Positive review from an additional (third) reviewer (endorsing the 2nd reviewer) against a negative review from the 1st reviewer

It would be strange for the editor to solicit the third review and then not even consider it: that sounds like a waste of at least three people's time.  However, as to how this will affect the final decision: as Nate Eldredge points out, the editor is not obligated to go with two out of three.  In fact an editor may go against the recommendations of all the reviewers, and this certainly happens sometimes, especially in our day in which so many journals have "very high standards."

Buffy says "Anything here would be a guess."  I agree, and here is my guess: if the editor solicits a third review and the third review is really positive, then the editor is likely to accept your paper unless the first reviewer comes up with new, relevant, significant negative comments.  (Why?  Because, again, the editor could just as easily -- and in fact, more easily -- have rejected your paper after the first two reviews.)

However, in some hard-nosed decision theoretic sense, you don't need to know the answer to this question, by which I mean to say that you will find out eventually and until then you have done the optimal thing.  If that doesn't cheer you up: look, if two out of three reviewers are really enthusiastic about your paper, then even if this journal doesn't accept it, some other, similar journal probably will.  Congratulations on your good work.


Could I continue in my preferred field whilst working on a post-doc in a different field?

There are many whom I know have done their post-docs in a field far different from their primary area of research and work. I don't see this as a problem. Post-docs and PhD dissertation may also widely differ from person to person. I have not seen such a phenomenon affecting their career.


Showing research to professor who is not my advisor

First of all: you should really be asking your advisor this,  not strangers who don’t know your circumstances.

In any case: if you have a result that you feel is ready to be shown to others, why not write it up and put it on ArXiv yourself? That way no one could do this to you.


How to ask the editor of a journal whether our manuscript fits the scope or not

Broadly, I would encourage you to review the information for authors provided on the journal's website in greater depth. First, it seems that some of the feedback you are seeking is related to the format of the manuscript (you mention asking about length, for example), and as these requirements are generally laid out online in the journal's instructions to authors, the presubmission inquiry is not an appropriate venue for getting those types of questions answered.

Second, many journals that regularly field presubmission inquiries will have a description on their website of what this inquiry should include and where to send it, although the level of detail they provide may vary. I refer you to PLOS Biology's Presubmission Inquiries page for a good example (http://journals.plos.org/plosbiology/s/presubmission-inquiries), as the points they ask authors to include in their inquiry could, I think, be broadly applied in cases where the journal has not provided much guidance regarding what they're looking for. Bear in mind, however, that it is necessary to do your own research regarding your particular journal's guidelines; Nature, for example, wants a fully referenced first paragraph of your article.

Final point--a positive response to a presubmission inquiry does not guarantee that you will receive a favorable review, or even get reviewed at all. It is a good start to the review process, but just a start.


Planning to do PHD, Masters Thesis important? (USA)

Your last question is a bit of a non sequitur, frankly: I don't really see the connection between going into industry versus doing a master's thesis with the rest of the question.

That said, JeffE's comment above is essentially correct: if you are interested in doing a PhD in the near future, an industrial job is probably not going to get you the research experience you need to be a competitive PhD applicant.

With respect to what you need to do to convert your project into a master's thesis, that's really something you ought to discuss with your project supervisor. Without knowing the specific policies of your department, as well as the specifics of what you did in the project, it's difficult (if not impossible) for us to know what needs to be done.


Direct quotations and quoting 'questions'

No

I don't see a strong case for plagarism here. According to Google:

  [Plagarism is] the practice of taking someone else's work or ideas and passing them off as one's own.

It doesn't sound like you've tried to do this if: despite not being in quotation marks, the quotes were clearly indicated as the work of others. Furthermore you've corrected your mistake which shows good willing. I'd rest easy and wouldn't lose sleep over the matter.


Age limit for research position or postdoc in pure mathematics?

As mentioned in the comments, the answer is that there are typically no age limits.  What postdoc positions occasionally limit (e.g., NSF postdocs) is the number of years since you've gotten your PhD, and there is often a preference to hiring recents PhD, which is what we mean typically mean by "young mathematicians."  (We usually look at dates of degrees rather than age specifically when reviewing applications.)

Many mathematicians started off in other fields first, and there are quite a number of successful mathematicians who have gotten their PhDs in their 30s-40s.  See this MO question for examples.  Also, here is a related MSE question.

To be honest, I haven't seen enough examples personally from the hiring perspective to know whether there is some bias against age in hiring postdocs or not--I imagine there is at some point, e.g. at 60 or 70, people may not think it's worth training someone who may not have any good years left and such a candidate would need to have done something truly amazing to be competitive.  But at 40, this is not as big of an issue as it might have been in the past--many mathematicians nowadays do great work after 40 (including people on the MO list above) and are recognized as such.  This is corroborated by the fact that research universities regularly hire professors who in their 40s and 50s (though it is rare to hire someone to do research someone who is already in their late 50s or 60s).  So, I wouldn't worry too much about a bias against your age.


There is no hard and fast rule on whether to include calculations in papers that have appeared in other papers. It is a judgment call on the part of the author. For my papers, I have sometimes included these equations (either in the main body of the paper or in the appendix) sometimes I have omitted them and directed the reader to the bibliography, and sometimes I have just provided a brief sketch of the argument.

The reason to include them is because sometimes they are convenient for the reader. The main reason to exclude them are because they detract from the focus of the paper. As an extreme example, if your important new ideas in a paper take up 3-4 pages, it is strange to include 50 pages of previously published calculations, say, even if it is in an Appendix. It makes it harder for me as a reader to understand exactly what is the main point of your paper, and I might get the impression that the authors are adding fluff to make their contribution seem more important than it is. You want to keep your novel, important ideas at the forefront of your paper.

And don't discount the page length: even if they are no explicit page limits in a journal, you generally want to convey your idea in as few pages as possible. First of all, is the possibility that potential readers might be discouraged from reading your paper if it seems too long. Secondly, journals do hold longer articles to higher standards. When I was submitting to the top ranked journal in my field (which had no explicit page limits) we were told by a senior professor that our idea was worth publishing there if we could keep it under 30 pages, and probably not worth publishing there if it hit 40. In other words, there was a sense where our idea was not worth wasting 40 pages worth of someone's time, although it was worth wasting 30 pages worth of someone's time.

In summary, papers don't necessarily have to be self-contained, and how much to include previous work is a judgment call on the part of the author. I will add that as a student, it is probably best to defer to the advisor when making these judgment calls, as the advisor will be more familiar with the conventions and culture of your research area.


Why do publishers allow distributing preprints?

Although this is speculation since I don't work for a publisher, there are a couple of reasons I can think of:

Due to pressure from funders, who want the research they funded to be publicly available.
To take away the focus from gold open access. Publishing preprints is known as green open access, and means that authors are allowed to post their work elsewhere. Often, however, this is with restrictions: only the non-peer reviewed version is allowed, and only after a certain period. This discourages academic libraries from cancelling their subscriptions, and appeases the funders who might otherwise call for the published version to be publicly available immediately. (Note: I think this was mainly a motivation before the publishers figured out they could heavily charge funders for the latter requirements.)
Because it might be hard to argue in a legal case for publishers to restrict access to research that they haven't been involved with at all (i.e. not yet been peer reviewed, layout done by the researcher themself, etc.). Yes, they often coerce authors in transferring copyrights to the publishers, but they might rather not test the strength of that argument in court.
As a courtesy, to maintain goodwill. It's clear now that it doesn't really threaten their business model (no subscriptions appear to have been cancelled in response to preprints being available), so they can easily do this.


Is it advisable to have a master or PhD thesis topic in mind before entering graduate school?

There may be advisers, departments, universities, countries (academic cultures) or fields where you need to come up with your own idea. I would not think this is the norm, however. In many cases Phd positions are financed by project funding so that the project is largely defined. This does not mean that the entire PhD is staked out in advance but the direction is. When you start a PhD you need an adviser which would imply that the field and direction of research of that adviser will determine the direction of your research. In many academic systems you directly apply to a PhD project which is pre-defined. I could probably come up with more cases that point away from come up with your own thesis topic.

That said, however, it is not inconceivable that someone could enter a system with an own idea but since coming up with great ideas commonly involves having a deep understanding of a field, and that in itself being one of the goals of a PhD, it would be a very rare case.

So depending where you are or where you are heading in the academic world, you do not need to know the thesis topic in advance. You will be looking for topics that may interest you and once finding positions announced decide if they fit your interests. It is rare that you find exactly what you dream of so many go for positions that are "close enough". Another point here is that you would probably not select a topic only, you would also consider the academic milieu and if you think it would be good for you and your endeavour into research.


Repositories of funded research projects in different countries?

In the US, the government funded agencies usually publish lists of funded projects. For example, you can search the National Science Foundation database for all of the funded projects relating to "beer". Each of these entries lists the name of the project, the NSF program that funded it, the PI's names and contact information, the amount awarded, the date awarded, and an abstract, among other information.

Here are the databases from other US government funding agencies:

National Endowment for the Arts
National Endowment for the Humanities
Environmental Protection Agency
Department of Energy
National Institutes of Health

There are other agencies probably, but all you need to do is go to their main site and search for "funded projects" or "Search awards" or "recent awards" or something like that.

One agency that may be hard to search would be DARPA (Defense Advanced Research Projects Agency), which is the scientific research arm of US military.


Have researchers any incentive to publish negative or confirmatory results?

There is certainly incentive to publish negative results: a good negative result that clearly establishes, "X is not possible" or "X is not true" can be extremely valuable.  I've published some negative results myself, and am proud of the work.

Negative results, however, typically must hew to a much higher standard of evidence than positive results, in order to distinguish between "X is not possible" and "I can't figure out how to do X." For positive results, showing "I can do X" automatically implies "X is possible," but the syllogism does not hold in reverse.  I think this is one of the main reasons why publishing negative results is so difficult. Also, it's easier for reviewers to argue with negative results, and harder to argue with positive: with negative, it matters strongly why they are negative, while with positive the "why" can be relegated to discussion and hypotheses for future investigation.

Confirmatory results, however, are much harder to justify in absence of an explicit mechanism requiring them, as for medical studies.  Typically, we get confirmatory results not directly, but indirectly through the development of new results building on the prior results: the prior results get confirmed through their use in the controls in the new study.


Software for submitting and testing programming assignments

The open-source web program CMS (Contest Management System) was created by people at my university (CS institute, university of Pisa). Screenshots here.

It has been used also in the international informatics Olympiad and several other international programming contests, so it is mature and well tested.

It is in use since a few years in the undergraduate course on Algorithms in our CS degree. It allows students to submit their source code online, where it is executed in a sandboxed environment and scored automatically on the basis of some test cases. It supports out of the box C, C++, Java, Python, Pascal, PHP, and other languages can be added (although I don't know how easy it is).


How to present the motivation for a book on mathematical research?

What the publisher is looking for is a book that will attract many readers.  If crowds are already clamoring for a book, then the decision to publish it is easy, but that's uncommon.  Instead, the publisher generally has to try to predict whether an audience for the book will materialize when nobody knows they want to read it yet.

The "motivation" the publisher refers to is anything that makes people want to read the book.  You need to demonstrate to potential readers that the material is interesting and exciting, that reading the book will be useful, that it connects to a larger scholarly conversation, etc.

Right now, it's clear that you feel the book is valuable and would like many people to read it, but you aren't giving potential readers a lot of motivation.  For example, in Section 1.4 of the current draft, you write

  Somebody might ask, why to study it? My approach relates to traditional general topology like complex numbers to real numbers theory. Be sure this will find applications.

and

  This book has a deficiency: It does not properly relate my theory with previous research in general topology and does not consider deeper category theory properties. It is however OK for now, as I am going to do this study in later volumes (continuation of this book).

Basically, this amounts to saying you don't yet know how it will be useful and you aren't connecting it to the literature.  The lack of applications is a serious disadvantage, but not necessarily decisive by itself (some things can be published in mathematics just because they are beautiful or seem like they should be useful).  However, not explaining the relationship with previous research is a major problem.  It's nearly impossible to get an academic book published under these circumstances.

I don't mean to be overly discouraging, but my impression is that writing a book on your work is premature.  Instead, I'd focus on connecting your work with the rest of the field, with the goal of getting a group of other researchers building on your papers.  Once you start to get more citations, you can bring them to the attention of publishers as evidence for a community that values your work and would benefit from a systematic presentation in the form of a book.


Difference between Computer Science, Computer Engineering and Systems and information engineering master'sdegrees

Computer Science is mainly theoretical with a heavy "cutting edge" theory and research focus. This is where you would study things like memory management, compiler design, programming language design, artificial intelligence, etc.

Computer Engineering is mainly hardware focused and is usually a subset of electronic engineering. This is where you learn to design processors and build hardware devices.

Systems and Information Engineering is like Computer Science, but is more "practically" focused - it is more about application to real-world problems, with a focus on information systems. This is where Security often falls, as well as other fields like human-computer interaction, information systems, and other applications that are closer to the user.


Is there anything to do while waiting for results of a thesis examination?

From reading the examination instructions it appears that if I get my degree, it could be between 6 weeks to a year.

Have you talked with your advisor about the time frame you should expect?  University policies often allow for a wide range of possible schedules, to account for differing circumstances.  The advisor generally has a clear idea of which part of the range a student is likely to end up in (although of course there are no guarantees).

When you reach the point of graduating, there should be little uncertainty left about the quality or value of your work, because your advisor should have been offering feedback and guidance along the way.  If your advisor is genuinely unable to predict whether it will be closer to 1.5 or 12 months more, then it is a worrisome sign (suggesting inexperience or negligence on the advisor's part, or that they suspect something may be wrong with your dissertation).

  Considering the time-frame is so variable, is there anything else I should be doing or planning?

I agree with the comments above about job applications.  In the cases I am familiar with (mathematics in the U.S.), academic job applications are due around December, which is typically about six months before graduation occurs.  This includes both faculty and postdoc applications.  Practices may differ in other fields or countries, but it's almost always a good idea to begin looking substantially before you actually graduate.


Where can I find hard data on students' reasons for being students?

This is an active area of inquiry in US academia, as market research for admissions departments and also as part of the larger investigation into student "success". Our dean likes to remind us that the main reason for going to college used to be "to get an education" but now it's "to get a job" (and thus we need to be more get-a-job focused). I don't actually know which study he's quoting, but an article out this month seems to support his contention.

Twenge and Donnelly have published a retrospective study of students entering college between 1971 and 2014 surveying the students' reasons for pursuing higher education. From the abstract:

  Millennials (in college 2000s–2010s) and Generation X (1980s–1990s)
  valued extrinsic reasons for going to college (“to make more money”)
  more, and anti-extrinsic reasons (“to gain a general education and
  appreciation of ideas”) less than Boomers when they were the same age
  in the 1960s–1970s.

(Twenge, J. M., & Donnelly, K. (2016). Generational differences in American students’ reasons for going to college, 1971–2014: The rise of extrinsic motives. Journal Of Social Psychology, 156(6), 620-629. doi:10.1080/00224545.2016.1152214)

Other articles that may be of interest (by no means an exhaustive list):

Balloo, K., Pauli, R., & Worrell, M. (2015). Undergraduates’ personal
circumstances, expectations and reasons for attending university.
Studies in Higher Education. Advance online publication. doi:10.1080/03075079.2015.1099623
Bui, K. V. T. (2002). First-generation college students at a four-year university: background characteristics, reasons for pursuing higher education, and first-year experiences. College Student Journal, 36(1). 3+.
Kennett, D. J., Reed, M. J., & Lam, D. (2011). The
Importance of Directly Asking Students Their Reasons for Attending
Higher Education. Issues in Educational Research, 21(1) 65-74.
Kennett, D. J., Reed, M. J., & Stuart A. S. (2013). The impact of
reasons for attending university on academic resourcefulness and
adjustment. Active Learning in Higher Education, 14(2). First
published on June 10, 2015. doi:10.1177/1469787415589626
Phinney, J. S.; Dennis, J.; Osorio, S. (2006). Reasons to attend
college among ethnically diverse college students. Cultural
Diversity and Ethnic Minority Psychology, 12(2).347-366. doi:
10.1037/1099-9809.12.2.347
Schultz, J., & Higbee, J. (2007). Reasons for Attending College: The
Student Point of View. Research and Teaching in Developmental
Education, 23(2), 69-76.


To avoid legal battle, in bussiness world reference letters are written extremely terse. How do academics get away with this?

My impression is that the difference is largely cultural.  The academic community in the U.S. has developed a culture of relying on written letters of recommendation, and this practice has a lot of inherent stability.  Someone considering suing knows that a questionable lawsuit would permanently ruin their career, in a way that wouldn't necessarily happen in the business world.  (For one thing, academia is a much smaller, more tightly knit, and more philosophically coherent group.)  If a student or job applicant did sue frivolously, then it would probably be cheaper to settle, but the university would not do so: proving a point would be a higher priority than saving money.  (By contrast, for-profit businesses are less likely to make unnecessary expenditures to try to defend their principles.)  University attorneys know that if they advised faculty not to write or require letters, everyone would ignore them and it would just hurt the university's reputation.  The culture takes on a life of its own, regardless of the legal context.

However, I believe U.S. legal precedents are actually pretty favorable for academic letters of recommendation.  The key phrase is "academic deference," which as I understand it is the theory that academic judgments are not subject to legal review because the courts aren't even capable of evaluating these judgments.  (Of course I'm not a lawyer and so I'm probably at least overlooking subtleties.)  You can sue for reasons like discrimination, but you can't successfully sue someone who made a good faith effort to judge your academic performance or potential on the grounds that you think they judged it wrong.

The academic deference doctrine is based on a number of precedents, but it's somewhat controversial.  For example, people argue that it makes it too easy to get away with discrimination (since it makes courts reluctant to examine evidence), and that lots of non-academic judgments are equally difficult to evaluate but don't have a special doctrine protecting them from review by the courts.  See this article by Moss for a review of the precedents and an argument against academic deference.

Depending on the circumstances, there may also be other legal issues.  For example, it's much harder to sue someone for libel based on their evaluation of your published scholarly work.  In particular, you have to prove actual malice since publishing the work makes you a public figure for this purpose.  In other words, it's not enough to prove that the evaluation was wrong; instead, you have to prove that they knew it was wrong or at least had reckless disregard for the truth. (See, for example, Posner's wonderful opinion on whether calling someone a crank is defamatory.)  I believe this is much more clear cut and better established than academic deference is, but it is not relevant for unpublished work or other recommendation letter content.

Returning to the cultural theme, it's also worth thinking about psychological factors.  If I run a business, then my ex-employees could be applying for jobs at competitors, partners, or companies that are irrelevant to my interests.  Among these possibilities, partner companies I'm actively working with are only a small fraction.  The generic case is that I won't care about the new employer or will actively harbor ill will towards them.  If a lawyer advises me that it's best not to say anything, I may seize on that excuse even aside from the lawsuit potential.  By contrast, academia is a world in which we're all partners, and that feels very different.  Universities do compete against each other in some ways, of course, but there's a much greater feeling of good will and cooperation than you see between most for-profit companies.  It's no surprise that very different norms and practices have developed in a far less competitive environment.


Is it allowed to re-format a post-print version of a published paper?

Since you obtained the permission for the journal to use a post-print version of the paper, you should be allowed to do that.

Technically, you have two options (depending also on the thesis requirements of your department/university):

add PDF pages to your thesis (which will look inconsistent with the rest of the thesis - and you are not interested in this option)
reprint using the thesis style

In the latter case, you might do the following to the page with your Chapter title (I would also make the chapter title = Paper title, but I don't think it's mandatory):

Chapter N

Chapter Title

@2000 Publisher. Reprinted with permission (Mar 15, 2003), from J. Doe, Paper Title, Journal Title, January 2000. DOI: XX.XXXX.XXX

Page break, followed by the reprint of the journal paper with thesis formatting.

Notice, it is explicitly stated who holds the copyright (Publisher or Journal) and that this chapter is a reprint with a permission obtained at a certain date (you might want to hold either to the email from the publisher or screenshot with the permissions).

That is exactly how I added my already published papers (2 IEEE conferences and 1 IEEE journal) to my thesis according to IEEE permission.


PhD Applications: Can a good academic record in my master's compensate for a horrible UG academic record?

In short:

You need to do some research-type work during your Master's to evaluate if your desire to get a Ph.D. has some foundation.

You certainly would have a chance to get into a Ph.D. program with strong enough application. However, you would have to work hard during your Master's.

There are several things you need to consider:

you have not yet finished (or, I guess, even started) your Master's degree. Therefore, you are planning way ahead.
you certainly want to do a research-based Master's degree with a thesis, as opposed to doing a pure course-based Master's. Doing research during your Master's would allow you to understand if you like doing research in the first place. Also, it would strengthen your potential application for a Ph.D.
a carefully written Letter of Intent would be crucial.
sometimes, only a GPA in your last two years of the undergraduate program is used for applicants with a Master's degree.
you should make a decision of industry vs academia closer to the time you are finishing your Master's degree. Moreover, even if you get into industry, nothing prevents you from applying to a Ph.D. program several years later if you still have research interests and, especially, if you position at industry had a research component that you were excited about.


Can call numbers differ between libraries?

Normally, when already available, Library of Congress classifications are usually found after the title page, and should thus be constant across different libraries. For publishers.

In any case, this should be a fairly easy hypothesis to test (at least to a certain degree). Most university library catalogues are on-line and freely available. You could sample a cross-section of titles from different subjects and see what happens: my suspicion after a few cursory checks of my own is that call numbers do vary somewhat, but primarily at the "secondary level" (in identifying the author, rather than the subject).


How to secure recommendations and apply for PhD after having worked outside of academia for two years?

I'm not a computer science guy, so I don't really have experience with the norms of a CS department in a university.  But I can give this general advice:

If you want to do a PhD, you should at the very least: 1) know you enjoy research; and, preferably, 2) have specific research problems you really want to work on. Don't enter a PhD program if you don't like to research. If you're not sure, start with a master's in a program that has a history of allowing master's students to graduate into PhD programs and in-so-doing take advantage of their master's coursework.
References: get them from people who make you look good and make sure your letter-writers know what makes a good grad school letter of recommendation. If you have a good manager who can attest to your capabilities as a learner, sure, have him or her write a letter.  However, not all managers are going to know what graduate schools are looking for -- so educate the writer. Grad schools want people who can learn and work independently above all.  Emphasize that. And, of course, if you are interested in a certain kind of research, make sure your letter-writer knows that and can comment about it!
The personal statement matters. In your post here you mentioned your strengths (professional experience at a good firm) and weaknesses (disconnected from academia, non-academic references).  Be straightforward about those in your personal statement. More importantly, use the personal statement to discuss what you want to research, why, and your prior experience in the area. Furthermore, explain why you are a good fit for the department...
Fit. You need to fit in at your department. This basically means you should apply to programs where you can have an appropriate mentor who is an expert in what you want to study, or expert enough to guide you along. Do not just apply to any-old program, or a program with a good name. Read through the department web site, figure out the kind of work they are doing, and contact possible mentors/advisors with questions that show your interest and help you decide if the program is a good fit. Having prior rapport with the faculty will help you, and if the department knows you want to be there, this will bump you up a little in the stack of applications. Of course, having good credentials and clear research interests is what makes for a successful application, but departments don't want to waste giving offers and potential funding to candidates who are unlikely to attend the program should they be admitted.

Hope this helps.


Publishing while working from home independently, what affiliation to give?

Generally speaking, you should not put any institution as your affiliation unless you are currently based there, or did the work while you were based there. In this case, unless you did the research while at Linkoping, you should not give Linkoping as your affiliation.

See, for example, this discussion.

If it helps, it's worth remembering that the "affiliation" is in many ways an "address" - it evolved out of simply giving an address at which you could be contacted, and some journals still refer to it this way. It's not unknown in some fields for independent researchers to give their home address, but it's perhaps more common just to say "independent".

If you have no current affiliation, you can simply say "Independent researcher", or similar, and leave it at that (adding an email address is good, if not asked for elsewhere in the paper).


Paper getting rejected from many journals after no proper review - What could be the problem?

I don't think there is only one reason for all the rejections you got. The first journal seemed to reject you because of a formality, which could have been prevented (abstracts usually never have citations). Maybe they think if you can't follow the submission guidelines to every last bit you don't deserve to be published (which can be unreasonable).

After that your research was already 14 months old. Did you do a new literature research? The novelty could have faded during that time. Journal 2's and 3's rejections seem legit and happened in a relatively reasonable time frame.

I guess journal 4's answer does look like the editor/referee didn't read it in detail. But before accusing them of lack of interest or ethics, you should ask yourself if your research has the quality and novelty to be published.

You also need to overthink your choice of journals. High-impact journals are often not the best choice for your research due to their high standards. They also tend to not publish very specialized articles.

My concrete advice: Review your article and try to improve it. Get criticism from colleagues and take it seriously. Compare your article to similar articles from your field and apply those same standards. Then choose a journal that is common in your field and that published articles related to your work and try there. Good luck!


Is it common to review papers assigned to your supervisor?

It is not uncommon for the advisor to ask a student to review a paper. Let's face it — reviewing is a chore, takes a huge chunk of your time and most people do it not out of interest for the paper, but rather a necessity (it factors in promotions within the organization and recognition within the society) and probably some feigned interest in the "role of an academic" and "giving back to the society".

Usually, the papers that an advisor passes on to their students are

tangentially related to their interests
only mildly interesting or borderline stuff
are not from top-tier journals

As a student, you should never pass up on these opportunities. It can be a very rewarding experience to review a paper and discuss with your advisor. Some of the things you'll learn are:

that you didn't catch on to some inconsistency/mistake after a month of review, but your advisor did it in 15 mins of casual reading.
to write an effective critique while at the same time not putting the authors down. Contrary to what many may think, a review is not all about "your math sucks!". While yes, it should be pointed out if it indeed sucks, there are ways of saying that. If you spend a lot of the review finding faults, then it is also "fair" to throw in a couple of nice things about the paper and balance it.
you'll also learn to not nit pick on minor quibbles and focus on the technical content (I hate it when a reviewer makes a huge deal of 'data are' vs 'data is').
You'll learn to do this while juggling other activities, so it's also an early lesson in time management.

In the end, the quality of the review is partly your advisor's responsibility and he's not going to allow it if it is completely shabby. So, take this as an opportunity to learn about how to write a review.

Speaking for myself, I reviewed a couple of papers for my advisor in my early years and now, after I have a few publications to my name, I get invited to review papers on my own (i.e., not via my advisor). Recently, there were a couple of opportunities that my advisor passed on to me, but the difference this time, is that he trusts me to do a decent review and so requested the editor to officially ask me to review, so that I'll get credit for it.


What are the pros and cons of being a Mathematical Reviews' reviewer?

For background, MathReviews are reviews written by mathematicians of published mathematical papers and typically describe the content of the paper. Such reviews are available on the online database MathSciNet.

Here are some reasons to do it

Writing reviews forces you to read some papers that are not in the focal point of your interests. Since there is no decision to take, I find it less time-consuming and stress-generating than refereeing a paper.
A good review is a service to the mathematical community: it allows mathematicians to find relevant papers and decide wether a paper is worth searching for and/or reading.
You get paid $8 for each review that you can use to buy books from the American Mathematical Society.
Your name might appear in MathSciNet as a reviewer next to some nice authors and nice papers ;-)

Here are some reasons not do it:

Reading a paper and writing a review takes time.
You are not anonymous. If you are not careful enough in writing your review, you might upset some authors.

Here are some tips to have a good experience:

You can set up a limit of the number of papers that you accept to have at once. Set it a reasonable level for your workload.
Choose carefully the AMS classifications that you are interested in. A poor choice can lead you in reviewing papers that do not interest you. (Afterwards, if you receive many uninteresting paper, you should consider mentioning that you are not interested in their AMS classification.)
Reviewing a book takes much time. Think carefully about it when asked.


Are there accepted criteria to define an author's institutional affiliation?

This is pretty old, but I will provide an answer to an increasingly relevant question. Affiliation is understood to be where the major part of the work was done. If this is not the author's current primary employment, then those details should be included in the contact details and/or acknowledgements. Any paid affiliation is unethical. Surprisingly, I did not find any reference to this "creative affiliation" in the COPE standards https://publicationethics.org/.

Many publishers include a statement about what to do if affiliation changes during the publication process - i.e. how to credit the institution where the work was begun and the institution where the publication was finalized. For example "Present/permanent address. If an author has moved since the work described in the article was done, or was visiting at the time, a 'Present address' (or 'Permanent address') may be indicated as a footnote to that author's name. The address at which the author actually did the work must be retained as the main, affiliation address." from Elsevier Guidelines for Authors (https://www.elsevier.com/journals/journal-of-archaeological-science/0305-4403/guide-for-authors, but they all include this). It seems that what the OP describes is so unethical that no one has addressed it explicitly (yet).


Can I use a professor's letter of reference as a recommendation?

Three things:

1) It's polite to ask someone before putting their name forward as a reference. It's a huge turnoff to have someone get in touch with you unexpectedly saying that you're a reference for someone you didn't think you were a reference for.

2) It's smart to ask someone before putting them forward as a reference, because it gives them a chance to respond to you. It's possible that this person may not be able to give you a good reference at this point in time, and nothing will destroy your chances faster than if the admissions committee follows up with a reference who then says they would not recommend you.

3) In this case it sounds like the letter of reference might be highly specific to that institution: "I have the funding to work with this student and want them to do a PhD with me." That's a nice thing to say about someone, but it's not really a general purpose reference. Ideally, applying to a PhD program, you want a letter to explain why you're a great asset to a research program.

If you still want to use this letter, then be sure to ask the reference before you do so.


Is there benefit to publishing the abstract of an English article in multiple languages?

I am Spanish, so I think I can argue why it would make sense to publish abstracts in two languages, in some fields, based on the Spanish context.

Most people in Spain are not fluent in English, and many have a lot of trouble understanding even the basics. This is more true when you consider older people, some of whom studied French as a second language, rather than English, which is currently the overwhelming choice.

Most people actively carrying out STEM research (I will leave out humanities since I don't know much about the situation there) will be able to read and write technical documents in English, however some papers are intended to be used also by people who are not actively engaged in research. Obvious cases are most engineers and those medics who do mostly only clinical work. Even many clinical research studies carried out in Spain are published in Spanish, because 1) many medics who can benefit from the information would not be able/willing to read it in English, 2) the authors are not able/willing to write in English, or a combination thereof. The paper you link is in a field of medicine, so it does not surprise me at all that the abstract is also in Spanish.

That said, I do not believe that in my particular field, physics, where the overwhelming majority of people interested in reading a research article are themselves actively engaged in research (and therefore routinely exposed to technical English), we would benefit from bilingual abstracts.

So, in summary, it makes sense in some fields but not in others.


Adding a short example after explaining the part of the method

Illustrating your method with a brief example is perfectly acceptable, especially if you do it in a reader-friendly way. Indeed, paragraphs often start with a "topic sentence" (which introduce the main idea, e.g. a concise description of your method), followed by some "supporting sentences" (which substantiate your main idea, e.g. by providing examples), before ending with a "concluding sentence". Such a paragraph structure enhances readability - so go for it!


Transcribing non-native speakers of English who are presenters at an international conference?

I assume you mean that the language of the conference is English and that people will be trying to do their best to speak English.

I think that, while it might be possible that you do it yourself, you are trading time for money. It probably can't be done quickly by a single person, no matter the skills, so a service might be much quicker. I assume that transcribing the talks into "better - more standard" English will require some consultation with each speaker on various subtleties. So, yes, a huge hassle, though do-able if you have the time.

I think it would be even harder unless you are familiar with the native language of each speaker.

I think you will also want to get each speaker to sign off on your transcription, however it is done. Some may have questions or even corrections.


How common is it to switch to a tenure-track position from a non-tenure-track position in the same institution?

Like many things in academia, the answer will likely depend upon the institution.  In most, I would think that a non-tenure-track and a tenure-track position are actually different positions.  You aren't just changing a title, but you are leaving one job and starting another (at the same institution). I would imagine that most do not have official rules about the number of times you can change jobs, although there may be unofficial scuttlebutt to the contrary.  This should be outlined in the faculty handbook/guide.

  Is it ever a good idea to ask when interviewing for a non-tenure-track position whether there is a possibility of switching to a tenure-track position down the road or what the institution's policy is surrounding switching tracks?

If you are interested in a tenure-track position, I think this is a very important question to be asking, and is not viewed negatively by any reasonable person. The chair or hiring committee should be able to let you know about this possibility.


Are there any specific teaching techniques to handle "virtual" classroom sessions?

When I read this question, I immediately thought of this TED talk.
In it, Peter Norvig, who taught a huge online course on AI, shares what he learned about teaching to a large virtual audience.

His main points:

Mimic a one-on-one teaching style by positioning the camera overhead as you write and speaking as if it is a single student.
Alternately, use a livescribe pen (I've had experience with this for a math class; loved it)
Make short, <10 minute videos to retain attention
Ask questions to check understanding (they will pause+answer) and then go over them
Have due dates for watching the videos; students need motivation to watch them in a timely manner
Encourage online forums because peers are great tutors they "remember what it's like to not understand"


Normally, you can't just change an already published version. However, this does not mean that you should just publish the correction in another journal. The best way to deal with it would be to contact the editor of the original journal and discuss things with him, as this error also concerns him, not only you. He will then be able to tell you how to publish the correction.
In case that you aren't the only author (e.g. you have an advisor, colleagues, etc.), they should also be informed before taking action.


US Master Admissions, LoR: Academic vs. Employer

For graduate study, what the committee looks for is primarily ability to do research. You need LoRs that highlight that aspect of your work. If no faculty can attest to it (or you in general), a letter from a previous boss at work might do.


Do the results of evaluating cutting-edge methods in an industrial setting constitute new knowledge?

Science focuses on the acquisition of new knowledge.
"Does this really work outside the lab?" is a valid question on which to acquire knowledge.  Industry usage of a method often requires changes in scale and context which pose fundamentally new challenges to overcome.

Not all industrial evaluations, however, would be meaningful science.  The distinction is whether the information acquired by the evaluation constitutes a contribution to human knowledge or if it is just a recommendation for a decision by the company.

For example, I saw a talk yesterday which included future work to evaluate a new membrane material in an industrial water-treatment facility.  Let's see some examples of how this evaluation might be science or not:

Science: When used at scale, is water quality maintained to appropriate standards? How well does the material hold up over time?
Not Science: Will this be easy to integrate into the current procedures of this particular plant?  What business and legal contracts will be necessary to switch suppliers?


Is it common to seek outside letters for the third-year renewal of an assistant professor?

I don't know whether it is common, but a version of it, a 4th-year review, exists (determined by department pattern of administration) at Ohio State, and it's actually useful. It gives the candidate a good feel for what the actual tenure review will be like the next year, and alerts them to problems that can be remedied. Letter writers are usually asked to update their letter for the real review (though not if they wrote a crappy letter for the 4th year review). Similar letter-inflation exists in Alaska, Vanderbilt.

I take the point that this is a form of bureaucracy- and service-inflation, but it actually gives reviewers a longer time to read the papers, in case they are not familiar with the candidate's work. The problem-detecting function is quite valuable, I would say.


Why bother publishing papers in journals?

There are a number of reasons to do so, never mind the existence of self-publishing on the internet.

Some of the reasons are institutional. If you don't publish in reputable journals you probably don't have any future in most of academia. You will be judged, at least in part, and largely in some situations, on your journal/conference output. Some of this is just inertia, of course, but much of it is really valid.

Your answer to another question on this site expressed skepticism of the review process. I think that view was too dim. People, even if unpaid, consider it their professional duty to contribute to the community by making a good faith effort in reviewing. Journals normally use several reviewers for a given paper so that the occasional poor job can be discarded. One person reviews papers so that other people will be willing to review their own papers fairly and honestly. The review process does two things. First it helps authors improve papers even if they are already pretty good. Second, it keeps junk papers out of the mainstream.

So, authors and the community at large get a benefit from the publishing process that wouldn't be in place if everyone just self published.

But there are other reasons as well, some of them going back to fair and independent review. In a world in which there were no gatekeepers on publishing (and there really aren't now - since you can publish on your own) every reader of every paper has to work hard to validate everything that is said. The effect of this varies by field.

In mathematics it is fairly easy to write a paper that doesn't hold up, but "sounds good" due to the use of specialized mathematical symbols and terms (jargon). If I find a paper online, I have to work pretty hard to determine if it has value. If I find it in a good journal, I have some assurance that others, with skills like mine, have already done this and have found it worthy. So my task is eased and I can be more productive myself. Errors occur, of course, so mathematical skeptics are welcome.

In some other fields, especially those relating to health and public policy, a lot of garbage gets published in the "popular" press. The anti-vax community, for example, has caused a lot of harm. Without the vetting process that occurs in reputable publishing, where people independent of the author have an important judgement, the garbage will start to obscure the gems. Enough of that happens already.

And comments on self published work are just about worthless as a judgement. The reader of a bunch of comments has few ways to judge the veracity of the commenter. And bots and trolls are rampant in flooding the space with mis-information on some topics.

A third issue is that if you only publish yourself, then it will be hard to find you. And even harder for people to make a judgement about whether what you say has value or not. An internet search on most topics will turn up a lot of things, of course, but it is, again difficult to sort the treasures from the trash. If I already know and respect some individual, then it is easy to find their work online. But not so easy to find the work of a recent PhD who doesn't yet have a body of respected work (probably in journals and conference proceedings).

Publishing is a public good. It isn't paid for with public money, however. This is both good and bad. Having it be a private undertaking keeps the possibility of governmental interference (censorship) out of the game, but also requires that the money come from other sources: subscriptions, author fees, etc.

So, publishing is an effective and sufficiently efficient (for now) way to make one's work known to a community who might need to see it and may use it to advance the state of the art.

And, for most researchers the "high paywall" doesn't really exist. Many people use grant funds to obtain the materials they need, as well as to pay page fees required by some journals. But even a poor student can obtain free access to nearly everything just by going to a decent library and asking for a copy. You don't even need to go physically anymore. An email to the librarian may be enough if you are an enrolled student. The libraries pay the fees if needed, sometimes using public funds. This avenue may be open to nearly everyone, actually, provided that you have access to a library that, itself, has academic connections.


How to write a PhD thesis in three months?

Make an outline and a schedule, then follow the schedule.  Include time for revision and feedback in your schedule.

If you know all the content already, the writing can be done much faster than that.  In my field, it is only necessary to write about 90 generously spaced pages, so three months is less than a page a day.  In more verbose fields, your thesis need not be more than 500 pages, so that's an achievable 6 pages a day.

The real problem is when you do not know the content you need to write - that part we cannot help with here.


Is it safe to use up all the words available in a word count limit when submitting a journal article?

If you have 9,000 words, do not try to add new words only to get closer to the limit.

If you have 9,999 words, do not remove words merely to get further from the limit.

Submit no more than 10,000 words unless you ask permission (sometimes there is flexibility in the word count, sometimes not).

In summary, use the limit as given and don't concern yourself with gaming the system beyond that.

These sorts of strategies and games might have a place in standardized testing but they don't have much place in research.


Is offering to use personal funds for research a good idea?

I think you shouldn't offer private fund to supplement a research budget, and I also think people won't let you for the two following reasons (among others):

1. It's not your private responsibility to fund your research. For the sake of your own self respect, you shouldn't pay to work. It will give a bad signal, even subjectively, about the quality of your work. It's important for an academic career to be able to show that you can secure complete funding for your research.

2. Personal funding is not reliable:
People reviewing your application will see that the project is underfunded and will doubt that you will effectively be able to compensate with your own money. There will be no ways for the institution to enforce a funding commitment like "the project will be supplemented by personal funds". Funding is generally secured via contracts or other forms of legal documents.
Besides, any institution that relies on researchers breaking their piggy banks to pay for equipment is doing a sloppy job and it's going to hurt its reputation.


Does posting my work on the Internet protect me if someone else tries to publish it with peer review under their own name?

There are sites like arxiv.org where you can publish something, which isn't peer-reviewed yet, but which becomes public and stakes a claim to the idea.

However, that's usually what some people (usually at universities, not companies) do when they have a full-fledged paper to release. In your case it sounds, if I read this correctly, like you have some general ideas you have not yet had a chance to pursue in depth.  You're considering putting them out and inviting others to run with them, but want some credit.  I would say that if you simply put out a general idea, that is worth an acknowledgment in a paper, not co-authorship.  Being an author means actually doing some of the work -- writing text, doing experiments, etc.  I don't think what you describe rises to that level.

One thing you might consider doing is putting out enough information to tease people into inquiring for more information, then trying to work with anyone who inquires to be more directly involved in the work as it proceeds.


In general, single subject studies often do not require IRB review in the United States because they do not meet the federal definition of research (they are not "generalizable.")

However, there are some exceptions to this rule. For example, a single subject oral history study or a single subject retrospective case study does not generally require IRB approval, but a single subject clinical study that involves collection of data that would not ordinarily be collected in the course of treatment does.

If you'd like to be sure, I suggest an email to your IRB.


How often should I meet my direct mentor in bachelor's thesis?

My undergraduate project meant I had a meeting once a week for 10 minutes... Some meetings left me with 3 weeks work... So it depends but for an undergraduate, once a week is ample.

Some PhD students have daily conversations, others less often, but that depends on the topic, field and the people involved.


As a European doing a PhD in Hong Kong, I've had the occasion to TA a few CS undergrad classes as well as take my own higher-level courses. I honestly can't say that I noticed much difference in class structures beyond the fact that people are much more shy about talking in class.

So, how will it affect someone not used to it? You will stand out a bit if you ask questions in class, or if you are the type to yell out answers immediately when the lecturer poses one to the class (this is usually met with resounding silence). If you are someone affected by peer pressure, you may end up asking less questions during lectures. Join the trove of students surrounding the lecturer after class for answers.

How do they maintain their educational standards? As far as I can tell, "rote learning" mostly is code for "exercises out the wazoo" here (newspaper articles abound about kids having 30 minutes a day of play time, the rest being occupied by school and homework), and there's nothing better for learning to do a thing than doing it over and over.

TL;DR I'm sure people here had a radically different experience in primary school, but by the time they reach university it seems to all come out in a wash.


What's the best way to progress and prioritise my reading?

Yep, I definitely feel the same way - but I think there's hope. I've found that it's best for me to save a list of the articles and books I want to read, just like you suggested. (Personally, I like to keep separate lists for work-related reading and leisure reading.) Then, at the end of the week, I'll set aside a day or even just a few hours for reading time.

Research Papers

During my reading time, I first just read through the abstracts of those papers - a well-written abstract gives enough information to give me an idea of what's out there without getting me into the nitty-gritty details, and I'm able to get through lots of abstracts in a short time (1-5 minutes / abstract). Then, for the abstracts that caught my eye, or where I want a better explanation of what the paper's about, I'll go back through the introduction and discussion (this might take 5-10 minutes / paper). Finally, for a few papers that seemed especially relevant, I'll go back and read through the methods and results to really understand what they're doing. This can take a while (30 minutes - several hours / paper), so often I'll only look at one or two papers in this final step.

This approach gives me a high-level overview of what's out there, and at the same time allows me to get into the details of a few papers that most interest me. I hope that over time, I'll get to the point where I've thoroughly read and understood many of the well-known papers in the field.

Nonfiction

For academic nonfiction, I'll take a few hours on Friday afternoon to read something work-relevant. I try not to approach this from the standpoint of "how many books can I finish?" Instead, I try to just read a chapter or a section that I find interesting, and sometimes this naturally leads me to go through whole books over time.

News & Leisure

That leaves me a bit of time in evenings or on the weekend to do a bit of light fiction reading if I'm in the mood for it. If I'm not in the mood for it, then I just let it go; no point in reading to relax if I don't even feel like reading in the first place.

For news, I try to take about 10 minutes or so each day, either when I'm eating breakfast or when I'm standing in the lunch line, to read a news site (I use Reuters) to see what's happening. I find this keeps me reasonably well-informed about current affairs.

The biggest challenge for me is to avoid getting bogged down with the feeling that I'm falling behind in reading. Although there are thousands of papers and books that I would enjoy, there's just no way that I can churn through tens of papers per week and still truly understand each individual paper. It's a process, and I've accepted that it will take time. I try not to think of my reading list as a "backlog"; I try to think of it as a list of ideas for my next reading time.

Obviously, there are many other ways to manage reading, so in the end it just depends what works best for you. I'd suggest experimenting with a few different strategies until you find one that works well. Let us know when you come up with something good!


How to not feel offended by comments/edits during manuscript drafting as first author

I often get the same feeling as you when receiving comments from coauthors. I find the key to not letting it get to you is to view it as constructive criticism and discuss the matter with that individual. Even incorrect criticism is constructive, as it tells you if your work is inadvertently challenging a common misconception. In any case, the solution is to have a level-headed discussion about it.
I came to this way of thinking when I realised I was doing the same thing as your coauthors to my students. It caused them an understandable degree of frustration. But, I was making those changes to the manuscript because I believed they would make the manuscript better. Sometimes I was right, other times I was wrong - but by discussing the changes we ended with a paper that really was better.
My point is that your coauthors are probably trying to do what's best for the paper. Sometimes those efforts might be misguided, but the point is that the intentions are good. I would thank them for their interest and their time, and then ask them to justify their changes to you.


Should I address all my research experience in my personal statment?

A personal statement is not a narrative version of your CV - rather, it's a description of your research interests, and how what you have done before helped shape those interests, and how they leave you qualified to start graduate school to pursue those interests.

If some of your experience turned out to be a dead end, and it doesn't fit said narrative, there's no need to include it.


Failing students when it might cause them economic ruin

You are responsible for teaching the students to the best of your ability, and to judge their capacities to use what they have learned.  That judgment is made based on their grades.  So you have several things to think about here.

Are you teaching the best you can?  Teaching does not mean "downloading facts", as I'm sure you're aware.  It means "transferring knowledge, skills, and attitudes".  That "transfer" part is the important bit — transfer means that the student is able to reproduce and use what they've learned.  Is your teaching enhancing this transfer?  This is a tough nut to crack — how do you know?  Are you planning your assessments so that you can really tease out the nuances and to see which students really understand, or are they just assessments because you need to assign a grade somehow?  Your institution might have a center for teaching how to teach, and if you feel that you aren't teaching your best class then start there.  Otherwise, lots of books and resources exist, which I'm sure we can all provide.
Are you assessing fairly?  Fairly doesn't mean easily.  It means that you are creating assessments that actually test understanding and that a student with reasonable ability will be able to succeed at.  It also means to understand their context.  It's easy to make a "really good" assessment that everyone fails because they also have three projects and two midterms in their other courses.  Are your expectations clearly communicated, and are you ensuring that you only assess what you've asked for? (that doesn't mean that you can't expect students to go above and beyond, just that you need to tell them you expect them to)
Are you assessing accurately?  I'm distinguishing this from "fair", but you can treat "fair" and "accurate" as two sides of the same coin.  Accurate means that your assessments are set up so that appropriate weight is given to appropriate topics, and that your tests actually enable students to display their understanding and capacities, rather than whether they memorized the example or found the answer on stack exchange.  Creating fair assessments is challenging, but there is a lot of research and resources available.
Are you giving every student the chance to seek help?  I often find that if students are slipping through the cracks, setting up a regular meeting with them to keep them on track can do wonders.  However, I am in a job in which I'm required to work with students like this, so it's easy for me to do.  If you are a busy research professor who is teaching two courses per semester while juggling other things, it's a lot harder.  Ultimately, the final exam is not when a student should find out they failed the course.  They should know that they are on a bad path long before then, and should have opportunities to get on track.

If you are doing these things, then you are not causing them financial ruin.  It's similarly not fair to say that the students are causing this — you don't know their context and can't make the judgment.  Perhaps they went to a bad high school that just didn't prepare them, or perhaps they are always on the train to another city because their parents are sick and they can't attend classes.  It is not your responsibility to help them in this way unless you are capable of providing everyone the same help.  Which brings me to the most unfortunate reality of post-secondary education:

Not everyone can make it.  For whatever reason, some students simply will not demonstrate that their abilities are up to the standard that has been set.  Notice the wording I used there — I didn't say that they don't have those abilities, but that they will not demonstrate that they have those abilities.  Provided you are assessing them fairly/accurately, teaching the best you can, and giving the help they pay for, then you are providing them with every opportunity to demonstrate those abilities.  If they are unable to do so, then it would be unethical to let them pass regardless of the reason.


How to deal with administrative duties killing the research spirit?

First, I absolutely do appreciate your disaffection with the situation.

I would wager that some of your disappointment is due to pointlessness of some of the administrative activities, or the pointlessness of trying to "over-perfect" things that only need to be "good enough".

Also, some administrative problems will never be solved/resolved, but only "stayed", and require a certain (perhaps small) effort forever. Expending more effort at this moment will not solve those problems. Staying up late will not solve the problems. They're like laundry or dishes that just have to be dealt with, regularly, and "doing a great job on laundry" this week will not really reduce the laundry burden for the next week.

But, yes, these administrative things are very important to keep things going. So there is some exercise of thought to see how much of one's motive force to allocate to "routine" tasks, etc.


I would say that hiding information in anything of this nature - a CV, a resume, and so on - is always suspicious and usually unethical.

I would provide a brief explanation in your personal statement.  Given it has to do with a situation that is unquestionably out of your control, some universities might forgive less-than-exemplary marks.

Getting a masters degree before a PhD could improve your situation further - in this way, you can further prove yourself as a good programmer and book worm who wants to do research.  Naturally the CS field wants more than just these traits, but you seem willing to learn.

Edit: If you're going for an undergraduate degree, all the better!  Simply proving your aptitude should be sufficient.


Can a paper get rejected after acceptance due to incorporation of reviewer comments

What you've described sounds like a 'conditional acceptance', but I'm confused how you got to the proof stage without addressing the comments suggested. How did that happen? Also, no, do not make major changes during the proof stage.


Can we withdraw a manuscript after acceptance but before publication?

As noted by @Joe_74, it is possible but very bad form.  If there is not a good reason for such withdrawal, the authors are subject to poor reputation at a minimum and sanctions (such as a ban) at a maximum.  You haven't said why you wish to withdraw.  As Joe said, if there is an error, it is unfortunate, but withdrawal is probably best.  If it's like another recent post, and it's because of simultaneous submission or some other less ethical behavior, you would deserve whatever comes your way.


Is the PhD thesis needed for a faculty appointment?

One of the general prerequisites in this day and age for a faculty appointment is an earned (as opposed to honorary) PhD from a (typically accredited) degree-granting institution.

Consequently, asking to see either a PhD thesis, a transcript, or the degree certificate is would be ways of ascertaining that you do, in fact, have a valid degree. This by no means implies that only your PhD matters in the hiring process; just that it's part of the process to ensure you're eligible. I wouldn't read too much into this beyond that.


How to determine effectively whether my paper is in scope

I don't know of PC chairs who would deliberately "game" the acceptance rate for a conference, especially an important conference. On the other hand, they do want a lot of submissions. Often they want to build a variety of viewpoints and research into the program, so your "outlier" may actually be a good thing to them. A lot of submissions makes the reviewing more tedious, of course, but allows the program committee to build a more inclusive and "interesting" program.

Of course the reviewers will give detailed feedback to the chairs and the conference program committee so the answer you got isn't indicative that you are more or less like to have the paper accepted.

Some conferences have very narrow scope, of course, and I suspect that the answer from the PC would be different if your abstract didn't sound relevant to them.

I suspect that you already have the best advice you are likely to get.

The only caveat I have here is that if the conference is so gigantic that the PC can't really respond to such questions they just have boilerplate answers to all conferences. But usually, someone would take a look at it. Committees are generally big enough that someone will look.


What to do when research leads to poor results?

I recommend that you record your failures and not just your successes.  In your case, I suggest you write a technical report giving all the details (the implementation, the comparison, the conclusion).  It may not be considered as a publication worthy of your resumé, but at least it serves to document your efforts and may prove to be useful in the future (in case other people are thinking of using your proposed method).

Also note that your method may appear worse when compared to others using a certain metric (say, time complexity) but may appear better when compared to others using a different metric (say, space complexity).  You might want to look at your method again.


How bad do your teaching evaluation scores have to be before you should leave them off your resume?

In my experience, people don't generally put teaching evaluation scores on a CV at all, regardless of what they are.


A new model for publications where papers evolve over time?

Versioning of articles is supported by arXiv for exactly the reasons that you mention.  Each version of the article remains accessible and has a unique identifier, so when citing an arXiv document, it is best to use the version identifier.  A person following the link, however, can see that there have been updates since the referenced version, and use the updated information.

I'm not sure if any other publication venue offers this, though. I think that bioRxiv does, but it doesn't make it clear the way that arXiv does, and talks about replacing an article with a link to the final published version.  It's pretty new, though, and its policies may well be in flux.


Computer Science degree Vs. Software Development degree

There is widespread confusion and lack of clarity in education when it comes to "computer science".

Formally, computer science is the rigourous study of information theory and other abstract notions; it would be better called "computing science". You're not likely to do any computer science in a real job unless you're doing computing research, though an understanding of some of the fundamentals is useful: in particular, some of the less rigourous parts of computer science may be seen to include algorithms and data structures, an understanding of which is almost always a job requirement.

However, the "computer science" course offered in many universities is often in fact a software development/engineering/programming course, with very little theory and instead a focus on actually creating computer software. I posit that these courses are misnamed but it's so widespread as to be unavoidable.

In a University that offers both Computer Science and Software Engineering courses, I recommend taking the latter if you want to become a professional software developer. That being said, it's impossible to predict what some arbitrary company is really asking for on their job description. You'd really have to ask them, or just wing it.

In a University that offers only a Computer Science course, read its syllabus as you will probably find that it's really a Software Engineering course anyway, or is a mix of both disciplines and will still be useful to you in all likelihood.


What is the proposed penalty for students that paid an essaywriting service to complete their papers for them?

The official punishment already has a fork, being the first time and honest can help them to get a suspension closer to 6 months than to a full year. Also, you can help them get a speedy process, so the penalty starts counting as soon as possible.

It is important that there is an official record of this event, so they can't pull the "it is the first time, I promise" again. They now have a record, and they know it.

This said, I can't believe they didn't know they were doing something wrong, so I don't think one should be very forgiving.


Can someone explain what is being said here in color publishing in the American Mathematical Monthly?

By default, color figures will appear in color online and black and white in print. If you want them to be in color in print, you need to pay the rates they indicate. All their papers appear both in print and online, it is not that you choose one or the other. They also advice on the required quality (resolution) of the figures (regardless of color) and ask that if you use the default option the colir figures are understandable and meaningful when rendered in black and white.

Other journals have an option for slightly different figures for color and black and white, which may make things easier sometimes (for instance, in black and white you use different kinds of shading as different "colors"). It doesn't hurt to ask if this is also an option here.


Why do people in academia tend to write their email address with "(dot)", "(at)", instead of ".", "@"?

To avoid email harvesting spam-bots. (As if someone can't write a Perl script to make the appropriate substitutions.)


Should Figures and Tables follow a certain order or be at a specific location in a document?

There are many policies that publishers imply considering figures. The most common ones are:

All figures or tables (so-called floats) have to be numbered and get a caption.
All floats have to be placed at the top of the page, or at a page solely made of figures and tables.
All floats have to be referred in the text by their number.
Every float has to appear no sooner than on the page where it is first mentioned (i.e. if it's first mentioned on page 5, it shouldn't be placed on page 4, but it can be placed on page 6).
Numbering should be consecutive (i.e., no 1 then 3 then 2).
The first reference to the floats should be consecutive (with the exception where you basically only "confer it" (with "cf." or alike).

Some journals want you to provide figures and tables separately, some don't care, some have typesetters that do it themselves, some don't force captions, some allow in-text placement, etc. Just check what you have to do. If nothing is said, I recommend complying with the rules above.


How to explain blackballing by previous program in PhD application?

So here's what I see as the issue you need to overcome: If I'm told that a whole department or university conspired against a student to force them out, I usually tend to think that that is a silly allegation and that the person who makes this allegation is delusional. That's because it requires that a whole bunch of people (who also happen to be my colleagues!) would have had to act unethically, as opposed to just one person coming up with claims that have no factual basis but support their self-interest in believing that it's someone else's fault.

I have no idea which side is correct in your case, but as a member of an admission committee, a story like yours would certainly not make me excited about the candidate.

So you have two options in your explanations to the department you are applying to now:

You provide incontrovertible evidence that your claims really are what they are, and that the colleagues of the admissions committee members are all unethical blokes waging a vendetta. You may not have the space to sufficiently support your claims.
You make up some other explanation that sounds plausible for why you left that program. This may include "having had personal problems that you have since overcome through personal growth", or an admission that you really did something wrong but have come to understand by now why it was wrong and that you have learned from it. In either case, the explanation ought to be credible and probably ought to address the issue at hand in some way, though it can also be a bit nebulous.

The point I'm trying to make is that leaving a program, for whatever reason, carries with it a stigma that usually falls on the person who left the program, not the program itself. It is your job in the new application to address this.


What agreement will allow the publication of research based on (anonymized) private data?

This is a tricky question. There are established approaches for biomedical sciences, and they include specific consent forms. However, if you are talking about schools you might have minors involved, and this would much complicate any matter.

In the absence of a specific agreement between participating individuals and researchers, you need to obtain, in my opinion, the approval or waiver from an established institutional review board.

In addition, you need to be able to accurately deidentify your data, in order to make impossible to recognize the school or the subject. This is easier said than done, as just by looking at case mix, number of pupils, and type of subjects taught a very smart researcher could recognize one or more schools.

The safest way to address this would be to report only aggregate data, with effect weighs, such as done by the US National Inpatient Sample project.


This is probably best evaluated in the context of the individual institution. Standards differ and both the student and the professor should have a common understanding. Some places it is sufficient to give a good summary understanding of a deep problem or area of research. Others requires some new results, which may be minor or not. Some require publishable results.
So talk to some colleagues and get an understanding of the local culture. It is harder, of course, if you are an external evaluator. In such cases ask someone at the student's institution for a bit of guidance and ask whether you should evaluate based on their criteria or that of your home institution. Some places use external evaluators (also at the doctoral level) to assure themselves that their own standards are correct.
But at this level, the literature review might be more important than other parts, since one of the purposes of the MS thesis is to give the student some practice in carrying out deeper research where the lit review can make or break problem selection.
During the defense, you can be as hard as you like, but you need to evaluate answers for "reasonableness" as much as literal correctness. If the student can demonstrate a reasonable approach to something it may be enough. Requiring correct answers to difficult questions under duress is probably too much. But they should have ready answers to foundational questions, of course.


How do I cite a paper by a person plus a company?

In deciding who to list as the author of the paper, I wouldn't pay any attention to the copyright line.  Academic standards are not concerned with who owns the paper legally, but who actually made it.

For a recent paper I co-wrote, we signed over the copyright to the publisher.  So if you look at its copyright line, you'll see "American Mathematical Society".  That doesn't mean you should cite the paper as having been authored by the American Mathematical Society.

What name(s) appear on the article's title page, right under the title itself?  That's who you should credit as the author of the paper.


How much reputational value is added to a journal by being indexed in various abstracting and indexing (A&I) databases?

Reputation of a journal matters for two at least two things. The first is whether a library will subscribe to a journal. If you are looking for subscriptions, the more places you are indexed, the better. As your journal is open access, libraries are unlikely to pay money to subscribe, so I do not think this matters. The second is whether academics are willing to publish in the journal. I think serious academics choose journals based on what has been published in the journal in the past. Indexing is like advertising: it might make me think about publishing in the journal, but if everything in the journal is crap, I am not going to publish there.

As for faculty recognised journals, this sound fishy to me and I hope you are not talking about mainstream Western universities. Presumably, in these crazy faculties, if a researcher thinks your journal is good quality, they will fight to get the journal recognised regardless of where it is indexed.


Sounds like there was a conflict between the two behavioral researchers that left and the rest of the department about the direction of the department. The behavioral researchers lost. Such conflicts can be very nasty. The fact that the conflict was "resolved" by the departure of two faculty, points in that direction. In that case all remaining faculty will be very relieved that that is over, and the department is not going to start that all over again to accommodate a PhD student. In that case, you can either become a non behavioral researcher or switch to another department/university. It is unfair, but if my description of the situation is correct then those are the only realistic options.

You can ask the researchers that left if they know a department that fits your interests. Switching departments for this reason is perfectly acceptable, this is not your fault.


What are good principles for creating figures?

There are many books on this subject, as Peter Jansson points out, as it is something of an Art/Science in its own right.

However, if you don't feel like buying and reading one or more books on the subject, here are a few basic things that I consider both important, and easy to follow:

Consistency: While people can generally argue for hours over the merits of one colour scheme over the other, what is more important is that you use a consistent one for all your figures. Same goes for fonts and line styles. Also, if you're going to use blue squares to represent some thing in a figure, be sure to use blue squares for nothing else throughout your entire paper.
Conciseness: Try to reduce each figure to making a single point, i.e. try to think in terms of "what is this figure trying to say". It's tempting to pack more and more data into a single figure, but in the end this will usually dilute the message. One figure, one statement.
Clarity: Once you've decided what it is that your figure will say, remove anything from it that does not contribute to this single statement. E.g. do you really need every data point/curve you've drawn? If your statement refers to part of a flow chart or class diagram, do you really need all the other, less relevant boxes/labels/methods there too? Also, if the salient feature of your figure is not immediately clear, don't shy away from adding an arrow or something to highlight it.
Completeness: Holding the balance to clarity's minimalism, make sure there is also nothing missing from the figure which is needed for the statement you want to make. Figure axes labels are a favourite.

Funny how they all start with "C". This is not intentional.


How are some academics able to publish so many papers per year (e.g., 50+ papers per year)?

If you look at big names in science, you'll see their name at the end of a ton of papers (in many disciplines like chemistry and biology, standards can be different elsewhere) and this is why: providing the money and the lab space gives "senior authorship". Usually they review the drafts coming out of their labs/collaborations, along with guiding students/postdocs at the idea stages (which is considered worthy of authorship by NIH/NSF and journal standards). People with big labs get to put their name on the end of every paper generated from not only their lab, but from their lab's collaborations and whatever their grants funded.

Of course, some people are just crazy productive, but it's more likely that someone with tons of papers is getting a lot of them through their large labs.


What is an effective note taking procedure?

You can keep 2 sub notes per topic, one of them can be composed of excerpts lifted from books/internet, the other can be on your thoughts/summary of the material.
You can use a standard numbering scheme for both notes to keep track of content; e.g. in notebook 1, 1.2.4 can be Geography>Rivers>Nile in both sub notes.
Take care to paste searchable text and not images of text, for ease of later access.


How can I quickly learn advanced math concepts for my PhD in engineering?

The truth is: There is no magic bullet. You didn't learn engineering in two months, and you won't learn math in two months.
If there are specific mathematical concepts you need for your work, you can of course select books from that area. If self-study is not fast enough, you can also consider paying a tutor to walk you through material. But short of that, mathematics is like any other field and language: It requires years or studying and practice to become fluent and productive in.


In how much detail should one describe their past and projected future work for a junior scientist application to CNRS?

It may be dependent on the field and even on who is in the jury. In particular, the jury changes every few years and they decide by themselves what procedure they will follow to judge the applications.

Two of my colleagues who have been on the CNRS jury in different STEM sections in different years told me the following:

Your file will probably be assigned to one or two of the jury members who know most about the subject of your proposal. They will have an in-depth look at it and initially defend it on your behalf if they think it is worth it. These assigned jury members are the only ones that have to read your file. The others can choose to do so if they wish.

Besides this I can tell you the following from applying for a CR2 position myself (several years ago):

I described my past research, point-wise per university where I worked. This was 2 pages in total.
I described my research proposal in 11 pages. It included figures, preliminary data and references (much like a research paper). I described a short-term (5 years) research goal as well the many possibilities to expand the research later on.

This must have been reasonable because I was invited for an interview. Of course there are surely many other ways to do it that may be equally good or better, but all I can say is what I know, and wish you good luck (you will need it. It is well known in France that the jury often wants to fund around 20 equally good proposals out of ~200 applications, but they only have the money to fund a couple).


Is there any research direction which is closely related with map reading?

Since I'm not really sure what is available in the GIS field for research I won't try to answer that part, but when I was in university I did some consultant work for a GPS company called baseline geo.

They had me in to help with some database stuff, but much of what they did seemed to be making custom gps/gis maps for various clients. For example they might have a client who is a fisherman that needs a map of all his fishing areas, or where his traps are. Another example could be a wildlife preserve where they need to keep track of the animals with gps trackers in realtime. Either way it would fit both your skillsets. This is just a industry example and you seem to me more looking for a research position or ideas.


One line thank-you emails to lecturers/professors - yes or no?

It doesn’t matter all that much. But in general it’s good practice to thank people when they help you with something. And the extra workload imposed by dealing with such thank you emails is too insignificant to worry about.

When in doubt about these sorts of questions, apply the rule “professors are people”.


The genuine benefits I think all fall in the category of "distinguishing oneself" ... from other applicants to grad school, for example... much as with the IMO (Int'l Math Olympiad).

That is, an otherwise merely-very-good record (out of 100s?!?) can distinguish itself from others by a pretty-darn-good Putnam score. What does it "really" mean? Well, maybe not so much about higher-level mathematics, but the "exclusivity" of "having pretty darn good Putnam score" is undeniable. It's a thing that can be capsulized and "explained" to the public in PR, whereas it's harder to popularly explain progress or work in genuine mathematics (without severe distortions...)

Even at beginning-undergrad levels, kids who do at-all-well on the Putnam get substantial recognition within their math dept, often are treated more forgivingly of other quirks or inconsistent performances in routine coursework. (Given the stodginess of much of the routine undergrad curriculum, this is a good thing, since it is completely reasonable to not quite be able to consistently comply with the apparent requirements...)

The flip side is that there's a hazard here, as in all contest-math, that the quick gratification (if one receives it...) may make long-term study and research look less rewarding in comparison. In happy cases, one can "warm" to more prolonged projects, and more-delayed gratification. But quick contest-things like Putnam can be encouraging, and are noticeable pluses on a CV or grad school application. Just should not be over-interpreted.


There are professional/ethical rules at many universities relating to dating between students and staff, but these do not extend to imposing a permanent moratorium on dating between people who have previously attended that institution.  Essentially you are asking if there are any professional or ethical issues in dating another adult who has no connection whatsoever to your current employer.  I cannot see any issue.


open-note essay exam with the questions given ahead of time, what is considered cheating?

I think the other answer is a bit more scolding than is necessary.

Your professor has your email to your mom, didn't comment on it, and forwarded it to the person responsible for recording grades. It sounds like what you are worried about is not a worry to the professor, and it sounds like your professor is quite a reasonable person where technical issues are concerned (i.e., by accepting your evidence that the work was done).

If I were in your position I'd concern myself more with making sure your submissions are fully accepted in whatever software you are doing the submission with in the future - hopefully the software provides some sort of feedback or way to check.

You can also consult the course syllabus to see if there are any specific policies on what is allowed and not allowed for exams. I don't think you are crossing any lines by asking for proofreading help (presuming you are not taking a course where proofreading is a major skill that is being taught). I also don't think it is necessary to explain yourself to your professor unless you find a written policy that makes what you did clearly against the rules: by sending the email, you haven't made any attempt to hide what you did so there isn't really anything to come clean on.

Besides that, I would stop worrying about this and focus on any other studies and responsibilities you have. You're doing fine.


external grant on application for SLAC/PUI

Four-year colleges are extremely diverse as to their educational philosophies, attitudes toward faculty research, and financial stability. Do you want to
begin your career at a place that would react unfavorably to this potential
opportunity of yours? @AlexanderWoo's suggestion to 'outsource' the bragging
to your supervisor's letter of recommendation seems sound. But you should
be able to mention this research connection in your cover letter in an
unobjectionable way.

One hopes that cover letters will result in interviews. A common question
in interviews has to do with your ideas how to balance teaching and
research. Your continuing research connection provides a fine opportunity
for you to think how you will deal with that question when it is asked.

Professional travel and participation in conferences can be crucial to
your continuing professional development at a four-year college. You can
hope that the subaward can help with that. On an assistant professor's
salary, you may be very happy for the prospects for some additional
summer salary.

I wonder whether it's possible to know in advance if or how
you can use these funds for undergraduate research. Obviously, that
depends heavily on the nature of your research and on the quality and
interests of individual students. Not so obviously, it may depend even more
on whether the financial officer handling the subaward at the
four-year college is knowledgeable and flexible enough to handle
paying appropriate students out of subaward funds.


What is the effect of a journal going open-access on its impact factor?

A few years ago there appeared a nice article in Science:

Open Access and Global Participation in Science

The authors convincingly show that going Open Access widens the readership of journals and improves citation counts.

There are some interesting references in that article too.


No-paper-year in one's career and getting faculty position

With respect to getting an initial faculty position, I'm not sure that there really is a penalty associated with having "no papers" in a given year, especially with the vagaries of the publishing system. Is a person with one paper in two successive years a stronger candidate than a person with no papers one year, and then three or four the next? Or was it just that one paper took too long in review for one candidate but not the other?

I think one has to look at the overall record to make a fair determination. Besides, the relative significance of the articles will also play a role. One paper in a top journal in your field is probably worth more than two papers in a random low-impact journal.

Spend less time worrying about things that aren't in your control, and focus on what is: doing solid, publishable research and writing a strong application.


What versions of a paper do I still hold rights to?

After accepting the article, the journal will ask you to sign a copyright transfer.  This document should describe in detail what rights the publisher gets, and what rights you retain.  If it isn't acceptable to you, you can try to negotiate; your institution may have an intellectual property office that could help. If all else fails, you can withdraw the paper and submit it to a journal with different policies (perhaps even an open access journal).

It is pretty common for the author to retain the right to distribute preprints.

Congratulations on your paper!


Refering to the data of another study as a source of data for you work?

It is absolutely okay to use data from another publication for your own analyses.  Indeed, this is one of the main reasons why often raw data must be made public (unless there are specific contractual or ethical reasons not to). Once the data is published it is in the public domain that there is no requirement to ask permission and the original authors have no right to object to you using it - if they wanted other not to use it, they shouldn't have published it. You do need to cite them however.


My department is splitting. Should I be on one side or get a joint appointment?

As in comments, for sure avoid getting yourself in the cross-hairs of political fights, as a tenure-track person.

Next, indeed, having mixed allegiances is not a good thing when you come up for tenure.

Possibly "being interdisciplinary" is a good thing, depending entirely on departmental politics. I've seen it go both ways (in my U.S. R1 univ): evidence of not being a real mathematician [sic], or, alternatively, being one of a new breed of mathematician.