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Is grad school typically time-intensive?
I would like to know what is graduate school supposed to be like? I started grad school for mathematics 2 months ago and I find myself studying all the time with no time for anything else (except activities of daily living). Is this typical?
Some notable advantages that I have:
I commute from school to home.
I am a U.S. citizen and obviously did not have to venture outside of home for any of my schooling.

It should take up a lot of your time, but not all. Be sure to get regular exercise, and find a way to socialize with people outside your department at least occasionally.

How far along in the program are you? I found the first few semesters the hardest because I had to spend a lot of time on "foundation" skills (e.g., using LaTeX). If you moved to a new city or country, that also makes it harder -- you suddenly don't have friends and family around to rely on and you may be suffering from culture shock.

I would further like to support the point made by @FrankThorne about exercise. Attempting to be healthy through various activities outside of work is both, a sanity check as well as a stress reduction tool for me.

Graduate school is an experience and like any other experience, it differs for different people.
You may or may not let your work overwhelm you. That is entirely your choice unless you have to catch up with your cohort. Time management is one of the most important skills to learn in graduate school and as I understand, it carries over to real life significantly later on.
Therefore, specifically in response to your question, your current experience is typical for certain graduate students but not all graduate students.

"That is entirely your choice" -- I disagree. Good time management skills certainly help, but even David Allen is limited by the number of hours in the day.

That is a different premise in my humble opinion. Hours/day is also a relative time scale. One of my advisers always tells me that if you cannot do all that you need to do during the time you set aside for work, then you are not doing something right.

Most graduate schools take a "firehose" approach in the first semester or two, so a heavy workload is to be expected, although it's certainly not desirable. That said, however, it should not be all-consuming—but it's also true that it can eat up all of your time, if you allow it to happen.
One of the things that I tell all of my students is that time for relaxation and non-study based activities is just as important as finding time for classes and preparing for examinations. In fact, not having the "outlet valve" can make you less productive overall; mentally and physically such behavior is not sustainable over a long period of time.
Therefore, I tell my students—as well as undergraduates that I mentor who intend to go to graduate school—that they need to schedule relaxation time into their week. What they do and when and how they do it is up to them; but there needs to be something to balance the stress of being a graduate student.

Short answer: Yes.
Grad school is an extremely time intensive activity. Depending on where you went and what you did for undergrad, you may feel overwhelmed. Rest assured that grad school is designed to eat up all your time and you are expected to dedicate your life to it. That said, it should eventually be somewhat enjoyable.

I disagree. Graduate school is not designed to eat up all your time. Time management is key.

I have had a slightly different experience that what is mentioned here - I have worked full time while completing my PhD.  That means a lot of time management, as well as stress management is required.
Break up each task into smaller manageable subtasks and allow yourself rewards and most of all, as has been mentioned, time to enjoy some hobbies and recreation.  This is critical - you'll potentially burn-out other wise.
Having a job (volunteer or paid, full or part time) is also a good way to force you prioritise tasks and deadlines, the job also provides a break from study and vice versa - this is a mindset that develops over time.
You will be busy, but be sure that you are doing something that you enjoy, it won't be a chore, it will be something to look forward to.

In addition to the other good answers, "Yes." It is a situation in which there's no such thing as "being too good", of course. People who've been easily top-in-their-class are now "average" in the population. Very disorienting. Also, as noted, there is a pretense that people "catch up" at super-high-speed by doing 30 hours of homework each week, etc.
So, yes, the pretense, the hype, the mythology, and the disorientation seem to tell people to spend every waking moment "studying".
Among the bad/silly side effects or versions of this is the one wherein one merely frets all day, rather than doing anything constructive. Or "obsessing" about small things, individual homework problems that are of dubious significance, etc. Pointless.
Also as noted, it is important to get sleep, exercise, and reasonable food, to say the least. Chronic sleep deprivation (and dubious diet) is all too typical in the relevant age-group in the first place, and having added seeming-motivations to sacrifice sleep, exercise, and diet just makes everything worse.
As many people have said on many occasions, getting a PhD in mathematics is not a "career choice", because it's waaaay too much work in comparison to the (extra-mathematical) rewards. It only makes sense if one is fairly obsessed with math in the first place, and can continue to have that degree of irrational interest despite workload and temporary loss of self-determination.
That is, by normal standards, it is not reasonable to aim for "a normal life", whether in grad school or thereafter, because it's maybe not possible, any more than performing musicians have "normal lives", whether classical or jazz or pop or...  The idea is that it's a hobby that, quasi-miraculously, pays a living. (This is different than engineering, apparently!) If one can keep that feeling, then it's fine!

Short answer is yes.  Grad school can be very time intensive, especially if you are coming from a small undergrad program into a large grad program, as your background knowledge may not be up to snuff.


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Applying to a Math PhD program which doesn't require GRE as a physics/math major
I finished BS degrees in math and physics, and doing MS in physics.
I will be applying for PhD programs (mostly physics), interest in mathematical physics, and have taken only the Physics GRE. I found that Stony Brook mathematics dept does not require math GRE, so I am asking:
Can one expect to reasonably predict if it look bad to apply without a math GRE score, given that my background in math is (all pure courses starting from multi-var calc/linear alg/diffeq two semesters of analysis one semester of abstract algebra, undergrad diff geom., two semesters grad. diff. geom., currently in grad. analysis (and of course self-taught measure theory and point-set topology, complex analysis)) all A's.
No publications so far, but independent study in physics in understanding solitons of various classical field  theories, and string theory interpretations (used a little diff. geo (ADHM)).
And could one be able to predict if recommendation letters from at least one string theorist in a physics department will have as much impact as a rec. from a mathematics faculty?
Thanks

I don't think it will prevent you getting accepted.  I followed a similar path (Physics + Math BS, Physics GRE only -> Applied math PhD).
But I recommend that you decide who you would like to work with in the places you'll apply to, and write them a very polite, short e-mail explaining your qualifications and interest.  If a faculty member is interested in you, GREs won't matter at all.

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Is there such thing as too many references for one paper?
I'm currently reviewing a paper that has an uncommonly large number of references compared to the average number for that particular venue (more than 60 versus around 30). This is a regular paper, not a survey one, and although there does not seem to be wrong references, it feels like some are not really necessary, and the fact that one particular author is cited more than 15 times makes me worry that this paper is used to inflate the number of citations of that author (the submission is anonymous).
Should I mention this in my review, and try to examine which submissions are "abusive", or just let it go?

Does the journal have a policy on number of references allowed? Many do (mostly print journals), and would force authors to cut down the number of references.

As far as I know, there is no limit on the number of references, only on the number of pages, which is respected.

There is probably some discipline influence at work. In the social sciences, it is not uncommon to have around 50 references in a journal paper.

@shion: as I said in the question, the number of references is quite large w.r.t. the average number of references for papers in that venue

agreed. just wanted to point out a slight possibility.

I once wrote a paper that contained all references to papers not referencing themselves.  That was too many.

Accusing people sounds like a bad idea. Why don't you just try to remove some of the references? Are you allowed to do this?

It's really a judgment call… some people consider that more references is good, because it gives the reader a wider perspective into the issue, and some people consider it a bad practice (in old times because it wasted paper, but nowadays mainly because it obscures the more valuable information inside a long wall of text).
I have, as a reviewer, sometimes asked authors to cut down on the number of references, so it is certainly an acceptable practice. Here are some factors you may consider when making the decision:

Does each individual reference bring something to the paper, i.e. is used to back up a fact, idea, or to give credit for a specific (and relevant) new idea that it introduced?
Are references cited in block? I tend to consider it is very bad practice:

A series of recent experiments have shown systematically that current human-powered aircrafts are not suitable for mass transportation [refs. 9–21]

Each paper (or group of two or three papers, at the very most) should be used with regards to a specific point in the discussion.
Somewhat disguised form of the earlier: are long lists of claims and references justified? Sometimes many citations are used as “examples”, where a few would suffice.
Could some of the citations be replaced by one or two reviews on the topic?
Are the work cited really the seminal work on each topic/idea/experiment, or are there also less “worthy” works cited?

Finally, it is true that there are some unethical practices that can lead to inflated number of citations. Excessive self-citation is certainly one, but there are others. For example, some authors cite very widely papers from all groups in their field, even when it is not really warranted, in an effort to help their chances at peer review: the idea is that the reviewer is less likely to be harsh to a manuscript that cites 5 of her own papers.
And in conclusion, if you believe that self-citation was the motivation, there is nothing wrong with reporting your doubts to the editor.

I agree with @F'x.
But how we can respond to the reviewers' recommendation to add their papers in the references (as I guess from those recommended papers  comes back to special authors only)?

Blocks of citations are an accepted practice in the physical sciences.  There are often multiple papers that make the same point and are published about the same time - they deserve equal citation.

One1 thing2 that3 hasn't1,4 been5-7 mentioned8 yet1 is3-5 the9 effect10,11 on2,7,10 readability.12  References13 are14 a15 necessity16 but17 loading18 up19-21 a22 manuscript23,24 with25 too26 many2 will27 often3-5 make5-7 it28 more9,29-31 difficult17 for32 me33 to34 follow35,36 and37-39 can40 be3-5 a13-15,19,21-23,25-27,29-33,35-37,39,40 deterrent.41  If2,3,5,8,13,21,34 a3,14,15,19,26 paper2,7,18,28 turns1,6,18 off1,4,14,21,35 its1,7,32 readers,2,23 it's4,8,15,16,23,42 not6,28 doing1,2,4,8,16,32 its2,3,5,7,11,13,17,19,23,29,31,37,41 job.42

This answer may be too exaggerated. But, I still like it.

This answer is an example of the kind of paper that "turns off its reader", should this be downvoted then?

Very Nicely done!

I can only see one way to resolve this and that is to critically assess if all references are necessary. Self-citation can be a problem but it may be perfectly fine in situations where the author is a leader in, for example, a small field. Excessive citations can also be a sign of the author not being able to weed out the critical papers from the "mass". In some cases, it may be tempting to provide all the literature found on a particular topic wher perhaps a review paper or relatively new paper summarizing past work could be referenced using the form "(e.g. author, yyyy)", indicating it is one of several possible references on the topic. I think it is perfectly fair to ask for such changes if the excessive referencing is clearly just excessive.

I do not think that there are inherent problems with citing some "extra" papers, if they are appropriately relevant. The purpose of citations is to help us form a network of research. If a paper is not cited, then it will not join that network. However, one does not need to cite every paper that an author has written in the past 5 years in order to maintain that network!
Rather than spend time examining each citation, perhaps you could ask the author why there are so many citations. If the author(s) has been inflating citations without due cause, then any academic worth their salt should promptly correct that indiscretion.

I wonder if the authors considered the question When you reference an article, is it always expected that you have actually read it?
I can imagine multiple likely reasons for the high amount of citations by one particular author:

The over-referenced author is a member of the same group as your paper's authors (or even themselves) and they try to promote their own work. This may be adequate if the cited papers honestly led to the new one, but if they are just loosely related (if at all), the amount of citations should be severely reduced
that author is one of the big-shots in the field, and the submitters either want to acknowledge that fact or they know that person is likely to also review the submission and would insist on these citations anyway - maybe this is actually already the reaction to such requests. And don't say this doesn't happen...

Unfortunately no matter the reason, to judge fairly you basically have to read at least the abstracts of said citations and check their relatedness. However, as F'x' answer suggests, if there are "obvious" signs of over-citation, e.g. block citations of more than, say, three publications, you shouldn't bother with that and rather directly state your concerns in your review.
Once the amount of references surpasses a sensible amount, the authors should maybe more directly justify the citation themselves instead of forcing each reviewer to figure that out on their own...

There should be a Goldilocks-range for this, and what this supposed to be depends on your field, topic (whether relatively new or not), and most importantly, your advisor and thesis committee.

(Image ref. PhDComics.)

What references are for : to justify statements only, including background.
When should one put references : when making a statement which needs justification not provided in the article.
When not to tolerate multiple references :

Careless scattergun references "on the topic".
Reference stuff to boost citation indices.

Why is this important :

Because a paper which does not reference precisely is a waste of the reader's time.
Because boosting citations is wrong.

Multiple references may be acceptable only if there are independent angles to reference.

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Can I put the editor in the Acknowledgements?
I am currently having an exceptionally good and fair editorial process with a paper.
One of the two reviewers suggested a rejection (still providing many suggestions for improving the manuscript).
The editor was able to understand that many issues raised by the reviewer were because of how the paper was written instead of the actual research design and the results of the study. Additionally, the editor was also able to understand that the study is multidisciplinary and that some issues were born on the side of the non-familiar discipline for us (both the editor and the reviewers are expert in this discipline). These issues were not severe but quite a few.
Instead of rejecting the article, the editor requested major revisions and actually provided substantial suggestions for improving the manuscript. Exactly how the reviewers did.
I revised the manuscript and acknowledged the "help of two anonymous reviewers". However, this time I truly feel that I should thank the editor, as well. I have never seen this in a paper. Is there a reason for that? Can I acknowledge the editor in my paper?

Note that some journals specify in their manuscript rules that you should not thank the reviewers/editor.

Thanks for reminding me that, @Bitwise. It seems it is not the case for this journal. However, I will check that in my future submissions.

There is nothing wrong with acknowledging an editor that goes beyond what can be expected. It is of course not customary to provide such acknowledgement in most cases. Editors do not expect it and it may simply appear as inappropriate attempts at flattery. It is difficult to draw the line where acknowledgements are appropriate but, I have probably acknowledged editors in a couple of percent of my own papers. I have also been acknowledged a couple of times in my capacity as editor (out of editing hundreds of papers), all in cases where I have felt my assistance would save a paper that could otherwise be buried undeservedly. In any case, your description seems to fit a case where the acknowledgement is appropriate, although no editor would probably expect it.

Thank you. I would limit myself to just acknowledge the editor (by name) in the same way that I acknowledge the reviewers, for their insightful suggestions.

@dgraziotin: beware that some journals list on each paper the names of the involved editors; and in any case, the editorial board is public. So, acknowledging the editor by name only could seem like you are close to him or her, and might have gotten a favor treatment. It might therefore be better to specify that you acknowledge help provided during the editorial process.


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Do textbook publishers really offer ethically questionable inducements to professors to adopt or retain their book?
I teach at a community college, and my experience with textbook reps is that they're very friendly and persistent, but ultimately all they've really done is to give me a copy of their book and try to convince me to adopt it. There are certainly many unethical things about textbook publishing, but as far as I could see, they were decisions made by executives in New York (e.g., bringing out new editions to kill off the used market, or shrinkwrapping the book with useless trinkets so that it couldn't be returned). In online discussions, I've often heard people who seem to be students make claims that professors were "bribed" to use a particular publisher's book. I never believed these claims, and when I asked these people to supply evidence, they never had any.
But recently I was talking to a colleague in another department, and he told me that his department would never change their book for a particular course, because his colleagues got ethically questionable inducements from the publisher. When I asked him what they were, he said that the publisher would, e.g., repeatedly invite faculty who were using the book to "meet-the-author" events in Florida. He said that these faculty had grown to expect this as a perk that they were regularly offered as an unspoken quid pro quo for continuing to use the book. I didn't ask him for hard evidence of his claim, and I don't know what form of evidence he would have available.
Is there really any hard evidence that publishers do this sort of thing, or is this an urban folktale?

repeatedly invite faculty who were using the book to "meet-the-author" events — Why would anyone want to go to a meet-the-author event for an academic textbook, let alone repeatedly? I'm amazed that people think it's a valuable enough "perk" to impose the book on their students... I know that textbook reps/publishers do try to sugar up the faculty and I've usually heard that they offer to, say, provide X free books/yr (any from the publisher) or a generous discount, etc.

@yoda I think the idea is that the perk is a free trip to Florida, not a meeting with the author per se.

related: http://academia.stackexchange.com/questions/29492/are-there-situations-where-taking-an-honorarium-for-trying-a-textbook-on-a-class

Wait -- it can't be -- next you're going to tell me that drug companies sometimes engage in ethically questionable practices to ensare doctors.

There is some hard evidence that textbook publishers do occasionally offer inducements to professors for adopting their texts. The abstract of this paper in the Journal of Marketing Education reports that

With respect to publisher incentives, 32 respondents reported that they had been offered and 18 reportedly received an inducement from a publisher related to textbook adoption...

Ricki Lewis, author of Freebies and Other Inducements found that "monetary enticement to adopt a book, although not rampant, does happen, and not just in economics. In science, these extras are encountered in large introductory biology and chemistry courses--but less so in physics and geology classes, which tend to attract fewer students."

A couple of years after asking this question, I came across the following article:
"Selling Out: a Textbook Example," Thomas Bartlett, Chronicle of Higher Education, June 27, 2003
The article is paywalled, but you can easily find the full text by googling. It documents a number of clear instances of such inducements, and even quotes several teachers who explain that they knew it was unethical to take the money, but they did it because they wanted some cash. Some choice quotes:

I bought a house in June, and I needed a washer and dryer.
I think most people are susceptible to twinges of guilt. I'm not susceptible to those twinges of guilt.

Apparently the most common form that this bribe takes is that teachers are paid to review a textbook. In some cases they get paid regardless of whether they adopt the book, but in at least one case documented in the article the company, North West Publishing, only paid reviewers if they also adopted the text. In many cases, the payment is made to an entire department and is said to be in return for contributions of material to the book by faculty members, but the payments are disproportionate to the value of the contributed material.
In November 2015, I heard about another instance of this kind of bribery. State legislation in 2012 created the California Open Education Resources Council, made up of faculty from the UC, Cal State, and community college systems. The council was supposed to pick 50 core courses. They were then to establish a "competitive request-for-proposal process in which faculty members, publishers, and other interested parties would apply for funds to produce, in 2013, 50 high-quality, affordable, digital open source textbooks and related materials, meeting specified requirements." As of 2015 this appears to be a second failed initiative (the first being Governor Schwarzenegger's free digital textbook initiative for K-12), and one of the roadblocks appears to have been a controversy over a practice by the publishers of paying faculty to adopt their open-source books. On the face of it, this seems a little odd -- why pay people to adopt a book that is free? The publishers' illogical public justification is that they are doing this because making the materials free takes money out of the collective pockets of faculty who have written books. This makes very little sense, because the people they're writing checks to are not the same people as the ones who have written free or non-free books. Presumably the motivation for paying for adoptions is that the publishers intend to make money off of ancillary products and services, such as $120/semester subscriptions to mandatory online homework systems.

Thanks for following up on this. It's too bad that the CA initiative fell through, I had really high hopes for it at the time.

Other leading tricks: (1) Offer a lucrative "accuracy checking" gig to recent adopters, (2) Create a special university-specific version of the text with e.g. an appendix of university-specific requirements and "share" the revenue with the "coauthor" department.

I haven't been offered any free trips by publishers yet, but in my area (mathematics) someone once pointed out a different incentive the publishers provide to our discipline.
At the largest mathematics conferences in the U.S., there are "exhibits" which publishers use to show off their books. There is a significant fee to rent space for these. Publishers also purchase advertising for the conference program, provide name tags with the publisher's name, and other such things. This has the effect of subsidizing the conference, reducing the cost for faculty to attend.
I think there is an ethical question to consider about this framework. In the end, students who buy the textbooks provide the funds that the publishers use to purchase exhibit space and advertising, which in turn defrays the cost of the conference for professors.
It seems reasonable to ask whether this helps to discourage the professional societies who sponsor the conferences from setting up committees to develop free courseware -- committees of that sort seem like one way to get "respectable" freely reproducible course materials, and the lack of action by mathematics professional societies seems particularly noticeable.


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Applying for postdocs: mention two-body problem in cover letter?
My spouse and I are both finishing Ph.D's in math and applying for math postdocs in the US. We work in different areas of math, but there are many departments in which both are prominently represented. A postdoc position in the same place is not an absolute must but a big plus for us, and would likely be a deciding factor if choosing between offers.
My question: would adding a statement in the cover letter to the effect of
"My spouse xxx is also applying for this position" be helpful, or is it more likely to disqualify both of us in the eyes of departments? We have different last names, so someone who does not know us well personally would probably not know we are together.
The advice for tenure track applicants seems to be not to divulge such personal information until the interview, but there are no interviews for math postdocs so I'm not sure whether the advice would be different.

As someone who actually has experience chairing a postdoctoral hiring committee in math in the US (maybe F'x has? s/he is an international wo/man of mystery...), I think the answer is "it's unclear."
I think there's no question that mentioning your spousal situation in connection with a job will increase the probability of you both getting jobs and decrease probability of either of you getting jobs; it's impossible to be sure how those things will balance.   There's an extremely real danger that if a school knows about your situation, they'll just decide they have no chance of getting you and give up; on the other hand, if a school has a reasonable number of positions (for example, the University of Michigan), and you and your spouse are reasonably hot commodities, there is some chance a school will try to grab you both, but only if they know before whatever crucial meeting they have.  That's not a very likely turn of events, but it has happened (note the importance of at least one, and hopefully both, of you being a hot commodity, and of the school in question having a large number of positions; if they have only one position, this won't work very well).
In part, you have to decide for yourself how scared you are of not getting a job vs. how scared you are having to take a job separating yourself from your spouse.  No one on this site can tell you, but maybe your advisor or another trusted mentor can help you work that out.  If you're planning for a research career in mathematics, you should also give some thought to doing the best postdocs possible (maybe requiring separation) to have better leverage on the TT market (I know that sucks, but the two-body problem generally sucks).
If you decide you would like the committee to know about your spouse, you then have to figure out when and how to tell them.  I wouldn't depend on anything being noticed in your cover letter; there are a lot to read, and such a subtle thing will go unnoticed.  As other answers point out, there is some chance of coming off as presumptuous. It's probably more reliable for one of your letter writers to mention it (bonus: this requires you to have a discussion with the letter writer about your situation).  You can also broach the subject with someone you know at the school via email (or ask your advisor to do this).  Another useful trick is to include a link to your spouse's homepage on your homepage (though that could be easily missed as well; still I'm more likely to read a homepage than a cover letter).

No, I have never chaired such a committee… my answer was based on my non-US experience, which I have now made clear. Thanks for your detailed insight!

I think the advice that applies to tenure-track applicants also pertains to postdoc applicants. Employers aren't allowed to ask about two-body problems in terms of interviewing and hiring candidates. There's no need to force the issue ahead of time.
If you get an offer, then you can discuss the two-body problem. Otherwise, I wouldn't make an issue of it before then.
(Of course, the challenge is trickier for postdocs in most fields outside of math, because in those disciplines, postdocs are normally hired by individual faculty members, rather than at the departmental level.)

I'd not risk it: you have more to lose by mentioning it than to gain. It seems fairly unlikely that this would be a motivating factor for the department to offer you both a position, but it could be interpreted badly (such as “I won't come if you don't offer us both a job”).
This answer is not based on personal experience with US post-doc committees, but post-doc hiring in general.

What if we look at it differently; me and my wife also have the same situation but we are in computer science instead of math. Don't you think it gives the motive to the employer to think of further pushing his/her research boundaries and apply for bigger grant for both of them, especially in Europe where EU grants are available?


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If research design, data analysis, and results only are good, where is the line between suggesting major revision and rejection?
Disclaimer: I am quite fresh as a researcher, even more as a reviewer.
I am reviewing a paper that appears to report a well-conducted empirical study, with proper data analysis. The results of the article are interesting and relevant for the journal.
However, I am very concerned with how the paper was written. I will provide some of my concerns of the report here:
Besides many grammatical errors - which I forgive as English is not my main language as well - the article is badly structured and often confusing. It fails to clearly state the research questions. No all the hypotheses are well supported by the literature review. It omits several key studies in the literature review. It often makes strong claims without a proper reference. It often fails to quantify stuff, falling to the tedious "a lot", "many", "few", "circa", etc. It is quite mysterious on certain aspects of the research design-e.g., a control group is suddenly mentioned without really clarifying what constituted the control group, and the paper reports that the experiment is not even a controlled experiment.
In sum, for the first sections I have nearly a comment for each of the manuscript paragraphs. I will do my best as a reviewer. I will provide all possible suggestions for improving the manuscript. Whereas I am confident that the results of the study are interesting, and that the research design is sound, I don't know if failing to clearly write the manuscript is a reason for suggesting rejection or for recommending major revisions.
Where is the line in this case? The journal does not clarify this in its reviewer guidelines.
In case of suggesting a major revision, what if the authors still fail to provide a clearly written and organized manuscript in a second round? Could I still request for major revisions?

Whichever box you choose to tick, make sure you explain in depth your decision. You can even add a private comment to the editor, indicating that the manuscript is borderline (if it is). That, in addition to comments from the other reviewers, will help the editor make a decision. (You only advise, but he is the one who has to decide, so give him all the information you can.)

Sounds like a classic revision scenario to me.

I would recommend reject, but without prejudice (i.e. encouraged resubmission)

I would recommend emailing the journal editor to ask for some of these clarifications. There might be certain unwritten policies endemic to that particular journal.
In general, you can ask for multiple rounds of revisions (major or minor) until you are satisfied. Peer review is supposed to be an iterative conversation. However, as I mentioned earlier, there could be certain journal policies regarding the number of revisions which you might get addressed if you talk to the editor.
As a reviewer, if you feel that the article should be rejected, you are free to make that claim. However, personally, I always give at least one chance to a paper (however horrible it is) to redress my comments.

Journal instructions vary so exactly what can be done may also vary. But, as a reviewer you re "only" suggesting a verdict based on your review. An editor will make the final decision based on your and one or more reviews.
One question you can ask is whether the revisions you suggest can easily be accommodated within some reasonable time frame. As an example, I edit a journal where we allow six weeks for "major revisions" (three for minor). Unfortunately, this time frame may not be obvious to anyone but the editor. But, you probably get a sense if the paper contains enough good science to be worth waiting for or if a new submission at some later time would be better.
Usually, you provide a report that is passed on to the authors in some way but you also provide a confidential note to the editor. I suggest that you detail your qualms about the paper and try to explain your thinking about the potential for this paper and whether it may benefit from either rejection and possibly later resubmission or by taking it down the "major revision" route. You can then provide you sense of how much time might be required for the changes so that the editor obtains a sure footing for the decisions. It is always good to receive a little of "pros and cons" from the reviewer.
In the end the editor will make the choice and it will be based on more views than just yours. Providing the best substantiated view you can will most likely be welcomed by the editor

It fails to clearly state the research questions. No all the hypotheses are well supported by the literature review. It omits several key studies in the literature review. It often makes strong claims without a proper reference. It often fails to quantify stuff, falling to the tedious "a lot", "many", "few", "circa", etc. It is quite mysterious on certain aspects of the research design-e.g., a control group is suddenly mentioned without really clarifying what constituted the control group, and the paper reports that the experiment is not even a controlled experiment.

I strongly recommend including this paragraph verbatim in your referee report.
This description is not obviously consistent with your claim that the paper "appears to report a well-conducted empirical study, with proper data analysis".  Is it actually possible, even in principle, to have a well-conducted study without a crisply stated research question or a clearly-defined control group, or a proper data analysis that uses "a lot" and "circa"?
These are very basic flaws, independent of the authors' first language.  If they were spread throughout the paper, they would be sufficient to recommend rejection.  If these problems appear only in the introduction (and later sections clarify the research questions, experimental design, and so on), then they may not warrant rejection, but they certainly require major revisions.
The discrepancy between the initial sections and the body of the paper suggests that a student wrote the former, and the PI wrote the latter.  At least, I hope that's what happened.  It's appropriate to be gentle (but firm) with the student, but a bit less forgiving of the PI for not advising the student better.

In case of suggesting a major revision, what if the authors still fail to provide a clearly written and organized manuscript in a second round? Could I still request for major revisions?

Yes.
If the authors' revision does not sufficiently address the concerns in your initial report — regardless of whether your concerns are about presentation or content — your response to the editor should be "The authors' revision does not sufficiently address the concerns in my initial report; therefore, I cannot recommend acceptance."

The difference between a major revision and a rejection can be thin, because after a rejection people can of course still significantly improve the article and resubmit.  Many journals have a deadline to submit a revision.  In this case, I think:
If the required work can reasonable be performed in the time scheduled for a revision, then recommend a major revision.  If the work is so substantial that it would take a lot more time than that, then recommend rejection.

So, I'm in your place, reviewing the paper, and these are my (=your) findings:
The good:

"A well-conducted empirical study"
"Research design... [is] good"
"proper data analysis"
"The results ... are interesting"
"The results ... are relevant for the journal"

The bad:

"I am very concerned with how the paper was written." -> suggesting it could be written otherwise
"grammatical errors" -> Rectifiable.
"article is badly structured" -> suggesting a different structure would be good.
"article is ... often confusing" -> given what you've written above, the confusing parts can be rewritten or removed.
"It fails to clearly state the research questions." -> So it could state relevant questions; or none.
"No all the hypotheses are well supported by the literature review." -> What, people can't make their own hypotheses? What you can really complain about is:
"Omits ... key studies in the literature review." -> Solution is obvious.
"makes strong claims without a proper reference" -> Claims can be weakened to fit the actual results.
"Fails to quantify stuff [:] ... "a lot", "many", "few", "circa", etc." -> Rectifiable.
"It is quite mysterious on certain aspects of the research design" -> Still, you decided it was well designed. Mystery could be dispelled, apparently.

Recommendation: Resubmit after major revision
Plain and simple. If the good part makes you want to publish the thing given a perfect writeup, then at worst they need to rewrite their paper. No "lines" here.


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Is a break-of-study a hindrance to getting a PhD?
I live in a developing country. I want to go to USA for higher studies and plan to acquire a PhD there. But since I do not have enough money to go there, I need to have a job first to collect my money. May be the job is not relevant to my academic field of interest.
Are these types of break-of-studies hindrances to getting PhDs?

A "break-of-study" is not a hindrance per se. It has side effects (you get older, acquire a family, and so on), and some of these can make it a little trickier to get a Ph.D. In particular, you might find the answers to this question: Can one excel in graduate school with a demanding family life? very relevant in terms of the challenges of doing a Ph.D with a family.
But again, a break-of-study in and of itself is not a bad thing. Now if the job you are looking for takes you far away from your intended field of research, then you might have to explain your background on your application and somehow establish that you have a continuing interest and basic knowledge in the field (which may have changed since you graduated). You can do this by taking courses online, or by doing research projects on the side, and so on.


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Difference between transactions and journal
I feel a little bit ashamed, but I have never understood the difference between transactions and journals. This question is quite related. However, I could not find any clear differentiation.
For example, in my little field (software engineering) IEEE Transactions on Software Engineering is considered the top venue. However, there is not an IEEE journal on Software Engineering (or whatever name). To be honest, I have never seen any publisher on software engineering having both transactions and a journal on software engineering. This is also why I fail do differentiate them.
This is what IEEE writes at its FAQ page.

What is the difference between IEEE Journals, Transactions, Letters, and Magazines?
Journals, Transactions, and Letters are the primary means for
publishing technical papers concerning original work in IEEE fields of
interest. [..] The primary purpose of
Journals, Transactions, and Letters is to disclose and provide a
permanent archival record of original technical work that advances the
state of the art or provides novel insights. Papers in Journals,
Transactions, and Letters should be of lasting value to the
professional as judged by the authors’ peers through a formal review
process. [..]

The omitted part is about letters and magazines, so it is not related. Am I really missing it, or they do not really differentiate?
What is the difference?

I don't know the answer in the case of the IEEE, but in the case of the American Mathematical Society, all the following are journals, despite their various names: Journal of the AMS, Bulletin of the AMS, Proceedings of the AMS, Transactions of the AMS, Memoirs of the AMS. They differ in the type of articles published: Journal is the top tier journal, Bulletin publishes reviews, Memoirs publishes monographs, Proceedings publishes short papers, and Transactions the longer ones. Notices of the AMS is a magazine, publishing popular articles.

Also, what's the difference between a street and an avenue? There is a clear difference in Manhattan, but it's not inherent to the names.

Transactions used to have a very specific meaning. From the New Oxford American Dictionary:

transactions
  published reports of proceedings at the meetings of a learned society

In this historical usage, it is synonymous to proceedings, i.e. it is a published report of a conference or a set of meetings. Many learned societies have transactions: Philosophical Transactions of the Royal Society, Transactions of the Faraday Society, Transactions of the AMS, etc.. Some other institutions use the term “proceedings”, e.g. Proceedings of the National Academy of Science.
These transactions or proceedings were separate from journals, which do not have to coincide with a conference or meeting. However, with time the customs changed, and many of these reputable publishing venues became independent from actual meetings or conferences. But, because they were reputable (and famous is some cases), the name remained.

I have seen some ACM Transactions that have started recently. For example ACM TIOT: https://tiot.acm.org/.
So, why are they not called journals?

There is no difference.
In particular, IEEE Transactions on Software Engineering is a journal, as are all the other IEEE Transactions.

From IEEE:

IEEE Transactions generally contain major manuscripts
  approximately 8 to 10 printed pages or 24 to 30 double-spaced
  pages.
IEEE Journals follow the same length criteria as Transactions,
  but often are focused on selected topics and more
  specialized areas of interest.
IEEE Letters are generally short papers of approximately
  three to four printed pages or nine double-spaced pages.
  "

For all practical purposes, there is not much of a difference between IEEE journals, transactions, and letters. On the IEEE website, they are all included under the broad category 'Journals and Magazines.' However, they publish different article types. While journals publish articles on more specific topics or specialized areas, transactions publish articles of a broader interest, while letters usually refer to short communications rather than full-fledged research articles.

As per my general understanding (not by any technical definitions), Transactions are more focused venue whereas Journals are broader in topic coverage.
I decide where to submit my manuscript based on this understanding.


text:
How to effectively manage a new collaborator?
As a 3rd year PhD student in a Canadian university, I've been given the opportunity to work directly with my supervisor's long-term collaborator, who is a young faculty member in an Australian university. I shall be visiting him for a month to initiate a (STEM-theory) project and am looking for advice on how to make the collaboration fruitful.
More specifically, it took time for me to understand my own supervisor's priorities, strengths-weaknesses and way of working. With that understanding, I have been able to work effectively with him. How can I quickly learn the best way of working with my new collaborator?

He is your supervisor's long-term collaborator, right? Your supervisor will have the best answer for you.

Make sure you come well-prepared.

I could not agree more with gerrit's answer. Based on my own experience, preparation prior to meetings with external collaborators is critical to the success of the project.

@gerrit, 'just came back to say that your advice was most helpful. Thanks!

I just wanted to comment that your choice of words in the question is somewhat inappropriate: you do not "manage" a new collaborator when your collaborator is more senior than you are. As a graduate student, you cannot have any reasonable expectation of asking for and receiving commitments from a professor—if anything, it's the other way around, even if you will be the one doing the majority of the work!
However, this also tells you something about how to handle the process. Remember that the professor is quite likely to have many more time commitments than you will. Therefore, you will need to be cognizant of that when making plans. What takes you a few days of effort may take your collaborator substantially longer, if he has to do it himself. So it may be very useful to find out if there is another point of contact you will be working with in the other professor's laboratory group, and ask if you can coordinate things directly what that individual.

I disagree, so long as one is using a fairly wide definition of "manage". As a PhD student, one is frequently told that one may have to "manage one's supervisor". The same applies in business, and I don't see why it shouldn't apply to external collaborators. Obviously it isn't a supervisorial type of management, but it's management nonetheless.

I understand your objection to my choice of words. By manage, I meant understanding and acting according to his priorities, strengths-weaknesses and way of working.


text:
Is there a case for SLOs?
SLO stands for student learning outcome. At the community college where I teach, what seems to have happened is that our accrediting body told us we had to have them, and since they effectively wield the death penalty over us, we complied. Administrators may also have bought into the idea at some point.
What is the history of SLOs? Is there any published, intellectually rigorous justification for them?
I'm inclined to be extremely skeptical of them. They seem to be an incompetently executed type of standardized testing, without any of the scientific rigor that has been built up over a century of development of the field of psychometrics. In particular, standardized tests are supposed to be both valid and reliable. A typical SLO is probably not valid (because it tests too small a subset of the subject matter) and not reliable (because it is too short an instrument to produce a result with a reasonable variance). We could fix these problems, and then we would have ... a professionally developed standardized test. E.g., in my field, physics, we would have something like the AP physics test, the physics portion of the MCATs, or the physics GRE.
Administrators and accrediting bodies seem to believe that SLOs could be used, for example, to measure whether a particular educational innovation has been successful. The problem here is that one then has to interpret the difference between one set of test scores and another set of test scores, but the difference between two low-reliability (high-variance) numbers is essentially meaningless. This is also a problem that plagues "value added" measurements (Baker 2010), but it would be far more severe for SLOs because of their far lower reliability.
Arum 2011 (p. 140) discusses this sort of thing in the context of the seepage of NCLB-style testing from K-12 into higher education. They discuss the Spellings Commission report (Spellings 2006) as an influential document, although I think the fad for SLOs began to get underway before 2006, and the report suggested standardized tests such as the CLA, rather than what people now refer to as SLOs. A disgruntled member of the commission (Zemsky 2011) says that in retrospect the main outcome was to transform accreditation from a pro forma exercise into an audit-like procedure designed to give the federal government coercive power over colleges and universities.
Is the whole thing a Dilbertish emperor's-new-clothes exercise, or is there some intellectually rigorous case to be made for SLOs?
References
Arum and Roksa, Academically Adrift: Limited Learning on College Campuses, 2011; summarized online in http://www.newyorker.com/arts/critics/atlarge/2011/06/06/110606crat_atlarge_menand
Baker et al., "Problems with the use of student test scores to evaluate teachers," Economic Policy Institute briefing paper, Aug 29, 2010, http://www.epi.org/publication/bp278/
Spellings et al., Commission on the Future of Higher Education, "A Test of Leadership: Charting the Future of U.S. Higher Education," 2006
Zemsky, "The Unwitting Damage Done by the Spellings Commission," Chronicle of Higher Education, 2011, http://chronicle.com/article/The-Unwitting-Damage-Done-by/129051/

Are you talking about learning outcomes as in Bigg and Collis SOLO taxonomy? I'm not an expert on this domain, but it seems there has been published work.

@CharlesMorisset: No, that's something unrelated. I haven't actually seen a clear definition of what an SLO is supposed to be, although we are required to do them. But the basic idea seems to be that you state three or four goals in your syllabus (e.g. students will be able to analyze the forces on an object and draw a free-body diagram), and then you test that (e.g., with one of the questions on the final), and then preserve the data and possibly aggregate it with others teaching the same subject. Different sections of the same class would theoretically have the same SLOs and comparable data.

Talking to a colleague, I learned a few relevant things about how this happened here in California. The idea of requiring SLOs started out in about 2000, and it was a political compromise between government, which wanted NCLB-style standardized testing, and the professoriate, which wanted to retain their traditional self-determination. Political changes ca. 2005-2010 resulted in accrediting bodies such as ACCJC using accreditation to impose SLOs, and in particular there is a very controversial case in which San Francisco City College is in danger of losing its accreditation.

While this is not a perfect answer (not a rigorous study of the costs and benefits of learning outcomes) I hope it will give some insights.
Learning outcomes are not all that rare, although I do not remember seeing them much in the US when I was there.
One of the key reasons for learning outcomes is to be able to evaluate how closely Module A in School X matches to Module B in School Y. If you are teaching a subject titled "Contract and Negligence Law in New Zealand" then the learning outcomes kind of write themselves. If you are teaching a subject titled "Modern Business Practices" then it is less clear what it is that students who passed that subject actually learned.
So, leaning outcomes, I believe, are mainly for the benefit of administrators so that can 'map' modules across universities. However, I also believe that they have great value for us as teachers. I believe the more we can formalize, in writing, what students will learn, the more transparent we are being and the fewer (unhappy) surprises people are likely to have. Students will better understand what they are supposed to learn, as will their parents (if they are involved in the process) and other teachers will be able to see how our modules fit together with their own simply by reviewing the learning outcomes.
Typical learning outcomes might include (in my field): Understanding teamwork and team development. In this case, you do not need to look at differences in test scores. The outcome is not an improvement in knowledge (take a module where you have already learned the outcomes and you will likely learn very little) but rather an absolute "The student will understand this." If the student did not understand before, they should understand at the end, or they should fail.
I do not believe the goal of the learning outcome is that it is one-question on a final exam but rather it is what gets assessed by the assessor. How you do that is up to you. For the example of team work I have several tests to see if students understand the key points that they should have learned.

Are you in New Zealand? Does New Zealand have something similar to the UK system, where different schools critique one another's year-end exams?

No, actually, I'm in Asia teaching through a UK school and the admins have to line up how our modules compare to other modules from other schools for credit transfer purposes. We don't have the kinds of critiques you mentioned (at least not that I'm aware of) other than UK people (school admins, people from the accreditation agency, etc.) coming on site (1-2 times per year) here to make sure everything is above board.


text:
Using comments from examiners in a CV
I have just received feedback about my PhD (in my University, we do not do an oral defense, our dissertations are peer reviewed) - and I have received great and useful feedback and criticisms which will be a breeze to respond to.
Also included in the feedback are some very kind and positive comments about me as a scientific researcher.  This leads me to my question, would it be appropriate to use the positive comments from the examiners when applying to academic positions? This of course, while preserving the anonymity of the examiners themselves.
Something along the lines of "Examiners to my PhD dissertation recognized my ability to perform task, stating positive comment".

Hum, I do understand the impulse, but I don't think a CV is the right place for that. You don't want it to look like the back cover of a crime novel :)
In my country (France), PhD thesis undergo both a peer-review and a formal defense. Thus, you usually come out of it with two written reviews of your thesis, and one written review of your defense. It would be quite uncommon to quote these in a CV, but in many applications it is fine (and sometimes mandatory) to actually attach them to the application, as supporting material.
So, unless it is common to do so in your system, I wouldn't recommend quoting praise for yourself in a CV (a CV is a list of facts, mainly, not opinions), but you can try to include it in the application if it is allowed. Either raw, or you could quote it in the application letter, statement of intent, summary of your work, whatever:

The research topic of my PhD was to study the influence of UV irradiation on bacterial growth rate in the lab's fridge. I quantified the extent to which it was detrimental to the life of these poor innocent bacteria. I also made the case for a new classification splitting part of the UV range currently known as “UV-C” radiation into a new “UV-D” category, based on its distinct harmful effects on fungal growth.
This work was well received by the community, with a total of 4 published papers and 3 conference talks during my PhD. The thesis peer-review committee called it “a brave and well-inspired revolution of the old dusty classification of UV radiation” and characterized the end product of the thesis as “a clean lab fridge: the greatest service you can render mankind or, at least, labkind”.

ah yes, an application letter may be indeed the better option.

+1, if only for the funny imaginary application letter extract.

I don't know if I would include these in your own application materials, but I would certainly try to have this examiner write a letter of recommendation for you (many jobs will allow extra, optional letters if this one is an "extra"). It's going to sound stronger coming directly from a respected third party than if you provide the quote yourself, even if the actual material is the same.


text:
Funding for PhD students in the UK for EU student
If I wanted to do my PhD in the UK at a renowned university in the natural sciences, how likely is it that one gets access to a fully funded PhD program?( living costs + fees).
The reason why I am asking this is, that I see a lot of scholarships on the websites of the universities but I have never heard of an actual percentage of PhD student(coming from the EU) who got such a scholarship. Does anybody know? It does not have to be an actual number, but maybe you know something about this.

I do not know actual numbers unfortunately but I will tell you what I know from my experiences in a Computer Science and a Statistics department (of different universities). Your question is tricky because there are a lot of different cases:

BBSRC, NERC or EPSRC funded places (by far the most common). UK Research councils are the standard funding bodies for PhD programs in UK; they usually do not cover maintenance fees unless you are a UK national. They pay only the registration fees for EU students. (I know, I am one). The success rate for something like this is the highest compared to the following options; it generally equates that of a PhD program acceptance rate to the university you are applying to.
University/departmental funded places. Generically also called PhD bursaries. UK universities have self-funded places but they are not very common; usually not more than 2-3 places per department. In most cases those are money on hand but registration fees are occasionally lifted, I think because you are an EU national that might be easier (I know that for an Indian national fees where not waived.) their acceptance rate is obviously harder than those of option 1.
Industry (or goverment agency) funded places. Industry collaborations do occur, I have seen some brochures but I don't know anyone that got them. Pretty much the same situation in terms of fee coverage as option 2 but they tend to be even more rare. I would guess it is not "harder to get" than usual departmental funded places given you actually apply to one. Almost certainly these are tighten with a faculty member and they are not "up for grabs" by all applicants.
General university scholarships. These are usually merit scholarships and you compete against the whole university. They are hard to get: In the medium size university I am now this translates into 25 places. They do not differentiate between costs, they give you a lamp of money (about £13k-15k) and you are on your own. It is not completely unusual to get one if you are an EU national and you have already a registration-fee-only scholarship. Obviously these are really hard to get, but selection is non-random: if you are great you might get them.
Supervisor money. Usually they are tighten to specific grants/research programs/etc. It is almost the same as option 3. This is weird money for you to directly tap into. Essentially they are money a supervisor/department has and it is decided that they'll be used to fund a PhD. They might not even be advertised. I know two cases, in first one fees were waived, in the second one not. Success rate? I have no idea, probably the probability of really impressing with your research potential, a successful and well-connected professor with a shortage of good PhD students (Given you are good, the hard part is actually finding the professor; not many people have a couple tens of thousands of pounds to allocate to a person they think is awesome.)
EU programs. Sci-fi. I know only post-docs that got these kind of funding. I can not give any estimates, I am just mentioning them cause I know  they exist. I have come across them in relation with the Erasmus Mundus program, worth checking.

From what I understand, if you are an EU national registration fees are somewhat easy to be waived (ie. paid by the university or a funding body). Getting the extra money is the hard part but if your supervisor wants you, strings can be probably pulled. Teaching also pays good in UK in comparison with other countries. In general, do not let finance hold you back from applying to places. Especially for an EU national if they believe in you they will find a way to make you a somewhat good offer as your registration fees will not be horribly high to start with. Good luck!


text:
Will I be allowed to reapply for a mathematics NSF postdoc next year after declining one this year?
I am a mathematics PhD student in the US graduating this year. I recently received a very good 3 year postdoc offer in Europe, which I have to accept or decline in early December. Not being a big risk taker, I am leaning toward accepting the offer.
I have also applied for an NSF postdoc, which I would prefer to the European offer but am obviously not a shoe in to get--and the results of which won't be known until February. If I accept the European offer, I will have to decline the NSF postdoc if awarded.
If I do that, would I be allowed to reapply for the NSF next year?

If you accept another position before the NSF Mathematical Sciences Postdoctoral Research Fellowships are awarded, you should officially withdraw your NSF application.  The way the NSF postdocs work is that there is no second round of offers: if you are awarded one and turn it down, then it won't be offered to their next choice of candidate, who might have received it if you had withdrawn your application.  Furthermore, I believe withdrawing will preserve your eligibility for next year, while you will not be eligible if you decline an offer (according to the official instructions).

I think Anonymous Mathematician has left out something pretty important here, which is that often these situations can be finessed.  Have you spoken to the people at the school in Europe about the possibility of you getting the NSF postdoc?  Often you can spend one year at wherever you applied to for your NSF and then move to a different place.  It's also probably worth speaking to the project officer for the NSF; a lot of things about the fellowship are really up to him/her, so it's possible you could get approval to transfer your NSF to this new place.  There's no guarantee, but it's possible with the timing they'll be understanding.  You'll never know until you ask.
I completely agree that you need to withdraw your application from the NSF and any other jobs if you know you won't accept them this year.  That's just common decency, and it will save people trouble.

Great point!  If you know in advance that you can't accept the NSF, then you should withdraw your application, but it's certainly worth checking first whether there would be other options if you receive the fellowship.


text:
How long does it take for a citation to show up online?
How long does it take for a cited paper to show up online? I can see a couple of papers that were cited very recently and the papers containing those citations are currently online since a week or two. How long should I expect it to take before those citations show up as citations through Google Scholar or other indexing services?

I'm voting to close this question as off-topic because this is not a question considers academia. Rather, the question is based on indexing algorithms of particular websites.

I have timed this before and it takes about 4 days.

Google Scholar, Web of Knowledge, Scopus and other indexing services have their own ways how the papers get into their database. For Scopus, the journal has to be registered there, and then actively send the data. It's similar for Web of Knowledge I think. Google gets the data from who-knows-where and I doubt you can control it efficiently. In general, it takes couple weeks to several months.
As dgraziotin pointed out in comments, Google Scholar indexes citations from arXiv quite quickly, in couple days. However, by many people and many institutions, arXiv papers are not considered at all regarding citations, unless they are published properly elsewhere and properly Journal-ref'ed; even then, many people don't trust that the arXiv version is correct, because nobody makes any check of this (I mean, you can put whatever Journal-ref to whatever your arXiv paper, so it's not trusted).

With the exception of arXiv papers in Google Scholar. In my experience, it takes GS 3-5 days to index an arXiv entry, citations included. It seems it has got quite a preference!

@dgraziotin However, arXiv is not recognized as "a paper", unless you speak about e-pub arXiv journals, which do exist.

I use arXiv to self-archive my published papers, so I mainly employ it as a safe hosting platform to free up my papers.
You are of course right that arXiv-only papers do not count in many institutions. I do not like the current system, but that is another story.

With Google Scholar, it depends at least in part on the deal the publisher has made with Google about how soon they are allowed to scrape.  For this reason, Google Scholar citations for a year keep going up for months after that year has ended.

It took four days for a Science paper (four days from online publication, three from official publication / print.)


text:
A year + for first review, one referee report in, want to withdraw paper
A paper of mine has been under review for more than a year now. About 6 months ago I heard from the journal that one referee report is in while they are waiting for the 2nd. The editor promised he would get in touch with the Associate Editor to speed up the process.
In any case, nothing has happened until now.
I am thinking of withdrawing the paper citing excessively long review times. Could I ask for the one review that the journal received on my paper?
What is a good way to frame the withdrawal email with the request for the journal office to be kind enough to share at least the single referee's report they received?

What field are you working in? The normal length of the refereeing process varies wildly across disciplines.

At any case, I doubt the journal would send you the review. As well, I would as them to make it within a month (or similar reasonable dead-line) or you withdraw the article. That way you can actually gain a lot, because they might make it in one month, which is the shortest you can get in your situtation IMHO.

Just as an info how else such a situation could be handled on the side of the journal: I once had a similar situation, which was however handled completely differently by the journal editor. We received an information after some months that they had trouble getting the 2nd review, and were now looking for a 3rd reviewer instead. Some more months later, the editor emailed that he hadn't gotten any other review, but considering the delay would go on with one report only.

To answer the question I must acknowledge the comment that times vary between disciplines (and to some extent journals). You should therefore check what applies to the journal where you submitted your manuscript. Based on what you find you can start thinking about withdrawing the paper.
From my perspective what you describe sounds like good grounds for withdrawing and trying a different journal. In my field (Environmental sciences) and in the journal where I am editor-in-chief, the time from submission to acceptance can be anything from a month and a half to slightly less than a year, but then the long times involve revision and a second round of reviews. If what you describe happened in "my" journal i would be very sympathetic to a request to withdraw. One could argue that because you have received a review you should feel obliged to stay because of the work the journal editors have put in, but then one must also consider the work they have not done, which is following up on the lack of response. It would not be too much work to assign a third reviewer when lack of response from the second becomes obvious. So in the end I think the journal seems to suffer from internal problems. A lack of response from a reviewer (which is not uncommon) should not halt the process for a paper. So with the assumption that turnover times in your field are within what I see as normal in mine, I think you have a good case for asking to withdraw your paper.
So, in my view, this is what I would do. I would write a polite letter to the editor explaining that you have decided to withdraw the paper because of the (severe) delays you have experienced. You do not need to point out the obvious short-comings of the journal but explain how the delays affect your personal situation. We all need publications to strengthen funding applications, job applications, promotions, evaluations etc. so significant delays have negative effects. Now it is of course not a responsibility of a journal to help your career but in a case like this, there is little point in blaming a (failed) process within which you have no insight, so focus on the effects it possibly has for you. And keep it brief.

Hi Peter. Your answer does not address asking for the one review. I'm curious what policies, if any, journals have about such a request.

@FaheemMitha Good point. If one withdraws a manuscript, it will be up to the journal if they want to share the review. If one requests the review, it is more or less equivalent to committing to stay with the journal. There are not rules here so the above is more about courtesy than law. The review does not belong to the manuscript author so placing demands will probably not be taken well. I am sure the editor(s) realize their failure so constructive suggestions are the best way forward.

I actually had a similar situation some years ago. I don't think my experience is very useful, but I will briefly recap it in any case.
I submitted a paper to a journal in October 2009. In April 2010, after several requests, I was told that one referee had given a report, and the journal was still waiting on the second report. The journal then sent me the report at that time (in April), though I gather that was not standard procedure, and as far as I can see, I did not explicitly ask for it, though I had been repeatedly asking for feedback of any kind. The journal wrote:

In fact, we got a report from the first referee. The referee's opinion
  is rather negative. As a rule, we do not send a negative report before
  we get a report from the second referee. Taking into account your
  will, we send the first referee report to you - please find it below.
SInce we have not yet got the second referee report,
  there is no editorial decision concerning your paper.
  We hope to receive the second referee report in April.

I don't know exactly what was meant by "taking into account your will".
The second report never arrived, and I withdrew my paper in September 2010, slightly less than a year after submitting it.
I suggest that you ask your journal for the one report. You might want to wait on withdrawing it till you hear what the report says. You could say that you would like to use the first report to improve the paper while waiting for the second.
If they refuse, I guess you could then say that you are withdrawing the paper, and then ask for the report again. If you are going to withdraw the paper, this marks the end of the process from the journal's point of view, and I don't see why they would refuse feedback that might help you. Of course, they might refuse regardless. I imagine that individual journals would have different policies about such things.

The reason why journals refuse you to send the report is that they don't want people to expect to get the report. It's similar to situtation when you make some work for a client, and in the end he refuses to pay and end the contract; you don't gain or lose any money by giving them the result at the moment, but you of course don't do it, because it sense a bad habit.

@tohecz: In this case, this is a case where the 'work', i.e. reviewing was not completed, and the 'client' has lost out and wasted some time (a year in this case), so I don't think that is really a good analogy.

@FaheemMitha Still, from the perspective of the journal, they "didn't do anything wrong" (can you hear the sarcasm?), so it's the client (author) who "is over-acting".

@tohecz: Yes, I suppose the journal could well look at the matter differently.


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How to effectively explain casual research assistance projects on CV
Recently, alongside my day job (high school teacher), I have been taking up casual short-term research assistant jobs - these are not only paid, but also include me being a co-author of the paper(s) that result.
On my CV, I would like to have all this information, what would be an effective means to include all achievements of these projects?
I am hoping for specific examples if people have done this before.

In order to answer your question, you need to first understand who your CV is written for. If your CV is for you, and you are simply trying to document what you did, then you can simply list each research involvement as something like:

January 2014--July 2014 Research volunteer, Dr. Bigwig's lab. Collected samples from subjects and ran computer simulations. Contributed to 5 publications.

Ideally, you will also be able to list the publications to which you contribute.
If you are building the CV because you want to actually use it for something (getting a raise, getting another job, going back to school, etc.), then you should seek to formalize your relationship with the lab:

Do you have a title? If not, ask for one. Since you say you are being paid, you probably have one already. You should know the title and list it.
List the dates of the appointment. Typically they are for a year or a few years, even if you are only being paid for a small fraction of that.
Since you are currently a high school teacher, you may wish to list your research appointments in a different section of your CV than your teaching appointments.

Good luck.

Detail the employer and your role, make clear that your work was part-time or casual.
Indicate that you contributed to a number of reports, perhaps even citing the number of reports that you contributed to.
Make a specific reference to any reports that are appropriate to the job you're applying for.

For HR specialists reading your CV there will be important not just employment history, but also another perspectives of your CV.

a project history you have done or participated, then they need to know short one simple sentence of project description and your role on the project.
publications you have made or co-author.

If this is significant enough, put this to the Overview, what should be on the front page of your CV. Overview generally should contain teasers for the rest of CV. How many projects, how many publications, etc.
Take an example of different perspectives for example from Linked-in portal, which are: Overview, Employment history, Project history, Personal initiatives, language skills, Certifications, Courses, Skills, Education, Recommendations, Publications, Organization membership, Prizes, Academical Results, Patents, etc. Order is up to your priorities.
Example: So, I can imagine you could have Overview, Education, Project history, Academical results and Publications in top order.


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What should I read or know before I prepare my bachelor's thesis?
I am about to start planning my bachelor's thesis in computational linguistics, and I'm looking into how I can make the process as smooth as possible. So far, I've found that using some sort of version control system for keeping track of one's changes seems like a good idea. I've also started collecting papers using Zotero for easily exporting to BibLaTeX and keeping notes.
But those are only tools. What I'm most uncertain about is the actual writing process, especially since my native language isn't English. Is there a collection of common mistakes I could benefit from reading, or other every day tips and tricks? Anything, really!

Version control systems are good. I recommend Mercurial. LaTeX is also good. To improve your writing, the best thing is to practice. Aside for your research writing, you could do worse than post questions and answers to online forums. The Stack Exchange sites for English and Writers are quite helpful.

@FaheemMitha any particular reason for recommending Mercurial instead of git, svn et al.? Just curious.

@dgraziotin: Well, this is a bit OT, but distributed version control is technically superior to centralized in all ways that matter. I use Mercurial and like it. I think (as do others) that it is has a better user interface and is more "friendly" than git, though of course git is preferable to svn. These topics are discussed to death on the net, so you could take a look at comparisons.

@FaheemMitha I am using all of them regularly (software engineer). That is why I was curious!Let's end the OT here, or a flamewar might start :-) Thanks!

This is a pretty broad question, but if you are looking for a general guide on how to write there have been a number of books suggested to me.
Writing for Computer Science (Zobel) This is a decent book on explaining the principles on why and how you should write computer science articles. It's very computer science specific, with a bit more emphasis toward databases and operating systems, but I think it's applicable to most technical fields (of which computational linguistics should fall into).
I like this one because it's a general guide to writing that outlines the process and the structure.
Elements of Style (Strunk and White) A commonly-recommended book that a lot of people swear by but I found it a bit too low-level for my liking and actually had a hard time finishing it. A professor described it as "too prescriptive".
Bugs in Writing (Dupre) This is an okay book as a reference manual for improving your prose, but isn't a good guide for figuring out the writing process. There's good advice in this book (and it's actually rather fun to flip through just to learn about various style points) but can be difficult to use as an actual guide.
Style: Toward Clarity and Grace (Williams) I've gotten through a few parts of this book and it gives very specific advice on how to proceed on improving your writing, especially explaining specifically how to introduce ideas in paragraphs, how to flow them together to create longer manuscripts, and how to restructure and correct text so the main ideas come through. As I surmised, it is in fact very analytical and detailed and does describe the rationales behind its recommendations. I think this book is a great resource for those who have some words written, who know they have to make their writing "flow better" or "more clear" but aren't really sure how to do it. It appears to be an especially valuable book for the "second pass" through anything, where you have written down your initial ideas in part-writing, part bullets, and are trying to convert it into a real readable piece of work. (Previously, I wrote: This book was JUST recommended to me and I haven't read it, but it is apparently very analytical and detailed, and outlines the rationales behind why one should write in the way it discusses. In fact, I think there a jab at the Elements of Style in this book where the author laments that "Be clear" is GREAT advice. We all KNOW that. The real problem is, "How is it that I can actually implement 'be clear' in my writing?" However, I haven't gotten far enough to comment on it yet.)
So there's a little about what to read. As for what you should know? Well, that's a more difficult question :)

Thank you! I have been reading through half of Writing for Computer Science and it certainly seems like a great book to keep close for reference in the writing process.

Best thing you can do is have a well defined topic. Since you don't mention that in your question, I don't know if you have a research topic/question yet. In my experience, that's by far the most crucial thing in having a thesis go smoothly. The student who know what they want to work on usually have everything fall into place.


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What does "restricted admission" mean in German universities?
While browsing the web-sites of various German universities I have come across the term "restricted admission". What does it mean?
Do German universities discriminate students on the basis of their age?
Is there anything called "unrestricted admission"? If so, what does that mean?

I believe they are simply saying that they will not necessarily admit you simply because you apply and can pay. Your application must be accepted (and some will not be).

@earthling: No need to pay beyond a small student registration fee each semester. Public German universities do not charge tuition.

In Germany, access to universities is regulated by the Numerus Clausus system, which basically says that the number of students admitted to any given programme at a university can be either unrestricted or restricted to a fixed number of students.
For an unrestricted programme, students just need to fulfill the basic formal criteria (they need a german Abitur, or an equivalent). For most restricted programmes on bachelor level, prospective students need to apply and are then ranked based solely on their Abitur grades (plus a few exceptions for corner cases, foreign students with no german Abitur, etc.). For restricted master level programmes, many universities (including, apparently, TU Kaiserslautern, as linked by the original poster above) have adopted a more US-style admission system, which is based not only on previous grades but also on letters of recommendation, statements of interest, interviews, etc. TU Kaiserslautern also has its selection procedure online. This will vary per university, though.
Edit: to answer your subquestion (which I happened to have missed the first time around):

Do German universities discriminate students on the basis of their age?

No, not in general, and certainly not officially.

On your subquestion:

Do German universities discriminate students on the basis of their age?

I don't know any public state universitiy that does it, but in some cases privately founded institutions of higher education admit only persons up to a maximum age.

One example I found is the Hasso-Plattner-Institut (HPI), a institute that offers bachelor-, master-, and doctoral degrees in cooperation with the University of Potsdam.
At the applicants information page one can read:

Offen für alle Studierende unter 35 Jahren, die entweder in einem Bachelor‑, Master‑, Diplom- oder Promotionsstudium immatrikuliert sind oder ihr Studium vor weniger als einem Jahr abgeschlossen haben. [Open to all students under age 35, who either are enrolled in a bachelor's, master's, or doctoral program or have completed their studies less than one year ago.]

May the community add more examples in the comments. They can be added to the answer.

authors: نرگس قلی نژاد


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Independent research post-PhD strategies
After reading The nightmare of being an independent researcher, Applying for research funding as an independent researcher? and On getting reviews for research work as independent learners and reflecting on many a post PhD academic who, for whatever reason, are not able to get a foot in the door in academia after they complete their work.
I have seen this go both ways - the post-PhD after a while just gives up and gets any job they can, or they go down the path of independent research (usually, as in my case, while working full time).
From experience, this independent research is following on from the PhD topic, still in collaboration with others and at least one established academic, but it is the kind of situation where experiments are performed on the weekends in the backyard, using equipment borrowed or made, and more often than not, all self-funded.  Papers still get published and conferences attended (where possible).
What my question is, what strategies are there to maintain motivation in independent research?
Additionally, how well recognised are independent researchers?

Just to clarify, you're talking about experimental research as opposed to (say) research in mathematics ? The challenges are quite different.

@Suresh yes, I am referring to experimental sciences (Physics).

By an "independent researcher", do you mean that you are not associated to an institution, or that you have become independent from your advisor?
The first case, I am not certain what to say; it really seems that if you are not associated to an institution, you have to deal with a lot of stuff; prejudice from more traditional academics (if he is good enough to be doing research, why is he not associated to an institution? Hence, his research must be terrible), difficulty in accessing published materials (although this is becoming easier and easier, where many recently published papers are in public domain one way or another), etc.
In this case, I suggest that you have at least a few very close academic contacts who are well-respected. These people should be able to explain your situation (about why you are not following a more traditional route) and become your champion. They can also occasionally get you the research papers that you cannot access otherwise, and should you decide to return to school, they will vouch for you by writing you letters, etc. They can also invite you to give talks, participate in conferences, and in general make sure that you are not forgotten in academia.
I think staying in academia as an outsider is much harder if you cannot find people like this, and in all the cases that I have seen, these people sooner or later leave academia. So you need to plan ahead -- if you are still in school, cultivate these relationships. If you have already left, start by getting back in touch with your advisor and close friends who may still be in academia.
In the second case, I think everyone feels some nervousness (and hopefully some excitement) from becoming independent. I think the most crucial thing is to make sure that you have some low-hanging fruits as well as the ones that are just outside your reach as your research projects. Keep yourself busy, and you will find that you have become a pretty good researcher during your time as a graduate student!

Yes, as mentioned in my initial question, collaboration with at least one established academic is needed

Hi @Scrooge, not getting the point of your comment. But anyway, I'm not talking about just collaboration. It should be a closer contact than that; you need a friendship, because otherwise the collaborator probably would not care about what others thought of you in academia. I personally would not want to do any research with an independent academic that I don't know well -- too much to risk, and not much to be gained is my honest opinion. As you yourself seem to be worrying about, independent researchers are usually not well-recognized at all. So don't aim for a collaboration; aim for a friend

Yes, I have several friends in academia, including my PhD advisors.  According to a few other independent researchers that I know, this is not always necessary.

@Scrooge OK. I am not (and do not plan to be) an independent researcher, so your friends may know better. My experiences from the other side always have been that the independent researchers who are taken seriously are the ones with many friends within academia; the friends will vouch for their personal circumstances that forced them to leave academia (it wasn't because they couldn't find a job; they just had this other issue, etc), and their competence as researchers. Good to hear some other perspectives, though.