to waste his time.


Massimo's comment reminded me of the old adage, "drink when you want to, not when you need to", and I think those are useful words to remember.

However, I also agree with what rnrstopstraffic said, and if you have no general problem with consuming alcohol, try it and see what happens.

I don't suggest going out with your friends, drinking 6 pints of beer and 3 shots of tequila before stumbling home at 2am and scribbling nonsense, however. One glass of wine or beer with dinner would, I expect, be enough to get the creative juices flowing (if alcohol is going to get them flowing at all). I also recommend that you wait until the following day to edit and submit.

I've personally never written academic work after drinking alcohol, but I have written fiction after doing so. For me, it definitely doesn't improve the quality of my writing, but it does help me put pen to paper (or fingers to keyboard) and just write. As Inkblot says, it's a lot easier to rewrite and edit when you have something on the page, even if it is total garbage.


What is a scopus indexed conference and how to identify the same?

There is no such conference.
Scopus is an indexing database which indexes the publications (journals and conference proceedings). Scopus does not index conferences.
What you are actually asking is: Whether the conference's proceeding is indexed by Scopus?
Many conferences publish their proceedings via popular publications such as Springer, IEEE, ACM, Elsevier. If it is a Springer-publishing proceeding: usually, it is LNCS (Lecture Note in Computer Science) and it's sub-lecture notes such as LNAI. Similarly, there is LNEE (electrical engineering), and many such. These LNXX proceedings are indexed in Scopus.
If it is IEEE, usually the papers will appear in IEEE Xplore (which is Scopus-indexed). Similarly for ACM proceedings, ACM Digital Library.
Elsevier publishes under the name of Procedia Technology or Procedia Engineering and few more. These are indexed in Scopus.
There may be other known publishers such as IOS Press, and many more. In that case, you have to check thoroughly where the conference publishes its proceedings and whether that publication is indexed by Scopus.


Grey literature, point it out as such in the bibliography?

References are references, and the reader already has all the information needed to make his decision on the quality of the source (the trust he has in the source) without you adding information. You don't need to separated references in different “sections” (which would make it much harder to read), or adding information. It is clear from the reference itself:

  boo2060, “A question on grey literature”, Academia Stack Exchange (http://academia.stackexchange.com/), 26 April 2013

that it is not a peer-reviewed journal paper, which would have a very different style:

  T. T. S. Boo, “A question on grey literature”, Academia SE Monthly, 17, 13-14 (2013)


Can I reuse part of a paper for my thesis?

Yes. It is certainly okay. Indeed, general practice when writing a PhD thesis is to produce a number of publications that add up to the thesis, whether directly (using staples) or by a good deal of massage. Some published material may be omitted and some additional material may be included. There's no reason why this shouldn't apply to a Master's thesis, too.

It is a good idea to cite the paper in the thesis (if the paper has been accepted for publication) and the thesis in the paper, if possible.


General vs field specific journals in mathematics

It's a bit difficult to disentangle this issue from prestige, since many of the most prestigious journals in mathematics are general.

At the very top of the prestige scale (Annals and a handful of competitors), there are no specialized journals at all.  Specialized journals start to appear a little lower on the scale, and they become more common as one descends further, as well as more specialized.

To a first approximation, prestige is the more important factor.  For example, given a choice between GAFA and Transactions of the AMS, GAFA wins on prestige despite being quite a bit more specialized.  There may be other reasons you might prefer the Transactions (for example, the publisher's policies, or a desire to support the AMS), but if building an impressive CV is your primary motivation, you should go for prestige.

On the other hand, going with the broader journal is a good heuristic if you aren't sure which is more prestigious or don't think there's a big difference, since it's correlated with prestige and therefore tends to give a good impression.

Towards the bottom of the prestige pyramid, people may raise an eyebrow at overly specialized journals, since a paper acceptance doesn't mean much if it's in a venue specifically designed to ensure that specialized papers not easily publishable elsewhere find a home.  Of course that doesn't mean the papers are bad, but they won't look impressive on a CV.


At least in chemistry the information you get at conferences is usually (nearly) done work. The presenter has at least a very big head start so it's nearly impossible to take an idea there and do it yourself even faster.

A bigger problem are grant proposals. Here most of the time no or only little work on this topic has been done so it's actually possible to scoop others and in addition as a reviewer you can prevent the proposal from going through. We had that happen before where a reviewer wrote absolutely wrong and nonsense statements to get the proposal killed, most likely to copy that idea since he works on the same topic.


Not including student who contributed very little as coauthor of paper

This doesn't seem like an especially unusual situation to me. You had a student for a fixed-term internship, during which time she pursued an angle that did not result in a publication. The student then moved on to other things, and so did you. You kept her informed of your work that is related to what she did as a professional courtesy, but she isn't interested in participating after the internship ends (nor does she have an obligation to). This kind of thing happens often, and nobody behaved badly here...

Do you have any indication that she expects to be a co-author on the eventual publication? (Corresponding with you about the work out of interest doesn't mean she expects to be an author.) She may not have any expectation of authorship credit.

If at some point she asks about authorship, I think you can just gently point out that her work did not lead to publication, and that you started working on the current approach (that did lead to publication) after she left.

If you do get the feeling that she expects authorship but she hasn't explicitly said so, you could say something to her like, "it has been interesting corresponding with you on this, X and I will be sure to thank you in the acknowledgement section of the eventual publication that he and I write." (If indeed you decide that you do want to do so.)


Should you request graduate school recommendation letters only from those that know you as a researcher?

Graduate schools admitting students are looking for evidence of ability as (or at least strong potential to become) a good researcher. Therefore, letters of recommendation that do not discuss research at all are simply not nearly as helpful to us than letters that do.

However, a mediocre letter of recommendation can be damaging to a student's chances of admission. Someone who isn't enthusiastic and immediately willing to write a letter should not be asked to write one; the "hit" to the student's admission chances simply aren't worth it.

So, under the circumstances, someone who is willing to write a very good letter that can testify to academic talent is certainly better than a weak to mediocre research-based letter. But a letter that only talks about a student taking tests well and "acing" a class is not really helpful. A letter that talks about, for instance, an in-depth class assignment, or can include details and observations from outside of class, would make for a much stronger and more useful letter.


In writing a job posting/ad, better to be specific or broad?

There is no straightforward answer to this. I would say it should depend on how important it is that the candidate fit the desired specialism(s). If you are willing to consider an outstanding candidate who does not fit the desired specialism(s), you should tend towards making the advert relatively open. If not, you should be more specific. In all cases, you advert should be open enough not to discourage serious contenders but specific enough not to waste the time of candidates who stand absolutely no chance. When advertising, it is also useful to clarify:

the history and modus operandi of any particular initiative/project/grant to which the position is connected (each institution and department has its own character and traditions, which may be obvious to an insider but may seem bizarre/confusing to an outsider); and
whether the purpose of the position being advertised is to

deepen an existing departmental strength or research cluster, or
broaden your department to extend coverage beyond its existing specialism(s).

Issues to consider with option (A)

it has the advantage of encouraging candidates with the corresponding specialism(s), who may otherwise not apply because they do not realise you are after those specialism(s) (because applying for jobs is very time-consuming);
it may discourage candidates whose profile is not a perfect fit (because they will assume that there must be someone who is a better fit in terms of specialism(s));
too specific, and people may assume that the vacancy is "fake" because you have already decided whom you intend to hire and are advertising to hide the nepotism (and thus not bother applying).

[but not all very specific adverts are stitch-ups: my current position had a very specific advert, but that was because it was to fill a post for which project-specific funding was already obtained; despite not knowing any of the people in any of the departments involved, I got the job, but I suspect I may have been the only applicant (the timing of the advert was unusual)]

Issues to consider with option (B)

you will probably get a lot more applications (no comment on whether this is a good or a bad thing); but
many/most of these applications will not fit your desired specialism(s); and
some candidates who would be a perfect fit, not being aware of the fact, may not bother applying;
people may assume that the vacancy is "fake" because you do not really intend to hire anyone, but are just "testing the waters".


Is there difference between value of Scopus- or ISI-indexed paper in gaining acceptance for PhD?

At least in the US, PhD admissions committees do not care whether the journal an applicant has published in happens to be on one list or another (there are plenty of really low-quality journals in both of those lists, and high-quality journals not in them). Rather, they care whether the journal is reputable and highly regarded, and whether the paper itself is any good.

tl;dr Aim to publish solid, high-quality work in a journal that is known for publishing solid, high-quality work.


Applying for scholarship with prospective advisor support, but not taking the scholarship: possible consequences

If you have a definitive plan in Europe, then there is no problem rejecting the opportunity in Japan, it should be ok as long as everyone gets notified. The advisor may be get annoyed briefly, but they will soon not think about it (especially famous professors) as they have many things on their mind.

I am actually in a similar position right now in which I might decline a potential JSPS fellowship.


Is it unethical for a professor to demand students buy their book then force autographing it before they can submit any work for the semester?

Yes, some aspects of this are unethical. I'm surprised that a university would permit it to happen. They would, I hope, object if they learn of it. Especially if they learn of it from complaints to higher authorities.

In my personal view as a professor and author, I can, certainly, assign one of my own books in a course I teach. But I believe that ethically, I should return to the student any royalty payment that I receive from the publisher. To avoid student cheating, I can purchase their receipt for the book from them so that they can't simply return it to be sold again as new.

I think that the professor in question is trying to do something similar in part of this (autographing the book), but in an unethical way.

I would think that autographed copies can be sold back to the bookstore, but not simply returned as new. Some autographed works are worth more, actually. The professor doesn't profit from the sale of used copies, of course. Only the "first sale" results in any royalties.

I don't know how the professor "verifies" the purchase. Does he keep a list, or just ask to see an autographed copy?

But, the issue of profiting from students when you require a purchase in such a way as to guarantee a profit is clearly a breach. As you describe it, it sounds like a clear form of coercion that should not occur and actually can pollute the relationship between student and professor.

And obviously, most professor-authors think their own books are the best.


Can I ask conference chair to give me an early result?

You can certainly ask, but you should not expect or demand an answer. Conference organizers may have hundreds of abstracts they may need to sort through and it may not be possible to give you an answer until the notification date.


Transition from university teaching career to curricular assessment type jobs?

I suggest the following course of action when thinking about any non-standard career path:

Identify people who already have the job you would like to have. Get in touch with them, and ask them as many questions as you can think of (about their job, how they got it, etc.). If you can't find anybody, chances are that this job doesn't really exist in your area. For instance, I am not sure if my university employs anybody for "curricular assessment", although we have a few people who more or less work fulltime on program management and development (which may be close to what you have in mind).
Find out what qualifications these people have, and which qualifications they had before starting their job. It's well possible that you may need additional training before you can realistically apply for the job you are looking for (e.g., to become a program manager in my department, you typically want to be a mid-career academic with considerable pedagogical training and some publications in education-focused journals and conferences).
Let everybody and their dog know that you are interested in transitioning into such a position. One challenge with non-traditional career paths is that most people in your network may not even be aware that you might be interested in such a job if they happen to come across one. The only solution for this is to make sure that your entire network is aware that you are not looking for a standard faculty position.
Volunteer for every opportunity to take on a role in your department that comes close to what you want to do. Besides giving you valuable experience this will also help you become known as the person doing program development in your department (and, hopefully, beyond). If a suitable job opens up, you should be the first person that people are thinking about.

In a nutshell, it's really not all that different from how engineers transition into management positions in industry. First, you make sure that people know you are interested in a management position in the first place. Then you get the necessary training and take over more and more management tasks, until a suitable opportunity arises and you get asked to transition.


Can I use published data to do my analyses and publish?

They've published their data. The way academia works is that people build on other people's work. You're just expected to reference their work properly.

Copyright is not particularly relevant here. Copyright law varies from country to country, but in any case copyright does not prohibit you from, e.g., adding two numbers just because those two numbers appeared in a copyrighted paper. Here in the US, copyright applies to the presentation of a work, not to ideas or data. For example, telephone directories have been found not to be copyrightable in the US. Since copyright is not very relevant, neither is licensing. Copyright law is specifically constructed so that it will not interfere with activities like scholarly commentary.

You will of course want to behave well toward the people whose data you're using. It won't hurt to talk it over with them. They know it intimately, and they may be able to warn you against misinterpreting it. For example, you don't want to be in the position of publishing a "gee whiz, amazing!" conclusion based on their data, only to find later that it was a misunderstanding. It may be appropriate for them to be coauthors on any resulting paper. Even if the purpose of your analysis is to contradict the conclusions they drew from their own data, it still doesn't hurt you to tell them what you're doing, and be above board and respectful.


Should I comment on a cited paper in the paper-review part of my master's thesis?

I'm not entirely sure about what kind of publications you are talking about when you say 'published by vendors' (white papers, brochures, user manuals?). But if you are referring to scientific literature, my answer is: by all means.

I don't se why you would refrain yourself from commenting the possible limitations or drawbacks of published methods. Just stay modest and consider the possibility that these publications came out a while ago and that the general knowledge in the field improved since then.

Being critical, if done properly (give objective reasons), is certainly something to be encouraged at the Master's level, and yes the appropriate section for this is the "State of the art" section.


Difference between campus police and campus / public safety

In the US, most state universities will probably have police, but it is a state matter so it varies from state to state. Private institutions probably don't have police, but still need security for students and otherwise. Private institutions could, in theory, contract with local police for coverage (some places) but can't form their own police forces.

At state universities it is the state that is responsible for safety and security and it is probably cheaper/easier to integrate training, etc. if they are police. They also can speak and act with the authority of the state if they are sworn officers. And use deadly force, of course.

In New York, for example, the police on state campuses are separately organized from the town police where the campus is, but they have all police powers both on and off campus. They carry guns, tasers, etc. and wear bulletproof vests when on patrol. I think they have special training so that they respond more appropriately to young people than municipal police might.

But many of the campuses are in small towns, even villages, in which the overall danger/threat is minimal.

It is probably more of an administrative matter, combined with the paranoia of politicians who don't want to be blamed if something really bad happens and they can't claim to have taken all possible precautions.


Separating your publications into journals vs. conference/workshop

I happen to prefer a chronological listing. But it is really up to you. For example, if you work regularly in two different research areas you could even list publications and such separately for the two areas.

The chronological listing makes it easier, IMO, to follow a thread or trend in research where other divisions don't.

But, if you have access to examples of how others do it in your field it would probably be best to follow along.

You are asking here for what amounts to opinion and those opinions may not be valid in your field. Do what is expected, I think.


Is an invitation to 'chat' about a potential PhD position actually an interview? What am I to expect?

Yes, this is an interview. Or at least a part of an interview - depending on your location, there may be a more formal one later. As a rule of thumb, both for academia and industry, whenever you meet with a prospective employer, be it for a coffee or lunch, a "chat" or something else, it is part of the interview.
As for the chat itself. If he asked you to give a short presentation, you should prepare to give a rather thorough one; ie. be prepared to explain basic stuff as well. If you have no idea about the format (time, place, equipment, audience (eg. is it just him?)), ask him. In my field it would be common to prepare some slides for such a presentation, but for others you would do without. It is always nice to know roughly how long time you have when preparing. Important: If the prof. says that you have, say, 20 minutes, then prepare to stick to that.
You can ask about details of the research, what is expected of PhD students wrt. teaching, possibilities for traveling and other things you are curious about.


Found a figure duplication problem in an already published paper

You should definitively discuss this with your mentor, who presumably knows the conventions of your field. If conventions or journal policy are still unclear at that point you can always check with an editor of the journal what course of action they do prefer.
Take the following with a dose of salt, because my physics perspective probably isn't to be trusted in your case given that you linked to a medical journal. However, I'd think that if you can repeat the experiment (with proper approvals in place) to fix the mistake, and the mistake doesn't invalidate the main conclusion, then an erratum/corrigendum is probably the better outcome for all parties. The International Committee of Medical Journal Editors has some guidelines on how journals should handle corrections and retractions, which  seems to agree with my position:

Pervasive errors can result from a coding problem or a miscalculation and may result in extensive inaccuracies throughout an article. If such errors do not change the direction or significance of the results, interpretations, and conclusions of the article, a correction should be published that follows the minimum standards noted above.
Errors serious enough to invalidate a paper's results and conclusions may require retraction. However, retraction with republication (also referred to as “replacement”) can be considered in cases where honest error (e.g., a misclassification or miscalculation) leads to a major change in the direction or significance of the results, interpretations, and conclusions.

If even pervasive errors can be handled as an erratum, probably your case can too. Finally, here's an example of an erratum fixing a rather large image duplication problem by repeating the experiments. Also see this Retraction Watch post.


I have a strong suspicion and weak proof that the data in the paper are fake. What to do?

You should definitely report your concern, but assume good faith.

This certainly sounds like a significant problem.  However, fabricating data is a very serious (even career-ending) allegation. You shouldn't accuse someone of this without very strong evidence, and I don't think you have it in this case. There could be an innocent explanation.

You might have misunderstood what they are doing. For example, rather than running all new tests, did they use the same results for their algorithm, but then compare it to different algorithms?  (I'm not sure from the question whether this would be possible).
It could be a simple error.  For example, what if they accidentally opened the wrong image file and added labels to it?

I would raise the issue, but rather than saying "this looks faked", something like this:

  The authors purport to have run new comparisons, and yet the results on the graphs are exactly the same as in their previous draft.  I don't understand how this can be correct.  Could they please explain, or correct the graphs if necessary?

Another thing you should do is ask for more detailed results and more information about their methods. It sounds like their reporting on what they have done is far from adequate. How they respond to this request might give more evidence on whether the results might be faked. If they are unable to convincingly explain the strange results and fully describe their methods, you should then at least raise the concern with the editor.  I don't think you have enough cause to do that yet, though.

If there is further action to be taken, it will be the editor's responsibility.  Here is what the Committee on Publication Ethics recommends to editors in this situation.  If the authors cannot satisfactorily explain themselves, it should result in a report to their institution and an investigation.


How to fill "department" for the author actually without department?

I don't see anything wrong with "N/A". Don't overthink this --- odds are that no one with a say on the acceptance of your paper (editor, reviewers, editor in chief) will ever look at this field. They are only there for the convenience of the journal staff, as far as I understand.


Is verbatim copying of short technical phrases without quotes but with citation considered plagiarism?

I disagree with the two existing answers (gerrit and Patric).

In mathematical writing, it is not necessary to put quotation marks around very short fragments of descriptive text where that text is the obvious and natural way to express the idea.  For example, if Smith has written a paper whose main result is

  Theorem. Every even number is divisible by two.

then it is perfectly acceptable to write

  Smith [cite] shows that every even number is divisible by two.

without quotation marks and without clumsy rephrasings such as

  Smith [cite] shows that all even numbers have two as a factor.

The significant intellectual contribution of the work you're citing is the theorem itself, not the obvious wording that they used to express it. As you say, anybody who understood the concept would probably choose to phrase it in that way, even if they'd never seen the paper you're citing. Mathematical writing would be completely unreadable if every phrase that had ever appeared before was put in quotation marks.  After all, Smith was hardly the first author to talk about even numbers – are we going to accuse him of plagiarism for not acknowledging that the phrase "even number" is a quotation from somebody else?


My professor wants to know if his recommendation is helpful

You should not be nervous about the enquiry, he just wants to know the outcome. Many academics lose track of time and/or have unrealistic expectations about how fast things move. I would respond that you haven't heard anything yet, but will let him know, regardless of the outcome, when you hear.

If you get in, he will fell happy for you and if you don't get in he will feel a little sad for you. Even if you are unsuccessful, I would not tell a letter writer that the letter was "useless". The only case I might say something like that, and I would be much more positive about it, is if you chose not to use that individual as a reference. Something like: for that position, I was limited on the number of reference I could submit and I felt my other references were a better fit for the position.


Why are seemingly important topics not covered in textbooks?

An important distinction that needs to be considered, in the design of any course, is the timescale over which the knowledge is expected to be applied.

At one end of the spectrum are courses where the knowledge is expected to become obsolete only on a time scale of centuries, such as calculus or Newtonian physics (yes, they change: try reading a calculus text from 100 years ago and the notation is likely to be somewhat confusing), but are generally about fundamental knowledge and core principles and thus often rather removed from immediate applicability.
At the other end of the spectrum are courses where the knowledge is immediately applicable, but where it may become obsolete quite quickly, such as training in particular software systems or laboratory equipment.

Institutions then tend to organize themselves along this spectrum according to their goals:

Strong universities tend to focus much more on the long-term end of the spectrum, because they are trying to give their students skills to last a life-time, and indeed to help those students become the ones who create new systems and applications that render the shorter-term knowledge obsolete.
Vocational schools tend to have a mix that aims to give the students both immediately applicable skills but also enough foundations that they won't need major significant retraining for a number of years.
Professional development and other "on the job" training tends to be much shorter and focuses on the short-term skills that are needed now and where it's OK if you need to train again on the new system in six months.

Now, let's consider your example of search engine optimization: this is a rapidly moving target, since it's based on adapting to the current methods that the current search providers happen to be providing how the internet happens to be organized right now.  Cutting edge SEO techniques are being invented and destroyed constantly.  Pretty much any SEO technique from five years ago is totally useless today, and SEO didn't really even exist as a field ten years ago.

As such, you should expect a marketing textbook or course at a good university to pay little attention to SEO, but instead to focus on more foundational principles.  On the other hand, if you search for SEO textbooks and courses online, you'll find a lot of more vocational or corporate resources available.

In short: educational resources adapt to the timespan over which they are intended to apply.  The longer a timespan an education is intended to cover, the less it will focus on "hot topics," and a good undergraduate degree is intended to last your whole life.