IEEE Transaction on Circuits and Systems Review Process I submitted a journal paper to IEEE Transaction on Circuits and Systems for Video Technology on June 12th. Today, after 40 days, I checked its status and it went from "In Peer Review" to "Awaiting Recommendation". What does "Awaiting Recommendation" mean? Also, Considering that it usually takes the review process about 100 days to finish, should I expect the manuscript to be rejected?

Thanks

It means that the reviewers already submitted their scores and now the paper is with the associate editor who will make a recommendation to the Editor-in-Chief.

The next step will be "awaiting final decision" which will be made by the Editor-in-Chief.

It will take probably a week or less to get a decision now based on my experience.

At this point, the paper could get accepted or rejected. You cannot infer anything from this status.

I recently submitted a TCAS journal paper and went through this process.


How important is it to cite the URL in bibliographies? We use MHRA Author-Date for citations, and the information about MHRA Author-Date online is usually contradictory and unhelpful. The guide I've always referred to from my university only specifies including a URL for electronic journals, as so:

But realistically, every journal I access will be online. I don't have print copies of the ones I need. Is it important to include a URL for every journal I access? I almost never see URLs given in real academic papers, so I'm trying to determine whether this is something I should include in my own work.

I haven't previously been penalised for not including URLs, but I'd like to know the general consensus on when you should include URLs in citations.

Including URLs and DOIs can be very helpful. For many if not most articles, a search for the title in a search engine is adequate to locate the paper. Though searching for the title takes longer than clicking on the URL or DOI in the paper, so it's still not preferred in that case.

Further, I've been surprised by articles which are not easily available in Google Scholar but are online. I've made quite a few interlibrary loan requests, later finding out that the entire proceedings of the conference I wanted an article from was online via the professional society which organized the conference. Google Scholar does not capture everything online at the moment. Many researchers do not know how to use the services of their library, so having the URL of the conference paper can be very helpful for many researchers.

Unfortunately many journals and conferences have their own citation style which may not use URLs or DOIs, but when you have the option, I think you should use it. My policy is to include as much helpful information as I can, and that often means more obscure citation information like OCLC numbers and ISSNs (which librarians can use to locate print only items).


How to paraphrase a paraphrased part? Lets assume that A wrote an article in 1999 and A included a part taken from B's source written in 1998. How do I paraphrase that part, and how do I cite it?

Like this; Blablablablabla blabla (A, 1999).
Or like this; Blablablabla blabla (B, 1998).
Or something different?

Why not include both?

Blablabla  (A, 1999, and B, 1998).


What does my colleagues' question really mean? I have been a tenured faculty member at a math department in the US for a few years. Recently two colleagues of mine asked (apparently independently) why I do not have PhD students. I honestly explained my reasons to each of them. Also I added that despite that, if it is necessary I CAN take students. Neither of them commented my answer.

Should I take these two questions at face value? Or did the colleagues try to let me know in an indirect way that I am expected to have students? Is there a way to make sure whether my department is unhappy that I have no PhD students?

It is impossible to read their minds, of course, but I think that they are at least expressing surprise that you don't have doctoral students. There may be a (very) mild rebuke in it, especially if it is thought to be a necessary element of the work.

But, there may be an implied warning, that, although they can't sanction you for not having students, there might be long term negative consequences for your career if you get by without accepting students. You don't say whether you have been asked to be an advisor and you don't say whether you have turned people down. If either is true then the warning, as well as the rebuke, might be a bit stronger.

But whether there are consequences or not depends on local custom at your place of employment as well as your other contributions to the profession.


How to build bridges between mathematicians, computer scientists and biologists? I am part of a recently founded laboratory in computational biology and we are trying to get all the parts (biologists, computer scientists, mathematicians, and so on) to speak the same language, or at least one we can all understand. To do so, we want to figure out some strategies beside seminars and weekly lectures.

I am not the only one who went through this challenge, see: [1]. For example, How to explain core biological concepts like evolution and selection to a mathematician? How to explain a mathematical formalization to a biologist (beyond the very basic models the majority of biologists know, such as predator-prey and logarithmic growth)?

There must be strategies; for instance, books that are in an effective middle (mathematically rigorous, but stepped enough that a biologist can understand it). This is a long term project and we need to devise strategies to progressively "retrain" ourselves. (Bibliography suggestions are welcome.)

[1] https://liorpachter.wordpress.com/2014/12/30/the-two-cultures-of-mathematics-and-biology/

Disclosure: I'm a mathematical biologist that came into it from the biology side.

I don't think it is necessary to retrain the biologists so they understand maths and retrain the mathematicians so they understand biologists, although these things should occur naturally to some degree with interdisciplinary work. Rather, I think it is important to understand the motivations of each 'type' and to tailor the language to the audience.

To grossly generalise, biologists are more interested in quantitative methods as a tool to answer interesting biological questions and mathematicians are more interested in the method/analysis used to answer that question.

So when mathematicians talk to biologists, they need to place less emphasis on the technical details of a model/analysis and focus on the general features. For example, if you are building a model to answer an evolutionary or ecological question, a biologist is more interested in the biological assumptions the model is making and whether or not the model is a reasonable abstraction of the biological system. In turn, the mathematician may need to explain why certain details of the system can't or shouldn't be included in the model (e.g. because they would complicate the analysis for little gain in intuitive understanding).

When biologists talk to mathematicians they need to frame their questions in a way that is conducive to a quantitative framework. If a mathematician is trying to build a model, they don't need or want to know every minute detail of a system. It's overkill and will just lead to confusion. What are the most relevant points? For example, if a biologist is interested in how the density of cows affects the density of grass in a paddock, then it isn't helpful for the biologist to give the mathematician a lesson on all the intricacies of grass growing and grass eating. It would be better if the biologist comes with a defined question, such as 'how does increasing the number of cows in a paddock affect grass regeneration?' and points out that the main elements in the system are 1. how grass grows (as some function of grass density) and 2. how grass is eaten (as some function of cow density).

If you want a book about mathematical biology that is written for biologists then I'd recommend "A Biologist's Guide to Mathematical Modeling in Ecology and Evolution" by Sarah P. Otto & Troy Day


Appendix in research paper? Should I include an appendix before or after the reference for my course physics project?
Thanks.

Appendices usually come before the bibliography (as you may need to cite things in the appendices). It's worth checking if your university has its own style guide, just in case.


What can I do with a book summary? I finished reading a textbook of about 250 pages. For my personal reference, I created a summary in note form of about 30 pages. Formulations are close to the original text with some variation on my part, and there are literal quotes. I don't consider it a replacement of the book (obviously?).

What can I do with this summary? Is it fair to give it to friends who are interested in the topic? What about students? Can I even publish it online?

I am aware that laws may play into this. The book has been published in the U.S., I live in Germany.

There are two questions, namely what you can do legally and what the community would consider acceptable.

Legally, distributing such a summary is probably a copyright violation if you borrow too much from the original; in the U.S., it would be considered a derivative work (the legal definition includes "abridgment" and "condensation" as forms of derivative work).  In that case, it would be illegal to distribute it without permission from the copyright holder.  On the other hand, you are not likely to get in trouble unless you offend the author or publisher.  The easiest way to offend the publisher would be if they view your summary as competition that might decrease sales of the book, but they might take a strict approach to copyright enforcement in any case (it depends on the publisher, and I would guess that a nonprofit publisher might be more understanding than a big commercial publisher).  In practice, the worst case scenario is probably being forced to take down any copies you had posted online.  You could be sued, but that seems unlikely to me.

The research community is likely to take a less strict approach than the law.  If you distribute the summary privately (e.g., just to friends or students), then nobody is likely to find out or care.  If you post it online, then it's more likely to attract attention, but it won't necessarily be negative attention.  That depends on how you've written it.

You should keep several things in mind to avoid causing offense:

You should be absolutely clear about what you have done: what's a direct quote, what's a mildly reworded version of the author's words, what's a summary in your own words.  You need to be careful about distinguishing your own interpretaton from the author's, and you can run into trouble in two directions, either by seeming to take credit for observations that are explained in the book, or by seeming to attribute your own ideas or organization to the author.  This is a difficult balancing act, which is easy to mess up.  Even if you are very careful, the author may still feel that you are distorting the emphasis on different topics, for example.
You should be very careful about correctness.  I would be unhappy if someone circulated a summary of a book of mine that had mistakes in it.

I would not recommend asking the author for permission, since that would put the author in an awkward position (of having to either endorse or object to your summary).  If the author discovers your summary and complains, then I feel professional courtesy requires you to make changes or take it down.

Personally, I would probably not post it online, but opinions could differ.


Is it normal to get an angry review that does not address any point of the work? I recently submitted a paper for publication. I was amazed to read the tone of one of the reviewers.
Previously, it was read by a pair of peers. I am completely sure that they would tell me if they found something wrong with the manuscript. Instead, their comments were positive.
This reviewer did not address any specific point of the work, just underestimated it as a whole. I could understand if his/her opinion was that the work is poor overall, but I perceive his/her comments as unnecessarily offensive.
As examples, the review contains the sentences:

It seems to the present referee that the author does not realize what constitutes the fundamental problem of molecular quantum mechanics as related to calculation chemistry.
The simple fact that the author ... and then he picks the "best" through statistics and numerology, reflects his attitude and respect towards the concept of THEORY.

On the contrary, very often my colleagues joke about (and many times we have discussed) my obsession with accuracy and scientific rigor. So, I am very convinced that the manuscript can not have an unusually high lack of rigor.
Although I have already published papers, I am inexperienced in publishing. This was the first time that I did the publishing process by myself.
I wish to know

Are these kinds of comments normal from reviewers? If so, what motivates them? I tend to think that the comments should be an objective appreciation of the work and not the author.
How are they perceived by the academic community?
Should I respond in any way?

Edit:
Just for clarification. I don't have evidence that the reviewer misunderstood the work. The only comment he/she made is the second quote that I previously included in the question. It is noteworthy to say that this point is far away from the central point or incumbency of the paper. The other thing he/she mentioned about the work is related to the title.

Getting angry reviews that, in your opinion, fail to understand your work is normal. It's sadly part of the territory.

It's hard to say why someone writes an angry review. Maybe they're an angry person, maybe they had a bad day and didn't like your work, or maybe they're one of those "tough love" people and get a little harsh when they disagree about something.

Your best approach is to ignore the tone of the review. If your paper got accepted, celebrate your publication. If you get a rebuttal, try to address their underlying concerns by politely pointing out why they are wrong and you are right.

If you are certain that your work is correct and the reviewer is wrong, think about what in your paper might lead them to believe what they did. If one person thinks you did something wrong, others might too. Consider rewriting that part of the paper to clear up any misunderstandings. It may be time consuming, but it will make your paper all the stronger in the long run.

Not to make any assumptions as to your research ability, but if this is your first time submitting a publication on your own, it is entirely possible that your technique is wrong. You can be rigorous in your approach and still do things incorrectly. It may be worthwhile to approach a more senior researcher that you trust and get their opinion on your paper with respect to the review.


Re-applying to medical school after misconduct I am a nontraditional applicant for medical school and wanted to ask questions about my application here. I was previously enrolled in another MD program. I had an undiagnosed disability that resulted in some abnormal behavior, including research misconduct (data fabrication). It led to me withdrawing from medical school program, but I have spent several years recovering. I have finished a PhD. I have published many papers including a few at top journals (Cell) since then.
I maintain a strong interest in academic medicine and I am ready to take another go at it.
How might my application be processed differently? How successful could an applicant like myself be? Do you have advice on how I can present myself in the best manner? Do I have a chance?

I think the road is uphill and very steep. Research misconduct is bad, but in medicine it is deadly. Literally deadly. You will need to find a way to convince people that the past isn't going to be repeated - has no chance of being repeated.
But it is difficult for a person to reassure others, on their own, that they will be good, now, where before they were bad..
I think your chances depend very strongly on what kinds of recommendations you can get from others who know you well and are aware of your past as well as your present capabilities and attitudes.
It may be that people will take your previous "undiagnosed disability" as an ameliorating factor, but even then will need assurance that it won't/can't return. Again, others can speak for you and if they are putting their own reputations on the line for you, can make the difference. But people will need to be wary, because of the possible consequences.
The same concerns wouldn't be there if you were studying, for example, CS or math. But medical research is qualitatively different.


How can I assess the quality of a paper outside my field? As per the title, I would like to determine whether a paper cited by a student comes from a reputable source or not, given that the paper's content lies outside my field. My first thought was to check the journal's website, as well as doing a Google Scholar search to see whether papers in other reputable journals cite papers from this one.

The particular case I am concerned with is a Psychology paper, appearing in AllPsych Journal [sic]. All the journal's webpage says is that:

  The educational articles and papers published in AllPsych Journal are written by mental health professionals, psychology students, psychology instructors, and other authors outside the field of psychology. *   They represent problems, solutions, and suggestions about everyday life and its relation to psychology.  For submission consideration, please contact us via our feedback form.

This seems dubious to me, but nonetheless, a Google Scholar search suggests that some reputable looking publications have cited works appearing in this journal.

I suppose I have two questions then:

Are there any other techniques I can use to assess the quality of journals outside my field for this purpose. Ideally these should take relatively little time.
Is this specific journal considered reputable in psychology?

This question concerns assessing the quality of papers outside one's field.

The question seems to be more leaning towards the quality of journals outside of one's field. Here's a brief list of pointers (some of which also appear in this question):

check if the journal has an impact factor (some good journal's don't and vice versa, so beware of false positives and false negatives)
find out the most prominent literature indexes in the area and see if it's in there (e.g., DBLP for Comp. Sci., PubMed for life sciences, etc.)
check the Australian ranking tables (don't take them too seriously: there is no such thing as a total ordering of journals)
check for journal citations in Scholar/Academic Search/Scopus
otherwise check paper citations in Scholar/Academic Search/Scopus
find out if the publisher is reputable (Elsevier, Springer, a good university press, etc.)
check Beall's list to make sure the publisher is not "predatory"
find out if the editors-in-chief are established academics (e.g., high h-indexes in Scholar)
talk to experts in the area
apply common sense.

The last point is particularly important. Though it is easy to discover if a journal is excellent or terrible, in between those extremes, there's a lot of grey. For example, new journals may be much-needed and drawing quality work from quality people, but they won't have a high h-index or an impact factor, etc.

For those grey areas, talking to an expert who knows the field is important.

  AllPsych Journal

This doesn't seem to be a formal journal, but rather an informal way for authors to publish educational articles online. All papers are published on the web-site, there's no mention of an editorial board, a publisher, a means of submission, etc.

Of course, this says nothing of the quality/utility of the papers published there: just that it would probably not count in academic circles as a "traditional journal".

For the quality of a paper itself independent of the venue, check how many citations it has in Scholar versus it's age, check the nature of those citations, check the h-index and background of the authors, etc. (Of course these methods are only an approximation for reading it and making up your own mind as to its quality, but since it is outside your area ...)


Useful software resources for reviewing papers I have a paper for review and I would like to include comments (on clarifications/suggestions/errors) over specific paragraphs or statements.

What are some ideal software resources that could help reviewers? I would prefer them to be Linux-based.

If you have access to the LaTeX source, there are a number of packages that will help you. Some include todonotes and fixme.

However it's more likely that you have a PDF only. In that case, you need a PDF annotating package. A free cross-platform solution is Xournal, which runs on windows/linux (and maybe Mac).

If you're on a iOS device, then Goodreader is a nice app that does annotations.
There's always Adobe Acrobat as well. Both of these solutions are not free though.

Update: (by @atiretoo)

One issue to be careful with providing comments on a pdf or other document is maintaining anonymity. Adobe Acrobat (and probably other software), automatically flags your annotations with information about you unless you are careful to remove that from the document before commenting.


Should I provide specific acknowledgments in addition to a general acknowledgment? As a student I wrote a paper for a course. I am now preparing the paper for submission to a journal. My teacher will get a general acknowledgment for the discussions we had on the topic as a footnote on the paper's title (as is the custom in my field). There are a couple (~3) very specific pointers the teacher gave me, such as a relevant piece of literature. These are not vital for the flow of the paper but are useful pointers for the reader; they appear in footnotes. Should I add a sentence to such a footnote such as "I am grateful to John Doe for this reference"? Or is it kind of implicit in the general acknowledgment at the start of the article that the acknowledged persons have contributed such details?

I've often seen specific points included along with general thanks in a single footnote, something like "I thank my supervisor, John Doe, for numerous helpful discussions and, in particular, for calling my attention to reference [7] and for simplifying the proof of Lemma 2."


What's the proper way to (APA) reference a settlement agreement? I want to reference an exhibit from the following document (it's been split into separate parts):

Exhibits:
https://targetbreachsettlement.com/Portals/0/Documents/Settlement%20Agreement%20Exhibits.pdf

Agreement:
https://targetbreachsettlement.com/Portals/0/Documents/Settlement%20Agreement.pdf

Part of a class action lawsuit settlement agreement proposal / notice.

Court: UNITED STATES DISTRICT COURT
District: DISTRICT OF MINNESOTA
Case & MDL: 14-MD-2522-PAM/JJK
Document: 358-1
Filed: 03/18/15

Pursuant to: 28 U.S.C. § 1715

But I'm unsure of the proper rules to format such a citation.
I can't seem to find any information regarding the APA style for referencing settlement agreements and/or proposals in particular.

PS: More info on the settlement can be found here:
https://targetbreachsettlement.com/mainpage/Home.aspx

According to the table of contents (pdf) for the APA 6th edition style guide, the APA defers reference styles for legal materials such as court decisions, statutes, legislative materials, and administrative and executive materials to The Bluebook®, which requires a purchase.

However, the APA Style has a blog, which has about 10 posts tagged legal, which gives guidance for a generic Name v. Name court case as follows:

  Name v. Name, Volume Source Page (Court Date)
  e.g.
  Lessard v. Schmidt, 349 F. Supp. 1078 (E.D. Wis. 1972)

And for the in-text citation:

  Name v. Name (Year)
  or
  (Name v. Name, Year)
  e.g.
  Lessard v. Schmidt (1972)
  or
  (Lessard v. Schmidt, 1972)

A settlement is just a specific type of court decision, is it not?


Transcript error, college unresponsive - how to handle? I applied to graduate school this spring, and discovered that my undergraduate transcript has a substantial error: it omits one of my majors.

I contacted the university registrar, who indicated the omission was caused by a "system" issue that prevents listing a 3rd major if the student thas one. (They said their new system won't have this issue in the future, which doesn't help me at all.)

The registrar also pointed to a note on the bottom of the transcript that says I was "approved to pursue" the three majors. But, the comment is dated 2 years before graduation, and "approved to pursue" doesn't mean "completed," so I don't think this is sufficient, especially given the conspicuous blank spot next to where the third major would be listed.

Since replying to my first email right away, the registrar hasn't replied in weeks. They have not indicated that they plan to correct the issue.

How do I get the college to correct my transcript, preferably soon enough to submit to the graduate school?

A couple of suggestions. First, I think that having three "majors" is pretty rare, so a system error omitting the possibility would be easy to make.

Second, I doubt that if you are good enough, then the third major isn't going to put you "over the line" in any application when two won't. (Caveat below)

Third, just explain it somewhere else in your application materials, such as your CV or cover letter, and also ask that the registrar will back you up if asked. Alternatively, have a faculty letter writer make it clear on your behalf. It is best if someone else, rather than yourself only, makes the statement so that it gains credibility.

Caveat: If that third major is your specific field of interest in graduate school, then you may need to have a letter from the registrar as part of your materials. Though, if you are in the US, even that probably wouldn't be essential as it isn't an absolute requirement that you continue in grad school in the studies you did as an undergraduate. Other places are a bit more strict, perhaps.


Re-applying to the PhD Program after Illness I started in a combinded MS/PhD program and was on the PhD track, but for mental and physical health reasons I had to switch to the MS track. I had not yet made it to the research part of the program, so I don't have an adviser.

I really want to get my PhD, and the (then) graduate director in my department told me when I made the switch that I'd be able to apply to rejoin the PhD program after getting my Master's. I'm getting my Master's in the spring, so I'm working on the application now. I just don't quite know what to do with the essay.

The essay is supposed to be about my research interests, career goals, and reasons for choosing the program. I think my health issues will be sort of an elephant in the room if I don't say something about them, but I'm worried that saying too much will make me look like a weaker candidate than I am. I've had these health issues for most of my life and will continue to have them for the foreseeable future, but they're more under control now than they were a year and a half ago when I made the switch.

How much is too much to reveal about this whole situation? How much is too much of my essay to spend on it? Is there any way to spin this situation in a positive (or at least neutral) way?

(I wasn't sure how much detail to include in this question, but I'm happy to go into more detail if it would help.)

I'll slightly replicate my answer to this question: mention this, but don't be too melodramatic. You have dealt with an illness that was out of your hands and got a handle on it. This is not something that a reasonable admissions committee will see as a point against you, but be sure that they understand you are not looking to get accepted because of your illness. It is also might be illegal to discriminate against you because of illness, depending on its nature and the country you're in.

Good luck!


I changed a word from a source, how do I cite it correctly? I'm writing an analytical summary on Meditation II of Descartes from the compendium we have been given at school. We have been told to use this as our main source. Nevertheless, there is this specific part in section 12 of that meditation which I don't quite agree with:

  [...] something extended, flexible and movable.

As per Marleen Rozemond in Descartes' Dualism [Source] in page 93, this is a poor translation.

The reason I looked this up was because the word didn't quite fit the context, and then I saw other people had translated it as mutable, which is also a correct translation for the french/latin word.

Complaining about the poor translation in the summary makes little sense to me, as it's not part of the context, and I have a limitation of 600 words to care about. Nevertheless, I am citing from the source of a document which uses the "movable" word instead of the "mutable" word.

How should I approach this? Should I make a postdata explaining why I have done what I did?

For reference, I am using the APA referencing style.

Write:

  [...] something extended, flexible and [mutable].

You might like to elaborate in a footnote, e.g.,

  The compendium poorly translates original word as movable, but mutable is more appropriate, as noted by Marleen Rozemond in "Descartes' Dualism," page 93.

(Depending on the style, you might like to replace in "Descartes' Dualism," page 93 with a citation.)


Helping With Programming Q's I am a mostly self taught programmer. I read books and make things in my spare time. I want to go back to school soon for a CS degree and one of the ways I stay sharp is to help with stuff that's within my ability on Stack Exchange or Reddit. For example things like "How to print the reverse of a string" or whatever.

My question is that a lot of schools have policies against letting your work be used in someone else's assignment. As far as I'm concerned helping out on internet forums is just doing a public good but are there schools that see it differently? Could that come back to bite me when I'm enrolled somewhere? Should I hold off from answering questions until I'm through the educational system? Or is it a baseless concern?

Answering Questions from others on stack is one thing which is fine - it is outside your course.

Posting an assignment to get it solved for you or posting the solved assignment for others is not...

Students have long helped each other, by working through problems and applying the process etc but NOT by handing over a complete solution to a graded assignment - that is cheating and most institutions will be after both the cheat and the person helping them...


Does a PhD thesis have to be theoretical? I already asked a question in the past about the requirement to join a PhD program, but I am now wondering what makes a PhD thesis what it is. As seen on a lot of different websites and for example on this post, one of the goals of a research thesis is to contribute to human knowledge by researching and documenting said research.

My personal goal is to contribute to human knowledge, and I feel like some researches in computer science (from different offers and thesis I saw) don't create knowledge, but are rather focused on creating a product that could as well be developed by any company with a research and development field. Because of this, I have trouble visualizing if there is really a knowledge creation in those PhDs, as I feel like those are not in a "science" related field but rather in a technical field (even though it's in the name "computer science").

Just to be clear, I'm not in any case questioning the benefit those research made, I think I am misunderstanding something in what a PhD is, and want clarifications to make sure I'm joining a PhD program with the right state of mind.

Does a PhD thesis have to be theoretical ?
If not, what is the benefit of developing a technical product in a academic environment rather than in a private environment ? (for both the doctorate and the academic world)

While doctoral degrees in some specialized fields have a different designation, you can get a PhD in many non-scientific fields. English Literature or Philosophy to name just two.

But even in those other fields, a dissertation is normally theoretical in some sense appropriate to that field. Many are more like mathematics, actually, extending a thread of thought, rather than gathering data and applying statistical methods or other tools.

I question the premise that most CS dissertations are "product development" actually. None of them in my particular purview have been. All have contributed to knowledge, though that knowledge can often be commercialized in some way.

Some CS research in the language area results in the development of a new language, of course, but that doesn't mean a commercially viable language. They are normally written to test out some ideas of semantics or implementation and so really do extend the range of human knowledge.

But CS, in general, has been concerned for a long time with building things, so research that is closer to the "real world" is natural. But companies find it difficult to justify doing "pure research" that can't be turned into a revenue stream in a predictable way. That sort of thing is left to universities and to doctoral students.

And, of course, there are many CS topics if that is your chosen field. You can be as theoretical as you want to be. Some subfields are nearly indistinguishable from mathematics.


Is there any advantage of putting source tex file on arXiv? I don't really like other people seeing my source file. Are there good reasons to upload the source file (.tex) on arXiv over uploading just the PDF?

Arxiv mandates uploading the source of any PDF file generated from Latex code. You will not be able to upload only the PDF version in this case (unless you succeed to game the system).

Why do the require the source? This saves quite a lot of space (50k-100k source vs. 500-900k PDF) and there are some additional reasons. As the other comments mention - the full explanations are in http://arxiv.org/help/faq/whytex


When is applying for a postdoc too early or too late? I am in some kind of conundrum. Currently I am a grad student in Germany. Things are reasonably fine, but because of some bad luck I am not 100% confident that I will finish my thesis at the end of this year (as planned). I might need some more months (maximum 3, I hope), which in the worst case I could finish my work even without a salary. Still, I want to try and get done as close to the end of this year as possible.

Some sources (the Internet generally) tell me I should soon start searching for a postdoc position, especially because I am for personal reasons bound to a fairly specific location in the UK (not where I currently live, but where my significant other lives).

So what do I do? Start looking and applying for postdocs now, wait three more months (to give me the same leeway but with the added three months) or wait until I am actually done. Waiting until I am done is probably the morally right thing to do, but if it is taking me until March 2018 to finish, sustaining myself for potentially some additional months of job search will be financially problematic.

If I start searching now (or soon), what can/should I tell potential advisors? How common (if possible at all) is it to set the start day "somewhere between January and April next year"? I have a feeling this would hurt my application significantly, in favor of applicants that have a more well-defined timeline. What is the most common thing to do? I have seen others postpone their graduation, but most of them were planning to leave academia after that anyway, so had to prepare for a fairly different hiring process.

I am just worried that even if I find a position quickly after finishing, the start day might be months away and that would still leave me without any salary for a lengthy period of time. Any tips and experiences would be appreciated.

Actually, what you described seems very familiar and I'm sure it's the same for a large fraction of Ph.D. candidates. So relax a bit :-)

But - I have to say that, reading between the lines of your post, I'm uncertain that you should even be searching for a post-doc at all:

You express a desire to find employment that sounds at least as significant, if not more so, than your interest to continue your research.
You are not speaking in terms of what you want to do research-wise but where you need to be geographically.

1. First figure out / soul-search whether what you really want is to find a post-doctoral research position.

Are you absolutely sure that you want to pursue a career as an academic researcher, right now? Are you sure a stint in industry (or other non-academia employment) is not something you would find satisfying, interesting, relevant?

(To Op, specifically:) Maybe you are and your motivation and orientation is perfectly sound, but I'm getting a 'vibe' that this might not be the case.

If you're certain that a post-doc is indeed what's right for you to do next, then

2. When the conclusion of your Ph.D. duties is in sight, it is time to start searching for a post-doctoral position.

The research groups / departments with which you'll inquire about open positions are very well aware that prospective availability is sometimes up for change, particularly in your case. Do not hesitate to say "I expect to conclude my Ph.D. in between X and Y months". Now, it's possible that someone might tell you "I need an extra researcher who's willing to start yesterday to get ahead on some funded research project" - and won't accept you on that account. But, well, that's life - and they won't think less of you because you're not done yet; don't drive yourself mad in some impossible race.

3. Sometimes you don't find a suitable post-doc position even if you search diligently and on time. Think about contingencies.

Academia is never very well funded, positions are scarce, and in your particular case there are some tight constraints. I know this is not very encouraging advice, but it's better to recognize this possibility and learn to live with it than spending the last months of your Ph.D. in dread of it being realized. That's really not a good emotional state to be in - and it won't help your work, either.


Writing affiliation as a high school student I want to send an article to a math journal. As with many others, that journal wants a cover letter, which should include the author's affiliation.

I'm still a high school student and my school isn't in the U.S.
How should I write my affiliation?

My school's name is hard to translate to english, should I write its name as in my language? And, when I'm writing my school's adress, should I write it as in my language?

(If you see a grammar mistake and edit it, that would make me really happy.)

First of all, I'm impressed by your ambition here.  And I should warn you not to get discouraged if the math journal ends up rejecting your submission.  Do you have guidance from someone experienced in academic publishing, to help you through the process?

As @Nate-Eldridge pointed out already, you should simply state your affiliation, and the country doesn't matter.  But I will add:

If the submission is not double-blind, there is a risk that people will take you less seriously when they see the affiliation.  There's not much you can do about this, I think.
High school students do contribute to academic publications, though I was surprised to see this.  One was a coauthor of a paper in a very strong CS systems conference this year (others were at a university).

Good luck!


How can I narrow down my CS research interests when my undergrad institution doesn't have a large CS department? I am currently a 4th year CS senior from a smaller liberal arts school with a small CS department.  So far, I've pursued a few semesters of opportunities to do one-on-one research with my head of department, but these research opportunities have been limited to his Post-Doctoral field of work (classifier algorithms and biometric analysis).

I was hoping to get a better idea of other graduate programs that schools offer before attempting to apply to graduate school in a month or so.  Is there a good way to go about this given that my school's departmental resources are so small?

I'm in an analogous situation. I'm one year out post-undergrad, and am applying to programs this month as well. I also came from a relatively small program, and didn't have a great idea of what direction I wanted to go in.

What I did (and this is perhaps not the most efficient), is I went to the webpages of some schools I was considering, and looked through all of the CS faculty's personal pages. Be forewarned, many of them are badly designed, but a lot of them also have a short description of what the professor's research is about, in their own words. From these descriptions, I started to get a better idea of what did and did not interest me, and it gave me specific people to mention in my applications.

Of course, this approach relies on you having a relatively small list of schools that you're considering. If your list is more than 20 or 30, I could see this becoming too much, or if you have no idea where to start, it might also not be great.


What should I say about a publication that I have not contributed to? I am currently an undergraduate student and I am applying for research Masters/PhD in the US. I joined a research group before to help out on a part of a project. My coworker in this group, a PhD student has published a paper afterwards, which is irrelevant to the work that I have done, but since I have worked in his group, I was added to the co-author in his paper. I did not ask for it, but anyway, I have the publication, and I have to mention it in my application.

My fear is that, if, during the interview, I was asked about the publication, should I just say that I did not contribute to it? I do not want to lie anyway, but would that hurt my previous research group since they have added irrelevant people to the paper?

I do not think it is uncommon to have a coauthor that is not relevant to a project in my country. However, I am a bit afraid if they would take it seriously in the US.

Cut shortly, use it to your advantage, but be honest. If you're in the project, that means you should know the aims, tasks and problems of it. Even if you did not contribute to the article directly, experimental or literature research is still relevant and could be used by your colleagues. Try to figure out to see it clearly and be able to explain.
And of course if you include this publication to your CV, you should know as much as possible about the topic. That could be educational for you as an undergraduate.
Good luck!


How to overcome lacking teaching experience for admission to Master of Education I'm nearing the completion of my undergraduate degree in mathematics. The handful of experiences I've had tutoring students are among the most satisfying ways I've applied math to real problems. My academic record is good but not honors material. I'm convinced that teaching mathematics at the secondary school level is an excellent way to apply my math degree where it's needed.

I am applying to a 13-month Master of Education program at an American university. Through coursework and internships teaching at a local school, students are fully prepared to certify to teach Secondary Education.

This is a highly selective program.  Applications, essays, PRAXIS scores, and interviews are all part of the application process.

Does inexperience teaching totally defeat one's chances of admission to an education program? This may also apply to teaching at a university.  Is there any way to convince them to see past the inexperience? How does one overcome this?

Does inexperience teaching totally defeat one's chances of admission to an education program?

No.

I have direct experience in your situation: I entered a MEd teaching program at a top-5 U.S. university with zero teaching experience.  I did have five years of military experience, and I emphasized the leadership skills I gained from that, as well as the personnel management skills I learned. My college grades were mediocre (3.2 GPA in Electrical Engineering), GRE scores were decent but not phenomenal, and I entered the program to be certified in high school physics.

  Is there any way to convince them to see past the inexperience? How does one overcome this?

You are in the enviable position of wanting to teach math, and STEM teachers are highly sought-after and needed right now. That isn't to say that you won't be competing against highly-competitive peers, but for what it's worth you will probably be competing against fewer peers.

To overcome the lack of teaching on your resume, you should highlight any experiences you have had working with students or children (e.g., did you TA a class? Were you a camp counselor? Think outside the box to find something relevant, but don't stretch it too thin -- e.g., lifeguarding probably wouldn't quite fit the bill, but mentoring junior acolytes at your church might). You should certainly discuss why you enjoyed the tutoring, and how that informed your decision to pursue a teaching career.

Furthermore, you need to demonstrate your passion for teaching -- talk about the middle school algebra teacher who opened your eyes to the beauty of mathematics, or the calculus teacher who gave you the first real taste of a formal proof. Talk about why you love mathematics, and how important you think it is for upcoming generations to get quality mathematics teaching.

The admissions committee needs to see something special in your application that will make you a great teacher, and personal experience means a lot -- do you have 26 cousins that flock around you during family reunions to hear stories (you're a great story teller! This is a fantastic skill for a teacher!). Did you wake up every morning in tenth grade salivating at the thought of fifth period trigonometry class? (you've got legitimate passion! [and may be the only person in the world who loved trig at that age...]).

MEd programs are one of the few programs where I believe a well-written personal statement can truly make a difference in your application, so make it good. Have one or more people read your statement and give good criticism. Write it one week and re-read it a week or two later, and edit it if you don't see the passion coming out. Ask your reviewers to look for passion (or, rather, ask them after they've read it what they thought, and if "passion" doesn't show up in any reviews, re-write it).

Your letters of recommendation are extremely important, as well. You should make sure your letter writers know that you are applying to teaching programs (not research programs), and that's what you would like them to focus on. You don't want a letter that says, "X is a brilliant mathematician who can focus intently on minute details of complicated mathematical proofs for hours at a time. He has the potential to produce award-winning mathematics."  What you want is something along the lines of, "X was one of my most passionate students, who has a knack for coming up with succinct, meaningful explanations for complicated mathematical topics. I routinely saw him during office hours where we had enlightening discussions about the course. I learned as much from him as he did from my own teaching."

Your interview is obviously important, too. I suggest preparing something to teach for five minutes (high school level--if I were preparing something, I might choose compound interest -- you can teach it in about five minutes to a willing audience, and you end up with the beautiful definition of e in the end), and practicing it on someone. If I were interviewing candidates, I'd ask them to teach me something (maybe something particular), and if you have something in your back pocket that you've practiced, you'll be ready for the question if it appears. Be prepared to discuss why you didn't have the opportunity to teach (what did you do during your summers?  Were there TA opportunities that you could have taken?). Obviously, do a lot of smiling and be as personable as you can without going outside your normal personality. Have a very succinct answer to why you believe you will be a great teacher -- 30 seconds that will wow an interviewer. (one further tip: if you have an interview with multiple people, remember their names and address them with their names during the interview--this can make a very good impression).

Good luck!


Writing and publishing a technical note about an R package I prepared a developmental version of an R package specific to my field of study. Now I would like to encourage more people to use it and contribute code. My plan is to release a technical note describing the package in a field-specific journal. MATLAB is dominating my area of research so I don't think that usual R-specific channels (CRAN or The R Journal) would be appropriate to reach this scientific community.

However, I could not find R-specific guidelines to releasing technical notes about R packages. This relates not only to this particular journal but scientific journals in general.

To be precise, I would like to know:

it is a common practice to write a technical note about a package that's only available on GitHub (no CRAN version yet)
at what stage of development the package should be so that it can be
written up as a technical note
are there any guidelines to publishing technical notes about R packages

Can you think of any other considerations to keep in mind?

Thanks

I am aware of the submission guidelines to The R Journal but I think that my package is not aimed at the general public and it's at a rather early stage of development.

This question was previously posted on StackOverflow but the moderators suggested that I post it here.

Obviously you will need to do a bit of work to find the most appropriate journal for your field, but publishing an article about an R package is completely acceptable. In fact, "An R package for reading EPANET files" by Eck was published in Environmental Modelling & Software which describes itself as follows,

  Environmental Modelling & Software publishes contributions, in the
  form of research articles, reviews and short communications, on recent
  advances in environmental modelling and/or software. The aim is to
  improve our capacity to represent, understand, predict or manage the
  behaviour of environmental systems at all practical scales, and to
  communicate those improvements to a wide scientific and professional
  audience.


How to contact a foreign professor and ask him to cooperate in a research work? I have completed my Msc. degree and I proposed an invention based on my thesis subject before I had defended my thesis but I have not registered it till now. My professor offered me to fabricate the device that I had proposed, both with him and a professor at a foreign university. He told me that I needed to form a research group consists of 4 people, we two and a professor and a student at a foreign university. I am required to do the half of the job along with my professor and the other half at the foreign university which I am going to find. The whole process is supposed to take 1 year and is fully funded. At the time I am planning to apply for a Ph.D. position at a foreign university too. Can I apply to the same professor for a Ph.D. position who I am going to work with him on this project? Is it constructive and has a positive effect on my application process? If yes, could you please tell me how can I explain the situation to a professor to persuade him to work with me. I mean let me know how can I take the advantage of this project on my application process. Any advice or possible email content would be welcome.

Thanks in advance

Can I apply to the same professor for a Ph.D. position who I am going to work with him on this project?

Yes, at least at US institutions this would not be a problem. I don't know of any reason why it might be problematic anywhere else.

Is it constructive and has a positive effect on my application process? If yes, could you please tell me how can I explain the situation to a professor to persuade him to work with me. I mean let me know how can I take the advantage of this project on my application process.

As I mentioned in my comment above, it's often an advantage to have previously contacted a potential advisor and discussed working with them. Many prospective graduate students "cold email" professors to express interest in working with them, discuss potential research projects and--usually the primary reason for emailing--to make sure the professor recognizes their name and remembers them when actually reviewing applications.
Having a particular topic or project in mind tends to be a positive--as long as it's something the department or professor you're applying to work with is interested in. The only downside to having a specific project in mind is that it might be limiting if the professor isn't interested in it and you haven't expressed any interest in things they DO want a student to work on. That seems unlikely if you're selecting them as a potential collaborator because their work aligns with your project, but I'd make sure to explicitly state that while you want to work on this project, you are also interested in ___ (things that they study that you would be interested in doing for your PhD--read their webpage to get an idea of their broader research interests and ongoing projects).
In general, when emailing potential advisors/collaborators, keep the following rules in mind:

Be polite and respectful! Don't ever come off as arrogant/demanding/expectant.
Mention who you've worked with--you'll gain credibility if they know your advisor, respect your institution, etc..
Demonstrate that you've done some background research into what they do--mention work they've done that interests you, papers you particularly liked, etc.
What can you offer to them or their lab? Describe your background, strengths, interests, etc... show them (without being arrogant!) why you think working with you/taking you on as a student would be worth their time.
Show your enthusiasm!
Try to keep it as brief as possible while still including all relevant information--be succinct. Professor are extremely busy and get about a zillion emails a day. He/she will probably not bother reading your email if it's super long. Also on this note, make sure you include enough info to snag their attention in the first few lines, since that may be all they read if they aren't hooked by then.

An example email would be something like the following (reorganized/worded as needed):

Hi Professor ___,
I'm currently finishing my Msc. degree at [institution] with [your current Professor], and am planning to pursue a PhD in [field] this coming [whenever you'll be applying]. My thesis work has been on [describe your research].
I'm contacting you for two reasons: first, I'm considering applying to [institution], and was wondering if you are currently accepting new PhD students. I'm especially excited about your work in [topics], and [describe any particular topics where your interests intersect with his/her research, strengths you have that would be particularly helpful in pursuing this/these avenues of research, etc.--e.g., I think my background/experience in __ would be an asset in studying __].
Second, one of the outcomes of my thesis work is [describe your ongoing project], which I would like to work on as a [side project/chapter/Phd project/etc. depending on the scope of what you have in mind]. We have 1 year of funding to complete this [maybe include more details--mentioning the funding is very important since it means you come with support!], and are currently looking for collaborators to [describe what you need them to help with]. [Explain why you think he/she would be the perfect collaborator].
I'd love to discuss potential PhD research topics and collaborating on our __ work if you have time in the next [give them a reasonable but discrete timeframe--few weeks is usually good].
Thank you for your time,
Arash


Why are positions in math so hard to come by nowadays? Whenever I've heard math professors talk about job prospects in academia, they indicate that the job market has gotten much tougher over the years. Is it true that it is harder now than it used to be to find a good position? If so, why is that?

The number of tenured/tenure track faculty positions in the US has been on the decline in recent years, partly because of a substantial increase in the amount of teaching done by contingent faculty (adjuncts, full time instructors who aren't on a tenure track, and graduate student TA's.)

The number of PhD graduates in mathematics has been fairly steady at around 1200 per year.  Most of these new graduates want to ultimately obtain a tenured faculty position, but there are only about 700-800 such positions available every year.

There's a clear inbalance here between the supply of new PhD's in mathematics and the number of desirable faculty positions that they can chase.

A good source of statistics on this is the annual survey done by the American Mathematical Society.

http://www.ams.org/profession/data/annual-survey/survey-reports


Advisor suggesting a change in the PhD research direction resulting in less theoretically intensive thesis. I am worrying about the implications I joined for my PhD in mechanical engineering in a Canadian university almost 3 years back. I had completed the necessary coursework and preliminary exam last July. My advisor had approved my research proposal to develop a numerical procedure to predict the damage behavior of composities during a complex loading condition. It is a really challenging topic and I wanted to give my best in solving the problem. My committee members were also satisfied with my research proposal and projected timelines.

Howevever, till now, I have not been able to get any substantial progress on the research topic. I am facing a lot of theoretical issues and my research topic is very loosely related to the expertise of my advisor. As a result his technical suggestions are not quite relevant and helpful. There's no one in the department who can help me in this regard.

Last week, my advisor suggested to change my research topic to a different one within the realm of the grants objectives. The modified researh area won't require the development any numerical procedure. Instead I will be using a commercial software with inbuilt procedures to get the results. I won't be able to publish in a reputed numerical or theoretical journals and  will have to settle for decent application oriented journals. I don't want my PhD to just be one where I pressed some buttons to get the answer. I wanted it to be rigorous.

I am not sure what would be the implications if I accept to my advisors suggestion. On one hand the modified direction would guarantee atleast 3 decent publications. On the other hand, I don't know if I will be able to solve the theoretical problem soon enough to generate results. But if solved, will lead to a theoretically intensive paper and a lot of learning opportunity as a researcher.

What should I do? I will be funded for 5 years. And I would like to stay in academia in the future.

I'd suggest, pretty strongly, that you go with your advisor's guidance and turn the original project into a longer term goal. Your research career needn't end with the doctorate and it would be good to finish with some work done on a difficult future project.

But the short term goal should be to get out the door with good letters of recommendation and enough of a push to get you into academia. What you can do after that is up to you and the possibilities you can bring to bear on your research.

For what it's worth. I have a friend who is a reputed computer scientist. Top education, works in top level industrial gigs. But he also writes poetry. In fact, for more than ten years he has written a poem every day, without fail. The deadline for the poem is strict. But he described his methodology to me as something like, starting out with high standards and expectations for the day and continually lowering them until he has something acceptable. He gets the job done, and saves the rest for another day.


Completing undergrad in 4.5 years I'm currently in my junior year, doing CS and math double major. For the next year, I have the choice of spending a semester abroad at a top 20 CS program. I have completed nearly all of my required courses, except one.

The thing is that, if I cannot take an equivalent of that course in the semester abroad, I won't be able to graduate at the end of four years, I will need an extra semester just to take that.

On the positive side, in the semester abroad, since I do not have much course requirements, I will be able to spend time doing research (the school I will be going has undergrad research program).

So, my question is, how much one extra semester (probably with only one course in it) would affect my chances in graduate school admissions (for US)?

Note: I know that the extra semester would cost me a whole year due to the admission cycles. In that semester, I can stay at my current home instution (maybe again working with a professor), because double major students are allowed/expected to complete in 5 years.

Extra time you spend doing research will almost certainly do more to help your chances of admission in graduate school than taking >4 years to graduate will hurt - especially if you don't have other strong research credentials (with the caveat that admissions committees are full of people, and you might run into one person who for some reason decides that taking >4 years to graduate is the mark of a failure - it isn't really worth your time worrying about each of these possible types of people).

However, you should keep in mind that graduate admissions, particularly for PhD programs in the US, typically occur only at one time in the year, for fall semester, so you should have a plan for what you intend to do the rest of the year. If you can get hired in a university lab in your field of interest, that would be ideal for graduate admissions.

This answer is based on my experience in Biological/Biomedical Sciences in the US, and advice may vary by field and country; I also have in mind primarily PhD admissions.


Repeat acronym in conclusion Can I use acronyms and abbreviations in the conclusion of a scientific paper or should I avoid them?

Even though the main idea of acronyms and abbreviations is to avoid repetition, my impression is that acronyms should be avoided as a conclusion should be somehow self explanatory.

Is there a consensus on something like that?

The abstract should be self-contained, so any abbreviations used therein should be explained at first occurence (if a term occurs only once, then there is no need to introduce an abbreviation), and citations should be given in its full form (i.e., [Name, Journal, Volume, Pages, Year]). Then starting from the Introduction, one introduces abbreviations at their first occurence again, even if they were introduced already in the abstract.

And while I somewhat understand the desire to keep the Conclusions self-contained, too, at times when I wanted to do so either the reviewer or the language editor insisted that there should be only abbreviations once they are introduced. Personally, I don't like starting a sentence from an acronym, or a number, but the editors don't have such dillemas; so I usually just write so that there are none at the beginning of a sentence.

I once argued about it with the reviewer, but the language editor then again said to stick to abbreviations. I guess there are more chances to get it one's way in case of a very long paper (>50, or even >100 pages) for the sake of clarity.


When citing an arXiv paper, what year should one write? A paper on arXiv can have multiple versions. It is rather frequent (at least in math) that the first version and the latest version are even from different years. When citing such a paper, is it better to put in the year in which the paper was first published on arXiv, or the year of the latest version (and probably explicitly saying which version is cited then)?

Assume that neither the journal nor the publisher have any written guidelines about this particular scenario; for example, when one is themselves putting a paper on the arXiv.

I would cite the exact version you are referring to in your work. Therefore the year should be the year of that version. You should also use the actual arxiv identifier in the citation. This is to minimise the effect of potential changes in the cited work on your paper. Moreover, your goal is to provide the reader with a precise pointer to the cited work so that they can easily find it.


Traspararent evaluation in lab exams -- good or bad idea? In a traditional evaluation, instructors only let their students know their total marks when the semester results are released. The marks given for each student for each question is kept confidential.

In our institution, lab examinations usually occur before the corresponding theoretical exams. Hence, I tend to follow a more transparent evaluation where the students get to know their marks and know where they have gone wrong just after their evaluation. I do this so that they could rectify their mistakes in their upcoming theory exam. After all, the whole rationale behind education is that you get to learn wherever possible.

What are the pros and cons of this approach?

My experience (in the UK) is that provisional marks for all assessments, whether coursework or exams, need to be returned to students within a set timeframe. 15 working days is a common one, but this varies from university to university.

Early feedback is a good thing, as you said, as it lets students know where to concentrate their efforts. This may include subject areas, but also, sometimes a student receiving a lower mark than they hoped for, might be spurred to working harder towards the next element of assessment.

I say provisional marks as, although the marking standard will have been internally checked at this point, it unlikely to have gone to an external examiner to ensure that the standard is comparable with other universities. So, the mark could potentially still change after that process.

The question asked if there are any cons with this approach. I can't think of any, but I'm really not used to the idea of marks being held back unnecessarily.


How are trustees chosen? I thought that trustees of a university are leading people in the region or around the country (politicians, industrial leaders, donators, etc). I accidentally saw the Board of Trustees of Princeton University, and was surprised that one of the members is just a student from California.

It makes me wonder, how the trustees are selected? and what are the requirements for becoming a trustee?

Every university should have a documented process for choosing trustees, regents, etc. Ours are appointed by the Governor. See the link for what Princeton does. There are students on the Princeton board because a) there was a grad student among the 13 elected alumni trustees (2011 grad), and b) because there is always a graduating senior elected. Both of these kinds of alumni trustees serve for 4-year terms.


Does using a bibliography software actually save you time aside from when converting citation style? Does using a bibliography software actually save you time aside from when converting citation style?

I have used refworks and endnote for years and from 3 years ago I decided to ditch them both  and do the whole referencing business by hand because of frustrating problems they caused many times (references showing up incorrectly, having to manually add papers, references suddenly missing etc.). I only dump pdf files in them to keep a record of the references. I have been doing fine and I think it has been pretty efficient in three years I have had two change citation style manually twice which was painful but that was it.

I decided using endnote today again because i am writing a major review article. And already its painful! After inputting 15 references manually as the pdf files that can not be identified correctly (beats me why! clear pdf with OCR) and spending 30 minutes inputting the references, and then searching them to add them back in the paper I am doubting my decision!

Can anyone give me some motivation on why to use these tools really? I mean yes style change and finding duplicates can be good. But is that it? I feel like going back to basic but think there must be something wrong with me as it seems everyone else is using them without going insane!

It depends what you mean by using bibliography software. I think of bibliography software as doing three things:

They help you organize, search, and find your references. While
Pubmed and Google Scholar are quite efficient at finding references
for my field, I often prefer to search my own library of papers I am
familiar with when looking for a reference. I use JabRef for this
purpose and it saves me loads of time even when not converting
citation styles.
They help you create a reference list at the end of a
manuscript/grant/etc. If you have a database you simply need to tell
the software what papers have been referenced and what format you
want the reference list in. This saves you time when you convert
styles (and the first time you create a list). I don't think it
really does anything else. The key is that in my opinion ALL
bibliography software does this stage well for ALL styles. I see no
reason not to use bibliography software to create a reference list
at the end. This is the section where it is easy to make minor
mistakes and can waste a lot of time getting the style correct
They help you with formatting in text citations. This is where most
of the software falls down. In text citation styles have a lot of
variability (book, chapter, article, first time citation, subsequent
citation on a page, citation in a foot note, etc) that make
automation hard. Defining an automated system that can implement an
in-text citation style is no small task. Even if you can create such
a definition, many publishers have small in house tweaks. Create
software that is fully compliant with a style and allows for tweaks
to be made easily, is even harder. If you are lucky enough that your
software has the style you need, or that your target publishers are
easy going enough, then using bibliography software for your in-text
citations is a no brainer. If you are not so luck, you may not want
to use that feature.

In summary I would always use bibliography software for 1 and 2, but only for 3 if I am lucky.


Automatically checking retracted papers in bibliography Is there a program or online service to automatically check if there is a retracted paper in the bibliography of a pdf file?

As of today, nothing for free, and definitely nothing for PDF files. The best approach to developing such a program would be writing a front-end to the database of an organization such as Thomson Reuters or DBLP. However, you are unlikely to get free access to the interface of the database.


Are Asian-Americans considered an "underrepresented minority" in academia in the US? As an Asian-American I sometimes feel as though I am "stuck." There are certainly many Asian academics, but only a few Asian-Americans. This is complicated by the statistics. In absolute numbers, I think the numbers of Asian-American academics are small. Asian-Americans only make up a small percentage of the overall population of the U.S. (about 5%), and so from that perspective, a statistic that says something like, "9% of academics are Asian-American" (I made this up) can be regarded as saying that Asian-Americans are overrepresented.
At the same time, to my knowledge, I was the only Asian-American in my entire PhD program while I was there (not just my year - the entire PhD program), there were to my knowledge no Asian-American faculty in the department, and I can count on my fingers the number of Asian-Americans I see represented in my field.
(Edit: I also want to add that I understand that even the term "Asian-American" is messy because it lumps together several different ethnic groups)

There is no universal definition of "underrepresented" and also no universal definition of Asian-American, so it's impossible to answer this question accurately. A very rough answer is that it depends on the discipline (eg computer science vs anthropology) and also on which ethnicities are considered Asian-American.
Your personal experience notwithstanding, it is likely that Asian-Americans are overrepresented in academia overall, simply because Asian-Americans are overrepresented among Americans with advanced degrees. But this isn't a very useful metric from the point of view of diversity and equity.

Edit:
The NSF has a breakdown by race and discipline of US citizens awarded doctorates in 2016:
https://www.nsf.gov/statistics/2018/nsf18304/report/which-fields-attract-students/minorities.cfm
As for faculty, another reason it's going to be hard to find good data on whether Asian-Americans are underrepresented is that schools love to pretend that their faculty is more diverse than it is, so they often have rather creative definitions of "underrepresented."


What is the difference between repeatability, replicability and reproducibility? I have seen many instances where authors used the term "reproducibility" and "replicability" interchangeably in the social and behavioural sciences. Sometimes, they distinguish between the "repeatability" of experiments (same measurand/same measurement conditions) and "replicability" (same measurand/different conditions). If the three concepts are differentiated than, in most cases, there seems to be an inherent hierarchy between the three concepts:
repeatability < reproducibility < replicability
Where a successful replication means that the same finding has been achieved with different data (or sometimes methods) and reproducibility means that it is possible to get the same results given the data and analytical means from the original study.

However, it occurs to me that at least in computer science this seems to be different.[1]
I am not aware of the situation in other fields. Therefore, I am curious which definitions of repeatability, reproducibility and replicability are used in other disciplines.

What are the definitions most commonly associated to repeatability, reproducibility and replicability in your field?
Are the definitions the same but the concepts have substantially different meanings between fields e.g. because pseudo-random numbers generated by computer experiments are different from true randomness in biological experiments?

The American Statistical Association (ASA) has developed Reproducible Research Recommendations. The purpose of these recommendations are to create transparent science that can be recreated independently of the data creators and analyzers.  These recommendations have been motivated by several high profiles examples of studies being either retracted or not repeatable. The ASA includes definitions for Reproducibility and Replicability:

  Reproducibility: A study is reproducible if you can take the original data and the computer code used to analyze the data and reproduce all of the numerical findings from the study. This may initially sound like a trivial task but experience has shown that it’s not always easy to achieve this seemingly minimal standard.

  Replicability: This is the act of repeating an entire study, independently of the original
  investigator without the use of original data (but generally using the same methods).

I do not know repeatability fits into these definitions or if it has a formal definition. Also, this hierarchy seems to differ from yours. Reproducibility is using exiting data and recreating the same results using the described methods. Replicability is conducting a new experiment and reaching the same conclusions.

On a personal note, I have tried to reproduce studies while working with a statistician and most life science journal  articles do not include enough details to exactly recreate analysis unless they include their script (e.g., Python, SAS, or R code used to analyze the data). We were trying to recreate simple linear regressions and ANOVAs to find case studies for undergraduate stats courses, but often got different regression coefficients and test statistics. For example, people often make assumptions about NA values or transformations that are not described in their formal writeup.

For examples of replicability problems, search for psychology reproducibility problems. Also, notice the inconsistent use of the r terms here.

For examples of reproducibility problems, this lecture describes how a forensic statistician uncovered the Duke Cancer Scandal a few years back. Although outright fraud was occurring, there were other serious issues with the data analyzes.


How to finish my PhD dissertation before funding runs out? I am in the 4th year of my PhD and still has no paper published. I am working on my first ... but it has taken a long time because I had not been very satisfied with that piece of work and had been making modifications here and there. I have a second piece of work expecting to be published, but that one needs considerable improvement, too. My advisor is very grumpy about this, and he is now anxious to get me enough publications to send me off. Things are a tangled mess and I have no idea how to get out of this.

One, during the past three years, I had been working on something totally different from the main interest of my advisor. He is now sending me bits of pieces to work on in his main field. But I have little background knowledge, while still having to spend time writing that poor old paper and RA-ing on another project that supplies funding. I would never graduate in time were I to work on the new topic. I have not even identified a reasonable topic yet! On the other hand, if I were to incorporate some of the previous work into my dissertation work, it is different from my advisor's interest, and I fear another two unproductive years.

A second difficulty adding to the first one is, I find myself unable to discuss work with my advisor. The meetings are just like: I told him what I had, he made some comments, and then told me what to do next. Things never lasted more than 20 minutes. I feel lacking the big picture or a research objective. Sometimes I wish he could help me look at this piece of source code or that, but then in the meeting just failed to show it. Also, I am not a methodical or precise thinker, but my advisor is and he is very quick and sharp. I can make things clear on paper, but am terrible at taking facts from memory. This probably does not help him form any good impression. He also keeps mentioning I need more publications which are terrible blows to my psychology.

Finally, I have to graduate in two years, because funding is definitely running out by that time. In fact he is not even paying me at this time.

Seriously I want to quit, except to quit almost means the end of academic career. If I do not quit, what can I do to remedy the situation?

Here are a few ideas, hoping to help you get unstuck.

My spouse had a big-name, brilliant advisor who was impatient and rarely had time to meet with his students.  Fortunately my spouse found a person in the department who was able to be the mentor on the ground, the person to go to when a question came up.  He had a positive, supportive attitude, and was very knowledgeable, but was not able to be the advisor of record because he didn't have the right sort of title.  Perhaps you could find someone like this?  It might even be an advanced grad student or a postdoc.
Suppose your advisor is out of town for a month, but you and he still want to have some collaboration.  A good way of doing that is by writing a weekly email to your advisor, where you make an itemized list of what you've been working on and what questions you have.  I would suggest that you try writing this type of memo even when he is not out of town, and sending it to him the day before your meeting.  That can provide a helpful structure for your in-person meetings.
It sounds like you would benefit from having a study buddy.  This is someone who will listen to your troubles supportively from time to time, and help you stay on track with your goals.  It doesn't need to be someone you enjoy going to see a movie with -- this is similar to a study partner for a particular class, that you compare homework answers with.  Ideally this would be a mutually supportive relationship.

I would also suggest that you bite the bullet and resolve to spend some time learning the background material necessary for a productive collaboration with your advisor.  You don't have to continue working in that particular area your entire life -- you just need to get this PhD done, and it sounds like that's going to be the easiest way to do it.

Reassurance: it will probably not take as long as you fear it will to learn that background stuff.  Although you might not realize it, you are a more efficient learner now than you were a few years ago.  Also, I think you are motivated now to figure out how to do things methodically.

I can see that both you and your advisor have had your frustrations with each other.  I predict that as he sees you taking steps to meet him halfway, you will start to see more patience and a more positive, supportive attitude from him.


How to get title and pdf (and perhaps other metadata like author) from DOI I have a bunch of DOIs, now I would like to fetch the corresponding PDF and the title and authors, creation/publish date, keywords, abstract if possible, etc. I understand that many articles are behind a paywall so don't expect to get the PDFs for those. But I would still like to get the other metadata for those articles, even though they are behind the paywall (since I imagine that info is public).

To summarize, looking for some/all of these properties in preferably JSON or XML form (except the PDF, in PDF form, if freely available):

title
authors
journal
publicationDate
keywords
abstract/description

I tried looking here at the DOI API but it only seems to provide this:

{
  "responseCode": 1,
  "handle": "10.1000/1",
  "values": [
    {
      "index": 100,
      "type": "HS_ADMIN",
      "data": {
        "format": "admin",
        "value": {
          "handle": "0.NA/10.1000",
          "index": 200,
          "permissions": "011111111111"
        }
      },
      "ttl": 86400,
      "timestamp": "2000-04-13T15:08:57Z"
    },
    {
      "index": 1,
      "type": "URL",
      "data": { "format": "string", "value": "http://www.doi.org/index.html" },
      "ttl": 86400,
      "timestamp": "2004-09-10T19:49:59Z"
    }
  ]
}

I saw CORE, which might have the metadata, but it isn't public domain / free / open source for commercial use, which I would like. Also checked at the Elsevier APIs (Mendeley and Scopus), but they are not free for commercial use either.

the Crossref REST API is public and doesn't have a license - all our metadata are available for reuse without restriction. That's because we believe that metadata are facts and facts cannot be owned or licensed. (The license CC 4 refers only to the documentation on how to use the API :-))

We have 105 million DOIs about 25% of those have full-text links that go to HTML or PDFs. I'm not sure of the exact queries you'll need but if you end up using it and need help you can open tickets there on GitHub.


Visa interview: Will you return to your home country after your studies? Why almost all students answer 'Yes' to this question? Is this a must for student visa? I have applied to student visa from Iran to study master degree in Germany. I want to pursue PhD (may be in Germany or may be not) and I will apply to work for giant software companies after that.

I don't understand why people write this?

[UPDATE]

I will immediately follow PhD after masters either in Germany or somewhere else. Also all students have 18 months job seeking visa extension. Then why should we lie? Embassy definitely knows that everyone will at least give himself a chance to work in a better company.

Why almost all students answer 'Yes'?

The host country is not looking to accept immigrants when allowing students to come pursue degrees on education visas.  Each country has their own system, standards and procedures for allowing immigrants in the country, and if you appear like you're trying to skip that by entering as a student they will deny your student visa application.


Completing German master's programs in less than allotted time I'm considering applying to master's programs in mathematics over in Germany (e.g. Bonn, Berlin Mathematical School). The stated time for these programs is two years.

Should I get accepted and attend, are there any issues (ethical or otherwise), with bailing after a year to attend a PhD program in the US? If so, is it possible to complete the program in a single year if I come in with some kind of advanced standing (i.e. having taken many graduate courses beforehand)?

This is something that you have to ask the respective offices at the schools you apply.

You can savely assume that completing a Master's in Germany in less than two years is in general possible if you complete all required things in time, i.e. you've got enough credits in all required categories. It will not hurt if you double check with the "Studien-" or "Prüfungsordnung" of the respective programs.

If the program will award credits for courses that you have taken somewhere else is something that nobody but the program office can answer (and will probably finally decided on an individual basis by the dean of student affairs).


Sending a second follow-up email for a potential PhD position Four weeks ago I contacted the department of the University to ask whether there are PhD positions open. They emailed me some questions I needed to fill in and said that they will review my application and let me know if they have something available for me as soon as possible. After two weeks, I sent a follow-up email asking if there was already some news about my application, but they didn't respond.
Now, two weeks after that follow-up email, I still haven't heard anything. Is it okay to send a second follow-up email? How should I formulate it? I don't want to seem annoying and intrusive. On the one hand, I'm willing to be patient as I really want to pursue a PhD at that faculty, but on the other hand, if they don't offer me a position, I need to start looking for other positions as soon as possible.

It's typical to apply for multiple (10+) PhD positions simultaneously, rather than sequentially. Don't wait to hear back from this place, just send your other applications now. It's fine to ask again about your application, but this time ask for the date by which you can expect to have a decision.
Here's a suggestion for how to formulate the email (you can modify it according to the specific details of your situation):

Dear Prof. X,
Last month I applied for a PhD position in your department. Do you
have any further news about my application, or an idea of when you
might make a decision? I am really excited about this opportunity and
look forward to hearing from you soon.
Best wishes,
MDG1999


How Much Say Would A Prospective Supervisor Have In A Students Admission To An Applied Math Graduate Program? I am interested in applying to some applied math graduate programs but I have some deficiencies in a few math courses. However, I have reached out to a potential supervisor and our conversations are going well. So my question is, if a prospective supervisor wants to take on a particular student, but students have to enter a common pool of applicants, how much influence on An individuals admissions does a prospective advisor have in the process.

"Soft" influence
It's hard to judge how much soft influence a professor has. Every professor will have a different level of influence, and also a different approach in how they wield it. There is no way to answer this definitively. The most influential professors in departments that allow them to wield influence will have as much power as they want to choose students. Professors in other departments may have little to no influence at all.
"Hard" influence
In my experience, the more powerful control over admissions that professors have is money. For many programs, there are more qualified applicants than there are slots available for funding. That means that many qualified applicants miss the cut despite being qualified: there are simply too many other prospective students that either have better resumes or have a better fit to the program. However, the program still wants those students!
If a professor has resources to fund a student and offers to do so, that student can possibly skip the queue a bit, because they are no longer competing for the at large funding slots. In the grad program I attended, these students were referred to as "direct admit" students: they joined a lab immediately that offered to support them. Other students had a year to rotate and choose a supervisor.
Summary
I have no idea which of these categories your program and professor is more likely to fall into, if either. If you want to be a student, apply. It's better to apply and fail to be accepted than to not apply and guarantee you will not be accepted.


To cite an organisation correctly in IEEE style My tex based on Espanta's answer

@techreport{AAMI,
    title = {Recommended Practice for Testing and Reporting Performance Results of Ventricular Arrhythmia Detection Algorithms},
    institution = {{Association for the Advancement of Medical Instrumentation}},
    year = {1987},
    address = {Arlington, VA, USA}
}

which is shown correctly now after Espanta's answer in Bibliography.
However, the thing is shown in my text similarly as before :

where AAM (1987) is shown.
I do not know what I should have in the text body for this citation, since the citation does not have author but institution.
I think AAMI (1987) is good.

What is the correct way of citing this organisation in IEEE style?

I think what you are referring to is a technical report or white paper from certain company. Then it should not be misc type. I think if you change your item from misc to technical report, the IEEE style in latex will handle it.

The correct field in citation style should be
Authors(if any), title, publisher, address, year.


Can someone with only a master's degree promoted to a permanent full-time faculty at a two-year college? Long story short, I am a master's graduate it statistics, and I recently applied to enrol in a local two-year college program to land a job in my rural hometown (I prefer to have a career in my rural town than in a bigger city, due to personal health and other circumstances). The admission secretary at the local two-year college saw my educational credentials and forwarded my transcripts to the dean of the two-year college's university transfer program. The dean called me on my cell and wanted to interview me for a part-time instructor position. I passed the interview and I will be start teaching introductory university math/stat courses at the two-year college in near future.
As a person who is just starting out in the two-year college teaching career, I am wondering whether the fact that I only have a master's degree in statistics and not Ph.D. would later prevent me from becoming a permanent full-time faculty at this two-year college. The dean of the university transfer program has a Ph.D. in medicine, and I see some other faculty members who have Ph.D. in their teaching disciplines. Primarily, this college offers two-year programs in trades, social work, and nursing, and this college does not offer any bachelor's degree program (although they do offer a transfer program to 4-year university).
Do two-year rural colleges like this promote instructors with a master's degree to a permanent full-time faculty if they teach well? or does such a promotion typically only restricted to instructors with Ph.D.? I am located in Canada.
Thank you,

You should take a look at the faculty credentials at this institution and similar ones (in Canada). Their websites should provide this information. You can see whether any permanent faculty have only master's degrees.
After you have taught for a year, and presumably done a good job, you might ask the administration about the possibility of a permanent appointment.


Do academics get bored of research? I am wondering if academics (Professors, Researchers etc.) who usually have to spend their lives on research get bored of the subject or get tired of research?

In this case, I want to know how they stay motivated - for example Nobel Laureates more often spend a large part of their life (15 - 20 years) on specific research. So how do they stay motivated?

What helps, I think, is that "research" is not a single thing but a complex of many different activities. If I am feeling burned out on paper-writing, perhaps I find my joy in coding or mathematics or sketching new project ideas. Likewise when I am happy about papers but feeling burned out on something else. At a larger scale, even a "unified" line of research has many distinct facets that may feel quite different when one is actually closely engaged with it. Thus, I see no difficulty in the idea of remaining interested and engaged for a long period of time. I have been so for nearly 20 years (counting undergraduate research work as well) and I see no reason to expect my interest to fail any time soon. Funding, of course, is an entirely different story.


When suggesting referee names, where do you draw the line for conflict of interest? Journal submission guidelines in my field typically require the submitting author to provide the editor with a list of potential referees. The journal guidelines ask to suggest people with whom we have no collaboration, no joint publications and no conflict of interest.

Given how competitive academic research is, I sometimes wonder how conservative one should be in choosing potential referees. After a long career, if I am to exclude all people whom I have collaborated with over time, there will be few experts left qualified to judge the work! On the other hand, someone with whom I am just starting a project with, and has nothing published with me so far, would not be seen as a violation by the editor, yet would not be rally fair (if we work together, he has a vested interest in my success).

So, I am asking here what guidelines or principles can be proposed in this gray area.

The National Science Foundation in the US has clearly articulated guidelines for what constitutes a conflict of interest for reviewers of grant proposals.  These are probably safe — and certainly defensible — guidelines for you to follow.  Specifically (and for the reason you mention), research collaborations are considered to be a conflict only if they occurred within the last 4 years (there are other rules as well, please see the document).


Where to publish research if I do not want a peer review process? I have a few papers, one of which is on a topic that, after thorough checking, has not been researched from this particular angle before.

My question is where can I publish this without going through peer reviewed academic journals? I only have my undergrad, and am looking to publish the work to make myself competitive for a PhD finance program. The paper is on real estate finance.

I just need a quick- one, two, you're published! Will finance programs look highly on this, or will they ignore it completely?

"…a quick- one, two, you're published!"

That's not how it works.

What works is:

Make it a publicly available preprint (online repositories like
arXiv, a preprint series of some institute, university, maybe via your personal website or blog…).
Submit to some peer reviewed journal that complies with papers that are available as preprints (and there are journals that do not cost you anything; you will not get "open access" for free, but in many cases the preprint can stay freely available).
Put the paper in your CV and add "submitted for publication".

Then the paper will be visible and checkable and it also shows that you know how scientific publishing works.


Does Hill University (USA) have legitimate accreditation? I need to know if Hill University is accredited. Especially in the field of MBA degrees.

The Hill University's, website dead as of Sept 2015*, accreditation page did not make it clear which of their degrees were accredited, instead the two accrediting bodies (IOEAB and OKOLA) are listed at this random website as "fake degree accreditation agencies". They are also the accrediting agencies used by Speedy Degrees which would suggest to me that accreditation by those bodies is more or less meaningless.

Further, the web domain is .com and not .edu which is highly atypical for US universities. The requirements for .edu domain require a US location and "proper" accreditation. While not using a .edu domain could be related to the online nature of the university, it is also a warning sign that the accreditation might be questionable.

* Recent reports by NYTimes and UIUC list this university as a fake.