text:
How can I get around the 10000 search result limit in PubMed?
I'm working on a project to analyze PubMed abstracts over a given period. I'm using the PubMed API (Entrez) to get PMIDs over a given period. I'm submitting queries looking like this:
2001/06/03:2001/06/03[dp]
This would result in all PMIDs with a publication date of the 3rd of June in 2001.
However, for some days, over 10.000 PMIDs were generated.
What can I do to ensure that I get all PMIDs that were generated in a day?
If I could download them from another source, that would be perfectly fine for my application.

Go visit your local research librarian and ask them for advice?

https://www.reddit.com/r/labrats/comments/kem5ga/saving_more_than_10k_pubmed_results/

Pay the service provider for access without the limit?

There is no way (that I know of) to pay to increase the limit.

I have an idea, but first, could you indicate approximately the proportion of dates you have encountered that actually max-out the 10,000 limit?

To overcome the 10,000 record limit, use EDirect. The E-utilities in Depth page, says:

For PubMed, ESearch can only retrieve the first 10,000 records
matching the query. To obtain more than 10,000 PubMed
records, consider using EDirect that contains
additional logic to batch PubMed search results
automatically so that an arbitrary number can be retrieved

By downloading the UNIX based EDirect utilities you can run a command line search similar to the following:

esearch -db pubmed -query "2001/06/01 [dp]" | efetch -format uilist

which will produce many more than 10,000 records. Please note, however, that when I ran this particular command (without having particularly studies the documentation) I received the following error:

Actual PMID count 31242 does not match expected total 32637

I don't imagine that it will take much effort on your part to discover the source of the error and overcome it. The important thing is that the command line utility esearch, along with the other EDirect utilities, gives you much more flexibility than using the direct HTTP interfact.
An alternative approach, of which I give only a bare-bones outline here, is often referred to loosely as "divide and conquer". Note that this is different from the formal, recursive, divide-and-conquer algorithm common in some areas of computer science.
By divide-and-conquer, I am referring to the idea that if you cannot directly solve the problem you want, then break it down into a series of (preferably mutually exclusive but jointly complete) sub-problems, each of which is solvable. For example ... and forgive me, but I am about to illustrate my point with a division method that will not actually work ... consider the possibility that you wish to download the PubMed identifiers (PMIDs) for documents published on 2022-01-01. Assume also, hypothetically, that there are 34,567 such records. You would know that there were 34,567 records because PuMed would return a result that included the string:

<eSearchResult><Count>34,576</Count><RetMax>20</RetMax>

Your next step would then be to ask yourself what sequence of queries you could submit to PubMed which (a) taken together give you all the records you wanted, but (b) taken individually would each return fewer than 10,000 results. One obvious (but, as I said, unfortunately unworkable) approach would be to submit the following 26 queries:

2001/06/03:2001/06/03 [dp] a* [au]

2001/06/03:2001/06/03 [dp] b* [au]

2001/06/03:2001/06/03 [dp] c* [au]

... and so forth. That is, you'd that search for all records published on 2001/06/03 that also had an author whose name began with 'A', and then 'B', etc.
Unfortunately, although this illustrates the divide-and-conquer idea, it will not work for the reason that PubMed requires truncated names (i.e., those where a wildcard * is used), to be given with at least four (!) initial letters. However, you might experiment, as I have, with submitting queries that use the record creation date (CRDT) as the way of slicing and dicing the records for a particular publication date. For example, whereas

2001/06/01 [dp]

returns 32,637 results, the diced queries:

2001/06/01 [dp] 2000/01/01:2001/06/01 [CRDT]

followed by:

2001/06/01 [dp] 2001/06/01:2001/06/20 [CRDT]

chop the large, unobtainable, parcel of records into downloadable bundles that contain fewer than 10,000 entries. Clearly, you would need to submit further queries with a CRDT range beyond 2001/06/20.

Thanks a lot! That's a beneficial answer. I have downloaded the annual baseline and used that, but your method is much better aligned with my use case. Regarding the divide-and-conquer, I had tried several combinations and was getting a bit frustrated with the lack of ability to break the search up. For example, the limitations of the wildcard seem pretty arbitrary. But esearch seems to be the way to go then :)

Note my remark about the discrepancy between two sets of results. It appears to me that eResearch itself uses a slice-and-dice-BY-TIME approach. I have a suspicion  that the reason for the discrepancy between some eResearch counts and those from the  PMID searches is because eResearch might not slice-and-dice far enough away from the publication data. No doubt a little experimentation on your part will reveal the truth ... and you might even ask the folks as the National Library of Medicine who actually run PubMed.

From their help pages one finds:

Download PubMed data

Once a year, NLM releases a complete (baseline) set of PubMed citation records in XML format for download from our FTP servers. Incremental update files are released daily and include new, revised, and deleted citations. The PubMed DTD states any changes to the structure and allowed elements from year to year.

So it seems you should be using their FTP server.

That is a valid solution, but it requires me to download many gigabytes of data when I am only interested in the PMIDs and abstracts. I would be happy if I could just download the PMIDs as a list with a date of publication attached.


text:
Algorithms, Combinatorics and Optimization graduate programs
Does anybody know of any other ACO (algorithms, combinatorics and optimization) graduate programs besides the ones at Carnegie Mellon and Georgia Tech?
From what I have searched, these two schools were the only ones that offered such a multi-disciplinary program. I like this intersection in CS/MATH. The only other multi-disciplinary programs are scientific computing ones where the focus is in numerical algorithms, differential equations, and parallel programming. Scientific computing would be my second choice type of program.
There are TONS of scientific computing programs, where aren't there more ACO programs? I think both topics are fascinating, but I just have more fun with ACO types of problems. Ideally, I would enjoy a 70:30 ratio of ACO and Scientific Computing.
I really want to do an inter-disciplinary program because, in a general computer science program I would most-likely have to do systems (ewwww!) and in a general math program I would have to study analysis and geometry (which is cool, but I would rather focus on ACO!)

Are there any other ACO programs besides the ones offered at CMU and GA-Tech?
Why are there so many scientific computing programs vs ACO programs?

Thanks for all the help

Carefully read the actual course requirements for the programs you're looking at.  Some departments are extremely flexible, and your final course list may bear only tangential resemblance to the name of the department.  (In that case, you just need a suitable advisor.)

I know uwaterloo has such a program

There are plenty of other ACO programs.  They just call themselves "computer science".

ACO = Computer science where you aren't required to demonstrate knowledge in systems :)

You should consider applying to "Operations Research", "Computer science", and "Applied Math" programs (note applied math and not math), all of which can potentially have concentrations in your desired field of study. Make sure the schools have professors publishing in the journals and conferences that interest you. Courses you tend to take in these programs include. Every course below can be used towards a degree in applied math at Cornell (not sure about other places).
Analysis of Algorithms - CS
Simulation - OR
Machine Learning - CS
Combinatorial Optimization - OR
Algorithmic Game Theory - CS
Optimal Learning - OR
Theory of Computing - CS (complexity theory)
Stochastic Dynamic Programming - OR
Networks - CS
Mathematical Programming - code word for analysis with an eye towards optimization and algorithms
Nonlinear Programming - OR
I know that Cornell has a very strong theory component to both their OR and CS programs and you should probably look into them. No matter which program you choose at Cornell, you can bet that you will be able to take a lot of OR,CS and math courses and count most of them towards your PhD requirements (this may not be true at all other universities, you'll have to check). The above list is just a sampling of some of the courses offered at Cornell in OR and CS. Combinatorics is offered in the math department. The difference between all these programs will be in the required courses you have to take, for example OR requires stats, CS requires the theory of programming languages etc., but no one likes every single course they take in their PhD.
Edit: Actually at Cornell, Applied Math has the most flexibility of any program. As long as you have some background in undergrad algebra and analysis (which you can make up during grad school) You can affectively create your own curriculum, with very few requirements. Its very easy to focus on ACO there. Note that many applied math programs are not so flexible, so you really have to look around.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
How to keep track of current physics after graduating?
This summer I graduated from college, majoring in physics, but for reasons outside my academic career, I won't be able to attend graduate school for at least a couple of years. Despite that, I'd rather not neglect my physics education until grad school becomes possible.
I realize that a B.Sc. doesn't mean I should be able to read all the latest articles coming from the frontiers of research. However, I'd like to keep track of current affairs in physics to both be in touch with my field, and to help me decide on which sub-field I will focus once I return to the academia, and perhaps even decide where to go and under who to study. What would you recommend is the best way to do this, and what are the resources available that I should be aware of? (Note: I will probably not have access to paid scientific publications after I receive my diploma in the next few months)
Also, I wouldn't want my physics skills to rust in the meantime. Apart from participating here on the physics stack exchange, do you know of any good resources for physics questions/riddles/puzzles, hopefully at the appropriate level for a college graduate, so I can spend some spare time solving those to stay in intellectual shape in the next few years?

Check the relevant categories at arxiv.org every day.

Why not look at free online lecture notes and such? http://ocw.mit.edu/courses/physics/ has plenty of graduate level courses, which would probably contain information at the right bridge level between your BSc and your eventual PhD.

I am in this same situation. Here are some thoughts I have:
In order to retain the skills we learned as undergraduates, we have to practice them much like we had to 'practice' problem sets for assignments. I think that the MIT open courseware is an excellent tool for reminding and practicing.
Physicists don't write papers about stuff other physicists know. Most (or all) of what's in a paper could be new and unfamiliar to the majority. A BS does not bring you up to speed with the physics community (my degree barely got me into the 20th century) so there is still a good deal of study before you could pick a paper and read it with ease. Continuing with your own studies by advancing your knowledge of physics will do a lot to help you understand what is in these papers. Reading the titles of recent Arxiv papers is a fun pass time; you can sit down and read any that perk your interest.

As stated in the comment above, the only way is to stay involved. I would suggest reading as much as you can, particularly in the subfields in which you hope to specialize one day. If possible, try to stay in touch with professors you know from undergrad, and attend their journal clubs to stay in the research field.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
How to address the person being recommended in a recommendation letter?
How should one "address" the person for whom I am writing a recommendation letter in the letter?
Scenario:

I have known John Doe for many years and am familiar with his work. We address each other on a first name basis. I've been asked to write a letter supporting John's application. When I write about him, should I write

Dr [or Mr, in case of undergraduates] Doe's works are well-written ...

or can I get away with

John's works are well-written ...

Personally I feel a bit strange writing Dr Doe for someone I know so well, but I wonder if it is better to err on the more formal side?

For what it is worth, the field is Mathematics. And for future reference, I do not want to limit the question to a particular level of application (for graduate school, fellowships, or for jobs); I suspect that shouldn't make a difference in the answer, but if it does, feel free to indicate.

I have seen both used in recommendation letters, regardless of the strength of the recommendation letter itself. I would, myself, recommend Dr. John Doe / Dr. Doe for most professional relationships, except when it is clear that you have formed a close professional relationship (PhD student, or long-term collaborator or post-doc). In case you go for the surname, I would still use the full name at the first mention:

Dr. John Doe was a student of mine at the University of X, where I teach Y, …. He later joined my research group as a Masters, then PhD student. John is an extremely bright student, …

(Of course, that's merely an example and not a good letter wording, so do not look at the wording itself, only the use of names…)

+1 the student is now a professional researcher with a PhD. Using the more serious approach and writing Dr Doe makes this more clear imo.

Formality is particularly important in letters for female students/colleagues.

@JeffE “Formality is particularly important in letters for female students/colleagues” — WTF?

@F'X: Yep. At least in fields like CS where sexism is still rampant, if subtle.  See also: Female authors publishing with only first initials instead of full first names.

Since you specifically asked about math, let me say that in my experience (as a mathematician, reading recommendation letters written by other mathematicians), the pattern of

use the applicant's full name once.
use their first name (generally what you would call them in person) after that.

is close to universal amongst mathematicians in the US.  One does find exceptions, usually replacing the applicant's first name with their last name (so, writing "Doe's work has been..."), but they are actually quite rare.

I agree that firstname is most common, but I think "near universal" is overstating it. Semirandomly looking at a dozen or so letters gave a few lastnames and a couple Dr. lastnames.

Hmm, I also looked semi-randomly at a selection of letters before writing the post and had my impression was reinforced.  In particular, I didn't see any Dr. lastnames.

I looked through a file of the recommendations I've written in the past few years, and I see that, for students and postdocs, I almost (but not quite) always used their first names.


text:
DBA vs. PhD Perception within Academia
In my field (business administration) there are two main terminal degrees. One is a DBA (doctorate of business administration) and one is a PhD (business admin, economics, etc.). A DBA is focused on the application of theories (within a business) as opposed to the generation of new theories.
Is there any published research on the perception between these two terminal degrees? I'm concerned that a DBA is viewed as a "poor-man's PhD." While I am interested in what hiring committees think I am also concerned about the perceptions across academia.

@user11852 I agree with the first part of your comment, not the second half. Once you go down one route, it's hard to pull back and do the other one if you change your mind. Better make the right decision at the beginning.

@user11852 You are making the assumption that this is for myself. I must advise my students and, therefore, I would like to know how the two options are viewed.

While the experience that individual has gained throughout the course of their career is the best indicator of whether an individual has earned the respect of their peers, my impression is that the PhD title is generally more recognized with the public at large (basically those unfamiliar with how advanced degrees are awarded within academic institutions). This is purely a social construct that isn't germane to the field of advanced study.
I see the issue as someone calling a chiropractor a "Doctor" even though there is no award of an MD, or not understanding that a D.O. and an M.D. are basically the same thing.
Now, some universities in Europe do not traditionally award a "PhD" because they have a different three letter acronym for their doctorates. That does not mean that the individual is any less accomplished, its just a different system than the one in the US.
Perhaps one way to explain it to your students is to note what other fields have a similar award. In law, there are Juris Doctorates and PhDs; and in art there are MFAs and PhDs. The primary distinction appears to be what you have already recognized, that one is more about application than research.
To be a bit snarky, there are some fields of study altogether that do not get much appreciation, education being the main one with the award of the D.Ed. I do see some eye rolling when that one comes up, but I've also seen eye rolling from guys in the so called "pure" or "hard" sciences and their opinions of anyone in the humanities or "soft" sciences.
As to directly answer your question, Yes, there are published articles discussing the "perception" of one degree over another. I took a quick stroll on Google Scholar and found a number of published, peer-reviewed articles discussing this very question.
Here is one titled, "Doctoral Differences: Professional doctorates and PhDs compared".


text:
Is there a list of countries (or universities) showing which prefer direct communication with referee?
My students often request letters of reference from me. Sometimes to attend graduate school in the UK, Germany, Switzerland, and sometimes in countries not internationally known for their education system.
Quite often the student says the university wants them to enclose the letters of recommendation and clearly some universities do not want the student to be involved in that communication process.
My question is, how do I know when I am writing a letter to a specific university if they prefer the student to submit the letter or if they prefer me to communicate directly with the school? I could check with each school as I write the letter but that seems like a lot of work which need not be repeated for each letter-writer.

I may be missing something, but why do you care? If the student asks you to submit directly, submit directly. If the student asks you to send him the letter, send him the letter.

If such a list existed, I'm afraid it would go out of date very quickly. @xLeitix offers one useful guideline. I know people who will always send letters of recommendations directly to the target (finding out the correct addressee should be the requesting student's responsibility). This avoids any impression that the student might have gotten n+3 recommendations and only retained the n best ones.

@xLeitix I care because there may be some schools which accept either method and for those schools I would prefer to send directly, bypassing the student's eyes altogether. As it is now, I have students comparing their letters to those I have written for other students and I would like to avoid that whenever possible.

@xLeitix: I agree with earthling. By not having to give the letter of recommendation directly to the student, I can write a more useful letter. (When letters are public, they are more prone to be "safe.") That's why, as a rule, I always ask for a direct address to send the letter, if possible.

@aeismail ok, based on "I care because there may be some schools which accept either method" I can kind of understand the question, though, I have never actually seen a committee that takes 'em either way (my experience is more with faculty search committees, though).

I may be missing something, but why do you care? If the student asks you to submit directly, submit directly. If the student asks you to send him the letter, refuse and submit directly.

@JeffE Some misguided application systems automatically reject applications if the letter is not provided by the student.  Presumably this is to reduce effort required to administer letters.

Well, many good answers are already included in the comment section, but Let my try to summarize and extend this a bit:
First of all, there are good reasons for not involving the student (you can be more honest, the student can not pre-select). To my knowledge, ther eare at least three different submission types:

Student sends in recommendation which is written openly
Students has to submit letter of recommendation, but it must be enclosed in a sealed envelope
letter of recommendation has to be sent directly.

The chosen method might not only depend on the institution, but also on the funding scheme if the student gets financial support. The sheer number of possible combinations, combined with funding schemes which might vary from year to year makes the existence of a complete list extremely unlikely.
I would suggest to  follow the advice given by Stephan Kolassa to let the student figure out how the process works. It might be good to tell the student that if there are several options, you would prefer to send in the letter directly.

Note that the sealed envelope method is a pain if the prof does not have a secretary. Make sure to ask the student to ask for the whole number of required recommendations ahead of time rather them trickling in over time.

Adding a bit to this, for Japanese universities, almost all expect the letter to be open and included in the applications materials sent by the applicant (my experience here is for jobs -- not graduate school), then recommendation letters are submitted by the applicant in their package.
I gather this is also common in China. As an American, I find it bizarre, but it is what it is.

Does this also apply to asian campuses of western universities?

What you are asking for is impossible because Academia varies.  Letter-collecting practices can vary between departments, degree programs, and supervisors.  They can also change over time.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Is it ethical to request additional money for non-research related work in a research lab as a grad student?
I work in a computational research lab as a graduate research assistant. We're all funded under various grants to do research in our field and we are also working on a thesis, which may or may not be directly related to the funding source (it is if we are lucky!)
Our lab is also licensing the software we write to outside companies for their own in-house use. As a result, there are many "niceties" that should be added to the code to make it more user-friendly, but these have no bearing on our research, either the sponsor-funded or thesis-related.
Is it okay that we are expected to implement these things in addition to our funded/thesis related work? Is it acceptable to ask for additional money (assuming work done on this is in addition to funded/thesis work)?
Our advisor is considering hiring an outside company to come in and put in these features, but we would be expected to help them through the process of learning and understanding our code so it would be nice to cut out the middle man since we certainly won't get any extra money from advising the consultants.

It's not unethical to ask your professor. However, as Leon pointed out, it could be annoying if not done properly. A couple of perspectives:

Set your goals. If you have enough funding for your research moving ahead comfortably and your goal is to finish your degree and get some solid publications, then focus on that (and be happy the maintenance is outsourced). On the other hand, if you're not funded well enough, and think you can accomplish both the research and get paid to do the maintenance coding, propose it to your professor in a way that is positive. But beware of the risk. I have had a student who, once he got scholarships, stopped doing the teaching assistantships we offered him. The extra money wasn't worth the headache or distraction to him.
Funded research work is never 100% research. I have always had, at various points of my research career, tasks that were distracting and fell out of the area of what was "research".  The goal is to keep it reasonable and minimal. Complaining about "not getting extra money for advising consultants" is probably not a reasonable attitude to take with your professor. Negotiate with your professor how many hours/week you can reasonably spend (without taking you away too much from your research) is surely a better approach.

From one perspective, adding these niceties to the software increases the likelihood that the software will be used and thereby increases the impact of your research. So although these niceties are not research per se, they help achieve the goals of doing research (at least from a funding agency's perspective), namely making an impact. Such tasks are often a necessary part of the research process (and someone has to do them).
Whether or not it is ethical to ask for additional money to hire people to do this very much depends on the rules of the funding agency and how well your advisor is at selling and justifying the idea to the agency.

I'm pitching in my own experience in similar issues.
I've been in 2 research labs as a grad student, and in both of them, aside from my own research I did other tasks like server administration (we had our own local network), a bit of outsourcing, and the ocasional side project.
Now, in the first lab, all of these tasks were done pro-bono, meaning, I did not receive a cent for it, even though the server in place was really old and prone to failure, which took considerable amounts of time from my research time. The Professor, not even once considered paying me for the task.
In my second and current lab, the professor pays you for everything that should derange you from your research, I did a couple of projects for a company (on behalf of our lab) and I got paid. I also gave some tours in the lab as well as some demos, and I also got paid.
The moral is, it is usually up to the professor whether he pays you or not, if he is not paying you, is most likely because he either thinks is within your range of activities or simply he does not have the money.
Personally, I would not ask for money unless I had the precedent that other person did it before, other way it could set a bad relationship between you two.

Beware that some universities have ethics rules that make it harder for a professor to pay his/her students -- or if the rules don't bar it outright, the prevailing culture might frown on it.  These rules are often written to protect students, e.g., from a faculty advisor who pressures his/her students to spend time working on his/her startup company.

Our lab is also licensing the software we write to outside companies for their own in-house use.

Are those companies paying you? Correct me if I'm wrong, but it sounds to me like you have a product. Instead of asking for funding to implement the features that these companies want, why don't you ask the companies themselves for money? I don't claim to know the hoops about using a research facility to work on parts of software that aren't research related, so if you decide to go this route you should definitely clear it with the lab.

If it is an american University, all work done in a Lab is property of the University


text:
How I add a co-author to my Google Scholar profile?
I have co-authored some publications with an author who has a Google Scholar profile, but I see no way of adding him to my profile as a co-author.
How I add a co-author to my Google Scholar profile?

The recipe is this:

Sign In to Google Scholar.
Click on My Citations.
Type your co-author name in the search box provided (top right).
You will get a list of authors that match the search. Click on the "Add co-author" button on the right of the correct person.

If your author is not found, you will get a failed search.

If you click on the wrong person, you can remove them with the edit button at the top of your co-authors list.


text:
How to publish an academic book but make the PDF freely available online?
Background
I like the idea of writing an academic book.

It currently looks better on a CV when applying for jobs, grants, promotions, etc. than a blog post, or a website.
Libraries and people archive the work
Most of the best academic content currently seems to end up in books and journal articles, rather than on websites.
People have an attractive physical copy to engage with if they want.

However, I don't like the constraints imposed by a book. In particular, readership is limited to those who buy/borrow the book or have access to a library.
Aim
In some cases, I'd prefer to write something like an "open access book".

If readers want the physical copy, they can purchase the book. Ideally some of this revenue would go to the author, but I'm not too fussed if the publisher just uses this money to fund promotion, editorial assistance, production, etc.
However, access to a PDF of the book is free online.
The book gets an ISBN, archiving, availability on Amazon, etc. and all the academic recognition associated with publishing an academic book.

Questions

So, are there any options for doing this, and what might be best option?
Are there any case studies of others who have done this?

Have you considered making your book an ebook? This does not have all the advantages you list, but it does (sort of) have the first. You can publish these (more or less) by yourself which means you won't have to forgo copyright. This way you can still publish the text for free as well.

I imagine self-publishing would provide less benefit to your reputation in contexts like job applications, promotions, and grant applications.

see also this list of open access publishers: http://openscience.com/the-right-place-to-publish-oa-books-in-the-humanities-and-social-sciences/?utm_source=rss&utm_medium=rss&utm_campaign=the-right-place-to-publish-oa-books-in-the-humanities-and-social-sciences

These days someone will make your book freely available online whether you want them to or not. So it's going to happen anyway.

I know a case that works just like you describe it. Hardcopy for people to buy, online version freely available. Maybe you can contact the authors directly: http://www.deeplearningbook.org

If you want this as a credit for applying, grants, promotions, etc., then publishing by a known publisher will be much better than self-publishing.  But (as some answers show) you can negotiate what you want with known publishers.

Cambridge University Press allows authors to freely distribute electronic copies of the books that it publishes, at least in mathematics and computer science.  (Of course this has to be explicitly negotiated into the publishing contract.)  Two good examples are Allen Hatcher's Algebraic Topology and Steve LaValle's Planning Algorithms.
You could also just release the book on the web, let people create their own physical copies through a book-printing service like Lulu or Blurb, and rely on the quality of the text to bolster your reputation instead of a traditional publisher's imprimatur.  See, for example, Pat Morin's excellent Open Data Structures.  However, I don't recommend this route unless (a) you write an amazingly good book, and (b) you already have tenure.

Both Hatcher's and LaValle's PDFs are printable.

@CharlesMorisset: There ain't such thing as "not printable" PDF. Hint: pdftk is your friend.

@CharlesMorisset: I hear ya. But with content restrictions as they are these days, I'm more than happy to flip off content producers and obtain an alternative version of the content I already paid for. Example: obtaining an electronic version of a dead-tree book I own. I'd still pay for content that I don't have in alternative formats though. At any rate, this discussion is not for here, so let's leave it as it is :)

OTexts
I just remembered that Professor Rob Hyndman had spoken about his upcoming textbook Forecasting: Principles and Practice

The entire book is available online and free-of-charge. Of course, we
  won’t make much money doing this, but textbooks never make much money
  anyway — the publishers make all the money. We’d rather create
  something that is widely used and useful, than have large
  publishers profit from our efforts.
Eventually a print version of the book will be available to
  purchase on Amazon, but not until a few more chapters are written.

The publisher is called "OTexts".
It says on their website.

OTexts represents a new approach to university textbooks. All our
  books will always be completely and freely available online. Why spend
  hundreds of dollars on printed books which are soon out-of-date when
  you can have continually updated online books for nothing!

At time of posting Rob's book appears to be the first text book to be published with this publisher.
It says at time of posting under the "For Authors" section

Print royalties are shared 50-50 between the author and OTexts.

Reflections
On the face of it, this sounds perfect for an author keen to maximise academic impact.
However:

This is a very new company.
I'm not sure what the implications would be for grants, promotions, jobs relative to publishing with an established academic publisher.

For instance, you can try with INTECH.
From the website:

InTech is a pioneer and world's largest multidisciplinary open access
  publisher of books covering the fields of Science, Technology and
  Medicine. Since 2004, InTech has collaborated with more than 60 000
  authors and published 1720 books and 13 journals with the aim of
  providing free online access to high-quality research and helping
  leading academics to make their work visible and accessible to diverse
  new audiences around the world.

One possibility is to self-publish. DH Fremlin published his extremely well-respected treatises on Measure Theory with Lulu.com. The books (in fact, the TeX source files) are available on his website for free; all the while his books are well-enough received that many university mathematics libraries have purchased physical copies of the books.

A new link for this book's website: https://www1.essex.ac.uk/maths/people/fremlin/mt.htm - but it seems that the page linked in the post worked not too long ago. (I did not want to bump the old post - after all, maybe the old page will start working again.)

You may wish to investigate http://re-press.org/ in Australia. They are an academic press that is, I believe, affiliated with an Australian University. They appear to do exactly what you describe -- make the PDF freely available and simultaneously offer a print version. We will be offering PDFs of our books through Google Play, but haven't yet found a way to subsidize this; at this stage of our development, we still have to charge, both for print versions and for PDFs.

There's epress.com (appears to publish an online biology journal) and epress.com.au (appears to be a printing company) ; Do you have a link to the publisher?

Another open-access friendly publisher is Athabasca University Press.  They're currently in the process of publishing my textbook that @JeffE mentioned.
http://www.aupress.ca/index.php/books/120226
They've been pleasant to work with and, in particular, were fine accepting a non-exclusive license to publish the work.  This still allows, for example, a student society to print, bind, and sell their own copies if they can do it for less than what the publisher is charging.

Spartacus-IDH is a French science publisher. If I correctly understand the site, all books are freely viewable and some are freely downloadable as PDF. The catalogue is meager so far, but I see no reason why it shouldn't grow.


text:
How to publish an article that is only one page long?
I am interested in publishing a journal article that is only 1 page long. Most journals want more lengthy articles. The area of focus is Chemistry. How to sort through all the requirements without reading each journal individually? I think maybe a consultant knowledgeable in this area would be ideal.

Are you sure you should not add more introduction, discussion of related research, cite more references, ...?

@J.FabianMeier  It is possible to do so but some clarity gets lost.

Yes, but depending on the field, you might be rejected just because you did not make your contribution clear enough.

For fun, "The Ratio of Proton and Electron masses", Friedrich Lenz, Phys. Rev. 82(4) 554-554 (1951), is two sentences, three lines long (four counting the one reference cited, or 8 total including title and author affiliation). Further note that it was in the "Letters to the Editor" section that became Physical Review Letters. Older Nature and other journals also often had fairly short contributions. If it is clear and concise and makes a contribution, there must be some letters journal that would take it.

Have you considered publish it as a letter in the relevant journals? 1-2 pages long letters are common in Chemistry

Basically you’re asking to write a short letter, comment, or communication. Some, but not all, journals allow for such submissions, although usually they are in response to an existing article in the journal.

I'd walk back that "usually" to "sometimes" - my field has a large number of very short but unlinked to another article publications.

There are "letters" journals that specifically deal with short publications. But I don't see a lot of standalone "one-pagers." (I believe we are in similar areas, researchwise.)

For example, the January issue of Infection Control and Hospital Epidemiology has five one-page stand-alone "Letters".


text:
Employer contributions deducted from quoted salary—is this normal?
In order to help in future salary negociation, I wanted to know whether it is condiered normal in North America to be quoted a gross salary that does not take into account employer contributions to things such as a a mandatory pension plan.
Specific example situation
This question is based on a situation I am experiencing right now, so I will use this to illustrate more specifically what I mean. I have just accepted a postdoc position (in a Canadian university, in case this is relevant), for which my advisor offered a salary of $40,000.
He wanted me to start working very quickly and I was available, so I started working without having signed my contract. Two weeks after, he explained that the work contrat was ready, and that the amount I would see in it (ca. $36,000) was the $40,000 he had quoted minus the contributions towards the pension plan and group insurance.
It was not obvious to me whether the deducted contributions were my contributions, i.e. $36,000 minus withheld tax would be my net income, or whether he had deducted the employer contributions and my net income would therefore be $36,000 minus my own contributions minus withheld tax.
I sent an email asking just that, and my advisor came to my office, slightly on the defensive I thought, to explain that the grant he had for my salary covered only $40,000 per year in total but that he had decided he would pay for the employer deductions with money from a different grant, and therefore that a new contract would be drafted.
And here I am, wondering whether there was an honest mistake or misunderstanding, whether I'm being a diva and my advisor just doesn't want to deal with it, or whether someone has tried to screw me.
Your answers will help me address this concern but mostly, as I wrote, will be helpful to me and I suspect to others in knowing exactly how to negociate their salary in the future.
Disclaimer
And before anyone tells me, I do realise that I am getting an adequate salary in the current conditions and that I should consider myself lucky to have a pension plan and group insurance.

Your advisor is the wrong person to talk to about this... talk to HR/payroll.

I personally don't think CA$36000 (€26.5k, US$28.4k) before taxes is an adequate salary for a trained scientist with a PhD who can churn out papers, given access to a desk and a computer, with considerably less supervision than a PhD student.  But who listens to me? ;-)

@jakebeal, I suppose it would have been easier talking to HR, but my advisor seemed insistent on handling the whole process, including answering the emails I sent to both him and HR. I'm not sure whether that's usual in this university, or whether it's just his personality, or maybe it's just because he's the provost...

@gerrit, I meant "adequate" in the sense of "within the range of normal salaries". Given how many hours a postdoc works, that may just end up slightly below the minimum wage... I suppose that's the price you pay in order to have a chance of maybe someday lending a faculty job and multiplying your salary by a factor of three overnight. :-P

Some quick Googling reveals that this seems to be a normal postdoc salary in Canada. But just because it's normal doesn't mean that it isn't insultingly low. Unfortunately, it tends to be a "like it or lump it" scenario :(

To deduct employer contributions from the salary as well as employee contributions would be highly unusual, I believe. (If it were the norm, then there would be no need for a terminological distinction between employer and employee contributions.)
EDIT: Here is my guess about what happened (purely speculation).  Perhaps there are contributions that are classified as "employer contributions" for tax purposes, and the university requires these contributions to be made for postdocs as well as regular employees but only makes the contributions for regular employees, so for postdocs the money has to come out of a grant instead.  This situation has the potential to be confusing, so perhaps your advisor simply forgot about this until you reminded him, at which point he realized that he made a mistake.
In any case, the question you asked him in your e-mail was completely reasonable.

In general, unless otherwise stated, you are normally quoted gross salaries, which are of course before any automatic deductions have been made. If you were somewhere like Germany, you could consult tables which tell you how much your post-tax salary would be, but in the US, there are too many variables (what health plan is selected, how many exemptions you choose to declare, and how much you choose to put into various retirement plans) for either faculty or even HR staff to be able to give you accurate information on the net salary.
However, the employers' contributions are not supposed to be included in the gross salary, since that's not what you'd be expected to pay taxes on.

It seems to me that the OP is saying that employer contributions have been deducted from the salary as well as employee contributions.  This is highly unusual, I believe.  If it were the norm, then there would be no need for a terminological distinction between employer and employee contributions.

@TrevorWilson that is sufficiently succinct and on-point that it ought to be posted as an answer.

@mweiss Ok, I will do that


text:
Paper with editor for longer than two and a half months
I have submitted a paper to a journal 2 and a half months ago. Its status remains "With editor". From your experience, is this normal? If not, how should I deal with that?

This question is probably relevant here: http://academia.stackexchange.com/questions/5793/how-much-time-should-i-spend-on-reviewing

I'll add that anecdotical “answer” here: even in a given field, it depends on the journal, the editor, and the circumstances. My fastest submission-to-online-publication time (for a peer-reviewed journal) was 24 days, and my slowest was 11 months…

Related: http://academia.stackexchange.com/questions/10999/how-long-is-reasonable-to-wait-for-reply-from-an-editor#comment20229_10999

Don't forget it is summer vacation time, it can be quite difficult to find suitable reviewers. But you can always ping the editor.

The time frame you mention sounds long to me. But having said that, there can be several reasons why this is the case. I assume that the journal you have submitted to uses an electronic submission system?
Reasons can be:

The journal is crowded with papers
The editor(s) has/ve difficulties finding reviewers for the paper
The time frame is "normal" for the journal, "with editor" includes review time.

I suggest you try to figure out how long the time from submission to accept/reject (turnaround time) is for the particular journal you submitted to. If it is possible to see more details that would be good but knowing the average turnaround time allows you to assess if 2.5 months is long even for this journal.
Since I edit a journal I can mention our time frames as an example:

Choice of editor 10 days
Choice of associate editor 10 days
Chose reviewers 3 weeks
Reviews 3 weeks
Editor decision 3 weeks
Revision 3-6 weeks
Editor evaluation 3 weeks.

This puts the theoretical turnaround at 18-21 weeks (around 5 moths). What usually makes significant delays are reviewers not returning reviews on time and authors not providing revisions on time. But the bottom line is that for me 2.5 months is long and if you suspect your paper is held up too long you should contact the editor.

From my editorial experience, finding reviewers for highly specialized topics may take a longer time. It once took me more than three months once to send 15 or so invitations in order to find 2 or 3 reviewers... and I have to give them 2 months to complete their reviews, too.

Thanks, Peter and Damien. Unfortunately, I cannot find out the turnaround time of the journal. Being a Springer journal, I doubt that "with editor" includes review time.

One of my papers took well over two years to get published, thanks mostly to two review periods lasting around 10 months (IIRC).  So 2 1/2 months is not that outlandish.
But it does not hurt to ask politely about the status of your paper!  It may be well down on someone's list of things to do, and a polite reminder that you are interested in its fate may be all that's needed to bump it up near the top.  Presumably, if you ask, the editor will give some indication as to approximately when reviews might be ready, and then you'll know when to send another polite reminder if nothing has happened.

What was the typical review cycle stated for the journal on their website? The ones I submit to say 3 months. If the journal says 3 months, then a 10-month turnaround is not acceptable.

The reviewer might take a few months but it is highly unlikely that an editor will need 2 months in the status of "with editor".

Expectation of review time and time taken for the editorial decision vary widely depending on the field.
In my own field, chemistry, 2.5 months is about the time when people would start to send an email to the editor and ask about the status of the manuscript. A review of the reviewing process for Angewandte Chemie, one of the field’s flagship journals, shows a median “submission to editorial decision” time of 5 weeks, with an average of 6.8 weeks. I recommend this paper, because it's full of statistics, and contains many links to data and reviews for other journals in various fields:

How Long is the Peer Review Process for Journal Manuscripts?
  A Case Study on Angewandte Chemie International Edition
  Lutz Bornmann and Hans-Dieter Daniel
  Chimia 2010, 64, 72–77

You can find plenty of similar statistics for journals in various fields, by a simple web search: biomedicine, medicine, statistics, philosophy… This confirms my initial point that review times (and thus author expectations) vary widely on your field and the specific journal: the average review time in the Journal of Philosophy is 12.6… months!

Edit: oh, and I have to disagree with your comment below Peter’s answer… “with editor” most often includes the time spent in review. I would say always, because it has never been any different in my experience. Many web submission interfaces actually don't allow you to know the internal changes of status between the editor and the reviewers (apart from the American Physical Society system, where you can track every correspondence the editor and reviewers have exchange)

Thanks for your helpful answer. Usually, I get first "with editor" and then "under review".

I have only ever submitted one paper, but it is currently "under review", after being "with editor" for less than a week.

@AlexBecker there are plenty of different web submission software out there… some of those don't allow you to see the difference between “with editor” and ”with reviewers”, and some do


text:
How do you know the project you are working on is worthy of a PhD dissertation. How does it differ from MS dissertation
I am speaking of project scope here.
So suppose my advisor is working with an industry .And you are asked to build a prediction model for small section of that industry? Does that qualify as a Phd Project or a Master's thesis project.
Or does a Phd project has to be generic model , in the sense all companies in that niche can use that model as basis for their analytics?
I am trying to understand the differences in scope for a PhD and MS Thesis project.

I've had this discussion recently—the major differences are in the scope and independence of the work.
There is no easy, absolute method to say "X is a master's thesis" and "Y is a PhD project" without knowing the amount of work involved in each approach, and how independent the student needs to be.
Ultimately, a master's thesis represents a body of effort designed to show that you have successfully completed the project to the satisfaction of your supervisor. A PhD thesis indicates that you have produced a sufficient intellectual contribution to your field, and that you have the capability to be an independent scientist.

Standards vary a lot: for example, I've seen MS theses in theoretical computer science from Israel that are mini-Ph.D dissertations.
But more typically as aeismail says an MS thesis is a demonstration of mastery of a particular topic, and may or may not include original research as a part of this demonstration. In this respect, an MS thesis is closer in form to a bachelor's thesis, but the material will be more complex, and less structured.

The standards will vary quite a bit from field to field, committee to committee, etc. But having gone through this fairly recently, and having been in the position to advise some others:

Masters projects: Good Masters projects can be tied up in a single paper - and should be amenable to being published. But they are generally a single, coherent research question. Secondary analysis of existing data, a theoretical paper to support an empirical study, a meta-analysis, etc. are all good examples. There may be lingering questions (there are always lingering questions...) but by and large the student should be able to "walk away" at the end.
PhD projects, on the other hand, should lend themselves to multiple papers, at least the number of papers required for graduation, and preferably several more to accommodate changes in funding, research interests, dead ends, or the paper that seems to draw the ire of reviewers everywhere. It should be new, asking fundamentally unknown questions, or at least trying to get at known questions in a different way, and should be substantial enough that, at the end, the student should be able to consider that area to be their area of expertise.


text:
What if I forgot to bring my poster to the conference?
Until all conferences provide digital screens, this could happen. One may leave the poster at home/office or lose it in the train. I think what to do next should depend on the value of the work and the participation in the conference, the poster content, and the conference policy.
Options:

just talk about my work
present it on my laptop/tablet screen
print it on an A4 sheet, or get a larger sheet (e.g., from a flip-chart) and draw the outline and handwrite the key parts of my poster
withdraw from the conference (no poster, no presentation), but some people may be wondering why I'm not there.

What are the pros and cons of these options in regards to academic prestige and reputation? Usually, are there other better options?

Withdraw is the only bad option here! All the others are acceptable. As for academic prestige and reputation, I don't think anyone will care.

There are also software solutions to generate a 4x4 or similar print out of 1 file/image on "standard" sized paper - you can get something like that printed at any office store easily, add some double-sided tape an a nice poster-board and your done

Although @user2813274 's solution is not pretty, it is not too uncommon.  I know someone who actually won a poster award using a poster printed in greyscale on a series of A3 pages.

"present with laptop" -- if that's the fallback, some kind of presentation as you would have for a talk probably works better.

Print it locally.
Hopefully, your conference is in a city of some non-negligible size and not in the middle of nowhere.  Find a copy shop in the city and print your poster there.
Large conferences may even have their own on-site printing, although a last-minute print job may be expensive or even unavailable.
Some people do this in any case, so that they don't have to travel with a poster.
(Your university/employer may or may not be willing to pay for a 2nd printing of the poster)

+1 Always bring a PDF and the src files of the posters and in case it is stolen, you can always print in a local copy shop.

Last week my poster got caught in the rain while walking to my hotel. I printed a new (nicer) version in a local copy shop in A0 format.

I did this a few months ago when I lost my poster in the airport.  Do make sure to check the reprint, though: I didn't, and found to my horror that the local printer had corrupted the file and chunks of the reprinted poster were missing.  I ended up filling them in by hand.

@jakebeal what file format? With .pdf I've never seen anything that bad (I have seen files that fail to open)

@ChrisH It was PDF, and it was actually quite resilient: the file was actually truncated by the printer, and what came out was the document specified by the first N megabytes.  It was a quite bizarre failure...

@jakebeal that is bizarre, with sufficient digging I could probably figure out something about the pdf subtype you use -- certainly any compression was of a  very basic type.

@jakebeal I would produce another copy with reduced file size. Inkscpae once exported a PDF with a large file-size and unnecessary complex drawings. I opened it in a PDF reader and printed it using a PDF printer! The resulting PDF was lighter, less layers, and had smaller file-size. I also make sure it is readable by different readers, and that the fonts are embedded. I then put it on Dropbox and Drive.

This is basically what 24-hour Kinkos are meant for.

@schester What's wrong with a hand-drawn poster? Maybe even one that the presenter redraws while explaining? If done well, that can have a value >> many a poster I've seen, with cramped 10pt text all over it.

@schester Yes, definitely, except if you are able to basically wing a spontaneous flipchart presentation. (I have some topics I could probably do that for; others, not so much.) Hand-drawing a poster that was to be printed will probably end up being ... suboptimal. Follow-up question: would that be cheating? "I didn't get accepted for a talk, so let me hold the talk x times in front of a pinboard."

There are two levels of issues that you may have to cope with.
First, let's look at what to do at the conference:
You already suggested some options:

just talk about my work

This might serve as a last resort fallback, but it probably does not leave too good an impression.
Maybe more importantly, talking about your work might be more difficult than expected, because without a poster, you won't be recognized as a presenter. In my experience, poster sessions usually work in a way that the audience slowly wanders around, looking at poster after poster. If someone from the audience has any questions or wants some explanations, they will look for someone standing around next to the poster they are currently reading. Hence, if there is no poster, no-one might stop to talk to you in the first place, because you will be assumed to be just another member of the audience looking at the posters around or vice-versa of you.

present it on my laptop/tablet screen

That might be an option. Maybe you should make up for not providing a large poster by being ready to also run a small demo of your work, if possible, and if allowed by the conference.
If you happen to carry around a portable projector, you could even truly replace your poster.

print it on an A4 sheet,

In this case, I suggest printing tiles of it on several A4 sheets, so you can reassemble the poster.
As suggested in gerrit's answer, you can of course also try and find a way to print the poster again in its original size, which I too find (visually) preferrable.

or get a larger sheet (e.g., from a flip-chart) and draw the outline and handwrite the key parts of my poster

That's quite a valid replacement.

withdraw from the conference (no poster, no presentation), but some people may be wondering why I'm not there.

There are always some planned attendees who are not there (visa issues, ...). People who have already met you during the conference might indeed wonder, but a simple explanation like "unforeseen change in plans" should be sufficient for them, if anyone even asks.
However, as there are various workarounds, as described above, the possible repercussions from this might be too severe as to not try and use the workarounds.
Second, there is the question about your home institution:
First of all, the poster is (probably) university property, paid for by the university. Some universities might not care about getting back the posters, others do. In the latter case, things are not much different than losing your office laptop, or any other piece of equipment. (In fact, along with the poster, you probably lost a university-owned poster tube.) Unrealistic as it may be, these pieces of equipment are often not insured for business trips, or at least for trips abroad.
As such, be ready to provide a replacement. I am not saying your university, or your department, or direct superior, could not be lenient if this happens once. But be prepared that you may not get reimbursed for printing another copy of the poster at the conference location.
Then, there might be the more severe issue that occurs if you went to the conference with only the poster to present and nothing else. Attending the conference is probably worthwhile for you just as well, but chances are the business trip to the conference was formally permitted because you were "required" to attend in order to present your poster. This is why I would urgently advise against the option to withdraw your submission, if there is any other way, as otherwise, you may be found to have violated the basis upon which your trip is funded and thus end up paying the whole trip and conference fee yourself.

Good point that the presenter might not get reimbursed.  I added a similar point to my answer.

I have actually done this before -- finally managed to get the blasted thing printed out by about three in the morning, shambled home, left the poster tube on top of my bag, and still managed to leave it behind when I left the next^W later that morning.  There's a longer version of this story which involves much running around a building with flapping curtains of A0 paper, and mucho, mucho swearing.
Anyway, I managed to find and download a 'split up your postscript into A4' program, over the piece of wet string that claimed to be the rather remote conference's internet connection (no copy shops...), and with much help and sticky tape from the conference reception, assemble this into the original(ish) poster.
Upside: I had a poster that stood out!  And a funny story to tell, which together meant that I probably got a rather larger and more sympathetic audience at the poster session than the (in retrospect rather dull) poster actually warranted.
If there's a moral to this, it this: conferences are social occasions, with human people at them.  And if you can make a connection any way – whether it's a weird-looking poster, or a ‘here's me improvising with my tablet’ performance – you'll potentially make a bigger impact than if everything goes smoothly (well, that's what I told myself).

+1 for the final paragraph. The nice thing about poster presentations is that they're informal. That means people will forgive you if something goes wrong, and appreciate your creativity if you find some half-assed solution to present anyway.

It is possible to print a whole poster on A4 papers. It takes some number of them (5*5=25 for A0; it would be 4*4=16 with borderless printing) but that's something that is manageable. Then you only need scissors (to remove the borders on some sides) and glue or duct tape; and also some time. Reassembling the poster takes no more than 2 hours then.
This is certainly worse than re-printing the poster in one piece, but it's very likely cheaper (you usually pay less for 25 full-colour A4s from a laser printer than for an A0 poster from a huge prnting machine); certainly it's more professional than any of the options you list.
Also, depending on the branch of your research, it wouldn't be unseen to have an article printed in larger print (like A3 instead of A4) and pinned to the poster board in place of the poster. I've certainly seen this in math/TCS, and even in natural sciences once.

Indeed, careful with the last paragraph as it really depends on the field. I have seen only one "poster" that was actually a printed paper pinned to a poster board, and my immediate impression (corroborated by the very poor (not conversation-ready) English skills of the authors) was that they simply hadn't understood what a "poster" was supposed to be. (I'm in a CS field that is quite graphical and hence posters with too much text are frowned upon; other fields might differ.)

Rather than taping the pieces together, I'd recommend trimming (if necessary) and then just pinning, stapling, or tapin the pages directly to the presentation board (if the conference provides ones). Taping the sheets together (to each other as a full-size poster) will be an exercise in frustration that will likely not end up looking good.

"not unseen" != "acceptable solution"

I know this is not extremely likely to work, but if it does then it's a big win, so I'll just suggest it:
Ask the organizers to print it for you or to help you with printing.
Even if it's not a conference at which the organizers do the printing, they might still either have access to printing facilities for official conference materials, or at least, being local, be better equipped to help you get that printing done.


text:
Double blinded review but the appendix contains author's name
Before submitting a review for a manuscript, I noticed the appendix possibly contains an author name, but I don't know him/her. My file explorer automatically shows files' metadata, including author name.
The review should be double blinded. Should I inform the editor?

Are all papers from this journal double-blinded, or is it an option that authors choose? If the latter, the author is responsible for the double blinding, and if they don't do it properly, that's their responsibility (that doesn't mean it wouldn't be good practice to inform the editor that your review is only single blind though). If the former, I would have though the journal staff would be pretty hot at ensuring all author info, including metadata, is scrubbed. (Aside: the reality is that double-blinding effectively is often pretty difficult, which is why double-blinding isn't yet standard.)

When in doubt: yes.  Let them know when and how you found this potentially compromising information.  Especially if you think this may impact your objectivity (e.g. "I don't recognize this name, so I'm not going to trust him as much and may/will be more critical than I otherwise would"). But even if you think your evaluation will be unaltered, you should let the editor know.  They need to be the one to decide if the review process can still meet the necessary criteria, if the authors should be notified and asked to alter the file to eliminate the metadata, etc.
In your case it sounds like you did the entire review under appropriate double blinding, fully unaware of the authors while making the evaluation, and then at the very end of the process you gleaned a potential clue about the author name. If so, then the editor may accept that no actual problem has arisen, and may simply try to take steps to ensure such metadata is no longer visible to reviewers.
Things get more complicated if there are multiple reviewers for this paper: it now becomes possible that one or more of them saw this data early in the process, and it potentially compromised their review, but yet this went unacknowledged. This makes it all the more important to inform the editor.

+1 for "when in doubt: yes" Let the editor decide if this is serious or not.

Something to add: Everyone accepts that double-blinding is imperfect. In my experience, the reviewer instructions will usually say something about this. For example, they will say that it's OK if you know the author identities because you saw a preprint (but please disclose this), just don't go out of your way to identify the authors.

I have always informed the editor and in every case, he hasn't cared.  I seem to have a super-power in that I can recognize people by their writing style.  So I have always known who the author of the paper was, without any tell-tale flaws in data scrubbing.  There's nothing the editor can do to thwart my super-power.  (Well, perhaps he could have someone translate it into Chinese and then someone else translate it back to English, but it'd be better to just get a different referee.)  I just put in my comments to the editor that, "I can tell this is Bobby Boogy's work."  So I go for full disclosure and let the editor handle it as he will.

It's not only writing style, in some cases you can guess the author by the topic of the paper. Often, there are only a few groups working on a topic and you can easily identify them by their setups/methods or even style of figures and plots. This must not have any negative effect on the outcome of the review, since this is not the author's fault. That may be the reason why your editor does not care.

In my field there's no double-blind review (thank goodness), but since it's a very small field, I'm pretty sure that I'd be able to recognize most of the authors anyway.

Unless you think that this might have impacted your objectivity: No, there is no need to actively involve the editor. As you revealed the identity only after writing the review ("before submitting") objectivity is probably not an issue.
It is important to understand that double-blind is far from being perfect: In many cases the "secret of authorship" just does not hold for long. You know your colleagues, what they are working on, which tools they typically employ, their style of writing and so on.
Hence, so even if there are some common rules, double-blind should not be understood in a too formal manner. It basically is a code of conduct. (1) The authors agree to try their best to hide their identity. However, there is also the other side: (2) The reviewers agree to not actively try to reveal the author's identity.
In this realm you as the reviewer are supposed to not look into the PDF metadata. If you stumble across a single, apparently accidentally left-over name, try to ignore it. Yes, all this should not happen if the authors had done their job. However, we are all humans and as long as neither your objectivity is impaired nor you have the impression that the authors tried to "drop" their identity, there is no need to make too much of a fuzz about it.

Is it normal that the journal did not filter out the pdf metadata automatically in its submission handling system? That seems like a rookie mistake from their part.

@FedericoPoloni: I have seen it happening. Even more for conferences, though.

If everyone in the chain were to follow the letter of the double-blind process, then the paper either has to be rejected, or has to be reviewed by someone else, and your review may not be taken into account. So, if you like the paper and want to see it accepted, then perhaps you don't want to escalate the situation.


text:
Should I tell my supervisor that I will consult someone else?
I need an specific advice on a specific area (not the main one) in my PhD research (e.g. is it a good idea to include the factor x in the review and analysis of the topic y?).
As far as I know, my supervisor is not an 'expert' in this specific area.
I think that someone else, who has recently done a PhD in my department and has good connections with my supervisor, is an expert in that area and can help.
In academic etiquette: should I make my supervisor aware that I am asking an advice from that person?

Yes.  In the same tone that you use to describe finding a helpful book in the library.  Consulting experts, whether in the flesh or through their published work, is a normal and expected part of doing research.
The tone of your question suggests that you are worried that your advisor might be insulted by not being consulted first.  If this is a real concern, you need a new advisor.

+1 for In the same tone that you use to describe finding a helpful book in the library.

Yes. I am a graduate student and I have done this quite a number of times. Usually its no problem. In fact my advisers have always encouraged reaching out to various people in their specializations to ask for advice.
What I do is bring up the topic and then say something like "What do you feel about me reaching out to Dr. XX or Prof. YY about feedback regarding this analysis? Or this writing?"
Usually, they are very happy to agree or suggest alternatives. I recommend that you try this approach and see what comes of it.


text:
Which year for book reference: Copyright date or Library of Congress entry
The verso of the title-leaf says "Copyright (C) 2004 by Ken Author". A few lines down comes the "Library of Congress Cataloging-in-Publication Data" which in the second but last line has an alphanumeric code followed by the number 2003. The last line ends with a ten-digit number that starts with "2003".
Which date to use in citation?
While opinion-based comments are appreciated, a convincing answer should come with reference to some standard guide on citation, please.

The Library of Congress Cataloging in Publication record (the CIP data) is a record prepared by the Library of Congress for a book that has not yet been published.  You should use the copyright date.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Can students apply for Research Grants (US)?
I know you can apply for fellowships for individual students, but I'm not talking about funding only for one's self. Let's say I noticed a grant that was solicited on grants.gov and I wanted to apply for it. Can I do that?
The nature of these grants is to supply the awardee with funding for experimental set-ups, student funding (undergrad/grad), and other various research supplies.
& As a follow up question, is it possible to apply, if your PI is applying for this funding as well. Basically, could I send in a proposal and my PI could as well? Are there some restrictions here? I've read through the solicitation's eligibility and couldn't find anything about multiple names being on different proposals, or if we were to apply separately, then having the funding go to the same group under different names.
Just curious if anyone knew.
I'll write back, if I find more info.

Related: http://academia.stackexchange.com/questions/9611/applying-for-research-funding-as-an-independent-researcher

Technically, in the US, most grants are not normally submitted directly by the principal investigator, but are instead sent in via a "grants office" that acts as the interface between the principal investigator and the funding agency.
Consequently, in addition to the grant-specific funding rules you have from a specific funding agency, you also have to deal with whatever restrictions your university grant-office has. For instance, it's not likely that your grants office will accept a proposal submitted by a graduate student instead of by a faculty member or similar personnel (lecturer, research professor, etc.).
In general, though, you need to read the requirements of the individual granting agency, as well as ask your local grants office.

For your first question: you'd have to read the funding agency's rules for an authoritative answer.  I think the most likely case is that there are no restrictions on who may apply for the grant, and proposals from students would be considered, at least in principle.
However, your chances of getting such a proposal accepted would be somewhere between extremely slim and none.  The review panel is going to have serious doubts that a student will have the necessary experience and expertise to successfully manage and carry out the project.  Your proposal would have to convince them that you do, and unless your circumstances are very unusual, this will probably be impossible.  Given the substantial time and effort needed to prepare a grant proposal, it's almost certainly not worth it.
For your second question: the PI normally lists on the grant application all everyone participating in the project who will be supported by the grant, including students.  Those people are normally not eligible to apply for their own funding.  And if you are not on the grant, then you're nominally working independently of the PI, and why would an agency want to award grants to two different people to do the same thing?

the most likely case is that there are no restrictions on who may apply for the grant — Really? I would expect exactly the opposite.


text:
Is it a breach of protocol to contact people higher in the academic hierarchy for social reasons?
I met two people at a past conference and we had a nice conversation there, but no further contact. Recently, I've seen their names on the list of accepted papers of an upcoming conference I'm attending. Since I'll stay at the conference location for an additional day afterwards and don't know anyone else there, I planned to write them an email and ask whether they had any plans for that day.
However, during looking for email addresses, I noticed that they are both full professors, which I wasn't aware of before. I'm a PhD student. Would it be a breach of etiquette to contact them? While conferences are often used for networking, I don't want to make anyone uncomfortable.

Is there any reason why you can't wait until the conference to ask them if they have plans for the additional day? I don't think there's really any issue about etiquette or protocol, but I'd probably want to have spoken to someone more than once before making plans to spend time with them. If nothing else, we've all had experiences of the person you get on with well the first time, but not so much subsequently.

Also keep in mind that you'll meet lots of other people at the conference, and some of them may be around on that additional day. I've certainly been in that experience and found other people to spend time with.

It is great that you are thinking about networking as a PhD student.
My advice would be escalate the relationship by one step. Going from a "nice" conversation at a previous conference (where no email or contract info was exchanged) to a social activity outside of a conference is a bit like asking someone you had a coffee with once to go on a trip with you. It escalates the relationship very quickly and could get awkward. Furthermore, many people don't stay extra days at conference locations so it is likely to be unsuccessful.
Less intense ways to connect:

Send them an email saying that you noticed they were presenting at the conference, and you are looking forward to seeing their work and chatting again
Run into them at the conference (as Ian_Fin suggested) and ask what they are doing for dinner or lunch on a conference day


text:
The Importance Of Final Year Results In US PhD admissions
How important are final year ( more especially final semester ) results in PhD admissions?
I am on MEng course in the UK where final year results are usually released mid to late July, and I intend on applying to US universities, now when reading on the application procedures at many universities I noticed that the application deadline for a lot of US engineering PhD programs seems to be from late November to late January, with admission decisions usually being made around April.So I am curious to know how important final year/semester results are in a PhD application.

One comment here: decisions are usually announced by mid-March, not April. Student acceptances are usually due in April.

Admissions to US graduate programs are generally conditional on final-semester grades. That is, you are required to pass your classes, and in general maintain a reasonable GPA in them. Developing a case of "senioritis" and getting D's on everything could have an effect on your admissions offers. (Whether or not it will depends on the department and the school.)
However, the grades earned in the final semester do not influence the decision whether or not to accept you in the first place; that is determined by your grades up through the end of the first semester of your final year (or the last semester of your penultimate year, if the grades aren't available by mid-year).


text:
Career for a mathematician outside academia
Briefly, the question is: what are sensible career choices for a trained mathematician (with a doctoral degree) outside of academia?
The situation I've found myself in is the following. I have been employed as a teaching assistant at one of the top Polish universities for a year now. The salary of TAs in Poland is borderline acceptable (as in, if it were a little bit less, one wouldn't be able to make ends meet), but when I was signing a contract, I was promised I will be promoted to assistant professor after a year.
Now, I was informed a few days ago that I am not getting said promotion, but they'll be happy to keep me as a TA. It was stated very clearly that this is happening not because I am not doing my job properly (in fact, I have a pretty solid track record); apparently the university is in financial troubles. As a corollary, I may be stuck as a TA for quite some time.
I have a family to provide for, so this is unacceptable for me.
To make matters even worse, the timing of the information left me without any option to pursue a postdoc position. This got me thinking that -- even though I enjoy doing research and teaching very much -- perhaps it's time to take that step and decide on changing career path. The problem is, I don't really have any experience in work outside of academia. I feel that I am professional and disciplined enough to handle any kind of work, but sending resumes at random doesn't seem like a good idea.
I realize the question may be too vague, but I'm thinking maybe someone has already been down that road and has some advices to share.

The all-time top question on math.SE may be of use to you.

What is your field? I think a mathematician of topology and a mathematician of stochastic equations are quite different.

How about a part-time teaching job at some private university (just for the money)? Also, if your research record is good, perhaps a place like IMPAN (http://www.impan.pl) is also worth considering?

There isn't anything. Sorry, it sucks; I'm in the same boat, and I hate it. It's not hard to get a job in industry with a math degree, but you won't be doing (nontrivial) math.

What did you do in the end?

The past few years, many friends, either mathematicians or people from physics/chemistry who knew how to write code, have gone other to various financial companies to do algorithmic trading, data analysis, that sort of things… and some others have joined web startups. In short: their coding, algorithmic and reasoning skills were more valuable than their specific academic knowledge.
What I would advise you to do is to look where alumni from your department have moved. Ask the department for statistics or listings, if they publish them; otherwise, look up people's names on the web or professional networks (LinkedIn comes to mind). See where they are now: this will give you an idea of who is hiring people with your skills (and network).

+1. From folks I've spoken to (so this is hearsay, but I'm repeating it accurately :) ) the skills developed doing high level education in math (computer work, grasping abstract concepts quickly, etc) are considered very transferable. And if you want to stay in academia, try looking around other departments. For example, I made a jump from researching statistical model fitting to bio image analysis not too long ago, as they have loads of big datasets to process and funding to hire someone to do it. Just look around - compared to many, you're really not in too bad a position to find something.


text:
Should conferences do early rejection?
A number of conferences have moved to a two-phase review system, in which for example all papers get two reviews, and then any paper that has received at least a "weak accept" advances to get two more reviews.  In the conferences that use this, I'd say that typically 1/3 are eliminated early and ultimately receive only those two reviews.
In general, conferences stick to a single notification deadline.  If they opt for rebuttals and offer a rebuttal after the first phase, authors may withdraw upon seeing the writing on the wall.  But if there's no interim rebuttal, authors don't find out until the notification date that their paper was dead perhaps 4-8 weeks earlier.
I'm familiar primarily with computer science systems conferences.  In fact, I have served on a fair number of program committees, chaired a few conference TPCs, and serve on some steering committees.   I'm curious whether the two-phase review system is used in other fields, and if so, do any release the rejections early?  And of course I ask because I wonder if I should advocate that conferences I have any say in move in that direction.

As a datapoint close to you, ICSE used to do this (two-phase reviews, early rejection for already dead papers) I think two years ago, but it appears to have been a one-time thing.

@Xleitix,  I wonder why 1 time? Failed experiment?

I am not in the PC, so I can't tell. I think it just has to do with them moving on to a more common rebuttal phase.

Thanks for this post @FredDouglis.  if I may ask an off-topic question, that is, suppose a conference has ~25% acceptance rate, does that mean out of the approximated 1/3 that move to the 2nd round, ~75% will eventually get accepted?  (1/4)/(1/3)?  Thanks

@oikos99, I had said maybe 1/3 got eliminated.  That means 2/3 move to the 2nd round, but of those, only less than half would eventually be accepted.  But it all depends on the conference.

@FredDouglis thanks for the correction.  I understand now :)

I'm in the health and social sciences and I have never attended a conference that has used this format for submissions. This seems like a lot more work for conference abstract reviewers and program committees (all who are volunteers).
I have seen a movement towards "late breakers," where you can submit an abstract for a subsequent round of reviews, often after the initial acceptance/rejection notifications are distributed. You typically are not able to re-submit a rejected abstract, but could potentially revise or (ideally) propose a different project for the conference. I guess there are pros and cons of each approach.

I guess a response that says that a field does use this is much more useful than one that says they don't (which I think will be the default).  Regarding work, these are not abstracts, they're full papers.  They are being reviewed anyway.  The decision about moving to round-2 reviews is being done anyway.  My only question is whether having a button to press to say "tell everyone who didn't go to round 2 that they've been rejected" would be a good thing or a bad thing.  A bit of work for the paper submission system, but no one else.

Oh, okay - this is a little clearer now. I would advocate for sending out rejections as soon as possible, because this gives time for individuals to revise their work and submit elsewhere. Nothing seems to slow science down more than the review process! LOL


text:
Filtering spam invitation emails
Is there a readily compiled, contiunously updated list of email addresse and/or domain names used in spam messages from predatory journals or conferences, or phrases or keywords that could be used to safely filter out such spam messages in email clients (without removing non-spam emails)?

I don't know of any, but I made one for myself to filter out 'To Dr My Name' as I'm not a doctor!

I would expect this list would expand so quickly and would have to be updated so often (every hour?!), that you can just as good not use it. I tend to remove everything that says "Dr. Researcher", "Dr. M Mark", "Dr. orcidid://...", "Journal of [what the f.. is that?]", "Journal of [xxx and] Research". I find spam emails are fairly easy to recognize without reading more than two words.

I keep them in a separate folder, which I check, so no nothing goes astray for me. Work colleagues and I like to share them around and make fun of them, especially when they claim I'm an 'eminent researcher in a field' of which I do not work in.


text:
Can an editor examine a PhD student whose manuscript is under review in their journal?
Do conflict of interest arises when a journal editor, who is handling a paper under review, acts as an examiner of the author's PhD thesis?
Does it depend of the review stage? Will the answer change if the review is already finished before the editor is nominated as an examiner?

as long as it is not affiliated with institution, i dont see a problem

The rules for PhD thesis examination vary country by country and even unversity by university, so I don't think this question can be answered here. (For example, I submitted my last paper a few hours before I submitted my thesis for pre-examination; on the day the committee selected the examiners it was not even possible to know whether one of them would become an editor of the last paper. In some universities, this timeline might be impossible.)

In the US system, my main concern in such a situation would not be conflict of interest in the thesis examination but rather would be conflict of interest in the journal reviewing process.
In the US system, a good advisor generally ensures that the examining committee are people likely to approve if the student does good work (e.g., no philosophical enemies) and ensures that the student does not go up to defend until they are certain to pass.
Members of a thesis committee are thus typically either members of the same department or close external collaborators, who should typically be barred by conflict of interest from handling a paper from that student at a journal in any case.

Thanks. Could you elaborate on why/how thesis examination may cause conflict of interest in the editorial review process?

@Orion Examining the thesis doesn't cause a conflict of interest. However, the relationship that causes one to be added to a committee would also often imply a conflict of interest. For example, Alice and Bob are working closely on a project, so when Alice needs a committee member for her student Carol, she asks Bob. When Carol submits her paper, Alice will probably be a co-author, and Bob probably shouldn't review it because he collaborates closely with Alice.


text:
Waiving library costs if the student has own access
Costs of print and electronic resources including access to journals and books are usually part of tuition fees for PhD and MSc programmes.
Are there universities which waive such costs if the student doesn't need them, e.g., has his/her own or external adequate resources?

Libraries (usually?) don't pay for access per student, so I'm going to guess this is incredibly unlikely.

I agree with @MJeffryes - library access and many other things are lumped into 'overhead' - it isn't a long itemized list of support for various university facilities that you can cross this or that off of.

Also, I don't think universities usually have the infrastructure in place to exclude particular individuals from using library resources. At most institutions, access is available for anyone using the university's IP addresses.

I'm not sure why you ask this question. I hope you don't intend to choose an institution based on this. Likely there are such places. Likely they are rare. Among other things, such fees provide general support to the library and the containing institution.

Why would a student have so many subscriptions on their own? Are you enrolled in two different universities?

Could you specify "external adequate resources"?

I never use the south walkway behind the dining hall that goes past those statues on the way to the Fine Arts building. I always walk west from the dining hall, into the English building, and take the tunnel to the Fine Arts building. Could I get a tuition discount that prorates out the upkeep costs of that walkway? While we're at it, I never check out "A Tale of Two Cities" from the library because my uncle has a copy, I should get an additional 50 cent discount. Thanks.

@Robert. Irrelevant comment. I didn't call for tuition fees waiving. I asked whether there are universities which allow that. Thanks. ;)

I have never heard of such a thing.  Such access is always made available to all students, and any associated fees would be mandatory.  They might be waived on the basis of financial need, but not on an "opt out" basis.
With a policy like you suggest, I'd be worried about students opting out to save a little money, and then discovering they needed access more than they thought, with an adverse impact on their studies.
Also, on a practical level, these systems are usually not designed to be able to grant or deny access to individual students, so they couldn't easily restrict access to those who had paid.  Often access is on the basis of IP address range, so that all you need is to sit down at any computer on the campus network, without any further authentication.


text:
How to cite a published review report of a journal article?
I found an interesting idea that was discussed in detail in a published reviewer report on an article in journal X (an open peer review journal) and I want to mention it in my manuscript.
How to cite and reference that reviewer report in Vancouver style?

What is your reference management software (of the likes of Endnote or Zotero) suggesting on the matter?

@G-E How does that relate to the question?

the question is about how to cite, so a reference management software usually is used to help citing sources, and they usually have standard formatting styles available as settings, so Vancouver style might be an option available to automate the formatting of the reference.

What does the journal tell you when you hit the "cite" button on the page showing the review?

I haven't seen this issue raised previously but (a) it is likely to be increasingly common, (b) appear on the face of it to present unique problems, but (c) actually be accommodated reasonably well within existing guidelines (e.g. American Psychological Association style, MLA, Chicago, Vancouver).
It is probably most useful to give a specific example. Unfortunately, I could not easily find a suitable medical-sciences paper that, itself, used Vancouver style ... but I did find a paper in American Historical Review with the following basic information.
Here is some additional information about a specific open review:

Journal title: The American Historical Review
Title of the submitted manuscript: History Can Be Open Source: Democratic Dreams and the Rise of Digital History
Source web page for original manuscript: https://ahropenreview.com/HistoryCanBeOpenSource/manuscript/
Title of review: Reader's Report #1 (Second report)
Web page source of the review: https://ahropenreview.com/HistoryCanBeOpenSource/readers-report-1-second-report/
The final revised manuscript of the authors is available here: https://ahropenreview.com/HistoryCanBeOpenSource/second-revised-draft/

Vancouver
Now pretending that it is a medical-sciences paper using Vancouver style ...
For the review:
[Reviewer's Last Name, First Initial(s) if available]. *Reader's Report #1 (Second report)* [Internet]. The American Historical Review. [cited year month day]. Available from: https://ahropenreview.com/HistoryCanBeOpenSource/readers-report-1-second-report/

For the final revised manuscript:
Author(s) Last Name First Initial(s). *History Can Be Open Source: Democratic Dreams and the Rise of Digital History* [Internet]. The American Historical Review. [cited year month day]. Available from: https://ahropenreview.com/HistoryCanBeOpenSource/second-revised-draft/

In Vancouver style, you'd likely include "[cited year month day]" with the date you accessed the web page. Also, the author(s) name and details should be provided as they appear in the source. If multiple authors are present, list them in the order they appear in the publication.
APA
For the sake of completeness, given that my example is actually from the humanities ...
For the review:
[Reviewer's Last Name, First Initial(s) if available]. (Year).*Reader's Report #1 (Second report). In *The American Historical Review*. Retrieved from https://ahropenreview.com/HistoryCanBeOpenSource/readers-report-1-second-report/

For the final revised manuscript:
Author(s) Last Name, First Initial(s). (Year). History Can Be Open Source: Democratic Dreams and the Rise of Digital History. *The American Historical Review.* Retrieved from https://ahropenreview.com/HistoryCanBeOpenSource/second-revised-draft/

Note: Your should replace "[Reviewer's Last Name, First Initial(s) if available]" with the actual name(s) of the reviewer(s) if provided. If the year of publication is not explicitly stated on the webpage, use the access year or an approximation. Again, although I could see indicators of an approximate date, the web page doesn't seem to say when it was published.


text:
Promoting research papers with targeted ads
I've seen a targeted ad on Facebook about a new study by a public university (linking to a news blog). The ad was paid for by the university.
Is it common in academia to use targeted ads, paid for by a project's money, to disseminate research findings? Does it have any ethical issues?

You don't suggest what the "target" is. That might have a bearing.

I mean the target looks like academics in my broad field.

Likely benign, then.

Actually the practice is old, though using Facebook may be new. My old alma mater regularly sends out publications and news items "promoting" research at the university. I think the intent is more to promote the university itself, however, though some of the news items are worth a look if the research suggests new breakthroughs in, say, medicine. And, I suspect that the practice has always included a certain amount of "targeting", though using older technologies. A special newsletter for billionaire donors, for example.
But, yes, there are ethical issues, and the university needs to consider the impacts of such things. I have doubts about "using a project's money". I don't know if that was the case or whether it was just the normal PR practice from funds allocated for that. And promoting dodgy research would have serious ethical implications, of course.
Note that my alma mater is a large US State funded place (an R1). In a sense, what they are doing is saying to the general public: Look at us, we do great things here.
And that same general public actually provides serious funding for the place via taxes and grants. So, pretty natural, so far as that goes. In fact, not reporting back to the public in some way about how the money gets spent would have its own ethical issues.

There are research grants/funders that require promotion of the work done (it's called "dissemination", but it is not necessarily purely academic.


text:
Risk register for 'office-based' research
I'm writing a grant application for a 1.5-year research project in which

I'm the only member
a systematic literature review (some papers may be pay-walled) will be performed
the main study data (de-identified) have been already collected in a previous study
the only required logistics are an average computer (already provided by the University) and open source software.

Of course, the application includes conference presentations, travel to meet collaborators, and open-access publications, etc.
From the funders' perspective, what kind of risks that should be addressed in such a research project?

Is the funder asking about risks to human subjects?  Your local IRB or equivalent would presumably find that the risks to human subjects from this kind of meta-analysis were tiny or non-existent.

Which funder? The funder I work for would view your team (if it really is just you being funded on the project) as too weak and risky to give money too. Others might have a different view, especially if your project is cheap.

I guess there could be many, but:

The existing data might not be good quality or sufficient quantity.
Reliance on a single person may lead to failure if they have health problems, or get a new job.

Thanks. How these risks could be effectively addressed in the application?