The difference between literature review and background sections of a dissertation

Context: I'm in a US PhD program and thus my answer may not be fully appropriate for Masters in UK.

In the US, a Masters thesis is required rather than dissertation, which is required only in PhD programs.  In Social Sciences, a Masters thesis shows that you understand the relevant research in some depth and that you can also apply this research to some specific problems or questions.  In contrast, a PhD dissertation needs to contribute to research in some important way (even if the contribution is narrow or small).

There are no widely accepted rules for what is appropriate for Background or Literature Review chapters, or whether your thesis should include either or both.

What follows are my views, based on reading various theses and dissertations.

A Background chapter is best used to present contextual or prerequisite information that is important or essential to understand the main body of your thesis.  Perhaps there were some historical developments that set the stage for your research questions or thesis.  Perhaps there was some debate over key terms or scope of your subfield.  Perhaps you are bringing together several disciplines, and you need to explain which aspects of each discipline you are including and not including.

A Literature Review chapter builds a conceptual structure that ties together all the key ideas from all the relevant literature.  By "conceptual structure" I mean an organized way of linking individual ideas together so that their relative importance and interrelations are clear and obvious to the reader.  What are the main ideas?  What ideas support these main ideas? What are the contradictory ideas?  On what basis to people decide what ideas or positions to support or oppose?

Viewed this way, what becomes clear is that a Literature Review chapter is less about "literature" and instead is mostly about "review".

For what it's worth, in my dissertation I will not have either chapter. Instead, I've decided to have a chapter called "Foundations" to cover both of these needs.


Can self-funded international students be denied admission based on absence of scholarship/fellowship?

Of course they can (and often are). Admission to graduate school also includes an evaluation whether the candidate is likely to graduate, and having funding outside of a scholarship does not change that evaluation. An added problem is that being admitted to the graduate school is only one side of the coin - you also need an advisor willing to work with you. If your application is considered too weak for regular acceptance with a scholarship, it is somewhat likely that you will also have troubles finding an advisor - and admitted students without advisor are often a bit of an administrative headache that admission committees would like to avoid.


How to build relationships with colleagues as new faculty member?

Solve the social things by being proactive. Go to your colleagues individually, after committee meetings, or during their office hours, introduce yourself as the new guy, and offer to buy them lunch or a coffee. If colleagues go to lunch after departmental meetings, politely see if you can tag along. The "somehow" in your question is indicative of someone who did not look for such opportunities or dodged invitations. Lunch is probably the easiest time for colleagues in a work setting to begin their socialization. Everyone eats and almost everyone like some company.

As best as I can tell, there are only a handful of things that bring faculty members together for forced work, e.g. departmental committee meetings. That being said, departments have social and semi-social functions. Attend as many as you can. Volunteer to help with student move-in at the dorms. Volunteer to be a marshal and graduation ceremonies with other faculty. Find a hobby and check out the university club (exercise oriented ones like cycling, rowing, and running tend to be popular).

Solve this problem like it was your PhD. Set goals and be deliberate. Also, be friendly.


Loss of perspective after short-term postdoc

Reputation: Regarding if your publication record is a problem, it depends on the field. I suggest searching on Google Scholar researchers at the same stage as you (ending their PhD and those that have started their first postdoc) to get a better idea.

Network: If you are on good terms with your first postdoc PI, which I assume you are, then also ask them if they know of any positions. It is insufficient to be applying for postdocs, in some areas they are very competitive. Your advantage is that you have solved a big problem (apparently), but who would know that? Use those that do know to help you out, they might specifically mention you to so-and-so who is looking for a postdoc.

Publish-or-perish: Stepping out of academia will put you in a worse position, I think it will be hard to return.


Reproducible and exact calculations vs. approximate and slightly random results in experiment

It's probably best to answer a generalised form of your question first before getting to specifics.

Reproducibility is a tricky issue in applied Computer Science but the principles are the same.

The first thing you need to consider is what, precisely, the results of your experiment depends on:

Does it depend on hardware? (e.g., performance experiments)
Does it depend on data?
Does it depend on software? (e.g., an implementation of an algorithm)
Does it depend on configurations? (e.g., amount of memory set)
...

For whatever your experiment depends on, in an ideal case, reproducibility should make those materials available to third parties, either through links from the paper, or as details in the paper itself. However, hardware in particular is often a tricky issue in that you're probably not going to make the  machine you ran the experiments on available. For this, it is typical to try use conventional hardware insofar as possible and to provide details in the paper.

And sometimes there are practical obstables for even sharing data or software, such as commerical interests, patents, licencing of the software used, and so forth.

In terms of reproducing your results, another aspect to consider is the stability of those results. When someone reruns the experiments, you would like them to see the same (or "negligibly different") results as you published. This means that, for example, if your results vary in each run, you should publish some bound or confidence interval on each run to give an idea of the distribution of results over each run, or you should take a measure like the average of multiple runs to ensure a stable enough result from which to draw stable conclusions.

However, what does "negligibly different" mean? Well while results should be "as reproducible as possible" (one will never get the exact same runtimes, for example, in a performance experiment), what is more important to the scientific method is that conclusions are reproducible. For example, if a bunch of doctors produce a study of 1000 patients showing a significant and strong correlation between eating popcorn and cancer, it is not necessary that the details of the study be reproducible but rather it is even preferable that the correlation be reproducible (and perhaps strengthened in a further study to look for causation by isolating the bad part of the popcorn and injecting it into some unfortunate mice or something).

So if you have general conclusions, then you might want to think about how reproducible they would be on different hardware, on different data, on different software, with different configurations, etc. If you don't know how the results would change when a particular variable changes, then you need to include that variable in your conclusion. That is to say, if you don't know how the result would change for different data, for example, then all you can conclude about is the data you've experimented with and maybe propose a stronger result.

Of course, almost all applied CS papers I've seen (including my own) don't stick to these rules because peer-reviewers don't hold them to such standards, other than in the most blatant of cases.

And it is exceptionally difficult to account for all variables in a thorough conclusion since in applied CS there's so much to take into account, particularly for performance: the machine(s), the programming language(s), the compiler(s), how good the programmer was, possible bugs, the data, other things running in the background, caching, ... hence reviewers tend to be a little more relaxed (perhaps sometimes too relaxed).

Summary: Publish both results if you think they are interesting. Publish as much material as you can to allow the results to be reproduced. If you're worried that the GPU results are too variable in each run to be reproduced, take the average of multiple runs to get a more stable result, or provide an estimated upper and lower bound, or something to characterise the variance.

But all of that is just the icing on the cake. The real goal of reproducibility is to be able to reproduce conclusions. Be careful to craft conclusions that do not overgeneralise the data they are drawn from.


Are tuition subsidies taxables for research staff?

I am not a Lawyer or Accountant, and if you really worry, you should ask one of those or at the very least talk to human resources at your university.

But, based on my reading of the relevant law, part (d) [usually referred to, I guess, as Section 117-4] specifically states that if you are an employee of a university, then tuition reduction for you to take classes at said university should not count toward your gross income when calculating taxes.

The US code does not distinguish between in-state / out-of-state tuition.

Caveat: your local state laws may have different interpretation of "gross income".


Can research paper information be used in thesis writing?

There are two concerns here:

Does the publisher of your previously published work object to your reusing the material in your MS thesis?  This should be addressed in any copyright transfer agreement that you signed.  Most publishers are actually OK with students doing this but a few are not.
Does your institution allow students to reuse material from their published research papers in theses?  Some institutions have rules against this.

You'll need to check on both of these issues.


what is RARE organisation in the context of hypertext systems?

A little detective work reveals the following. From Chris Adie's Resume it seems that RARE is now called TERENA, which is "The Trans-European Research and Education Networking Association". Looking at the history of TERENA, reveals that RARE stands for "Réseaux Associés pour la Recherche Européenne", which is a little strange, as it is a Dutch organisation.

Incidentally, one of my old pals used to work for TERENA.


Where to publish (recreational) mathematics without a PhD?

Of the journals of the Mathematical Association of America, you can choose between The American Mathematical Monthly, the Mathematical Magazine, and The College Mathematics Journal. The three have (perhaps subtly) different scopes1, and short of you telling us exactly what your results are about we cannot tell you which journal is the best choice. (On the other hand, you can easily write to the editors of one of those three journals to see where your manuscript would best fit.)

As Dirk mentioned, The Mathematical Intelligencer is also an obvious choice (again, caveats about not knowing whether your paper fit in their scope).

If you aim the material at the mathematical maturity level between secondary (high school) education and first years of a college education, two good publications are Pi in the Sky which is published by the Pacific Institute of Mathematical Sciences, and Parabola which is backed by the University of New South Wales in Australia.

Another general mathematics magazine you can try is Plus Magazine based at Cambridge; the editors specifically asks you to contact them in advance if you want to write for the publication.

1 A very rough guide is that in terms of "mathematical maturity", the "age" of the readers are such that CMJ < MM < AMM.


Undergrad research supervisors want me to write conference paper I have no interest in

Note: this answer assumes that you might be considering pursuing research after your undergrad, by applying to PhD programs.

You have to balance two things here:

The value of an academic publication.
Pursuing your own research interests and career goals.

Firstly, it is important not to underestimate (1). Publications are academic gold. It doesn't usually matter so much that the area of the publication is the same as your interests. If you apply to computer science programs you would be able to list that you have this publication; you might be surprised that even though it is not in computer science it is still likely to look extremely good. Roughly speaking, I would guess that it is at least 50% to 75% as good as a publication in your area of interest.

Why does a publication look so good? It tells admissions committees: This candidate knows how to do research, and is successful at it. They have already worked with a professor in a research group. They are able to see a project through to completion, and they know how to write. Notice that the area of the publication is irrelevant for all of these factors.

However, you cannot ignore (2) either. Research flourishes only when you are passionate about it. In the long run, you need to pursue research that matches your interests and particularly that is true when you are interested in computer science, not civil engineering.

With that in mind, I would suggest you make a compromise. It is highly in your interest to see this published with your name on it, but you also want to minimize the time that you spend on it. So you can reach out to your collaborators (professors) and say that you had underestimated the amount of work this would involve, and you don't have enough time or experience in this area to write the entire paper, when you are more interested in pursuing computer science research. However, you would be happy to work on it a certain amount. For example, it would be wise to set aside a week or two to work on it, particularly if there is no one else who an write it. But set a limit up front; if this is going to require a month or two of your time, then it is no longer worth it.

If you do end up writing the whole paper, you should make it clear that you are not interested in any follow-up work. You just want to follow this idea through to publication, and then you can move on to your own interests.


Can I submit an article just for the sake of useful feedback?

Submit your research to a workshop. Workshops are the kind of venue you are looking for: their purpose is to provide feedback on work-in-progress, with a fast review cycle and reviewers focused on a specific area of expertise.

Submitting your research to a conference may lead to valuable feedback, too, but there's a risk that submitting work-in-progress research can leave behind a poor impression to some of the reviewers. In consequence, these reviewers may be inclined to give rather terse/useless feedback.


How to cite a website/manual where the authors are (mostly) unknown?

You can cite using @misc without Author field. To to that, you need to include a key field. Here is an example:

@misc{KubernetesManual2017,
    title = {{Kubernetes Manual}},
    howpublished = "\url{please put the url}",
    year = {2017},
    note = "[Online; accessed 04-Dec-2017]",
    key = "KubernetesManual2017",
}


How to neutralize an Ivy League obsession?

It's not hard to find Ivy League alumni who will readily admit - even adamantly defend - the statement that there are other colleges in the US which are just as good academically, and that you do not have to go to an Ivy League school to get a first-class education. Of course this is purely anecdotal, not any sort of logical argument, but then again people who feel like the Ivy League is the only way to get a top-quality education in the US are also not drawing their conclusions from logic, so perhaps an emotional appeal is just what they need.

If you're talking to someone who might be open to an evidence-based approach, try asking them to name what they consider to be the top universities in the US. Or better yet, look up a few college rankings and find out which names consistently appear near the top. For example, the US News and World Report rankings for universities are headed by

  Princeton, Harvard, Yale, Columbia, Stanford, University of Chicago, Duke, MIT, University of Pennsylvania, Caltech, Dartmouth

and for liberal arts colleges, by

  Williams, Amherst, Swarthmore, Bowdoin, Middlebury, Pomona, Carleton, Wellesley, Claremont McKenna, Davidson, Haverford

Forbes' top 10 are

  Stanford, Pomona, Princeton, Yale, Columbia, Swarthmore, West Point, Harvard, Williams, MIT

Beyond those I'm not sure of other ranking systems' reputation, but the Parchment rankings give as their top 10

  Stanford, MIT, Harvard, Princeton, Duke, Yale, Caltech, Pomona, Harvey Mudd, Brown

and the Academic Ranking of World Universities gives

  Harvard, Stanford, UC Berkeley, MIT, Caltech, Princeton, Columbia, U Chicago, Yale, UCLA

and so on (you get the picture). Anyway, whether this person you're talking to comes up with their own idea of the top colleges or uses one or more of these lists, it's rather unlikely that their list will match the list of Ivy League universities: Brown, Columbia, Cornell, Dartmouth, Harvard, Princeton, University of Pennsylvania, and Yale. Clearly, while a university's membership in the Ivy League is somewhat correlated with having a high ranking, it is not the only way to get one.

You could also mention that the Ivy League is actually just an athletic conference, like the Big 10. The member schools generally happen to be academically high-achieving, but membership in the Ivy League is in no way meant to be a certification of strong academics.


Is it okay to modify the LaTeX template for article submission with additional packages?

Unless explicitly forbidden, adding packages is usually ok and fully expected - e.g. in order to add support for listings, tables, symbols, encodings, operational utilities (extended macro/logic support), or specific features thereof. This should, however, never mean a general change in the appearance of the paper. Therefore, packages that globally alter fonts or font sizes are usually not allowed.

As for using a separate .bib file, you can usually work with that and (if explicitly requested by the guidelines - this varies a lot by publisher) copy the formatted information into the .tex file as late as for the camera-ready version (when nothing changes any more).


writing letter of support for H1-B visa applicant

If you can only talk about his grades from a few classes, have you considered telling the person that you might not be the best choice for a letter of support?

Even just a class can be enough to see a student's skill, for example if a project is a big component in the class or if the instructor closely examines sufficiently detailed assignments and exams. This is really the useful kind of component: "X is skilled at task Y, as evidenced by his work doing Z..." If you just say someone is skilled without much evidence, it won't be afforded much weight anyhow.

If there has been no actual work, you can at most comment on:

Their grasp of technical knowledge taught in the course
Their intellectual ability (how quickly they were able to learn)
Their discipline and professionalism (e.g. in showing up to class, studying and submitting assignments on time)
Their talent for that for this area of work based on their performance in the course

It sounds like not much, so as I said, perhaps you might not be the best person to write this.

If you really want to write the letter, I would advise asking fellow faculty if they have experience in such a situation and whether they can help you.


How to politely reject co-authorship offer from a colleague?

I don’t think the question of how to “politely” decline the coauthorship is really worth fussing about. If you want to decline the coauthorship, that’s absolutely okay, just say so in plain words and explain that you don’t think your contribution was great enough to be a coauthor. I can’t imagine anyone ever being offended by this, as long as you don’t imply that you think the paper is worthless.

With that being said, I do think you are perhaps a bit misguided in where you are perceiving the bar for coauthorship to be compared to where it actually is. Everyone knows that being a coauthor can mean a variety of things, which can range anywhere between “I wrote the whole damn thing myself and my coauthors just answered a couple of questions I sent them over email” and “I just answered a couple of emails”. So, if someone asks about the paper in your viva, just tell the truth and say that your involvement was minimal - that is nothing to be ashamed of, but also doesn’t mean that it’s unreasonable for you to be a coauthor.

To summarize, as I said it’s absolutely fine if you wish to decline, but it’s best if that decision should be fully informed and based on an accurate understanding of what coauthorship is understood to imply.


How to cope with regret and shame about not fully utilizing opportunities during PhD?

While sometimes it seems that spending more time working is equivalent to accomplishing more (especially in academia, where there's always that one colleague), this is not true in general. In particular for demanding intellectual work (as required in an academic environment) it is important to take breaks, vacations, and spend time doing other things to refresh ones creativity (see, e.g. Clark & Sousa, How to be a happy academic, or any of the numerous articles online).

I personally like to look at CVs / personal websites of successful academics, and it is quite common that they have some hobby which has nothing to do with their work which they spend much time on, like sports, chess, music, etc. So you don't need to feel guilty at all. It's very common that people struggle during their PhD studies, everyone has to figure out for themselves how to "make it work". If for you that meant spending time in solitude, that's fine.

  This has led to spending a longer time on my research than my
  colleagues. It will take me a little over 5 years to defend. My
  colleagues and friends have taken somewhere between 4-5 years for
  their PhD.

So it seems you didn't actually take that much longer. Another reason not to feel guilty.

  I should have invested my free time (...) doing things outside my comfort zone.

  (...) I am 30 years of age (fyi).

Why not start now? At 30, most of your life still lies ahead of you.


How to find related work in academic writing in the most time-efficient way?

I understand that you are prepared to do the work necessary for searching the literature, but that you are looking for tips that avoid swimming aimlessly and wasting time going down unproductive lines. In principle, this is resolved by having a clear idea of what you are looking for. That way, you don't waste time exploring interesting ideas that are not immediately relevant. (And since it sounds like you are intellectually curious, then almost everything is interesting.)

I have found that one of the most valuable things to focus on in a literature review is theory, which I define as an explanation of the relationship between two or more measurable concepts. So, what you can focus on in a literature review is:

Clarify the theoretical concepts that interest you. A theoretical concept is necessarily something that is measurable, whether qualitatively (e.g. Type A versus Type B versus Type C) or quantitatively (i.e. counts, dates, etc.). This is the absolutely most crucial step to identifying theory.
When you search the literature, you should look squarely for these theoretical concepts. You might not know the measures that exist in the literature at first, but at least you know that you are looking for the parts of articles that talk about measures of your concept of interest.
You ignore anything that does not talk about measures of your concepts of interest. This means ignoring articles that don't talk about your concepts of interest at all, and it also means that even if an article does talk about your concept of interest, you skip the parts of those articles that don't talk about the measures of these concepts. (That said, of course, you should read anything that helps you understand your focal concepts better, even if they don't talk about measures.)

For example, if you want to study conditions that make people feel threatened by robots versus when they warmly accept robots, the key concepts would be:

Concept A: Type of robot interaction
Concept B: Human reaction to the robot

With these concepts identified, then you would search for literature that describes:

Different types of robotic interaction (e.g. personal voice assistant versus hardware robotic device; "machine-looking" robot versus humanoid robot; robot assists work tasks versus robot replaces human job; etc.)
Different ways of consideirng or measuring human reactions to robots (e.g. a scale ranging from violent rejection, such as vandalism, to warm acceptance, such as using the robot many times every day)

The results of the literature review would be a theory that explains how and why certain types of interaction with robots provoke various human reactions. (The theory would necessarily need to be enriched with context such as human personal characteristics, legal frameworks, etc.)

What I gave is a very brief summary and illustration of a literature review methodology that I am still in the process of developing, but I have an older working paper that describes the core principles in quite some detail. Even though I have unpublished ideas on this that are much better refined, the section in my older working paper on searching the literature explains this approach that I summarized in more detail.


When / how should I ask about a manuscript's status in review?

I don’t know your field, but in mine (theoretical computer science), you have to get used to long review processes. My personal rule is to contact the journal six months after submission. Given recent events, my new, additional rule is to also state upon submission that I can suggest referees if need be.
As EpiGrad commented, the four weeks time certainly refers to the time allowed to the referee. But additional stages take longer: a first quick scan of your paper to decide whether it’s worth troubling an editor with it; then the editor has to find referees; and, assuming they all complete their reviews in time, the editor also needs a little bit of time to reach a decision based on the reviews. Moreover, your paper might not be their top priority.
As for the “how”, something like this would do:

Dear Editor,
I understand that you must be extremely busy, but I was wondering about the status of my manuscript [title, reference number] that I submitted on [date]. Have you heard back from the referees yet?
Thanks a lot for your time.
Best regards,
[name]


How does one go about doing a Ph.D. in Europe as an American?

I am not even sure it makes sense to speak about “graduate schools” in Europe. In the countries I know, the big divide is between the master's degree and the PhD program, and not between bachelor and master programs. A master's degree is mostly another diploma with slightly higher requirements/more focused topic but otherwise not unlike a bachelor's degree in the way it's organized. There might be some exceptions here and there but it would be highly unusual to enroll in a PhD program without a master's degree.

Since tuition fees are relatively low in many countries, funding is not an issue in the way it is in the US (you still need to pay for the costs of living obviously but that's already the case for a bachelor's program). In some countries (e.g. France), people coming from abroad to study are treated exactly the same (which means paying something like EUR 250 plus some money for health insurance and a few other things), in others (e.g. the Netherlands), they have to pay a much higher fee (EUR 13000 per year where I work). In Germany the situation seems to be very fluid, with the rules set at the provincial level and changing all the time but I think fees are at most EUR 1000 per year.

Because local students don't have to pay that much and the fees don't differ much if at all from one program to the other, it's not surprising that you didn't find information about whether the master's program is “funded” or not, it's not a distinction that makes sense at this level. Furthermore, in many countries, support for students who face financial hardship is available from the government and not through the universities. Either you qualify and you can choose the university you want or you don't and you have to pay but you wouldn't specifically look for a “fully funded” program.

After the master's degree, the status of PhD candidates also varies a lot from country to country. In Switzerland, Scandinavia, the Netherlands and increasingly Germany, you are an employee with a reasonable salary (people will tell you it's less than what professionals with similar qualifications get, which is true, but you can still live comfortably). Some form of funding (from the main university budget, a research grant, European grant, corporate sponsorship, foreign government grant, etc.) is therefore a prerequisite. In France or Italy, you are considered a student and working conditions are often poorer. In STEM fields, PhD positions are usually funded and you do get some money and resources for your research. In the humanities, it's not uncommon for PhD candidates to have no funding, sometimes not even a desk and to scrap a little money to get by through teaching or even another job.

Here again, tuition is usually not the issue but living costs are (for at least three years, at a time where you might want to start a family, etc.) Even an unfunded humanities PhD candidate in France does not have to pay much to the university. Unlike bachelor's or master's degrees, I don't know any university where PhD candidates from abroad would have to pay more to be admitted or be categorically barred from some funding (but the situations are so diverse that it might exist somewhere I guess). The only hiring restriction of that kind I know are research fellowship from the European Space Agency.


Tuning the PhD journey for Industry jobs

If your goal after grad school is to get a job, then during grad school

you should do the things needed to impress the people you want to hire you and to be accepted and esteemed in their community.
Slightly more concretely, find people who now have the career that you would like to have, and during grad school do stuff that they have done.

I still think networking is key, but now you may be networking with a different group of people.


Suggesting an alternative to referee/reviewer recommendation

In my reply to the referee, I will explain why I did C and why I think that approach C is better than A and B

This is essentially all you need to do. You don't need to follow reviewers' recommendations slavishly, but if you do decide to deviate from their recommendations, you should explain why. Which you plan on doing. In the end, it comes down to the editor's decision, so you should always strive to make his life easy, by explaining what you do and why.

  "I am open to the possibility that the referee might still prefer approaches A and B. If that is the case, I will switch to these approaches in the eventuality of a further revision, should the referee request it."

This adds a nice touch, without appearing subservient. I'll keep this in mind for the next time I decide not to follow a reviewer's recommendations ;-)

Bottom line: I'd say you are doing exactly the right thing.

EDIT: Bonus points if you can and do write something along these lines in your response to the reviewer:

  "In addition to C, which is described in the manuscript, I also did A and B, as suggested by the reviewer. The results, as measured by Y, are similar/inferior/whatever to the results of doing C, in the following way:..."

And I do see the point raised by @xLeitix in his comment. The "open to the possibility" should not come across as "I'll use an inferior approach just to get published", but rather as "if opinions about A/B vs. C can differ reasonably, I am open to..."


How would an undergrad fund a conference trip with a single author paper?

Many universities have funds specifically for student travel to conferences. (For example: University of Washington, Wayne State University.) Even if there is no special fund at the university level, your department may be willing to sponsor all or part of the trip. While it's more common in my experience for student travel to be funded directly by their advisor from their research grants, my department has, on occasion, been willing to pitch in (e.g. under circumstances where a student has no advisor, or the advisor can't sponsor the trip.)

Many ACM SIGs (special interest groups) and IEEE societies offer student travel grants including travel costs (up to some amount) for their conferences. Many conferences in computer science arrange student travel grants from a government funding agency and/or industry sponsors. So you might consider submitting to one of those conferences instead, if there is one relevant to your field. There are also special grants for minorities, e.g. this one from ACM's women in computing.

Regardless of the funding issue, I encourage you to find a faculty advisor to give you feedback on your work. (Also, every travel grant I have ever applied for required a letter from an advisor.)


Waiting for one more reviewer due to being unresponsive - what to expect?

Closely related: What happens if a reviewer withdraws himself from peer review process?

If the reviewer is unresponsive, they effectively withdraw. Again the same basic options are available to the editor: they can find another reviewer, or they can make a decision based on the single review they've received. When you get the decision you'll be able to tell which option they took.

Does the fact that one of the reviewers who has already provided his/her reviews bears any significance in terms of revision, acceptance or rejection?

I suppose the fact the reviewer went unresponsive indicates that your manuscript is not so groundbreaking that people are actively excited to review your manuscript. But even drawing this conclusion is dangerous - the reviewer could simply have fallen ill, for example - so the brief answer is "no". It's simply something too circumstantial to draw conclusions about.
On the bright side, having one review completed is progress, so you should expect to receive a decision in a shorter time than if you withdraw and submit the manuscript at another journal.


Is it safe to list my publications on the Internet if I am being stalked?

There's a small chance it might help but probably not.

If your page has been on the internet for any length of time then it's already going to be stored in a number of library archives  like archive.org

It's possible to remove pages from the site but it takes time and there are other archives.

Example:

http://web.archive.org/web/20141124181833/http://www.statcan.gc.ca/pub/12-591-x/2009001/02-step-etape/ex/ex-publication-eng.htm

Also your publications are likely to be searchable through a number of online systems for finding papers such as google scholar.


Advantages of taking the Subject GRE exam in April

Your approximate dates for start of term and for graduate application availability are correct.  Some are open through January and some even as late as February, although most PhD applications do close in December AFAIK.

If you're not finishing until 2018 then the only real advantage is that taking the GRE in April will allow you to take it again in September if you need to improve your score.

Of course you could also take the October one if it's offered in your area, but you won't get September's scores back until after the October registration deadline.  And the October test's approximate score reporting date of December 9 may be too late for some applications.  IIRC, some applications close on or very close to December 1, but TBH it's been a long time and maybe that's not right.

On the plus side, there's a new rule in place ("new" relative to 2006ish) where you can submit only the score(s) you want to the schools.  In the past you had to submit everything on your score report, good or bad.

Sources:

https://www.ets.org/gre/subject/register/centers_dates
https://www.ets.org/gre/subject/scores/send/asr

My recommendations:

If you really feel like you're fully prepared for the April test, then take the April test.  If you don't do as well as you wanted then you'll have time before the September test, and you'll have time to earn extra money to help pay for it.  Tutoring is always an option, and if you tutor subjects that are on the GRE then that's a double bonus.
If you aren't confident you can be fully prepared for the April test, don't take the April test.


Is there a standard order for the preliminary pages of PhD theses?

There is no formal order that applies 'worldwide' no. Though you should consider getting in touch with the service responsible for thesis publication at the university (usually the library I'd expect), there may be a format that you need to meet regarding the front page, back page and potentially abstract page.


How to address having been plagiarized by senior scholars without ruining the relationship

It is difficult to say if this was intentional or only an oversight - though an improper one. But the fact that they cite you generally, seems to imply sloppiness, not malice. Ask for a correction.

I would simply point out the passages to them and provide them a proper citation for them. Since this is a book, it will likely go through several printings and it may be possible for the future printings to be corrected. Published books often come with an errata page, usually online these days.

You don't need to make accusations, just point out the correction.

If you get a poor response from the authors, then try to contact the publisher, starting with just the same information and request.

But if you get a favorable response, then thank them and, if you desire, say positive things about their work and point again to your own. From a bad situation it might turn in to a good one. But that assumes good will.


What are pros and cons for an adjunct professor job at a community college for an IT professional?

Without wanting to sound harsh, this whole post is all about you and how it will benefit your further career (after leaving this job). You seem to forget that you will be teaching real, young people that need a good teacher, in order to get the education they deserve. So, unless you refocus on them first, perhaps you should reconsider getting this job for simply "overcoming your fears, developing leadership skills, which you could then use in private sector" and leave it to someone more passionate about it.

To directly answer your question: Getting a job you are not sure you are going to like and risk being bad at it or prematurely leave, always looks bad on any resume. So, unless you are really passionate about this, perhaps you should stick to what you already know.


System for organising printed papers in folders?

Separate the semantic ordering from the physical ordering. It keeps your organization flexible, since you can assign each paper to several topics and projects, and change the assignments as you see fit.

This can be achieved by using a filing cabinet or folders on the one hand, and a bibliographic database (be it electronic or in paper) on the other.

Label each paper with some identifier. I recommend the date or month, but also a running number will do. The label doesn't have to carry any meaning. Collect the papers with a certain range of labels in one folder. For example all papers with labels January to March go in one folder called "Jan-March 2018".

In your database, each entry should also carry the corresponding label under which the paper can be retrieved, in addition to the bibliographic data, and any semantic information such as projects and topic keywords.  Use the database, not the physical location, for organizing the papers by substance matter.

How the database itself should be organized is another question. I use folders for projects and keywords for topics. Creating a systematic ontology or adopting an existing ontology (e.g. the Dewey system) seems overkill. Instead, I recommend creating keywords on the fly ("tagging") and combing through the keyword list once in a while. This will be more difficult with a paper-based organization than with an electronic database, of course.


Why dissertation has no score in GPA in United States?

Yes, this is near-universal in the United States.  Dissertations are not graded, and the GPA includes only course grades.

For the most part, people do not care about course grades in Ph.D. programs once you've completed your dissertation.  The GPA is understood to refer only to courses, so the GPA is also not considered important.  In particular, it is not viewed as a summary score for the whole program, but rather only for the initial coursework.

Dissertation quality is measured by reading it, gauging where it was published, or reading letters of recommendation.  For any job where the hiring committee cares how good the dissertation was, they will be reading recommendation letters, so there would be little benefit in having a numerical score in addition to the letters.


Ethical Problems Brought by Academic Paywalls

This seems contrived, as normally you can at least read the abstract to find out if you need to read the paper.

If you do need to read the paper, you have valid ways to do it, such as interlibrary loan, without paying $40.  It's not free, but not a huge expense.  You can opt to not read the paper, in which case you'd be doing your professional practice a misdeed.

Lastly, there is ALWAYS similar research by other people, who have not seen or heard of your paper.  It is NOT plagiarism to independently come up with something on your own.  There would normally be no charge of plagiarism, and you are wasting your effort serving as a patent troll.

If you are a publisher charging exorbitantly for access, you would build up your reputation, hire editors of stature, maintain a staff that keeps papers moving through the business, maintain a list of good referees, and do many other things to try to add value to your service and repository.  If you build up your reputation, institutions would subscribe.  If you can't establish a reputation, you'd go broke.

  Should the poor guy suffer a plagiarism charge just because I kept my
  research behind a paywall that he/she cannot reach?

The most likely scenario is that the person will not face a charge because no plagiarism occurred, as your paper has not been read.  Another likely scenario is that the paper were acquired through legal and nonexorbitant or free means like interlibrary loan, prepublication sources as required by NIH under the Public Access Policy, etc.

There are sound reasons to advocate for open access, but the fear of forcing plagiarism probably isn't in the hit parade.

Lastly, I encourage you to find the papers you need by legal means, so no, I don't feel acquiring the paper for free through extra-legal means is the way to go.


How to interpret reviews that focus only on grammar mistakes but a decision of "consider after major changes"?

Possibilities:

There are so many grammar and spelling mistakes in the manuscript that they pointed out a few by way of example and sent it back for English language editing before a full review. Given the quality of writing in the question, this seems unlikely.
There is a missing review that was not sent to you that has asked for more major revisions. Sometimes this happens if the reviewer uploaded their comments as a file. Log into the submission web site and see if you can find any extra review files associated with your manuscript.
The editor accidentally clicked the wrong button in the editing software and meant to send it for minor revision. This seems possible, but it is very strange that the reviewers did not comment on the results at all, and suggests a very poor review process.
The editor doesn't like the paper very much themself and has sent it back hoping for a major revision, but has been too lazy to provide review comments that would help.
The editor is particularly annoyed by grammatical errors and sent it back for a small number of minor errors to be corrected before being willing to send it to reviewers.

To me, the "missing review" hypothesis seems most likely. I would check the web site, and if you don't find another review file, contact the editor to clarify whether the grammatical changes you mention are really the only changes required.


Do I need to embargo my dissertation if I submitted portions to journals?

The general answer is: No, journals don't consider dissertations as previously published materials.

Some exceptions (that I don't know), may exist. If you want to be sure, here's a two things you can do:
1-Verify the instructions to authors.
2-In your letter to the editor that accompanies your submission, state clearly that this manuscript will be part of a dissertation.


Should I repeat experiment affected by external factors until achieving consistent result

No, you shouldn't do the experiment until you get the desired result.  This is poor science and borderline unethical.  (I'm sure you had no ill intent and that you are trying to deal with real-world complications.)

An experiment is flawed if it is run n times but only the results from n - 1 are used and reported. (Or anything less than n).  See Peter Norvig's page under the section "Warning Sign I2: Ignoring Publication Bias".

Beyond this, I believe that your experimental design is flawed.  You shouldn't run an experiment assuming an ideal environment when in fact the experimental environment is not ideal.  Only in theoretical models do you have the liberty to idealize your environment.  In laboratory experiments, you control the environment so you can idealize as much as possible. What you have is an experiment with confounding factors, which is not uncommon in real-world settings.

The best thing to do is to estimate the effects of the confounding factors through analysis of a theoretical model or a simulation.  In your case, which sounds like a queuing theory problem, a statistical simulation should be relatively easy.

With this estimate, you should be able to restate your hypotheses, essentially reducing the expected effects by the "loss" associated with "the shared pool not fully allocating resources when requested".


How much time does it normally take to get certificate of participation in a conference?

Not all conferences provide a certificate of participation. Some will provide such documents only by request. Many participants would not need such certificates at all, so it often makes sense not to provide them by default.
If you require a certificate of participation, write to conference organisers and ask for it.


Somebody made comments and suggestions on my drafts – can I be reasonably accused of plagiarism?

Based on what you said I have the impression that you are the main contributor to this work and he only had some editorial comments. Therefore, you publishing this work, cannot be classified as plagiarism. (If you think his contribution was sufficient for him to expect you to give him some credit (e.g. second author) then you have to be careful because it may cause further complications between you and him. Besides, it is your responsibility to make sure he gets the credit he deserves)

Most of the times people won't actually act against each other in situations like this. I remember a few years ago, I was stuck in a situation where someone decided to publish a team work with his name as the first author, while it was clear to everybody that he was not the major contributor. My adviser sat me down and told me to let it go (and I accepted because he had good reasons). What I'm trying to say is that in cases like this your supervisor would usually mediate and smooths things out before it gets serious.

However, I think the chances of him even trying to accuse you of plagiarism are very slim. But even so, if you publish this work before him, he needs to have enough evidence that he had major contribution to the work. I assume that this is not the case and it is clear from the emails that were sent to you.

I suggest you to simply let your adviser know that you will try to publish this work and don't worry about the PhD student.


Should I seek professional help because I have a lot of math books?

Personally, it seems to me that he was just making a joke. Awkwardly, perhaps, but still, just a joke. Your personal library seemed to him (and me) to be so "over the top" that it was hard to fathom. Had he said something like "Wow, are you ever intense?" it would have had about the same meaning.
It is possible that he had a negative feeling about it, but I really doubt it.
Or maybe a meaning like "Wow, you need to learn to relax a bit."
But if you are so intense that you are ending up hurting your health, then professional help is actually advisable.


Publishing on arXiv effect online scholarly profile

Both Google Scholar and CiteSeerX can detect arXiv publications.  I know for certain on Google Scholar because it has detected mine (and it is also adding to my H-index on the site).  For CiteSeerX, if you search by publication venue, you will find many publications in arXiv.  Both systems will, however, attempt to merge versions (and Google Scholar at least allows a person to do this manually as well), so a subsequent journal publication can supersede the arXiv version, making such an arXiv version apparently invisible even if it is part of the profile and collecting citations.

Neither system makes any guarantees, however, about how quickly it will detect papers in particular venues, so it is possible that arXiv is updated less frequently or more erratically than others (particularly for CiteSeerX, which is often plagued by maintenance issues).


Do you need a certificate to validate your publication?

Published conference proceedings suffice for proof of publication.


What are "advance articles" and how to cite them?

Some journals publish preliminary versions of articles. The final version will appear in a published volume, the preliminary version might not, since changes may be made.
You can cite a preliminary version, just like you would cite any manuscript. You cannot list issue/volume numbers, because they don't exist. You could label such manuscripts as "preliminary" or "to appear" or "advance article" or "advance article, final version to appear" ...


Sub-referencing work from the referenced work

Cite the database, and in citing it and/or in context, provide a way for your audience to know which version or part of the database was used. Ideally, you should provide sufficient details for your audience to know how the authors of work [X] produced their metric.


Which methodology of a research paper around a proposed software system

What you've described is called design science or design science research; it is most certainly not a case study. In a comment on your original post, @XLeitix nailed it as the pattern:

  problem -> proposed solution -> evaluation [rinse and repeat until results are ok]

In conducting a broad-based literature review of research on Wikipedia, my colleagues and I had to come up with a list of different research designs. Design science is in a category of its own, because it is quite different from the methods in social sciences. Design science is the default approach to research in computer science and software engineering, and so no one is going to explain the "research method" when they follow this pattern. It arises from the engineering paradigm where the goal of research is not to discover what exists or how or why things work, but rather to create something that is useful to people and prove that it is useful (usually by comparing its usefulness to some specified benchmark).

Ironically, the name "design science" does not come from computer science or software engineering, but rather from information systems (IS) research. IS research is primarily social science research, and so IS researchers had to come up with a name or a way to describe this type of research that is so different from social science, and yet scientifically rigorous. There are at least two major articles that describe its scientific characteristics in depth:

von Alan, R. Hevner, et al. "Design science in information systems research." MIS quarterly 28.1 (2004): 75-105.
Gregor, Shirley, and David Jones. "The anatomy of a design theory." Journal of the Association for Information Systems 8.5 (2007): 312.


What percentage of admitted PhD students comes from waiting lists

This will depend upon the department, but I would expect that relatively few students would be admitted via a waitlist.  Departments usually have a pretty good estimate of how many students who they accept will take their offer and enroll in their program.


The only way to improve writing (technical or non-technical) is by writing and submitting your work to the criticism of peers. Thankfully, in mathematics there is a culture of blogs. When you learn something new, write it up on your blog and share it with your friends. This will help you better understand what you wrote AND let you practice writing. At first, you won't get much feedback, but as your audience grows you will naturally learn from the feedback they provide.

Another great tool is math.SE and mathoverflow; on these sites you are guaranteed feedback. Ask and answer technical questions, this will let you practice your writing. As your writing and clarity improves you will also notice an average increase in number of up-votes, etc. This will give you useful positive reinforcement.


How does a professor know when a research project will get expected results?

The interaction between student and professor should not be a one-shot set-a-problem. Instead, they should be talking frequently, often once a week, and adjusting the nature and direction of the project based on what is being learned during it.

The project starts with some idea, from either the professor or the student, that the professor thinks likely to lead to an appropriate outcome within the available time.

As time goes on, the student should come to learn more about the project than the professor, and be reporting progress or lack of progress. The professor should be continuously evaluating whether the current line will lead to a good result, and encouraging redirection if not.

I am sure my doctoral dissertation was not at all what my advisor would have expected when I started on the project - it was a result of things I learned during it.


Quitting a PhD because you realise afterwards that it's not the right path for you is fine. A fellow student during my PhD did so (due to homesickness, primarily), and immediately started a PhD at a university in his home country. The supervisor/group leader/etc were disappointed but didn't hold it against him.

Quitting because you only accepted the position as an insurance policy is a very different matter. If it's not for personal reasons, such as those above, leaving mid-course for another university will be seen as a very selfish act. Even more so if anybody finds out that you were hoping to do it before you even started. From your description it sounds like your field is relatively small. That means people tend to know each other, which means this could very easily hurt your reputation far more than attending MIT (or whichever other prestigious institute) would help it.

In short: you shouldn't accept a position unless you intend to stick with it. You have an offer on the table, you can either accept it or reject it. If you accept it, the right thing to do is to withdraw any other applications which haven't yet responded. If you aren't willing to commit to it, the right thing to do is to reject the offer. There is a third option, too: you can ask the European university if they'd be willing to grant you an extension to the decision deadline. How likely this request is to be accepted strongly depends on many things, including national and institutional cultures and the length of deferral you're asking for.


How do government research labs compare to research positions in academia and industry?

So what I’m wondering about is how research positions in government run research labs with organisations like Australia’s CSIRO or America’s FFRDC labs compare with equivalent positions in academia and industry.

I work for a US Government Research Agency, so here is an answer based upon my experience (i.e., n = 1):

  What are their pay and conditions like, relatively speaking?

In this US, some labs are run by contractors (e.g., some DOE labs like Sandia). Others are run by the federal government (e.g., other DOE labs). I am an employee of the US federal government. OPM describes our benefits (link here) and the GS pay scale is here for 2019. Most research scientists are between a GS-11 and G-15, which a post doc starting as a GS-11 or 12 depending upon the agency. Some federal scientist become Senior Positions (ST), which are above the GS pay scale (OPM page here).

Most research positions in the US Government are "Research Grade Evaluation" (link here, which means we have a review ever 4 years (similar to tenure), where the panel of our peers can recommend our we say in the same pay grade, be promoted, or demoted a level. Some agencies like NOAA and DOD have switched to pay bands rather than the GS pay scale.

  How much job security do you have?

Probably similar to a US public academia setting. But, rather than be subject to the whims of state-level politics (US public universities), we are subject to federal politics.

  How much control do you get over your topic of research?

This depends upon the position. I am free to study anything falling within the mission area of my agency and my local center, as long as I obtain funding for it through internal or external funding mechanisms. This is less than an academic in theory, but in practice, if you like the applied science of your agency, this is enough freedom for many people including me. Plus, I like directly working with managers to see my research applied.

Here is a link to an obligatory PhD Comic on Intellectual Freedom.

Last, as another answer noted, your questions are largely specific to a given organization. I suggest researching different agencies you might like to work for and reaching out to researchers at those agencies to conduct information interviews. During those interviews, ask similar questions to the ones you posed here.


The chances of postdoc position higher in PhD country

In my surroundings (Germany, Switzerland), normally it's not a problem to get the first postdoc after you get a PhD in the same country.

However, a PhD in some country that is (sometimes wrongly) believed to have an inferior level of scientific merit may actually block the further scientific degree carrier abroad: impossible to start PhD studies a second time ("already has PhD"), and impossible to get a postdoctoral position as well ("bad PhD").

As a result, it is important to weigh the situation and think where and how to earn the PhD degree. I know people who have dropped basically complete PhD works right before defence just to be able to restart in another country.


Is it possible to do research, in your PhD, on the same topic that you did for your Master's dissertation?

Researching the same topic for a Ph.D. as a Masters is entirely possible, and not necessarily even all that unusual (it depends on how you define "same").  If the Masters is a first set of results on the topic, and the Ph.D. then pursues a significant advance thereupon, that would be an entirely reasonable progression of research.


Got Ph.D Degree from India on the basis of Ph.D Comprehensive Exam + Ph.D Thesis now thinking of doing Course Work in another university

If you are planning to take a big step of re-doing a PhD just based on this one interview you had, then I'd recommend reconsidering the thought. Have you received similar responses in the past? If yes, then may be the university that awarded you a PhD, doesn't has a good reputation. In that case too, a second PhD is not the best option. You can think of some Post doctoral certification or Post-doc research work. That would enhance your profile and would not count as a repetition.


How much depth should I have into a topic before I can claim it to be one of my research interests?

You can be interested in Japanese even if you don't know more than 3 words in Japanese.

You can say it is your interest.

If they ask about your research experience - then usually a publication is a good indicator that you have some knowledge of the topic.


Publishing a comment or contacting the authors privately?

There is nothing stopping you from contacting the authors directly. In fact that might be polite. It may, however, be unfruitful. Submitting a comment is not considered less polite than contacting the authors directly first. Remember, the authors have, in your view, published poorly referenced/researched work (reviewers and editors are partly also to be blamed). By writing a letter/comment, you perform a scientific debate where you wish to correct a problem with said paper and that is clearly within the realm of what we can and should do as scientists without feeling impolite.

Before you do anything you should perhaps solicit colleagues to discuss the matter over. Since the results have been published, some form of publication discussing the problem must also appear in a publication. It is for this reason you should carefully discuss the matter, start writing a "letter to the editor" of the journal where it was published. The letter should contain the information that puts the "novelty" in perspective. Under such circumstances the authors will have the possibility of a rebuttal which typically is published at the same time as your letter, it is their opportunity to "defend" themselves. This is what typically is done.

Now several things might happen, for example, the authors get angry, the editor refuses to publish your letter. This is why you are better off not being alone behind anything you write. If the letter is refused, then publish it elsewhere. But, remember, the point of writing a letter is to set the faulty perspective of the paper in a more correct one so that the paper is not taking credit where not credit should be had. Do not stray from this endeavour.


How do I acquire research experience for a PhD in Computer Science after I've started working in industry?

Actually, you probably already have more "research experience" than many (most?) students entering a doctoral CS program in the US. I doubt that you need anything else. I'm also wondering if you have misconceptions about the purpose of doctoral education. This is where you get a "first" significant research experience and show the world that you can do that.
It isn't a place where you go to prove that you don't need to be there.
If you have an MS from a good place (yes, you do) then you have the necessary background and more to enter PhD studies in the US. Just make a few applications to some places that support the specific sorts of research you are interested in. Get accepted. Find an advisor. Discuss mutual research interests.
But, absent an advisor with "mutual research interests", the way to proceed as an independent would be to try to find some collaborative relationship with someone who (like an advisor) will work with you and already has some experience. You might be able to find some such person(s) through work contacts or visits to university departments, but it seems to me to be just spinning your wheels when it is admission to a program being what you really need.
Most US applicants to doctoral programs hold only a BS/BA and not many of them have significant research experience. And almost always that will have been guided by some professor.
Ignore your age. It isn't relevant. But make sure that you are able to spend three years (or so) with vastly reduced income.
But if you want it - Do It.


Outdated letters of recommendation for graduate fellowships

It is perfectly normal to have one letter from your current research, since you presumably only have direct, extended experience with only one faculty member.

In picking your letters of recommendation for fellowships, the most important criterion is who can comment meaningfully on your potential to become a researcher. Whoever can provide the strongest letters should be your top priority.

However, I would tend to lean against asking someone who has never written for you before to do so after a gap of some years without providing more recent information on what you've been working on since.


Is it standard for graduate students to get gifts for their advisors?

No not standard (at least in Canada) and depends upon the tradition, it may actually seem as an odd thing. If there is a social gathering before Christmas then I believe that is fine to bring chocolates or whatever to all of attendees.
I would be very cautious to give my advisor gift every christmas. A verbal saying before the holiday starts is normal and acceptable;  nothing more nothing less.


Are Indian assistant professors eligible for tenure-track positions in the US?

Yes with caveats -- and the caveats have nothing to do with being Indian and everything to do with being outside of the American educational system:

There are particularities of the application process that are culturally bound and that you may not be familiar with (the style of the cover letter, its importance [or not], the style of your research and teaching statements, the format of your CV, who you ask to serve as a reference).
Your references may also be unfamiliar with American letters of reference styles. I find that foreign letters tend to be much shorter and much less enthusiastic.
Search committee members may not be familiar with your universities and its rank, with the ranking of the journals you've published in, and the significance of your teaching and service. They may be concerned that you do not know how to teach to American student audiences or that you may not be able to successfully apply for grants from American grant agencies.
The provost (who oversees searches) may be unwilling to authorize the search committee to bring in an international candidate due to the cost of airfare.
The university may be concerned about whether or not you will be able to obtain a visa to work. Even if you are able to get a visa, even under the best of cases, an international candidate who accepts a job offer in March may not be able to start by August of the same year because of visa delays. This may have programmatic repercussions (i.e., they need someone to teach CS101 in the Fall).
Rarely, some jobs are closed to non-Americans because the government grants or cooperating agencies require security clearances or have other restrictions. This is more common in the engineering and physical sciences.
In Canada, some positions are required to be offered to Canadian citizens before they are permitted to open to non-Canadians. The same rule technically applies in the USA for immigrant visas, but is not scrutinized as much.

etc.

As you can see, none of these have anything to do with you coming from India, and everything to do with being an international candidate. You'd have much more luck if you were applying from inside the USA (e.g., take a post-doc in the USA for a year or two and apply while on that).


Can my supervisor prevent me from publishing by affecting reviewers opinion?

In a biology / bio-engineering discipline, the authorship standards almost certainly dictate that you must have your supervisor as a co-author.
As such, worrying about contacting journal editors is beside the point: you can't ethically publish without your supervisor's permission---not because they're your supervisor, but because they're your co-author.

The biology focus also may help explain your supervisor's reluctance to publish, as it's (unfortunately) common for biologists to spend years building up a "perfect publication" with no incremental publications in order to try to get into a "glamour" journal like Nature or Science.

Given this context, I would recommend simply including the work you've done in your Ph.D. thesis (which does not preclude glamour publication).  That will make it very clear that you have done the work, such that your name must remain attached to it.  Beyond that point, I would recommend not worrying about the author order either: in biology, it is typical to put the student first and the supervisor last; since "last author" is also a significant and prominent position, I would expect that your supervisor is unlikely to have a problem with you being first.

Finally, I would recommend that you have a clear discussion with your supervisor about the criteria for publication.  Not "when will we publish?" because the answer to that will probably be "when it's ready," but "what else needs to be done before we publish?"  Get that agreement clearly worked out between you, then confirm it afterward via email to create a timestamped written record, and then you can also feel it is less likely that publication can be delayed by shifting goalposts.


How to present work that includes replicating results of another study?

I think the best way to approach this is to write a polite email to your collaborators showing enthusiasm for the work and letting them know that you were able to extend it. You may also want to propose if they would like to contribute to the poster. This can strengthen the relations and may result in a fresh collaboration.


How I can subscribe to conference/seminar/workshop alerts?

There are several sources I get information from:

Mailing list: See if you can find a mailing list specific to your area. Ask your advisor and colleagues about them.
Friends and colleagues in the field.
Word of mouth at other conferences: Ask participants about their favorite conferences & workshops.
Invitation emails of various kinds.
The academic sub-twitterverse
Wiki CFP: http://www.wikicfp.com/cfp/

Note that there are many conference/workshops that are not worth going to. And some of them are right out scams. I've read a number of horror stories about them (e.g. https://scholarlyoa.com/tag/predatory-conferences/). I suggest you choose carefully.


Should I mention that I'm able to self fund my degree in my SOP?

At least here funds to finance graduate students are scarce, so somebody who will be an asset without cutting into said funding, is clearly welcome. You should definitely state that in your application, by attaching proof of your funding. If said funding is e.g. a competitive scholarship from your origin country, it should be a definite plus in your application.


How do I write a formal resignation letter to my toxic PI advisor

It can be extremely short and to the point. You don't need to give your reasons:

  For personal and professional reasons I've decided to resign my position in your lab.

Nothing more is required as long as your contract, if any, permits it at all. In particular don't say things that might be disputed by others.


Does publishing a book while employed by an academic institution grant them legal claim on the royalties?

In general, no. (This is based on my experience in the US.) One's employing institution does not have any claim on royalties from books written while a student or faculty member. However, it's possible that there might be exceptions: for example, sometimes a university may help financially in the publication of a book, and this might be reflected in the publication contract. Of course, in such circumstances the book is not expected to make any money, which is why the university is helping out in the first place.

A related and very common phenomenon is for the publisher to hold the copyright on an academic title. My own book is like this. I am entitled to royalties, but the press holds the copyright for some defined period. Again, this is due to the terrible economics of publishing academic monographs.

There have been cases where universities have tried to assert very broad rights over the intellectual property of their faculty employees (e.g., lecture notes as well as books, etc), but I think these have generally failed. It does still happen: here's an example where the University of Louisiana is trying to broadly claim rights to scholarly output, including royalties from books. These sweeping assertions of rights have sometimes been motivated by the desire of administrators to claim a share of some of the genuinely lucrative things now produced by some university researchers, such as patentable biotechnologies, with books caught up in the net but not really directly targeted. Patents are an area with real money at stake, where the university's investment (in laboratory space and so on) is much higher, and where university claims on income from work done while employed are strongly and successfully asserted. Books, not so much.


What is "salami slicing"? Does it preclude presenting similar papers on a similar topic at multiple conferences?

Salami slicing normally refers to a different practice; that of taking a result and slicing it up into several smaller results with the intent of getting multiple publications. Technically all of the resulting papers are different, but less significant than if all were presented together in a single paper (or smaller number of papers).
It doesn't really have to do with "similarity" as such. But some conferences would frown on "virtually the same" paper at their conference.
But it depends. If the purpose of a conference is simply to broaden the audience of a result then there may be no issue. But conferences in some fields, such as CS, are primary publication venues and the proceedings have the same weight (or more) than journal publication.
In the latter case you have issues about self plagiarism and multiple publication, both of which are best avoided.
But I know some people who give similar talks at multiple conferences (often by invitation) and there is no issue, since their talk isn't intended to represent new results. So, a bit subtle, depending on the conference.
So, while your idea may not be technically "salami slicing" you still need to evaluate its appropriateness.


Chair and one of directors insisted that my project is theirs... what should I do?

Please note before reading: The text below contains only my opinions.

Accusing someone with stealing ideas is as ugly as stealing the idea itself.
As far as I understand, the department chair really liked the project and trying to get on the gravy train. Therefore, I do not believe trying to be reasonable with these kind of behavior will get you nowhere. Especially including faculty members, who have literally nothing to do with this matter is extremely rude and unprofessional.

If I were in your shoes, I would do follow these steps:

Explain the situation to the students working in the project (if any).
Ignore his mobbing (yes, I think this is heavy mobbing), and hand in nothing including surveys, project reports etc.
Write to IRB about this matter immideately and ask them for approval that the work was submitted by me.
Ask him to file a written complaint with the evidence that proves the idea belonged to him originally.
Collect/copy/back-up everything that proves the project proposal does not belong to the department chair.
Write to the dean (or whoever he is subordinate of) about this matter, asking to resolve this by official methods (as I have stated, this is clearly mobbing).

It is your own decision to leave the school. I would do the same, probably. But please keep in mind that these kind of issues can only be solved by legal process. All he can do is denounce you, and at this point, he will do it anyways if you drop the project.

Also, I believe that keeping your so called "ideas" to yourself is a responsibility. Either you immideately execute your ideas, or you accept the risk that someone can do it before you.
And there is nothing to do after that happens.


How substitutable is Statistics for Mathematics in graduate admissions?

This can only be answered by the university in question, probably at the level of the math department. It might depend on the specific statistics courses that you want math credit for. As you say, statistics overlaps with math a fair amount and many of the courses depend on a mathematical outlook and way of thinking.

In general, though, I think you are more likely to have them accepted than rejected, but you still have to face the fact that there will be a lot of other applicants for whom no exceptions need be made. So in a competitive place it might be the competition with those having a more standard background that will work against you.

But you have to ask them, and, as usual, you need to make your own case for why you will be a success. The evaluation depends on many things not just a bit of bookkeeping.


What can a publisher offer to its best reviewers?

There are a number of quite reputable journals that actually do give public "outstanding reviewer" awards, and their value (while not large) is non-trivial.

If the journal announces their awards publicly online, as these tend to do, then there's no worry about faking a certificate or such. It's probably not going to win anybody a job, but it's another line on the "service" or "awards" portion of a person's CV, and it will be noticed in their community.


It may depend on who your advisor knows in foreign countries --- or who you can get to know in foreign countries.

I've known people who've done this, but my impression is that in grad school it becomes less about "doing a study abroad" and more about doing a "visiting scholar" program at a particular school.  That is, you wouldn't seek or find something like "I want to study abroad" or "I want to study in Country X".  What you could do is find a particular school, department, or researcher in Country X and arrange to visit their department for a certain length of time.  I'm in a department in the US, and we regularly have visiting scholars from a range of countries (e.g., Japan, the Netherlands, Finland, Brazil).  We currently have one of our own students on a visiting scholar stay in Germany and another is planning a possible study in Singapore.

The thing is that, like anything else in a PhD program, "studying abroad" can't just be "studying", it has to be connected to your particular research.  So you would need to build connections with particular departments.

Also, there can often be opportunities for shorter-term study abroad in the form of "workshops" or the like.  These would be more in the range of 2-6 weeks.  That's a lot less time abroad, but my impression is it's much more straightforward, because you just apply (instead of having to form specific personal relationships with other researchers).  These workshops sometimes have fellowships available to cover some or all of the cost, and even if they don't, it's likely to be easier to get funding from other sources if you can point to a specific "thing" you're using it for (i.e., "I am going to this workshop on these dates to learn about these topics" rather than "I'm going to Country X for a while to hang out").


What are the rules for applying for the same fellowship (scholarship) after being rejected?

This may be more of a long comment than an answer.

Much of what you ask about depends on the specifics of the fellowship/grant you are applying to. Many (most?) fellowships are limited to the X best candidates. In this case, the fact that you did not get it does not mean you did something wrong, simply that there are other candidates that are better. In these cases I don't think "personal growth" is expected, you simply need to be better than the other candidates. There is also an element of luck, since some years may have stronger competing candidates than others.

This does not mean you should not try to strengthen your application/interview.

The success rate depends on the specific fellowship obviously.


Submitting a manuscript dependent on another one also submitted

Is there a compelling reason to submit both simultaneously? In case (I hope this doesn't happen!) there is an oversight in A, and the reviewer asks for modifications to the method, the results in B may no longer be valid. So it would be better to wait for acceptance of A.

If you must submit both soon because of deadlines etc, you can cite A as "journal xyz- submitted" (i.e. 'submitted' in place of volume number etc). This does happen now and then, but in my field (materials science), most journals discourage it.


Research comparing paper and online student evaluations of instruction

There has been quite a bit of literature on this topic. Because your question is broad (regarding acceptability, security, reliability, and validity), I have provided a brief overview; these articles should provide you with a starting point to locate additional information.

Reliability and Validity

A recent article providing an overview of the validity of different student evaluation methods in general may be of interest; the article does address online administration as one component impacting validity (Spooren, Brockx, & Mortelmans, 2013).

In a longitudinal study of over 63,000 student evaluations over 10 years (comparing paper in-class with electronic out-of-class evaluations), no significant differences in evaluation scores were found due to administration method (Risquez, Vaughan, & Murphy, 2015). However, one study had nearly 200 business management students evaluate the same teaching with both on paper and electronically within two weeks (Gamliel & Davidovitz, 2005). Although the mean scores were similar between the two groups, stability of scores was higher in the paper method. Thus, if the same teacher were to be evaluated multiple times, there might be more variance if the method of administration changed. The authors suggest that paper evaluations may allow students to look at the written horizontal profile of their responses, which they may recall on the second administration. In contrast, electronic systems that display questions differently may remove this effect.

A small study of over 120 medical students found that those who submitted paper evaluations immediately after training gave more favorable reviews than those that submitted electronic feedback at a later point in time (Palmer, 2009). The author posits that it is possible the rapport between the instructor and students immediately after session lead to better reviews, while those providing electronic evaluations did not have that social pressure. However, they state it is also possible that the time required to log-in and take the electronic survey may have been irritating, resulting in more negative evaluations.

Response Rates and Timing

Adams and Umbach (2012), reviewed 135,000 online course evaluations completed by 22,000 students. They found that students were more likely to respond to evaluations for courses within their major, and less likely to respond for ungraded courses or if the student was receiving a D or F grade in the class. They also noted some differences in response rates across majors, and evidence of survey fatigue that may impact response rates. Similarly, a study of graduate students using online course evaluations found that those students who responded earlier had more positive course ratings and expected to get higher grades, while those who submitted information later had lower grade expectations and course satisfaction (Estelami, 2014). The author suggests that universities must be aware that early/late responders differ in several specific ways that may impact the data they provide. In contrast, Pegden and Tucker (2012) found that the timing of completing the evaluation electronically did not impact responses, as evaluations were generally stable regardless of when there were completed.

Another article based on online evaluations at the University of British Columbia provides guidance on how to assess adequate response rates to enhance reliability and validity (Zumrawi, Bates, Schroeder, 2014). Nulty (2008) provides suggestions for improving response rates for teaching surveys, and compares paper/electronic methods; he suggests a mixed method approach may result in the highest response rate.

Acceptability

A study of nearly 1,000 students found fewer students completed the electronic version compared to a paper survey; students reported frustration with the site’s complicated and time consuming log-in process and were concerned about anonymity (Dommeyer, Baum, & Hanna, 2002). However, those authors caution that these burdens may be reduced as technology improves. Indeed, a more recent study of over 1,000 students found that students preferred the electronic evaluation option because they felt it was more anonymous, convenient, and presented less time pressure than completing the survey in class (Kinash, Knight, & Hives, 2011). A study of student perceptions about what is important in an online evaluation system reported a list of student concerns related to anonymity, ease of use, and being made aware of the impact of their responses (Nevo, McCLean, Nevo, 2010); this study provides information on a range of student concerns related to the evaluation system, with suggestions for other universities to follow.

Anecdotally, my graduate school recently transitioned from paper to online evaluations. I prefer the online evaluations because they allow me time to gather my thoughts, and I can provide more structured feedback regarding the class. Log-in is simple and is based on the universal log-in for our university; I take it on faith it is de-identified before being sent the instructor. Given how small some of our graduate courses are, that actually feels more anonymous than turning in a paper survey with my handwriting. We receive multiple email reminders to take the surveys during the last two weeks of class, which indicate the overall percent of students that have already responded (a form of social pressure, I suppose). There are only two things I dislike about the system. First, the response period ends before the final exam period begins, so you cannot include thoughts about the exam in your evaluation (the survey ceases to function). Second, responses are only available to the department chair, tenure committees, and the professor being evaluated. At my undergraduate institution all course evaluations were public, so students could read the evaluations of past classes to determine whether and when to take the course.

Adams, M. J., & Umbach, P. D. (2012). Nonresponse and online student
evaluations of teaching: Understanding the influence of salience,
fatigue, and academic environments. Research in Higher Education,
53(5), 576-591.
Dommeyer, C. J., Baum, P., & Hanna, R. W. (2002). College students'
attitudes toward methods of collecting teaching evaluations: In-class
versus on-line. Journal of Education for Business, 78(1), 11-15.
Estelami, H. (2014). The Effects of Survey Timing on Student
Evaluation of Teaching Measures Obtained Using Online Surveys.
Journal of Marketing Education, DOI: 10.1177/0273475314552324.
Gamliel, E., & Davidovitz, L. (2005). Online versus traditional
teaching evaluation: Mode can matter. Assessment & Evaluation in
Higher Education, 30(6), 581-592.
Kinash, S., Knight, D., & Hives, L. (2011). Student perspective on
electronic evaluation of teaching. Studies in learning, evaluation,
innovation and development, 8(1), 86-97.
Nevo, D., McClean, R., & Nevo, S. (2010). Harnessing information
technology to improve the process of students' evaluations of
teaching: An exploration of students' critical success factors of
online evaluations. Journal of Information Systems Education, 21(1),
99-109.
Nulty, D. D. (2008). The adequacy of response rates to online and
paper surveys: what can be done?. Assessment & Evaluation in Higher
Education, 33(3), 301-314.
Palmer, R. (2009). Evaluation of teaching--paper versus electronic
methods. Medical teacher, 31(12), 1094-1094.
Pegden, J. A., & Tucker, B. (2012). Does the timing of evaluations
matter? An investigation into online student feedback and whether
timing has an impact. Studies in Learning, Evaluation, Innovation &
Development, 9(1), 55-65.
Risquez, A., Vaughan, E., & Murphy, M. (2015). Online student
evaluations of teaching: what are we sacrificing for the affordances
of technology?. Assessment & Evaluation in Higher Education, 40(1),
120-134.
Spooren, P., Brockx, B., & Mortelmans, D. (2013). On the Validity of
Student Evaluation of Teaching The State of the Art. Review of
Educational Research, 83(4), 598-642.
Zumrawi, A. A., Bates, S. P., & Schroeder, M. (2014). What response
rates are needed to make reliable inferences from student evaluations
of teaching?. Educational Research and Evaluation, 20(7-8), 557-563.


Should a Database Update be sent for publication in same journal where previous edition was published?

Nothing ties you, neither ethically nor legally, to publish your new work (your database update) in the same journal as earlier work on the topic. However, if the journal was a good venue for this particular publication some years ago, the same reasons probably still hold, which means it's still a good place to publish your update. If, however, you feel like changing, just go for it!

Regarding authorship, this should be discussed right now. If you have full charge of the database, did important work on it yourself, and write the paper, then you have strong arguments to be first author. On the other hand, if you're the new admin but contributed little to the recent improvements, your position is weaker. In the end, it will be the result of a negotiation.


How to respond to an e-mail asking me to suggest a doctoral research topic?

I would suggest, unfortunately, that you refrain from giving students research topics. That is, unless you are able to continue to guide them through their degrees remotely. I doubt that you are able to do that, hence my recommendation.

It would be different, of course, if the request were coming from the advisor of such a student. In that case, you can examine what it might be that the advisor is most capable of doing for the student.

As a positive response to the student, and a general one that requires minimal tailoring in each case, is to ask the student to connect with a local advisor and, if the advisor is unable to come up with something, to have that advisor contact you.

But I think that local advice will be needed for nearly every student. In the very rare exceptions, the initial letter will probably make that clear.


I'm afraid there's not really a lot you can do. Your best bet is, as always, to contact the departments you are interested in attending, and explain your situation to them. You'll need to have a very convincing reason why you weren't able to take the GRE subject test, and would need a waiver. They may be willing to make an exception; they may not.

Beyond that, I'm not sure what else you can do; the policies and deadlines are all well-known and published, and the departments are not required to give you special treatment.


How to do a PhD to equip myself for a job as assistant professor

It is true that there are far fewer postdoc positions than graduates with a PhD. So it is legitimate to ask what you can do to improve your chances to eventually get a postdoc position, and from there on a faculty position.

The problem is that the number of factors that influence whether or not you will end up with one of these positions is large. There are some obvious ones:

If you get a PhD from a good university, that helps.
If you have a famous adviser, that helps.
If you are substantially better, that helps.
If you work in a field with current excitement, that helps.

Of course, there is also the issue that if you work in a field that is "hot" but that you don't enjoy, you're probably not going to do well.

Many of these factors are either out of your control (admission to Harvard or Berkeley) or that you can't foresee with your current knowledge, given that you haven't been involved in research for too long. But, if you get admitted to a good university, take the position and go from there.

(I will note that -- having read maybe 500 grad school applications in math -- about 2/3 of grad school applicants want to eventually become professors at a research university. This is wildly unrealistic -- I don't know exact numbers, but would imagine that overall only maybe 10% of grad students will eventually achieve this. I'm telling you this because you will have to contend with the fact that basically everyone around you has the same goal as you: they all want to go to a good university, be advised by that famous professor, etc. You'll have to work hard to be better than all of those others.)


Removing outliers. Would it be called cherrypicking data?

One major pitfall is going into analyzing the data without an a priori protocol to deal with outliers. Time to time, tension rises between analysts and investigators on whether a point should be removed or not. Investigator may wish to keep it because it drives the significant result; analyst may be anxious to keep it because, well, it drives the significant result. Much can be avoided if there is a agreed-upon standard.

Anyhow, here are some suggestions (slightly scrabbled):

Reconcile if it's an instrument or data entry error.
If it's a plausible value but behaving like an outlier, a few methods exist:

Do not bury plausible extreme values in favor of showing the after-trimming data only.
Consider reporting with and without it, discuss the differences.
Use statistics that are more tolerant to extreme values. For instance: Non-parametric statistics or robust estimation methods.

Keep all written record about related changes, make sure date, time, person, decision made, etc. are all recorded.
If correction needs to be made, do not change the raw data. Do so using script/syntax and save that syntax for reference.
Explain all outlier-related data change in the report/manuscript. Reasons and methods should be provided so that your analysis can be replicated.
If there isn't a protocol, set one up now before more instances like this came up.
Do not identify outlier after data analysis results are known. If possible, discuss with your colleagues about the outlier without telling them the hypothesis test results.


As a DACA student, am I eligible for PhD funding?

The most common kinds of funding for PhD students in the US are research assistantships and teaching assistantships.  Typically neither of these types of funding have rules about the citizenship status of the student.  These types of funding would provide a DACA PhD student with tuition and a stipend for living expenses.

Some prestigious, higher paying fellowships offered by the federal government would not be available to a DACA student.  For example, the NSF GRFP requires permanent residency.  The NDSEG, being funded by the military, requires citizenship or national status.

On a broader note, if you cannot get financial aid including a stipend, you should not get a PhD.  If the university thinks you will be a good PhD student, they will be willing to pay you.  This advice does not apply to professional degrees.


Acquiring a bound copy of someone else's thesis

Print the paper yourself, three-hole-punch (or buy pre-punched paper), and use a three-ring binder. For 200 pages, it might be easier to do this at an office/print shop (search "print shop" or "printing" on Google Maps or something to find one near you). Sometimes these shops will do this sort of thing for you, and often they have self-service machines which can get you around wariness that employees may be trained in as far as printing work they are not confident they are allowed to print. As a comment mentioned, these shops can also sometimes do coil binding, which would hold together better on a shelf. Nicer binders would do okay on a shelf, though they would be best held page-side-down in a file drawer or horizontal rather than vertical.

It's not normal to bind someone else's work in a proper book, and theses are not typically printed as books for resale. Printing a PDF of a copyrighted work that you have digital access to for personal use is typically completely legal, and practically never going to be an issue even in some odd context where it isn't.

@cbeleitessupportsMonica also suggests a "springback binder" which I have never used personally but it looks like they might be ideal for this purpose.


Is it okay to submit a paper to a conference or publication from another field?

There isn't anything wrong with submitting to a conference that might not be a perfect fit. I would urge you to ensure that the fit is decent enough that you won't be wasting anyone's time, but cross-polination can be great for both fields.

When I was a graduate student and was helping my advisor review papers for a prominent conference, I read an outstanding paper that I didn't believe was on-topic for the conference, and I suggested to my advisor that it should be rejected it even though it had a novel (and cool) contribution. When I discussed it with her, she said that for really excellent papers, program committees will sometimes be flexible. If I was convinced it was that good, she said, I should give it a positive review and let the committee sort it out. In the end they accepted the paper. It was very well-received at the conference, and the authors were excited to get the paper into the competitive conference, where it would undoubtedly be seen by a lot of people.