Have there been any recent studies on the effect of age on PhD success rates in the US?

I don't have exact references handy right now, but a researcher at UC Davis named Dean Simonton did some work on academic and creative output and age. The upshot is that up until actual senescence--so certainly no younger than around 70 for neurologically healthy adults--the relevant variable is "career age" (the time one has been working in a particular field) and not biological age.


Anyone with or without a PhD can write a text book. Yet independently of how well-known the author is, text books are not particularly well-selling items, since the audience is very narrow.  And even if they sell well, you will certainly not get any significant money from the sales.
If you want to write a text book for teaching purposes and because you think you can write a high-quality text book, then do it, go ahead.  Yet its popularity will probably grow if you make electronic copies available for free.
I am writing two text books at the moment, yet not in English, so I expect the audience to be fewer than 100 people. :-) However, I am still writing them because they will be nearly the only textbooks on that topic in this language, and people have already been very thankful for the drafts.


One of the stand-out conversations that I'm still grateful for with my PhD advisers 15 years later went roughly like this:

Him: So, what do you want to do after you graduate in 6 months?
Me: I don't know. [... beating around the bush for a long time, wanting him to tell me that I'm talented, know my stuff, and that I should definitely stay in academia and become a prof...]
Him: [Not budging] So I hear a lot of reasons for basically every option. What do YOU think you want to do?
Me: [Beating around the bush some more.] But I think I really do want to go for a postdoc and try that professor thing.
Him: [Without hesitation] Well, see, there you go! If you really want it, I'm sure you can make it, but only then. YOU need to want it, not me.

The thing is that in academia, you compete with the best in your field, the most motivated ones, the hardest working ones. It's a tough environment to be in, and one you have to love. If you have doubts, if you have to force yourself to do something you don't love doing, then that's not your career.

And there is nothing wrong with that either: There are many other, equally fulfilling professions where you can make a difference for your country and society. Choose something you love -- because that's where you're going to make a difference!


Is copy-editing/typesetting the only step in the publishing process where someone other than the author makes changes to the manuscript?

In general, you are correct: in general the editors and reviewers can only make suggestions for changes while only the author actually makes the changes.

In practice, however, good and thorough reviewers (and occasionally editors too) may often make highly specific suggestions for changes (e.g., "Delete this sentence", "Change phrase X into alternate phrase Y", "Cite papers A, B, and C"). Authors are strongly motivated to accept these changes in exactly or close to their stated form, for two reasons:

Doing so is likely to please the reviewer and increase chances of acceptance.
The reviewer often has a good suggestion and there's little reason to choose an alternate phrasing.

Finally, note that in some cases copy-editors do significantly more than just formatting/grammar-checks/type-setting.  In particular, for publications with very broad audiences, it is sometimes the case that the copyeditor will actually significantly modify the words and phases used by the authors in order to make the text more accessible and more in keeping with the publication's preferred "tone."  In this case, though, the authors always have a chance to review the suggested changes and make corrections in case they introduce errors, though objections to style may not be accepted by the journal.


Teaching classmates who don't put much effort in

In my experience, undergraduate students are a lot like children. They will be as lazy as you allow them to be. They will resist learning. They will resist doing the work and putting in the time. It's human nature...and it is something we, as teachers, must get the students to change.

Were I in your shoes, I would make it clear how to do something (as any teacher should) but I would certainly NOT do the work for them. If they keep saying "I don't know" then you should tell them "It's OK. Not everybody gets it their first time. Perhaps you get it when you take this class for a second time." I usually see my students' eyes open a bit on this one as they see that you are being so compassionate and understanding while still being refused to be manipulated. They also get the clear understanding that they will fail if they don't do the work.

We need to help students. That includes helping them to not be so lazy.


Letter of support for promotion to full professor from an "unusual" student

The department asked you to write because they want your opinion.  Of course they also asked others.  If they do not ask you specific questions, then just give the reasons for

  I am super happy to be able to support her/his promotion because I have a great opinion of her/him and I genuinely think s/he deserves that,

If they do include specific questions in their letter to you, then answer those, or explicitly say "I cannot answer question 3 because...".


How to create HTML Slides with audio for online lectures?

If I read correctly, in all those HTML slide systems you write the HTML file directly, it is not produced by some external tool. So I think you can simply put an audio tag in it. Or am I missing something?


How to properly describe future works in Master's Thesis?

Science is never complete. If the work that you have done in your master's thesis has been worthwhile, the most likely outcome will be that other researchers will want to develop your work further. Since this is the standard state of affairs, there is a standard place for describing future work in your thesis. This place is at the end of the Conclusions chapter. If you are writing that chapter well, you can both address future work that remains to be done, and give the impression that the work in your thesis has been worthwhile.
Your Conclusions chapter will start off by recapping what you did in your thesis; a short, high-level summary. Then, you will refer back to the problem statement and substatements you posed in your Introduction chapter (or maybe you put them in a separate chapter; this is also fine). For each problem statement and substatement, you will now methodically describe how the statement has been answered in your thesis, with explicit references to specific evidence in tables, figures, or the text. Once you have described how the problem statements have been answered, you then turn to describing future work, perhaps in a separately numbered subsection of the Conclusions chapter.
By building up your Conclusions chapter like that, you can give proper space and attention to work that remains to be done, while also giving a clear overview of the contributions of your thesis itself. If you refer back to the problem statements at the start of your thesis, you make a very structured impression: the start of the thesis and the end of the thesis are connected, and you summarize what you have done. So you combine sounding unbiased with discussing future work while also keeping the focus on what your research achieved.


What do PhD admission officers look for when evaluating an undergraduate thesis? (CS)

I think that significant research at the undergraduate level is pretty rare, especially if it can be completed and published.
The problem is that there is seldom time enough to get the needed background and also follow up to completion on a significant problem. Research is really open ended, especially in time. It is why some doctoral students take much longer than others to complete.
If you are diving into the unknown on a research question then it is impossible to foretell where or when you will wind up.
For that reason, I think that pretty much any research experience at the undergraduate level will impress a doctoral admissions committee in the US. This would even be true if there are no publication (yet) but perhaps many interesting questions still to be answered.
What is acceptable to your own institution is, of course, up to them, but I doubt, given what you say, that you are likely to leave too many admissions folks unimpressed.


Grad applications: mediocre grades from an ivy league (top 10) and outstanding grades from a smaller school; what should I do?

Just apply and see what happens.  You can't change the past.

Typically a graduate application will explicitly say that you must submit transcripts from all universities you have attended (or "earned credits from").  So it is not appropriate to simply pretend that it never happened.

Grad school decisions would, in any case, be based mainly on your more recent work, so the first year of your studies will not carry much weight regardless.  I'd ask the question: considering students at your current institution whose records in their later years are similar to yours, are they successful at getting into grad school?  If yes, then I think you are in good shape.

There is no systematic procedure in graduate admissions for discarding grades that were affected by medical issues.  You can, if you wish, discuss the issue in your statement of purpose (or other similar essay), and it would be up to the admission committee to decide how to take that into account in considering your application.  However, my feeling is that you don't need to say much more than "I started at University X, it wasn't a good fit, I transferred to Y.  Now here are all the fantastic things I've been doing at Y..."

As you get ready to apply to grad school, you will want to have serious conversations with your faculty mentors. This is definitely something you should discuss with them (though you don't necessarily need to go into as much detail as you did in this post), but I suspect they will agree that it isn't a big deal.


Editor has requested major revisions to manuscript. Should I give up?

Based on the description, I would advise you to sleep on it, suck it up, respond to the reviewers, revise the paper, and submit your revision to the journal.

Yes, reviewers can be absolutely, disgustingly, and unnecessarily rude and mean. Read their review, filter their non-technical rants, keep whatever helpful criticism you can extract from their comments, and address them nicely and respectfully. It may actually be that the techniques you used were adequate but you failed to point out why and how it would be unnecessary to use more expensive methods. Always assume that they are right. If they are mistaken, respectfully point out in your response why you are right and edit the original manuscript to make the issue clearer to future readers.

For instance, if the reviewer wrote:

  The methods used in the paper are abysmal. The authors use an outdated
  and archaic method, which is also very uncertain, to measure the mass
  of the frogs, which is by weighting them on a scale. The atomic mass
  interferometer, which uses gravitational waves and is able to
  precisely infer mass with an uncertainty of one atomic mass unit per kilogram,
  is the state of the art in weighting.

You can write as a response:

  The reviewer is absolutely correct that atomic mass interferometry
  (AMI) is the state of the art in weighting. However, we opted to use
  analytical scales to measure the mass of the frogs because the mass
  variations that we expected to measure are of at least 1 g, a quantity
  signficantly higher than the uncertainty of even the most rudimentary
  analytical scales. We do, however, agree, that the quantum mechanical
  analysis of the molecular buildup in neural entangled channels in
  during frog electrophoresis, which is suggested as an interesting
  prospective investigation, will benefit from the low uncertainty
  provided by AMI.

  In order to make it clear that the methods used in our study were
  adequate, we have modified the original manuscript to include the
  following sentence in the second paragraph of page 5:

  While there are more precise methods to infer mass, such as atomic
  mass interferometry, analytical scales offer accuracies that are
  compatible with the 1 g mass variations that were found in this study
  (see Table 3, for instance).


Graduate school admission with a degree in a different field

Graduate programs care far more about your background and preparation than about which field is listed on your degree.  Even if the application requirements list a degree in X as a prerequisite, the department will very likely make an exception if you have a degree in another field but can demonstrate that your background is equivalent.  How likely this is depends on which of the three cases listed above you are in:

Extensive formal study of X puts you in good shape.  You should discuss this issue in your statement of purpose and make sure your letters of recommendation address it.  Letters from people in field X who say your background is appropriate would be more convincing than letters from those in other fields.
The overall strategy is the same as in the previous case, but you'll have to work harder to make a compelling argument for admission.  It's certainly possible to get admitted, but the rest of your application will have to be convincing enough to make up for not having courses in X on your transcript.  When you request letters of recommendation from faculty in field X, you should specifically ask whether they are prepared to endorse your background as sufficient for admission (to avoid getting letters along the lines of "this applicant is smart and hard working, but I don't know much about their background and preparation"), and you should strategize with them about how you can present your background in the best possible light.
It's unlikely that you can be admitted at this point, for two reasons.  One is that many people think they would like to study a field that's new to them, only to discover that it's more difficult or less interesting than they had expected.  The other reason is that time in graduate school is a limited resource, and it's inefficient to use it to study prerequisites.  You would generally be allowed to fill in a few gaps in your background, but not to begin studying the field from scratch.  Instead, if you want to change fields you can begin by taking individual courses at a local university.  It's also sometimes possible to enroll in post-baccalaureate programs aimed at helping people change fields (but the availability of such programs varies, depending on the field and location).

There is a notable exception to #3, and that is the handful of fields where there is no meaningful pre-graduate coursework in those fields. For example, there are vanishingly few undergraduate programs in epidemiology, and as such there is very little expectation that you have taken specific coursework, and nearly the entire admitted graduate class will be "switchers" of some form or another. In these cases, what is likely most helpful is to be able to articulate how your present program and course of study has led you to be interested in, and prepared for, further coursework in that field.


A university's odd rule that inevitably affects students' final grades

I am assuming this is US. I want to suggest an alternative. Kindly ask your references to add the situation in their recommendations. I don't think Bill Nace's suggestion is exactly the right one, simple because of this answer. From questions regarding SOPs and from some personal experience I understand that at least some admission bodies in US universities do:

only glance over SoPs
Eliminate a significant (sometimes even more than half) of the applicants based on numbers (gpa, gre etc.) without even looking at anything in the application.

Now, nothing you can do right now that can help you in the second part except for scoring really high on your standardized tests. Even that won't be that useful as anonymous physicist points out in the comments. I heard people joking about getting someone to read your application as being the hardest part of an application (in US). You will need to somehow manage that. Probably good portion of your applications will end before a pair of eyes can lay on it. When, if, you get over that stage, 1 applies. They will read your recommendations more carefully than your SoP almost always.
Also, I would strongly suggest looking into graduate programs in other countries. I had much better experiences with European ones. They were always free and much easier to apply (in my case). Instead of dumping another 100 hours to a menial test, I reckon you can find and apply to 20-30 suitable master's programs in Europe.


How good is the Google Scholar search Engine?

It's not so much "worse" as it is "different".  The base Google Scholar search uses a number of defaults that may not be optimal for a given search.  Check out Publish or Perish which uses the Google Scholar API and provides a number of additional means of searching such as citation counts, journal sorting, etc. that can be a lot more useful.  It also has an alternate option to use the Microsoft Academic Search API, which provides an alternative set of results.


Extra question for specific students on test/quiz

The goal of any kind of assessment in teaching is to check if each student has met the learning objectives of the teaching activity, and the test should therefore have essentially the same questions of the same level of difficulty for all students. Otherwise, we would ask more of certain students in order for them to have met the learning objectives.


Switching fields within biomedical sciences between PhD and postdoc?

My background for context: BSc Mathematics, MSc Applied Mathematics, PhD Mathematical Modelling in Electrophysiology, Postdoc Biomedical statistician in gastroenterology but I avoided statistics like the plague right up to the end of my PhD. I found switching fields overall a hugely beneficial experience, although not without its drawbacks.

Pros:

You learn a LOT. I've found it really interesting to see how other fields work, and I feel like I'm more competent in a wider range of scientific techniques than I was when I finished my PhD. I was nervous about starting in a second field. Now, I would not be nervous about starting in a third field.
That said, I prefer this field to my old field. I want to stay in this field beyond the duration of my postdoc. And if you decide you want to go back to your old field, you can.
You can contribute in ways that no one else in your group can because you can suggest methods that no-one else knew existed. Things that are common in your field might be unheard of in your new field, which is a very fertile ground for novel science (this applies in reverse if afterwards you go back to your old field).
Your naivety about the field just means that you approach things with fresh eyes. You ask "stupid questions" and it turns out no one had ever asked them and they are actually really interesting.

Cons:

The imposter syndrome is real. You start off and the 2nd year PhD students know more than you. It feels like you're a student, but you're a postdoc. People mistake you for a student because of your lack of knowledge of some fundamental principles. But from a PhD, the thing you will have learned the most is how to learn, which is a transferable skill, so you'll catch up fast
Everyone I worked with has been very patient and understanding that this isn't my field, but I can imagine situations in which this isn't the case and people see you as incompetent

If you're willing to spend a while feeling like a first-year PhD student again for the benefits on the other side of that hurdle once you settle a bit, I would recommend it


How is an LOR presented when applying for grad school?

The rules vary greatly by country and program. You should follow the rules as specified by each individual program.

For instance, in the US, the applicant should never see a letter of recommendation at any stage of the admissions process. Nowadays, this is circumvented by having the letter-writer submit the reference directly, with the applicant only "supervising" the process to see if a letter has been submitted. In the rare cases where everything is to be submitted together, it is usually required that the letter writer sign across the seal of the envelope, to ensure no tampering has occurred.

As for the format, it should again follow local customs—for example, in the US, being submitted on official letterhead is sufficient; a mailed letter in Germany would be considered suspect without a stamp mark. (An emailed letter would be an exception to this, but would still be expected to have an electronic or digital signature of some sort.)


Math PhD Applications: Is it better to show just my good GRE score, or should I also send my low initial score?

Send your best one. GRE is typically used simply as a filter and including your lower score will probably hurt you more than it helps.


Tax incentives for private companies to fund academic research

The US has substantial research tax credits; in 2005, tax credit claims came to $6.6 billion USD, though it's not immediately stated what overall private R&D expenditure was in that period. (I suspect it would not be too difficult to find out...). Similar programs exist in many countries; see this 2014 survey.

The Deloitte report helpfully summarises (pp. 54-55) whether subcontracted research is eligible under the various national laws (which would cover academic funding); for the US, they are but you get a reduced deduction, while for Austria (for example) there is a 1m Euro cap on the amount that can be claimed for subcontracted research, and in the Czech Republic it has to be in-house to qualify.


How to cite ACM Computing Classification System?

Since you want to use the ACM Computing Classification System as a data set, rather than a publication, I recommend to use rules, established in the publication style guide for citing data sets. The only potential change I would consider is substituting the type of reference from [Data set] to [Data set -- Ontology] or, even, just [Ontology]. That is, of course, if your institution is not too inflexible on deviations from publication style standards. Otherwise or if you want to be on the safe side, just use the standard [Data set] identifier.

Check the following relevant resources on citing data sets, based on APA as well as other publication style guides. It should not be a problem to convert your ACM CCS citation to BibTeX format by using @misc entry type and including [Data set] into a relevant field (location-wise).

Resources:

Official APA blog post "How to Cite a Data Set in APA Style";
Examples by MSU Libraries How to cite data: Dataset citations (various styles);
Excellent comprehensive article "How to Cite Datasets and Link to Publications".

UPDATE: (initial attempt - alternatively, delete publisher / address and use "ACM" as author)

@misc{Acm:2012,
  author = "",
  title = {{ACM} Computing Classification System {[Data set].}},
  howpublished = {Retrieved from \url{http://dl.acm.org/ft_gateway.cfm?id=2371137&ftid=1290922&dwn=1}},
  note = {Accessed: 2015-06-21},
  year = {2012},
  publisher = {Association for Computing Machinery, Inc.},
  address = {New York, NY}
}


Is social media helpful for research dissemination?

An article from 2014 "Do highly cited researchers successfully use the web?" suggests that most of the most prolifically cited researchers do not have extensive social presences.

At the same time, studies also show that using the social web can improve hit counts somewhat, which suggests overall that using social media can influence research, but may not have an enormous impact.

Now you'll have to excuse me while I go create a Twitter account for my research group. . . .


How do you respectfully give a teacher feedback about their teaching?

Basically, I agree that what xLeitix said is the gist of if: as long as you are respectful, you should be fine.

To elaborate a little, my only experience with giving feedback back to the professor is a bit specific: a fairly young professor, that just got the course for the first time and was trying to improve it. Like in your case, he also said that he would appreciate feedback.

I'll try to give some specific advice, with a specific example of my situation:

again, be very respectful

(In my situation, this meant that I didn't start loudly complaining in class as the reading material quality (made by the prof) steadily degraded during the year. Rather, when I found enough time, I passed by the professors office during the office hours and asked him if he would be interested in my feedback on his reading materials.)
be as informed as you can about the coursework for which you disagree with the teaching approach

(Basically, why would I take your advice on how to teach X if you don't even have a rudimentary understanding of X?)
be specific, and give argumented reasons

(For me, this meant, when he agreed to listen to my feedback -- he actually scheduled a meeting outside of his office hours for that class suspecting it will take some time -- I didn't just come and said the materials were getting worse. I had specific examples of pages and exercises that I had trouble solving, marked in the script. I also offered information like "it took me X hours to finish and understand the first script (good quality), while it took me 4*X hours to finish the second one (worse quality), and they are supposed to cover approximately the same amount of coursework". For you, it might mean explaining how and why you don't think the feedback you're getting from quizzes is not helpful.)
make specific recommendations or suggestion (but don't demand anything)

(Again, in my case, alongside some of the things I marked, like exercises and definitions I had trouble with, sometimes I had my own versions of definitions, or I would re-phrase the examples in a way that made it easier for me to understand. It also help pointing out the ambiguities in the original and saying why you think your formulation resolves it.)
be committed. The bigger the change you want to make, the more committed your will need to be.

(As you can see form the above, making a substantial change, at least according to me, will probably require you do to a substantial amount of work on your own -- without the professor's help -- to be able to give suggestions well supported by arguments. Of course, you don't have to take all the points super-seriously if you just opt for a short 5-minute chat giving some suggestions and examples.

On the other hand, in my case, where I loved the course, I thought it was important, I thought the prof was great and trying really hard, and I had a (young and naive) wish to make a change for future generations, I took a few days to prepare my notes, I came to Uni a few days after the summer break has started in order to have time to give all my comments in as much detail as the professor wanted, and it did help that the prof actually knew and remembered me from the courses and valued my opinion at least a little.)


When do you use superscript affiliations and when not?

If many authors share the exact same affiliation, use the superscript form.
If one or more authors each have multiple affiliations, use the superscript form.
If authors come from departments whose names indicate distinct disciplines, and these multiple expertises are relevant for the multidisciplinary aspects of the paper, do not use the superscript form.
Use these rules as rules of thumb, not as ironclad rules. In the end, this is a matter of personal style and opinion.


Should I ask for a letter of recommendation when my performance wasn't great at the beginning?

I think that the poor performance on the first exam might actually help you to get a good recommendation.  In general, faculty like for someone to learn from their mistakes and make up for it.

Or, the faculty member may not remember your performance on the first exam and just go by the final grade.  Especially if you ask after the semester/quarter is ended.

Other things that can help you get a good recommendation include asking for help in a polite and formal way (e.g. without complaining) by visiting during office hours, and asking for specific assistance with something.

If you have more classes and have the same instructor/professor, then do well there too.  Ask them, in person, "Would you provide me with a positive recommendation for graduate school" and if they seem to grimace or have another negative expression, immediately ask "How can I earn a positive recommendation from you?"  People, especially faculty, want you to earn.


How to formally report database literature search results?

This sort of thing is pretty standard when it comes to meta-analyses, since each begins with a search for relevant studies. Generally, descriptions of the search query and its results are included in the methodology section of a paper; in addition to including the keywords used in the search (and, preferably, the reasoning for their inclusion), the start and end dates of the search should, as you mentioned, be noted. A diagram may also be helpful for readers to indicate the way in which you selected studies for analysis from the initial pool of results, and the languages in which the studies you assessed were written.

There are many papers that demonstrate this; as an example, "Psychosocial factors and chronic spontaneous urticaria: a systematic review" published in Allergy states the following:

  We first conducted a search of the PubMed and OVID/Medline databases
  using the keywords ‘urticaria’, ‘chronic urticaria’, ‘chronic
  spontaneous urticaria’ – given that the definition of CSU was not
  clearly established in early studies, we also included more general
  terminology such as urticaria and chronic urticaria, but excluded
  articles clearly assessing physical or acute urticaria –
  ‘psychopathology’, ‘stress’, ‘depression’, ‘anxiety’ ‘life events’ and
  ‘axis I’ and ‘axis II’, including full-text accessible articles in
  English, French and Spanish. We then performed a meta-analysis that
  included all these studies (see Fig. 1) from 1 January 1935 to 1
  January
  2012. After two reviewers (M.B.S. and I.B.) independently evaluated all potentially relevant studies, we conducted statistical analyses
  using Stata® version 12 (StataCorp LP, College Station, TX, USA).
  Methodological quality of included studies In order to assess the
  quality of the aforementioned studies, we employed a standardized
  measure specifically tailored to this systematic review, based on the
  Newcastle-Ottawa Scale (NOS) (8). This approach included the appraisal
  of external and internal validity, as well as biases common to
  observational studies specific to CSU and psychosocial factors. The
  independent reviewers mentioned above evaluated the study quality
  separately and resolved the differences in opinion by consulting a
  third reviewer (A.R.) (Table 1).

To sum up:

Databases searched
Search terms used (potentially alongside their justifications)
Dates of publication included in search
A diagram which explains how you winnowed these studies down to the relevant ones (and a table for the ones you decided to include in your paper)
As a bonus, if multiple authors are responsible for assessing studies for inclusion in your paper, include how these decisions were made/conflicts resolved.

I've bolded some of these ideas in the paragraph above to give yo a good idea of how this works.


How to correctly cite a retracted paper?

If you cite the study, then the citation should appear in the list of references.

The exact way to note the retraction varies based on the citation style (e.g. APA, MLA, etc.), as Nate Eldredge mentions in his comment. However, the basic convention seems to be to note the retraction in parenthesis, as an additional part of the original reference. For example:

Ricaurte, G. A., Yuan, J., Hatzidimitriou, G., Cord, B. J., & McCann,
     U.D. (2002, September 27). Severe dopaminergic neurotoxicity in
     primates after a common recreational dose regimen of MDMA.
     Science, 297, 2260-2263. (Retraction published September 12,
     2003, Science, 301, p. 1454)

This example comes from http://blog.apastyle.org/apastyle/2013/01/retraction-action.html, which pertains specifically to APA.


How can this be explained?

Since the Google algorithm is closed source, only Google can tell.

  Anything i could do about it?

No. You could try to write Google but I don't know any case where this turned out to be succesful.


How secure is it to receive an offer of post-doc position in email?

An unofficial offer is typically a notification of intent to make a formal offer, and I believe not legally binding.  This is not to say that an offer in email is not official and cannot be legally binding---but according to you the offer is unofficial.  Even if it is legally binding, having to take a university to court to secure a position does not sound like a productive way to start a postdoc.

Assuming the postdoc is completely funded from a grant on which this professor is the PI, in all likelihood the only way this would not turn into a formal offer is if the professor changes his mind or is somehow incapacitated.  Also, formality standards of offers can vary.  Anyway, if you are worried about it, I suggest you ask about the terms (if you have not received them) and when you can expect a formal offer.


How to formally address two individuals with different titles for PhD cover letter

In all likelihood, nobody will pay much attention to this. But if anyone is going to take offence, I think it is much more likely they will be upset if you haven't given them the correct title than because you're "drawing attention to their different levels". So I would address my letter "Dear Prof. X and Dr Y".


How to become well-known in the research community while being a PhD student

The best way is to be highly active in your field. (Note: this will take work.) Here are my suggestions for accomplishing this, and I hope others will post more in the comments or other answers:

Do awesome work. It all starts here. As a PhD student, this typically requires being in an awesome lab under an awesome professor, but it is possible to achieve awesome work without that.
Publish in respected journals in your field.
Network within your field. This includes attending field-specific conferences, talking to other PhD students and professors in other labs, and forming collaborations.


Were the duration of Bachelor's, Master's and PhD degrees different in the U.S. 100 years ago?

In the U.S., the Ph.D. is longer now on average, especially in the sciences because of the influx of money for paid research, the use of grad students to do research, professors as almost pure managers and grant funders versus real working scientists, etc. It has become something like Renaissance painting done by subordinates.  Except I still think the painters got their hands dirty and gave instruction.
There is almost no apprenticeship in R1 science from the professor, just other students and perhaps post docs. It is essentially about milking the grad student for results to get more grants, travel, promotions, grow the empire, etc.  Thus the expectation for work product has gone up.  Add onto that, that the money has enabled way more actual Ph.D.s to exist, but not increased the number of geniuses in the population and fundamental advances are if anything harder as simple much of the low hanging fruit is plucked.  And you have a situation of volume of result being emphasized.  Not the trainee education.
And enjoy the job market at the end...
All that said, if you sniff around you can find profs or even departments that still emphasize the classic 4 years.  But you will have to search. It is abnormal now.


Research grants for international PhD candidates

It absolutely depends on the source of funding. Each organization has their own rules. By and large, the NSF (since you mentioned F-1 visas I assume this is US-centric) allows foreign students to receive funding from grants, but this intent has to be disclosed at the time of submitting the grant request.

DARPA has slightly tighter rules although I'm reasonably sure foreign nationals can be funded. But if you're from a "country of interest" like Iran, there can be other complications.

Finally, while these are not PI-requested grants, the NSF-Hertz graduate fellowships are exclusively for US citizens.

p.s This even applies to PIs. There's a large DARPA program that you're not eligible to apply for unless you have a SECRET clearance, for which a necessary but not sufficient condition is that you're a US citizen.


Understanding a proposed schedule of a journal special issue

What the different dates imply would seem to be the following.

1st date: you need to have your complete manuscript submitted by this date

2nd date: Reviewers must have provided their reviews by this date

3rd date: between the 2nd date and the third date you need to revise the paper and possibly have another round of reviews if necessary. This deadline thus includes work you the editor and you and possibly additional reviewers. The manuscript should be sent in so that an editor can evaluate it and possibly find it acceptable. This this deadline probably involves a lot less time for you than just the time difference from 2 to 3 implies.

4th date: You will hear about the fate of your paper by this date at the latest.

5th date: the publication is expected to be out in printed form or assembled on the web (depends on what is seen as the final product)

So the time line may seem straight forwards but particularly date 3 is possibly preceded by a lot of work from more persons than you. I am sure an editor will want everyone to on the toes fo that stage so as not to unnecessarily delay the process.


How to import the citation of arxiv papers to Mendeley that could produce the accurate citation format?

For this kind of problems usually, I go to the Google Scholar and search the paper and from the results section, you can click on the cite button as shown in the picture and download the citation in any one of the formats. This downloaded file can be dragged and dropped to Mendeley.


Finding a PhD scholarship with a Second Class Lower Honors

Unfortunately with your record. you have zero chance of getting an international student scholarship from Australia (formerly called "IPRS" and now "Australian Government Research Training Program International Fee Offset Scholarship").  Best to be realistic about this from the get go.

Equally, I cannot think of any academic who would be likley to provide a scholarship based on your record (low second class) and no evidence of research potential.  If you have a friend who did so, I think there must have been extraordinary circumstances (e.g. research publications) or else it was a very low tier university.

The only possibility you have is to get funding from Sri Lanka and then try to find a supervisor in Australia who will accept you.  This funding needs to have two parts - (1) money to pay the substantial fees that Australia charges overseas students and (2) money to support you living in Australia which is not cheap even living the student life.

The reality is that you are competing with people who have evidence of research capacity.  This comes usually through published papers.  If you have not done any research that is publishable in the past the options are to work in the literature and produce a review paper on a topic of broad interest.  This is a path that I have seen used successfully in the past.  Alternatively do you volunteer in a research lab, do you have experience in research procedures that you have developed through spending time in a research lab?

Without some evidence of a capacity for research, it's hard to be at all positive about your chances of achieving your goal.

Sorry to blunt!

Best wishes


Students requesting to switch partners mid term

I would consider asking the student who is not getting along with their partner, whether they would consider leaving their current partner and work on their own from here on out. That way, the student still would have to do all the work on their own, but no longer has someone benefitting from their efforts without contributing.

If the student seriously considers this solution, you can be more confident that the complaint is genuine: if the student would be willing to go it alone, it is quite likely that the contribution of their current partner is near zero. But if the student is not willing to entertain this solution as a serious option, then you can derive the information that their current partner does contribute at least something to the team, and the request looks much less reasonable.

Based on the information you retrieve from this process, you can still decide to allow the student to join a team of three, or reshuffle some other way; asking the question does not commit you to actually make the student work on their own. But it might give you relevant insights.


Scientific Topic on Wikipedia originated from a Scientific Article with Low Citations

Wikipedia is a volunteer encyclopedia. People write whatever they want to write about. Someone found Fubini–Study metric interesting enough to write a big article on it (you can look through the article's history to see who they are). This doesn't mean the subject is very notable, only that it meets Wikipedia's so-called "general notability guideline". Therefore there's no reason to expect that the scientific articles that initiated the Fubini-Study metric to have a lot of citations.

As an illustrative comparison: the relatively obscure Bowling Green State University has a much more comprehensive article than the more highly ranked, bigger, and richer University of Tokyo. This doesn't mean that Bowling Green State University is somehow more notable than the University of Tokyo; more likely it means that among Wikipedia editors there are more BGSU alumni than UTokyo alumni - which shouldn't be surprising, since these Wikipedia articles are written in English. Compare the same articles in Japanese.


What is the more efficient way of self-teaching, when the return is diminishing?

I can help you think about math and programming, at least. The key to both is to do a lot of exercises and get a lot of practice. In learning on your own, you need access to someone else who can give you feedback on your results. It is very hard to judge your own work and to draw the correct conclusions from mistakes or to overcome difficulties.

Some online course structures may be fine for getting that feedback, but not all are. You need more than just the correct answers. You need to get a sense of why you went wrong in an exercise and how to avoid whatever that error was in the future.

Reading and watching videos isn't sufficient and it will give you only shallow learning. Then, when you hit the next challenge, you aren't quite ready for it. If you have a good textbook (and there are bad ones as well) try to do every exercise. Try to get feedback.

One way to get feedback, if you are working without a good guide, is to work in a group. You seemed to indicate that this was the case with you. You can each do a few exercises (the same ones for everyone) and then exchange work and discuss what you did and how. But even the feedback of other learners is better than none at all.


Is there research on the extent to which complexity of the proposed method(s) impacts the acceptance rate?

I haven't seen any research on the correlation between the complexity of the methods and the acceptance odds of a work and I think it is relatively hard to do a study on this. First because being simple or complex is completely subjective and domain dependent and hard to quantify. One can not generalize a pattern that is seen in a particular scientific community to others. Moreover, the information about rejection of papers is not publicly or easily accessible making the hypothesis hard to investigate.

That being said, in computer science machine learning community, I have seen that people are pushing towards critiquing the unnecessary complexity of the suggested methods and putting more emphasis on the actual results rather than the simplicity or complexity of the methods. There are many simple methods that are being published because they actually work well. I personally don't think that simple ideas which show good results are necessarily prone to rejection, but the opposite argument (complicated methods having higher chance of acceptance) is sometimes true.

On a related note, explanation of the ideas and presenting a work in the most simple way for people to understand, is being emphasized more and more. One reason of people trying to complicate things is that they think the less it is easy for reviewers to understand their work, the higher their chance of acceptance. I personally think that ideas in the papers should be explained simply and clearly because if it can’t be explained simply, probably it can be done better. And reviewers should not praise the work they don't understand, because it is the duty of the writer to explain everything simply enough so that the corresponding community understands it well.


How can a distance education student get a copy of the lecture notes?

Some comments and the already given answer give advices that can be counter-productive in France. You mention that this is about a research level course so I understand that this is a "Master 2 recherche" course.

It is unlikely, for privacy reasons, that someone will give you email addresses of other students. My advice is to ask the professor to forward to a few targeted students your request.

Going to the department chair/dean will probably be useless. If you really want to go up the ladder, ask to the person in charge of the master 2. But it will probably be useless too since in the French system professors are free to do as they want for their lectures. For those surprised by that last sentence, keep in mind that having lecture notes in pdf and a list of recommended textbooks is something that you don't have in all lectures in France.


Are there advantages or disadvantages for a college to give high or low GPAs?

Actually, reputation matters. If a college were to give out uniformly high grades then they would pretty soon not be trusted. And organizations that do "ranking" would be pretty savvy about such things.
It would also be pretty hard for a university to manage such a thing, since grades are given by individual professors with individual preferences to individual students with individual skills.
Some places, however, attract very able students. So, a 3.4/4 earned at one place might be better than a 3.6 earned elsewhere where there is a lower standard.
If the firm "cut-off" really happens, I assume that it is pretty low and that other factors might provide exceptions. Such a cut-off might not be disqualifying, but only result in a "sorting" of applications so that the more promising ones can be handled first.
Employers, on the other hand, are looking for skills, not grades. But they, too, want to spend the effort in hiring on promising candidates. Grades are only a part of that.


Etiquette of publishing (continued) research after graduation with an MS degree?

The big issue here is the following: will you need to have your master's thesis advisor write you a letter of recommendation in the near future? If so, then it will be potentially a big problem to publish material from your thesis without his involvement. This will provoke a response, which could be damaging to, for instance, job applications or graduate school admissions. So tread carefully before trying to publish the MS work.

However, since your advisor has proscribed work in other directions as part of your thesis, you could certainly explore those on your own. In such a case—since it isn't an outgrowth of your thesis work, but essentially a "parallel" work, you wouldn't need to share co-author credit with him. This is especially true if you write the paper and direct the research yourself; in such cases, he has no real claim to being on the paper.


What to think when asked to self-fund research?

Answering for the UK and for not-STEM: YMMV in other locations or subjects.

In such a situation it is very likely that you have not been given the funded position. If I were to speculate here, the internal decision about the funded position was likely made and whoever contacted you assumed you had already been notified that you did not get it. However, it is certainly acceptable and appropriate for you to ask about the status of that application and you need not hesitate.

However, to put things in perspective, my subject area recently had over 100 applicants for 4 funded PhD positions (and 86 applicants for a single post doc position). It certainly didn't matter at all who applied first as no one looks at the applications until the closing date, and we don't look at them in the order they come in. While you might believe your application was strong, and it might be strong, if you are facing a similar applicant to award ratio, your prospects aren't good.


What is the value to a student of a professor offering to supervise their PhD?

The easiest way to get into a Ph.D. program is to have a professor who knows who you are and wants to have you as a student.  In many other questions on this site, people talk about the difficulty of standing out from the crowd amongst the large number of applicants to any decent Ph.D. program.  With this professor, at least, you have stood out, and that's quite significant... if you want to do a Ph.D. with them.

First a sine qua non: don't even consider it if the program doesn't guarantee some degree of funding.  Every respectable university should be offering support for its STEM Ph.D. students through some mix of research and teaching assistantships.  It should be the department and not the professor that guarantees funding (though if the
professor has funding, they may be able to give you more time as a research assistant rather than a TA, if that is what you both want).

Beyond that, key things to ask yourself:

Do you actually want a Ph.D.?  Getting a Ph.D. is a terrible, soul-wrenching process and it renders you unfit for most employment.  If you are truly drawn to research, however, it is the best and only course to take.
Are you OK with not being at a famous institution?  There are only a few famous institutions in any field, and getting into them is a gamble. Often, however, there are a great many solidly respectable institutions that can launch you on a totally reasonable career, especially since it is often possible to "upgrade" institutions through postdocs.
Do you really want to work with this professor?  You don't know what working with this professor will actually be like. One advantage of the high-profile institutions is that if you find things aren't working with your advisor, there are often many opportunities to switch to others.  In a smaller and less renowned department, you will likely have less alternatives should things go wrong.

Ideally, if you answer yes to all of these questions, you should start doing some work together now, so that you can get a sense of whether there's a good working relationship.  If so, embrace it and be grateful that you found a good match.


Is it unethical to use a published code in my PhD thesis work?

There are three issues:

Is it a copyright violation? This depends on the license under which the original code was released.  You'll have to read it.

Is it plagiarism?  No, you have credited the original author.  However, you may want to make it more clear that it is really a relatively minor modification of their code.  Your current wording, "developed based on work...", could be interpreted as "I got some ideas from their work but then wrote all my code from scratch", which would misrepresent the real contribution of the other authors.

Is it adequate for your PhD thesis? You could write an entire thesis that just used the work of others, appropriately cited, with minor tweaks.  It wouldn't be plagiarism, but it also wouldn't get you a PhD, because it doesn't demonstrate an ability to do independent research.  So, you need to make sure that your advisor and committee are fully aware of what parts are your own work, and what parts are the work of others, so that they can evaluate your research accomplishment based on what you did.  If they don't feel it's adequate, then you may have to do more work in order to complete a thesis that will pass.
The same applies when you publish a paper.  Here, the editors and reviewers need to evaluate your paper based on its novelty - what part of it is new work, versus what simply makes use of existing work?


Usually, such kind of notes refer to manuscripts rejected by the same journal, not by other journals. In this case, the IEEE transactions on signal processing. The manuscript ID of the previous submission allows the editor to recover information about the previous process.

The IEEE Signal Processing Society policy 6.16, though not explicit, hints at the above interpretation (bold mine):

  If authors indicate instead that their manuscript is a resubmission, then they are required to upload a supporting document detailing how the new submission has addressed the concerns raised during the previous review. Authors may also request that the resubmission be handled by the same Associate Editor, if the Associate Editor has not retired from the board. The Editor-in-Chief will do his/her best effort to accommodate the author’s request while taking into consideration the balancing of the workload among the Associate Editors of the editorial board of the journal. A new Associate Editor may also be assigned to the manuscript by the Editor-in-Chief.

Indeed, the highlighted possible request is feasible only if the resubmission is to the same journal.

Thus, you should simply make a new submission, without reference to prior submissions to different venues.

When, instead, you are submitting a revised version of a previously rejected manuscript to the same journal, you can report the previous manuscript ID in the cover letter.


Can I publish if I develop a tool, but it solve non important problem only? (Mathematics)

Based on your reply to @DanielHatton's comment, you may have some research to make in that subfield to know about uses of the tool you discovered. Make your research in the subfield your tool may apply to and talk to people.

If you find something: great, you now have an application for your tool
If you don't find anything: it doesn't mean your tool doesn't have any application, let me explain.

In my humble opinion, publishing findings which may seem to have no clear application at the moment could still be useful years down the line. There are examples in history where research work had no application for a long time before..it did (anyone having such an example in mind is welcome to edit).
(Unfortunately?) not all papers are ground breaking. Yours probably won't be (as the vast majority of papers), but it might, sooner or later.
So I would encourage you to write a paper about it. You also mentioned that you are a student and I think that practising paper writing is valuable for students. You'll have some experience in case you want to become an academic, and if you don't, papers always look good on a resume.


How might being disciplined for participating in a non-violent protest on a public college affect my academic career?

Probably not at all.  Most academic institutions support freedom of speech.  However, this depends on the goal of the protest and the type/location of the hypothetical institution.  For instance, I imagine some religious institutions might not hire someone who had protested for abortion rights.


Do I need to reason why I use a particular technology in my research proposal?

You have two (related) questions:

What does this mean?

This means you should explain why you suggest using YCSB (You already know the reasoning, given your last sentence.)

Does that mean I need to reason all the tools or technologies I have chosen to assist the research process?

No. If that were the case, the examiner would have asked you to. In general, researchers use direct/concise language. Do not assume that they actually/secretly want you to answer another question than the one they have asked you.


What masters level courses should one take to prepare himself for a future career in the Internet of Things?

Internet of Things (IoT) is a very large cross-disciplinary domain. Therefore, if you want to become a well-rounded IoT professional, I think that you would have to take core classes from essential to IoT disciplines, such as electronics engineering, computer science / engineering, embedded software development, information systems and data science. Obviously, if you want to focus your career toward a specific part of IoT spectrum, you would have to study relevant topics at a more detail than the rest (which is still important, firstly, to be well-rounded enough and, secondly, to be ready for potential changes in your professional interests). Reading corresponding Wikipedia article, which is quite comprehensive, should be a good starting point and provide you with more information on various disciplines and areas of study, relevant to IoT subject domain. Good luck!


When writing referee's report after paper revision, can I discuss the reports of other referees?

Review are not an appropriate location for a direct argument between the referees.

There are, however, appropriate ways to respond to what you see as a mistake by the other referee.

First, you can make a clear statement of the positive value in the paper, implicitly contrasting with the other referee.  For example, in this case, you can simply talk about how significant and publishable the authors work on X is.  If they now mention Y in their paper, you can note that you are not concerned about it, for the reasons that you stated above.  In your open review, keep it purely about the paper.
Second, however, every review form comes with a place for confidential comments to the editor.  This is the appropriate place for you to respond directly to the comments of the other referee, saying things like "I think Reviewer #2 was too harsh, because...", since it is the editor's job to synthesize the disagreements of reviewers into a decision on the paper.

Finally, you probably don't have to sweat it too hard: since the paper wasn't rejected after the first round, that usually means the editor thinks it has the potential for publication, with appropriate revision.


arXiv or MathSciNet statistics by MSC classes and time

If you use R, you can use this script I wrote for scraping ArXiv metadata.


First time opportunity to give a seminar

If you have presented your thesis before, the seminar could be something similar to it. However, a seminar is usually given to a wider range of audience, and thus you need to make it more accessible for someone in the audience who may not be familiar with the subject. Aim for an accessible introduction, and save the technical details to the second half of the talk.

As for how long the seminar should be, you need to ask the professor how much time you have to talk, and how much time you have for questions and answers.


How to interpret "I think you should apply broadly" from a prospective PhD supervisor?

You should interpret it as good advice.
Apply broadly. Find the program that's the best fit for you. Many graduate programs are sufficiently competitive that many qualified applicants are not admitted. It's impossible to admit everyone qualified who applies if there are more qualified applicants than slots, and there is a lot of subjectiveness and a bit of luck in who makes that cut.
Maybe the professor is gently saying you are unlikely to be admitted to their program and lab, maybe not; there is little benefit for you in attempting to divinate their meaning. There is lots of benefit for you in following their advice (more choice, higher chance of admission), and risk in failing to do so (no choice, chance of not being admitted and not having a backup plan).
Sometimes advice is just advice.


Should a professor give students a take-home exam when the answers might be available online?

To answer in order:

I don't see why it's unethical for the professor to give a take-home exam. I don't dispute your (implied) assertion that this may benefit those who are willing to ignore the professor's explicit directions -- but that's unethical of them, not the professor, in my opinion.
This is entirely up to the professor. It would likely be within their right to do so, but my guess is that most professors would shrug their shoulders and make a note to themselves not to ask that question on a take-home exam again. You'll argue that this is unfair to students who follow the professor's instructions -- and you're right. Unfortunately, however, the world is not fair. That doesn't mean I -- or the professor -- condone cheating, but the professor likely knows that this risk exists with a take-home exam, and has judged it an acceptable risk.
What is the dean going to do in this situation? Force everyone to retake the exam? This may not be feasible -- for example, at my university, some classes have online sections off students who aren't physically present on the main campus. This precludes in-person exams oftentimes.
My advice would be to use a throw-away email account if you're so inclined. Keep it anonymous, but alert the professor. Understand though that they may choose not to act on the information -- and there likely isn't much you can do.

I don't mean to this be harsh -- just realistic. A better solution for the professor might be to explicitly allow online resources, but then structure the exam such that those resources don't help students any more than memorizing the material would. The easiest ways I can think of doing this are (1) opinion-based questions and (2) time limits that make accessing such resources a costly waste of the available time.


Letter of Recommendation Expiration Date

In addition to other points already made, in most situations you do not send the letters yourself, but have the recommenders send the letters directly. Sometimes this involves simply uploading the letters to a web site, but this would be done _by_the_recommenders_, not by you.

Thus, some action will be required by your recommenders.


How can you get to do a Short Oral Presentation at the International Congress of Mathematicians?

Short answer:  I don't know, I've never been on an Organizing Committee.

Long answer:  You likely can look at statistics for attendance versus
capacity of venue.  At the last few  International Congresses I have attended, usually there are about 2000 or more from the host country, and anywhere from 1000 to 2000 from other countries.  There are about 20 plenary lectures, about 150 invited lectures,
about 1000 Oral Communications and not quite as many posters.  Also some interesting
prize lectures, roundtables, and a few other items.
(I am doing this from memory.  I don't think attendance has surpassed 5000 lately,
but I won't guarantee it.  I could be off on any of the numbers by a factor of 2, but I don't think so.)

I have submitted abstracts for short communications since 1994, and have had them
accepted in all but one case (and in that case there were facilities for last minute "impromptu" sessions: the organizers kindly let me have a slot for one of those).  My unscientific guess is that the rejection rate is determined mostly by capacity, and that about half the local attendees and more than half of the non-local attendees submit abstracts, which would lead to about 2500 petitions for 2000 slots.  My estimate of the population whose desire to satisfy vanity overcomes their fear of public speaking  would suggest that 2000 petitions are for oral communication, and so roughly half are filled.

FUZZY DATA:  I submitted two abstracts this year, one a week or so before the first deadline and one a few days afterward, possibly after the first and before the extended deadline.  They were given designation numbers below 1900;  this supports my guesstimates.

LESS FUZZY DATA: at this writing, about one month before the 2014 Congress, registrations are pouring in and number near 2900.  There are almost 500 posters accepted and a little over 700 short communications, with some designation  numbers reaching over 2300.  Not substantive, but if the code numbers reflect submissions, this would imply an acceptance rate near 7 out of 24 for oral
presentations, and a little less than half for all presentations.  Off by less than an order of magnitude.


Are citations in PhD theses indexed by Google Scholar?

My own PhD thesis has been indexed, but the citations in it haven't, while the citations in other theses published at the same time have been indexed long ago.

I suspect the reason of this is the fancy cover page of my thesis, which doesn't match the document format expected by Google Scholar. For instance, the title should usually be the first line of text in the document.


Academia research vs. industry research (computer science)

As a researcher in industry, let me first emphasize to you that "industry" is a much broader set of organizations and varies a lot more than most people realize.  Thus, the answer to your question may depend quite a bit on the specifics of the company that you are at.

That said, however, in most cases a key animating idea for researchers in industry is a notion that often goes by a name like "customer focus": i.e., who will care about the results of this investigation?

Sometimes this is pretty straightforward (e.g., "if widget-making is 5% more efficient, then profit margins on widgets go up), but in other cases the relation is much more abstract or indirect (e.g., some prior work I did on potential programming languages for quantum computers that don't currently exist, but where the funder wanted to see how thinking about this might affect their goals for other research projects).

In all cases, however, you always have to be aware that somebody is paying the funds to support your salary and the salaries of your team, and they are giving you that money because they want some benefit to come from your research. This is true in academia as well, but professors are typically more insulated from it because their salaries are generally mostly supported by teaching---and even graduate students can be supported by TAships. If you're being paid to teach and expected to do research on the side, then it doesn't really matter what you're researching in the short term---but you will have more impact if you work on more important problems.

So, to the heart your question: how do you actually go about doing that?

I recommend starting by trying to be aware that at all times there is a "frontier" of research problems that you could be working on. Whenever you do a piece of work, you are choosing to prioritize one piece of that frontier over others.  Notice this fact and ask yourself questions like:

Why did I choose this problem over those other ones?
How will solving this problem affect the other problems on my frontier?
Who else cares about the solution to this problem?

There can be lots of reasonable answers to these questions, but starting to ask them can be extremely helping in moving to a more conscious evaluation of your research choices and whether they're actually moving you in the direction that you want to go in your career.

For more thoughts and suggestions along these lines, I would recommend the following resources:

"You and Your Research" by Richard Hamming, a long-time industrial researcher at Bell Labs.
My own talk on "Surviving Life as a Researcher"


Is it appropriate to add a co-author at the stage revise & resubmit?

Absolutely you can add a coauthor in revision, if there is good reason for doing so: in fact, I have recently done so myself on a paper where revision involved some new experiments with the aid of a colleague not previously involved.

Most journals that I know consider authorship changes routine and even explicitly support such changes by asking you to review and, if necessary, modify author lists as part of submitting a revision through their system.


With some programming but no formal CS background, to develop fundamental CS knowledge should I get an MS or BS?

So, do you think it makes sense for me to go for higher studies now?

Depends what you are hoping to achieve, of course. However, as you are already working in industry, if your goal is to get better pay or a better programming job, this may not work out the way you hope it would. If the goal is actually to (as you indicate) learn about fundamentals in computer science, going back to university may be the right move. However, note that for these basics, an undergrad may actually be more appropriate. At master level, most programmes would assume that you have a solid working understanding of these concepts from the start.

  What will my chances be of getting into a good university?

What is a "good" university for you, and where? There is also the problem that you indicate that your undergrad was not in computer science - this will probably hamper your chances of acceptance to a great computer science programme quite a bit.

Somewhat related: I feel that you are also overestimating the amount of industry experience you have accrued. Frankly, after 3 years, most people would not call you an "experienced programmer". So it is unlikely that your work experience will be sufficient to offset your missing undergraduate degree.


Wrong PhD project choice for PhD - stick it out, change, leave?

I am going to assume as a funded science PhD, you have something in the region of 3.5 years of funding.

You're only a year in, so it's not too late to change. There is even time for you to change completely (though it could be a lot of work to get done on time before your money runs out).

Typically I would say the first year of your PhD will involve you gaining useful knowledge and skills, though a project that may well not end up being what you write about in your thesis. It's your second and more the third year where you have the skills and can really do some research for your thesis.

Saying that, don't hang about! Organise a meeting with your supervisor asap to go over the options with them, they are given the position of supervisor as they should know how to steer their students to get a good PhD, but they can only help you if you tell them that you're not happy and what you want to do. You will have gained useful skills, so the time hasn't been wasted, but you do need to sort it out sooner rather than later.

I would hope there are other projects available you can move into, but the worst case scenario isn't the end of the world. Like you say with minimal effort you should be able to write up what you have done and get a Masters, then move on with that qualification and experience.


How often do techniques/methods that are considered old or obsolete become relevant again?

There are some important examples of techniques and problems being "revived" after having lain dormant for many years. For instance, in my own field, one of the cornerstones of computer modeling was originally derived in the 1920's, and then basically remained undeveloped until the 1970's, when it was brought back in fashion. (It has since been replaced by faster methods, but it is still regarded as the "touchstone" for high-accuracy calculations.)

Similarly, entire fields of research may have been developed before the applications caught up with them. Again, bringing up an example from my own field of research, the class of materials known as ionic liquids was known as far back as the early 1900's, but again were forgotten until the 1990's (or so) when they were "rediscovered" because they were nonvolatile materials and could be used as replacement solvents in the chemical industry. (It also offered the ability to do "combinatorial chemistry," which was also coming into fashion.)

THe point of these examples is that sometimes theoretical and even experimental techniques may be developed in one era, but the ability to exploit the technology to its fullest extent has not yet been attained. Keeping awareness of such methods thus can have some use. Whether it should be taught to every student of a field is a different issue.


Is it rude to ask the lecturer whether there is any “effective prerequisite”?

I wouldn't phrase it in terms of "effective prerequisites".  But it's certainly fine to discuss with the professor whether you are adequately prepared.  You could visit their office hours, or send an email:

  Dear Professor So-And-So:

  I am interested in taking your course MATH 4321.  I see that no prerequisites are listed, but I was wondering what background knowledge is expected, and whether I'd be ready for this course.  I've taken related courses X, Y, Z and feel comfortable with the material from those courses, and have also had some experience with topic Q.  Does this seem sufficient?  If you can recommend specific topics to review, or additional reading, I would appreciate it.  Or, if there are other courses I should take first, that would also be helpful to know.

If you like you can attach a copy of your transcript.


Should my citation style exactly match the original title?

All-caps are just a typographical decoration or emphasis of the whole title. You do not need to keep them for the same reason you do not need to use the same font and font size (as used for the original paper title) when citing. Something similar holds for title case (i.e., capitalising the first letter of all words except of, the an similar) – it’s just a typographical choice and does not affect the content.

Italics (unless they apply to the whole title) on the other hand serve some non-decorative purpose. In your examples, they allow you to directly see where a potentially complicated species name starts and ends. In other cases they may signal that a word is standing for the word itself, such as:

  On the evolution of the in Old English

In those cases, keeping the italics may really ease reading and thus I would personally opt for it in general. Keep in mind that the italics of italics are upright if you choose to italicise titles in general in your style, and you would e.g. get¹:

  Aaron A. Aaronson, On the evolution of the in Old English, Journal of Definite Articles (2015)

Finally note that you may have no choice regarding this anyway, as your supervisor or the journal you are submitting to prescribe some citation style.

¹ LaTeX does this for you automatically if you use \emph instead of \textit or similar to italicise.


Structure of a review paper with author's unpublished data

Let's talk about three kinds of papers that are commonly distinguished:

Empirical paper with original primary research
Conceptual paper with no empirical primary research
Review paper that synthesizes empirical and conceptual papers in the literature

Despite my simplistic categorization into three types of paper, this might be better considered a triangular spectrum and any actual paper falls closer or farther from any of the three points. All empirical papers have some conceptual development and some literature review; all conceptual papers have some literature review (but rarely any original empirical analysis); all literature reviews have some conceptual development (but rarely any original empirical analysis).
Your question seems to ask about if it is acceptable to write a review paper that, contrary to the norm, includes a little bit of original primary research. I have a two-sided response to offer you.
On one hand, in principle, if you consider paper genres as a spectrum, then you can do anything that you want that meaningfully advances your arguments. If the original research supports your reasoning, then it could be reasonable to include it.
On the other hand, there are risks when you deviate from established scholarly genres. I see at least two concerns with what you are proposing to do:

First, there is a concern about scholarly rigour. Presumably, almost all of the articles in your review are peer-reviewed. That is, they have been evaluated and approved by editorial committees with invited expert reviewers that are independent of the study authors. Thus, their reports should be given greater credibility. However, that is not the case of your original empirical research. It is your original work that has not passed scholarly peer review, yet you are offering it as evidence on par--or even with more weight--than published, peer-reviewed work. What you should do is to let your original empirical work pass peer review first before including it in a review of the literature. It is awkward mixing unscrutinized evidence (your original empirical work) with scrutinized work.
Second, I began with three common genres of work. The advantage of writing according to common genres is that peer-reviewers and editors know what to expect and know how to evaluate that kind of work. When you break from convention, you risk the high possibility that peer-reviewers and editors would not know how to properly evaluate your work. So, some might evaluate it as an empirical paper (where it would be considered far too light), whereas some might evaluate it as a review paper (where they would object to the original empirical work). You might be willing to take this risk, but you should not be surprised if peer-reviewers and editors have a hard time understanding what you are trying to do because of your break from convention.

Overall, I recommend one of two paths:

Do not include your empirical research in the review paper at all. If you say it only supports what the literature already says, then it adds little meaningful. In that case, it is not worth the risks of breaking from convention. But if your empirical research is substantial and meaningful, then you can submit it for peer review for publication as an independent article.
If you feel that the empirical research is not sufficient to be published as an independent article (or it is not worth your time trying to do that), yet it does add something meaningful to your review paper, then place it entirely in an appendix to the review paper. You are free to refer to it in the review as evidence, but the fact that you are placing it in an appendix meakes it clear that you do not give it the same weight as the independently peer reviewed work that you review.


Should "extra credit" questions allow students to get more than 100% of the marks?

My experience with American grading systems has been that the extra credit typically means an effective higher percentage is possible, i.e., 100% + 10% extra credit = 110% max on the assignment.  And if a student gets 110%, then that's what they get on the assignment, and great for them!

Most students will balance extra credit with mistakes elsewhere, meaning that extra credit effectively ends up acting as "forgiveness" for mistakes.  Usually, however, the students getting a lot of extra credit don't need as much forgiveness as the ones who don't, so I actually don't think that extra credit shouldn't be thought about as really being about grades.

Instead, I think it is important to view extra credit questions as places where the instructor encourages engaged students to additional exploration of the course material. The extra marks are then just a means of acknowledging that exploration within the formal incentive system of the course.

Given this, and the fact that some unusually excellent students could end up with more than a 100% overall, I would only recommend that all the rest of the students still be graded as though 100% were the maximum in the class. That way, a student going above and beyond gets acknowledgement, but other students are not affected negatively by that fact.


How can I tell if a website is safe for conference registration?

You will not be able to get a definitive answer on this unless you contact the conference organisers.  Certainly the registration mechanism is - by modern western standards - backwards - and you are right to ring alarm bells and take extreme caution as it could well be a scam

That said, @GlenPierce answer is not the final word - and there are significant elements which indicate that the site itself is credible - these include

The actual payment IS done over HTTPS, and the certificate ties in with the domain name.  Of-course, this does not mean much, except that the domain has not been compromised.
The domain names associated with the site have been registered many years
The site purports to relate to academic.net - and, indeed, when you go to the academic.net website, the payment system does, indeed link to this domain name.   It is also relevant that most of conferences they have listed are held in China.
If you log onto the site, and change the meeting ID, it lists different headers for different ID's - that means that if the site has been hacked, its been hacked for a while, and there is a "non-trivial" amount of coding behind this - and yet Google have not flagged it as untrustworthy.

My inclination is to believe that this is more a case of incompetence then likely fraud (and this level of competency is not that uncommon in the parts of Asia I've been exposed to) - but I would still not register this site without confirmation from the organizer that it is legit.


Who Owns the Code I Write (Graduate Student)?

As indicated, this is a legal question and  not an academic one, however I do get asked this frequently by students.

Intellectual property questions are never simple. When you do work at a university, the idea that created the work may have come from a member of the academic staff. Ideas and techniques that are incorporated in the work come from classes created by other academic staff. Some of their ideas come from their education and books and papers they used. The university (their current employer) and perhaps some past employers may have contributed to that knowledge.

Then the student creates some artefact from that. Does the student wholly own everything intellectual in that artefact? Probably not, unless there is an agreement that says they do.

Without any agreement it would be for the courts to decide who owns what fraction of the intellectual property. Normally no one bothers, but when it is a valuable idea or artefact then the lawyers will follow.

There can be no simple answer to this question.


These things are almost always at the discretion of the editor. If you notified him that you need more time, you are probably in the clear. But even if for some reason the manuscript database of the journal decides that you took more than 2 weeks and forces you to submit your revised paper as a new manuscript, the editor will still send it to the previous reviewers and treat it as if it was a revision. That's because any other course simply makes no sense from the perspective of the editor.

In other words, the worst that can happen is that the date of submission on the final, published version of the paper is the date when you submitted the revised version, rather than the original. There are likely very few cases where that actually makes a difference.

In summary: Don't worry too much about this technicality.


How has the application review process for NSF graduate fellowships changed?

First off, as a single data point, I was awarded the GRFP this year with only three reference letters.

  Each application consists of the following components: a 2-page personal statement; a 2-page description of past research; a 2-page description of proposed future research

Currently, the GRFP requires a 2-page Graduate Research Plan Statement, and a 3-page Personal, Relevant Background and Future Goals Statement. This latter essay combines and shortens the previously required 2-page essays.

That's the only thing in JeffE's post that is obviously no longer true.


How to get students engaged in more basic topics in programming?

Create games that apply some basic concepts.  You'll need a progressive set of games.  Start out by setting up your game board (homemade is fine) and your paraphernalia.  Your student will prick up his ears right away.  Explain the basic concepts needed to play the first game.  The game should be exciting but quick.

Each set of paraphernalia should have a number of variant games that can be played with that set.

Suppose a game involves converting a decimal number to Base 2.  You don't need to explain in detail, prior to playing the game, WHY computer scientists are interested in Base 2.

Many games will involve rolling one or more dice and then doing something that requires applying some technique.

Example: each player will, on his turn, roll five 0-1 dice (each side shows either a zero or a one).  These five digits define a five-digit binary number.  Write down the number you've rolled.  Now figure out what that number is in Base 10.  Say the answer is 12.  Move your guy 12 spaces on the game board.  Set up your game board like a simplified Chutes and Ladders, to make it exciting.

Edit #1:
Responding to the new version of the question.  It is tempting to want to give students the background information needed before giving them a hands-on project, because from a teacher's point of view, that is the most efficient way for the learning to take place; but sometimes it's useful to throw something at the students and let them flounder a little.  Then you'll have their attention when you explain why something didn't work, and what's really going on behind the scenes.  Have you ever tried that?

Edit #2:
You could ask the students to program a simple game, and then have them try out their neighbor's program.


In US, is it possible to have a non-tenure position for the whole career

In the US system, it is generally not possible for a person to hold a tenure track but non-tenured position, such as being a tenure-track assistant professor, for longer than a few years (I think the typical tenure clock is 6 years plus extensions for life events like new babies).  After that, the person will either get tenure or else they will have to leave or switch to a different class of position, such as "research scientist."

Research scientists or non-tenure-track professors, however, can easily have a full and comfortable career with nothing even vaguely like tenure involved, all the way up until they retire, go emeritus, or succumb to old age.  This can happen both in traditional academia (see, for example, Dave Clark, or non-tenure professors at medical schools) or in alternate academic settings such as national labs and research companies.


At American colleges, are student evaluations of teaching subject to code of conduct?

Yes, they are subject to the code of conduct.  However, they are usually anonymous, so there is no means of enforcement.


Importance of order of authors in published paper when applying for PhD positions

It depends. Authorship order doesn't always indicate who did the most work or the most important work on a paper in many fields. Some fields are alphabetical. Some fields have the lab leader or the person who won the gran last. Hopefully the admission committee understands the norms of their own field and the field you are coming from (if they are different) to be able to make a good evaluation.

I've never served on a PhD admissions committee, but I understand that they generally will try to determine your contribution to your publications when evaluating your application.


Doing it part-time is rather common at least in places i have worked. At moment me and most of my colleagues work from home two days of the week (usually Mondays and Fridays for most and Thursdays and Fridays for some) on the days that no teaching is involved. If there is an important meeting we will show up otherwise we skype. I think i generally work on average 6.5 days in a 22 day work month from home.


Omitting subscripts in proofs/equations in math/computer science papers

Here are some ideas from a physics perspective. We often have to deal with long equations.
If you have the occasional over-long equation, then sparing use of the two-column environment or slightly smaller font size can be the good choices. (Assuming the journal accepts it.) Suppressing meaningful indices like this can be OK if they are repeated, but if the same equation contains both t-1, and t+1 you probably want to avoid it since it reduces clarity. A great alternative is to abstract more. Define new symbols containing part of your expressions, so that each shown equation becomes shorter - and if done right, easier to interpret. Of course, this comes at the cost of a higher total number of equations.
Finally, sometimes it's best to put a simplified equation in the main paper, and full expressions in the appendices. However, if the proof is central to your paper you probably don't want to do that.


I know that there is a preselected candidate for a position to be filled at my department. What should I do?

One important consideration that you should take into account is whether there is an actual case of nepotism or not. Nepotism is if the preferred candidate is objectively inferior to at least one other candidate from all the information that is accessible to the selection committee. Or, in other words, if the head of the department is willingly hiring a worse candidate because they like them better, owe a favor to somebody, or have some other invalid reason to give one candidate preferential treatment.

The problem is that many "not really open" open positions aren't actually like that. In practice, what I often see as the main reason why a department or selection committee quickly zeroes in on a specific candidate is that they know much more about one candidate than about the others.

The most typical example is as such: There is an open search procedure, and a number of external candidates apply plus Alice, a candidate that has worked tightly with members of the department before, and which has been explicitly invited to apply. What you now see is a tremendous information asymmetry - the department knows little about the external candidates, but before they even open Alice's application folder they already have a great deal of information about Alice. They know what she can and can't do. Where other candidate's past successes are just a line in a CV to the committee, for Alice they know the full story, how she achieved them, what she has learned from them, and how this would help her be effective in her new position.

Recruitment is always a risky proposition, in academia just as in industry. We all have seen candidates that looked great on paper but turned out unsuitable for reasons that were impossible to glean from an application package. Faculty visits help, but how much can you really learn about a person in one or two days, especially in a somewhat artificial and often strongly rehearsed environment? In this situation, a risk-averse committee (and, realistically, this is basically every committee) has a strong incentive to go with Alice over a candidate that may have a slightly stronger CV, but also a much higher margin of error. As a consequence, a committee may prefer the "known candidate" Alice despite her weaker CV for completely rational reasons (which makes it different to nepotism). In essence, them doing so may be the optimal move for them given the information they have and how much they are willing to risk.

  What should I do?

Depending on how close you are to your boss, I would carefully try to find out why they prefer one candidate so much over the others (i.e., talk with them about it). It is completely possible that you may find that their reason is solid given the information that they have. Even if you disagree with their reasoning, understanding it may make the situation easier to accept for you. And if it turns out that there actually is a clear-cut case of nepotism (your boss knows the selected candidate is inferior, but decides to select them anyway), you have a much, much clearer argument for any potential whistleblowing.


Doing high level thing great but forgetting simple things

Sounds completely normal for PhD level work.

Many people doing PhD:s are like this. Some people who are envious or feel threatened of your high level abilities may try to shame you or make you unconfident with your lack of low level skills. There really is only one advice to give for this...

Trust in yourself and don't let it discourage you.


Meaning of "Study curriculum with rankings"

Study curriculum means the list of titles of courses/subjects and their contents, credits, and so on. In other words, the syllabus.

The term 'Ranking' is generally associated with the institution. Probably they are asking for the ranking of the university/college you attended. 'Ranking' may also imply your position in the class of X number of students. It may also simply mean the semester-wise serial number of courses.

You can have a look at this link.


PhD Thesis based on published articles on different topics

First of all, writing a PhD dissertation in 2 months is one hell of a task. You should probably talk to your supervisor about more time.

I believe it is not uncommon, as Thomas stated in the comments, that people assemble a PhD disseration from the publications they had during their time. Many people work of different topics at the same time, but usually there is something that combines them. The title of your dissertation can be very vague and cover a wide topic. In your dissertation you can split it into different chapters of sections according to your covered topics. Of course, it is good if you find a common thread and can build upon that. Even if you don't, I still think it is okay. After all, that seems to be what your supervisor wants.

If you are really unsure, there is no way around talking to your supervisor about it. Ask for his expectations and tell him about your plans. Then, you will be able to meet somewhere in the middle.


Getting a coder to perform triangulation

Your reviewers are right! Having multiple coders is a best practice for this type of work. You could try to recruit:

Other PhD students (trades are best - I will code for you if you code for me).

Masters students in your same lab (may offer trade, co-authorship if they want to help with paper more generally, or payment)

Masters students you have taught (usually would offer payment)

Advanced undergrads who you train extensively (would likely offer payment)

To find these people, you could try to send an email on your department listserv. Additionally, many professional societies have listservs and you might be able to find other PhD students that way. You could also use social media to tap your network.


How should I respond when monetary contribution to potluck will affect grade?

I personally make sure to never require my students to spend money to actually do the course (i.e., if my courses require the students to do something that costs money, I find internal or external sponsors for it rather than having the students pay out of their pocket), but I understand that I am coming from the somewhat privileged position of teaching at a well-funded private research university here. I would guess from your question that this is not the case here.

I think you are not fairly representing what's happening here. The deal quite obviously is not really "exchange money for grade points" (that would indeed be very bad), but "exchange money for participation in a didactic event". This really is not very different than a school forcing students to pay for participating in a school trip.

I don't see how it makes a major difference that participation in the event is graded, but of course practicalities matter here. If the event was very expensive so that some students could not afford it in practice, or if the organizer would turn a significant profit from the event, I would understand why you disagree with this. However, as it sounds, this is literally "chip in a few dollars for food", and in this case I don't really think that there is anything unethical going on.

  What should I do?

If you are not opposed to the monetary contribution for the potluck in the first place, I don't see how getting some grade points for it changes anything. So, I suggest you contribute to the potluck :)


I think this mainly depends on the journal, and of course the specific study in question.

While the first order certainly does make sense, the second approach coule also be viable for certain studies.

An example would be a study where a somewhat small sample was conducted, and the results show a significance of some kind. You could go on and discuss the reason/interpretations for the significance, and later mention that to quantify/verify the effect, further studies with a larger sample size should be carried out.

Again, this is highly dependend on the study and the format, so if a journal specifically asks for the first approach, you might want to follow their guidelines.


You can't upload your patent application materials to arXiv, because they simply don't accept that kind of submission.

https://arxiv.org/help/moderation:

  arXiv accepts only submissions in the form of an article that would be refereeable by a conventional publication venue.

Your file isn't an article, and "conventional publication venues" (journals, conference proceedings, etc) don't publish or referee patent applications.    If you submit it, it will probably be rejected in the moderation process.

Whether it would be legally advisable to make your file publicly available some other way, or to write and publish an article about your invention, and how any of this might affect the validity of your patent, are questions that you need to ask your patent attorney.  It would be very unwise to rely on the advice of random Internet strangers for something like that.


Pros and cons of paragraph-based writing

Following the advice by @jakebeal, I am posting my comment as answer.

Follow the norms of your discipline, if you want to be taken seriously. If everyone else uses sections and  subsections and you do not, it will only look bad on you.