text:
Start the PhD research before taking my masters?
I was thinking about getting my masters in November 2015 or May 2016 (An 18 month masters) but I was wondering if its possible to start my PhD research from now, I have an idea of what my research would be and I think it will save me time when I actually apply for PhD, I understand that a lot of changes will come once i finish my masters and enroll for PhD, but the question is; is the research that ill start now would be acceptable and valid for my PhD?

What don't you do the research you want to do for your masters project, then continue when doing your PhD?

This will depend heavily on the university, department, and country in question.  My Ph.D. institution basically didn't have "Master's" students.  They were all technically listed as Ph.D. students, so that the Master's was more of a "you tried and failed, here's your consolation prize," or a "we knew this is all you wanted, but pretending you were a Ph.D. student who couldn't make it let us fund you" type of thing.  So for those going for the Ph.D., the Master's was just this meaningless decoration you picked up when you eventually remembered it.  I got mine months before the Ph.D.

I actually did what you are proposing, skipped my MS and went straight for a PhD in genetics instead. Also, based on my experience I had a bunch of concerns for you but I can't post much - the program insists I have untoward motives because I don't know your income situation, not that I want to know at all!  Great. Last time I'll post here.
There are positives and negatives to this decision and in the end, you may not think going straight for a PhD is worth it.  First and foremost, will you be paid a stipend while obtaining a Masters?  If so, will it be the same amount as you would make while working on PhD, and are he conditions the same, i.e. will you be a teaching assistant the entire time for both degrees or will the PhD allow you to focus mainly on your research with little other responsibilities for the stipend?
What they did to me was blatant "carrot" manipulation.  I was offered a lot more to enroll in a PhD program and skip the MS.  And hey, they had already accepted me as an MS candidate, they just targeted me as good slave labor :) I think I should have stuck to my guns and gotten the MS first.  The classes in my case would have been identical and wouldn't have been repeated moving onto the PhD if I had stayed at the same institution - find out about that as well - what is the curriculum like between the two degrees?  Will any classes have to be repeated, especially if you change institutions?  If you have a good idea where you want to be as well as what you want to be doing (and you are stating that you do know what you want to study), ask the second institution (or the first one if you plan to stay) about repetitious classes.
As far as continuing on the same or similar track of inquiry, make certain if you plan on staying in one place they are good with that plan.  But honestly, if you are getting two degrees, take advantage of the switch.  Use your Masters to gain extra skills (by classes or experience) that you may not have planned on picking up if going straight for the PhD.  The broader your education, no matter what the field, the better you will see the big picture and its underlying minutiae simultaneously.  A broader knowledge base can only aid you in designing strategies to solve problems and make testable connections between superficially disparate subjects. If you switch institutions, you might find it even easier to stay inline with your original goal.

Sorry again for the awful post above. It is truly devoid of solid advice based on my own experience and absent a bunch of pros and cons for you to weigh, based on me not knowing your exact situation and common sense. Sorry and like I said this is my first and last time I will ever use Stackexchange for anything.

I’m not sure why you feel such need to apologise.  Answers giving personal experience are often useful, provided they are honest upfront that that’s what they are, as yours is.

There are advantages and disadvantages to each. I did the MSc first, researching a topic that I had been interested in for years. I never thought my topic would have any commercial appeal... but after my MSc I got hired by a company based on my research. So now I'm doing a PhD, continuing my research (much of it on company time, since it has applications for them), and am getting a nice salary (much better than a PhD stipend).


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Is it necessary to ask permission before including someone in the acknowledgements of a research paper?
I had the impression that obtaining written permission before including someone in acknowledgements was required. Therefore, I just wrote to someone asking for written permission to include him in the acknowledgements of a paper, and he said he didn't think it was necessary. I don't recall where I got this notion from - perhaps the rules of a specific journal? So, I was wondering if there are any general rules about this or not, or are they perhaps journal specific?

For an interesting paper where people declined to be included in the acknowledgements, see arXiv:1003.6064.

@episanty You do realize this is a April 1st joke, right? So I don't think standard rules in academia apply here.

Of course I do. One of the best to grace the arXiv so far!

One good reason to check with the acknowledgee is to make sure you are spelling their name correctly!

When you list someone in the acknowledgments, you're just thanking them, as opposed to speaking on their behalf or assigning them responsibility (the way authorship does), so I don't see why permission should be required.  I've never asked for permission or been asked myself, so it's certainly not standard in mathematics.  I haven't heard of it in other fields, but of course I can't say from personal experience.
Of course it depends on what you say.  "I am grateful to Alice for her steadfast support of my research" suggests Alice endorses your research, and you should certainly ask for permission before saying something like that.  "The determinant calculation in Section 2 was supplied by Bob" suggests Bob is responsible if it's wrong or clumsy, so you should make sure he is OK with being thanked (but in this case you presumably already discussed with him your plans to include his calculation in your paper and attribute it to him without making him a coauthor).  And of course if your topic is really controversial, then you should be extra careful about everything.  However, if you had helpful background discussions with Carl and write "We thank Carl for helpful discussions about functional analysis", I don't think you need to ask his permission.

You said what I wanted to say, only better.

I also think this is a good answer.  I would like to see a complementary answer from an academic in the field of law.  The point of inadvertantly assigning responsibility/endorsement is key;  I am going to review my acknowledgment sections to make sure of less/no fallout.

I wouldn't take "I am grateful to Alice for her steadfast support of my research" as an endorsement. Is that really what it's supposed to represent?

@DavidZ: I'd take it as indicating that Alice at least thinks the project is worthwhile and promising (although not that she has checked the details).  It's probably not a big deal unless the research is controversial or of questionable quality, but I'd avoid saying this unless Alice has been unambiguously supportive (not just helpful), and even then it couldn't hurt to run it by her to make sure she's OK with it.  For example, one could write to thank her for her help and support, and include something like "P.S.  I hope you won't feel shy about being publicly thanked in the attached draft."

While Anonymous Mathematician’s answer holds for most fields I am aware of, this question and answer made me aware that some journals in the field of medicine and some mega-journals require consent for being mentioned in the acknowledgements, for example:

The Lancet:

Please include written consent of any cited individual(s) noted in
  acknowledgments or personal communications

Plos One:

Authors are responsible for ensuring that anyone named in the Acknowledgments agrees to be named.

I've never come across any rules about this. But I do often write to people to let them know I'd like to include them in the acknowledgements, particularly if I know them less well, and enclose a copy of the draft paper. It's a way of thanking them, especially as they might never come across the published paper, and it gives them a chance to escape if, for whatever reason, they wish to.

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Obtaining followup clarification/feedback from referees via the editor
[This looks like something that might have been asked already, but I have not found a question like this on this site.]
I recently had a paper rejected with resubmission from a top Bayesian Statistics journal. This was not a surprise. My main reason for submitting to the journal was to obtain feedback, which I did obtain. I received two reasonably detailed reviews, one more detailed than the other (the longer a bit over 3 pages), as well as a very short and somewhat cryptic (one short para) comment from the Associate (Area?) Editor. Also, these reviews were delivered very fast, which was good. I submitted the manuscript on 27th of April, and it was rejected on the 3rd of June.
The general tone of the reviews is captured by the EIC's one line summary

Your paper has been read by an AE and two referees. They have all found the topic interesting but with several major flaws in the methodology and implementation

Now, some points in these reviews are unclear. Would it be reasonable to write to the editor asking for feedback on those points from the referees? Perhaps something along the lines of

Is this what you meant? If so, the answer is this. If not, can you clarify, please?

or maybe just

I don't understand what you mean here, can you elaborate?

Assuming the message is forwarded and the referee replies, I suppose there could conceivably end up being a bit of a back and forth with the reviewers via the editors.
On previous occasions I have not tried doing this, but I have come to believe there is no sense in being too shy in such matters. If you want information, ask for it.
However, I wonder if this is considered unorthodox, improper or inappropriate procedure. It is relevant to note that I am not an expert in Bayesian methods. However, the editors and referees apparently thought my paper worth the trouble of reviewing in detail. Regardless, my lack of experience/expertise may hamper me in understanding the finer points of what is expected in the field.
I will of course do my due diligence in trying to understand the content/purport of the comments, but I don't see the point of my spending hours trying to guess what is meant when the referees could (hopefully) clarify the point in a few minutes.
So, to summarize, the upsides are:

If I get a response, my eventual fixes will be better and more targeted
I don't waste a lot of time trying to guess what someone meant. Maybe it was even based on a miunderstanding

The downsides are:

The reviewers/editors will not want to be bothered with responding to me. This will be especially true if this is not considered normal procedure
They might be annoyed by my (possible) cluelessness in the area.

If I don't ask for any clarifications, then I will just end up making my best guess as to what the referee means. I don't think that the results would be as good as if I was to get clarifications.

The simple answer is: there's no harm in sending the editor a polite email to ask. Provided your questions are broadly sensible, they're unlikely to hold a grudge against you for doing so.
However, I imagine that an editor is going to be wary of encouraging a discussion that might irritate his reviewers (who he wants to be able to use again in the future), or which appears to risk developing into a challenge to the review process itself. I suspect that you are unlikely to get a positive response unless your question is very limited in scope: for example, "Reviewer 1 comments that my results would appear to generalise the Jenkins-Smith theorem; however, I cannot find a statement of this. Would the reviewer be prepared to give me an appropriate reference?"
Have you asked a colleague to look over your reviews? Sometimes, counterintuitively, things are clearer to a reader with a shallower understanding of the intricacies of your work.

To be clear, I think that if I write (I'm not sure yet) I'll probably ask for a clarification of the reviewer omments, and not attempt to get into a discussion. As you say, this probably won't be received positively. Now that I did think about it, I did recently write to an editor, but in this case asking her for clarifications on her own comments. She replied. However, in that case the editor didn't have to try to get a reviewer to reply.

First, as an editor, I am not happy to see that you send manuscript to journals to get feedback. It is a terrible waste of time for reviewers and editors who work for you for free on their spare (or research) time. So, I suggest not using this as a strategy in the future but at least try to locate journals where you think you stand a chance to be published and also prepare the manuscript accordingly before submission.
To your question. There is no harm writing a letter asking for clarification. A service minded editor will at least reply. But, I doubt that you can expect much interaction with the reviewers, with or without the editor as a middle person since, as mentioned above, these persons are working to serve the community on their spare time and for free. If reviewers are known by name to you, you are of course free to contact the reviewer directly. Again, the degree of response depends on the willingness of the referee to indulge to such communication and, perhaps, their interest in the details of your work. But if your aim is simply to squeeze out information from an "easy" source, I think you need to think again because such behaviour could soon turn out a label.
In your question you specifically ask about requesting references, and I will add that it is not very helpful when referees just allude to references in their reviews without giving them, but then people tend to have different standards. This obviously goes for all sides of the process.

"First, as an editor, I am not happy to see that you send manuscript to journals to get feedback". Sorry, I don't understand what you mean. Are you suggesting that I had no plans to publish there and just sent in my paper to get comments? That is obviously not the case at all. In any case, as I said, the paper was rejected. To be clear, I don't understand what you think I did wrong.

"because such behaviour could soon turn out a label." Sorry, I don't follow this phrase.

"My main reason for submitting to the journal was to obtain feedback, which I did obtain." - FWIW, I interpreted this in the same way as @PeterJansson.

@avid Well, because I didn't think the journal would accept the paper. But that is hardly something to criticize me for. People submit to journals all the time expecting to be rejected. If I was wrong and the journal accepted the paper, I would of course publish it there. I still don't see what I am supposed to have done wrong. And now  after looking at the reviews I'll have to decide whether to resubmit or go somewhere else, but again that is my decision and not something to criticize me for.

Indeed. If one submits a paper to Science, say, one accepts that there's a good chance it will be rejected: this does not (of itself) mean that the paper is not fundamentally sound. On the contrary, part of the value of highly selective journals is that the editors cherry-pick from submitted research. However, it's not unheard of for people to submit work to journals that is fundamentally incomplete, with the hope that the reviewers provide inspiration for the 'next step'. This, I believe, is the practice that @PeterJansson deprecates.

@avid Well, that is not what I was doing here at all. For the record, the paper was as complete and correct as I could make, working alone. I spent a huge amount of time on it. I certainly didn't submit unfinished work to the journal. That would be unprofessional and disrespectful. Unfortunately, it seems the paper was still up to standard, but I did my best.

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How do I write a good abstract?
So, I'm sitting here, rewriting the abstract of a paper I hope to
submit shortly. The abstract I had was old and not very good.
I have on good authority that an abstract is an important part of a
paper, because it is often what makes a reader take a closer look at
the paper.
So, how does one write a good abstract that will make people take a
closer look? What are things to include and things not to include?
What are common mistakes, if any, to watch out for?
By way of example, here the abstract I am rewriting, in its current
form. This is for an applied statistics paper. Feel free to critique.

We describe and implement a method to select a Bayesian model for
      a collection of DNA sequences. This method assumes the DNA
      sequences are generated from one of a particular class of
      distribution models. These models capture long range correlation
      structure among the sites of the DNA sequences. We choose a model
      from the class by using a simulated annealing search algorithm
      with a scoring function based on the prior predictive distribution
      corresponding to the model. We apply this method to model human
      and mouse Recombination Signal Sequences (RSS). We use the
      posterior predictive distribution corresponding to the model to
      predict which of a larger group of sequences are RSS in the
      context of a cross-validation setup.

ADDENDUM: Please comment on whether there is a standard abstract length limit in your field, unless it is journal specific.
EDIT: Here is a second attempt at an abstract. This is based partly on the discussion at How to Write an Abstract, which is a nice discussion of the main points to think about. The results teaser at the end is a little unorthodox, but it is intended as an inducement for people to look further at the paper. @F'x, do you have any feedback?

Given a specialised set of DNA sequences, it is a biologically
  interesting problem to predict which members of a larger set of DNA
  sequences belongs to that set. In this paper we consider the
  particular example sets of Recombination Signal Sequences (RSS).
Problems of this kind are commonly addressed in the biological
  literature. However, we approach this problem by selecting a
  Bayesian model for this specialised set. This is an approach that is
  rarely used in this context, but as we show, can give good results.
We select our model from particular class of distribution models.
  These models capture long range correlation structure among the
  sites of the sequences. We choose a model from the class by using a
  simulated annealing search algorithm with a scoring function based
  on the prior predictive distribution of the model. We apply this
  method to model human and mouse Recombination Signal Sequences
  (RSS). We use the posterior predictive distribution of the model to
  predict which of a larger group of sequences are RSS in the context
  of a cross-validation setup. We summarize the results of the
  prediction in figure and tabular form, showing good results. Example
  statistic: out of 700,000 candidate sequences, 30 to 50 are actually
  RSS. The algorithm ranks these, in descending order, by how likely
  they are to be RSS. It ranks almost all the RSS (90\%+) in the top
  100.

A gem is a short paper on abstracts: Landes, K., A scrutiny of the abstract. Bulletin Of The American Association Of Petroleum Geologists. 50 (9), 1992-1999.
Which provides an excellent description of the abstract.

Hi Peter. Yes, I've seen this note before, but was hoping for some more detailed points to consider. Apparently the author does not like the word "describe", which I use. I'm not sure why, though.

Before the 1966 paper mentioned by Peter Jansson, there was a 1951 paper.

One of the things that is too much overlooked is that an abstract is read by a more diverse crowd of people than the rest of your paper. So, you have three different goals:

Give a take-home message to people who aren't interested enough to read the full paper.
Convince the undecided to read it.
Make it easier for experts to find it.

Nowadays, #3 is not so much of a constraint: Google and other search engines allow for full-text searching. So, focus on #1 and #2: be concise, crystal-clear, attractive.

Enough with the generalities. I love to critique, so I'll give it a try: I'm not in your field, which I think makes me a good test reader for your abstract, but also makes it harder for me to actually suggest actual changes to it. Anyway…
I think it's decent: no catastrophe, but far from enthusiastic. My main comment would be that it lacks a clear statement of the broader issue you are trying to address. You could start with it, something like:

The past few years have seen large advances in the statistical modeling of DNA sequences, mostly based on genetic algorithms. In this work, we explore the efficiency of an alternative and simpler route, and show how to efficiently choose within a class of distribution models.

I have filled in with semi-random keywords/buzzwords, just to give you a sense of how to achieve it. The idea is to put your findings in perspective:

Roughly, what subfield are you working in?
What is the main trend in this field?
How do you position your work with respect to this recent research?

Then trim down the rest of the text:

We showcase a method to select a Bayesian model for a collection of DNA sequences, generated from a specifically chosen distribution model capture long range correlation structure. We choose the model based its prior predictive distribution. Applying this method to model human and mouse Recombination Signal Sequences (RSS), we predict which of a larger group of sequences are RSS in the context of a cross-validation setup.

(I hope I did not lose or betray some of the meaning, it's hard when you don't get the finer points of the text… but you get the idea anyway!)

Thanks, F'x, that's helpful, and certainly food for thought. BTW, "loose" in the last sentence should probably be "lose". Also, ironically, as far as I can tell, nobody has ever used the approach I use in this paper (I've spent a fair amount of time trying to find something to compare it to), so I think the first sentence of your proposed revision is perhaps a little inaccurate. :-) In any case, I understand and appreciate the larger points you raise.

To be more specific, when I say first sentence of your proposed revision, I'm referring to the "statistical modeling of DNA sequences, mostly based on genetic algorithms" part. People don't generally try to model DNA sequences, and I've never seen anyone genetic algorithms. Though I wrote, simulated annealing. Does this fall under genetic?

@FaheemMitha yeah, I wanted to write something plausible-sounding to give you an idea of what I meant, rather that just advice… that sentence (and the use of genetic algorithms) was the first idea that popped into my head

Sure, I understand your intention, and the example is valuable regardless. I agree that I should try to put it in a larger context.


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Does peer-reviewing for journals/conferences which advertise to attract reviewers; harm one's academic reputation?
I always thought that the way journals elect their reviewers is that probably they or their editors ask some famous researchers to review some of their papers. I mean, reviewers are probably asked to review papers.
Recently, I have seen some journals and publishers which advertise on their websites saying something like

If you want to be a reviewer for our journal/conference, please send your CV to our email address; we will assess your background and if you are accepted, we will inform you where to start reviewing our papers.

This is very good opportunity for students who are not very famous in their field and want to start reviewing for journals and conferences to send their CV and assess their opportunity to review for a journal or conference; but I want to know if somebody does reviewing for these journals which have such system for attracting reviewers, and mentioning involving in such volunteer paper reviewing in his CV; will this harm his academic reputation?
Is it acceptable for academic community that somebody send his CV for a journal and ask them to accept him as a reviewer? How such advertisement on a journals website is considered? Do reputable journals and publishers have similar advertisements for attracting reviewers to their publication group and can such advertisements be considered a sign of a non-reputable journal/conference?

Refereeing is a burden and a time-sink.  Certainly one has the obligation to agree to referee a certain number of papers once you are senior enough to be asked to do so, but why on earth would you ask to be sent papers to referee?

@AndyPutman I think this is a good opportunity for young researchers to start reviewing, this probably helps young students to start reviewing and help them improve their CV and add value to their academic reputation.

Sorry @andyputman, but reviewing is a cornerstone of the scientific process and can greatly improve the quality of the works. A properly done review is inspiring. I do not disagree that it is indeed a time-sink and should be done properly, but a burden, I do not agree. Just because you do not get any direct profit from it, doesn't mean you shouldn't do it...

@AndyPutman: Yogi Berra is said to have remarked, "You should go to other people's funerals, or else they won't go to yours."  I think much the same is true of refereeing papers.

How on earth are people interpreting my comment (including the phrase starting "Certainly one has the obligation...") as saying that one should not referee papers?  Writing referee reports falls into the same category as "writing letters of recommendation", "reading postdoc applications", "serving on grant review panels", etc.  That is, it is a type of service that one should do when asked (in reasonable quantities), but which there is no point in seeking out.  Trust me, if you continue in this career you'll have more "opportunities" than you can possibly accept.

@EnthusiasticStudent: Refereeing does not improve your cv.  While it is fine to have a line item there listing some of the venues you have refereed for, it is not considered an "honor" and will not really help you with your career.  When you are a student, you should focus on your research.  Probably you should say yes if you are asked by a reputable journal/conference (though ask your advisor before doing do), but more for good karma than to help yourself.

I am hard-pressed to imagine a situation in which reviewing would hurt your reputation. It does pay, as your question hints, to check up on the journal you'd be reviewing for to be sure it isn't scammy, but asking for reviewers isn't much indication one way or the other -- almost every journal needs a stable of willing reviewers, and what harm does asking do?
Yes, editors do choose reviewers for a given paper as carefully as we can, but we mostly haven't the luxury of "who's the most famous person working in this area?" because Most Famous Person is swamped. So we keep a stable of folks who have signed up with us, and we look through it for potential reviewers.

In my corner of academia (mathematics), I am not aware of any self-respecting journal that advertises for reviewers. The only examples of this phenomenon I've seen were from obviously bogus/predatory journals. To my mind, advertising for reviewers is one of several clear warning signs that this is not a journal I'd like to either read or contribute to.
With that said, a. this only reflects my limited perspective, and b. even if my perspective is correct, refereeing for such journals is not likely to hurt your academic reputation, in particular since refereeing is anonymous so no one except the journal editor would know that you were doing it. As others have commented, your time may be wasted but your reputation is not in serious danger.

Although refereeing is anonymous; I have seen that some people in Academia mention the journals/conferences they have reviewed for. Does mentioning reviewing for such journals in CV hurt reputation?

@EnthusiasticStudent the potential for any refereeing activities to either hurt or help your reputation is pretty minor. You would have to do something fairly extreme, like boast about refereeing 50 papers a year for a journal that publishes pure garbage, for this to have more than a negligible effect. But yes, mentioning that you have refereed papers for really bad journals could in principle lead some people to question your judgment and have slightly diminished respect for you.

It's more a question of whether you want to be reviewing for a given journal. Doing your first few reviews can be extremely instructive, even if the papers aren't of high quality. Later on, you might become pickier.
As other comments point out, most people who write reviews see this a "service" to their community, and do it because being an active member in the community has many benefits.
To answer your question, then, reviewing cannot harm your reputation, except indirectly by wasting your time.


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How to decide whether a mistake is sufficiently relevant to publish about it?
How do I know my results are significant enough to be published?
I am a physicist and I have found a very common mistake that appears in every paper in my area of interest. I thought it would be nice to let the people know it should be corrected. However, it is a very simple mistake, very basic math. I thought at first I could publish that as a short letter, but then I realized that I am unsure what actions the significance of the error(s) warrant.
How do I know whether an error is important enough to write a letter to the publication's journal?

of possible interest http://academia.stackexchange.com/questions/18911/what-should-you-do-if-you-spotted-a-non-trivial-error-in-a-highly-cited-paper

If you do decide to publish (and have the time), you should do an analysis of exactly what the significance is. Work out the worst case and average error. Maybe do some simulations. Look at a few famous results based on the technique, and redo the work to show how the results differ. Think kind of thing can help you build a simple insight into a more substantial publication. However, be sure to make the page count proportional to the heart of the paper. If it's a simple mistake 2-4 pages should suffice.

Out of interest, could you update the answer with what mistake it was, or publish in comments, once you have figured out what to do.

I'm sure you'll agree physicists frequently make minor errors, or rather have different interpretations of certain concepts in mathematics. I see this in differential geometry and representation theory for example. Sometimes it's simply a matter of language. I would check with someone else whether this 'mistake' is actually worth addressing, and whether physicists are aware of it and ignore it as a very minor technicality, e.g. in the exact definition of the tangent bundle.

Does it affect experimental/simulative results? Are there cases where it would, but which haven't been explored (in which case you could propose an experimentum crucis)?

You should talk to colleagues from that area of interest to check whether it actually is a mistake or maybe a common generalization that, although not perfectly correct, is still 'good' in the systems that were discussed in the papers. Also writing a mail to the authors of said papers is a better idea before writing to the journals without any cross-check.

Many journals have special formats for such remarks, usually called comments. Though these are usually directed at single papers, there might be journals out there which do not impose such a requirement. Also, as such requirements are not carved in stone, you might just contact the journals which published most of the papers making the mistake whether they would consider such a comment for publication.
That being said, you should ensure that the presumed mistake is really a mistake and not just notational sloppiness or a standard approximation (see BPND’s anwer), which nobody wastes words about anymore.
Finally, you might consider to not only mention the mistake but perform and report about some research and demonstrate or estimate the negative effect of that mistake and thus increase the impact of your publication. Also, to address one of your questions: The existence of such negative effects is a good criterion for the relevance of a mistake.

This is where you define yourself.  There isn't a right and wrong answer to be suggested.  You're helping improve the wisdom contained within the Academic Establishment itself.
Otherwise, I'd say you don't have to know.  That's what the peer review process is for.  But it might save you some time to use this radical tool of the Internet, whereby you can be in informal dialog with peers across the world.

True, however, estimating whether it’s worth one’s time to invest a considerable amount of time to prepare a manuscript is quite something.

I find it remarkable that you should take such a condescending tone, as if to say "Oh, everybody knows you should discuss it with your peers on the internet." Well, everybody except you, apparently, since you only included that part of your answer after somebody suggested it to you!

@David, well I knew of the internet, and I assume the OP does also.  For example, he could ask his question on physics.stackexchange.com instead of here couldn't he?  I think a little condescension can be appropriate if used in a corraling manner.

Condescension is never an appropriate response to someone who is legitimately asking for help. It only serves to alienate people and push them away from ever returning to contribute here.

Funnily, this was not even what I was aiming at in my comment. Rather I wanted to comment that letting the peer-review process decide about the relevance may be quite uneconomical.


text:
Reference on how often "To the best of our knowledge" assertions turn out to be false
Quite often authors make some claims with some "to the best of our knowledge" disclaimer.
Example:

"To the best of our knowledge this is the first time this approach has been used to address this problem".

Is there any research/study/survey that tried to look at how often such claims are false? (e.g. some counterexample can be found)
I am mostly interested in the field of machine learning / data mining in English-speaking venues, however any reference on occurrence of such false assertions would be of value.

Quite often, I would hope. Appending or prepending "AFAIK" to a phrase is really only appropriate when you have a pretty good idea - but just aren't 100% certain - that what you're saying is true.

The example you give is of a statement that can be shown to be false, but can't be shown to be true (which is why the authors qualify it in the first place). So I don't know what it means to ask "how often such claims are true."

@ff524 I was trying to be positive :) In my mind true == failure to show it is false but yes you're right, the direct way is to come up with a counterexample. I edited the question to reflect this. (apparently I messed up my votes, I can't upvote your comment)

A meta-comment: @FranckDernoncourt, you frequently ask questions about researches or studies on a variety of topics which, really, do not seem to attract much research, at least by judging the answers you get, which, AFAIK, are mostly based on personal experience. If there is a thread connecting this series of questions, which do not seem to be driven only by curiosity, it would be nice to mention it explicitly, maybe you'd get more (meaningful/useful?) answers. Moreover, it would be nice if you add to each question which publications or databases you've already searched to find an answer.

@MassimoOrtolano Thread connecting this series of questions: often personal reflections on the organization of research, and I sometime wonder to what extent ideas stemming from open science could help research to be more effective. Regarding your second meta-comment, I generally Google + Google Scholar a bunch of words I put in the question. It sounds a bit tedious to list all queries I have made, and it might be counterproductive as results for a given queries depend on the location, time, etc., I only look at the few first pages of results, and I may miss some interesting results.

Like @MassimoOrtolano says, in most SE communities, when someone requests surveys or solutions to his particular problem he must also provide a) evidence of his efforts so far or b) share the information he has acquired so far to the community. You seem to do neither of those two things, which to my eyes is a bit rude.

@Alexandros a)  I generally Google + Google Scholar a bunch of words I put in the question. It sounds a bit tedious to list all queries I have made, and it might be counterproductive as results for a given queries depend on the location, time, etc., I only look at the few first pages of results, and I may miss some interesting results. b) I do share any information I have found so far, e.g. http://academia.stackexchange.com/a/27497/452 but as you may have noticed through the number of answers my questions asking for references (as Massimo did) it's unfortunately often tough to find.

@FranckDernoncourt It is hard to believe that in more than 10-20 similar questions you have posted, you have not found a single reference or survey. It seems more probable that you actually found something that you did not want to share.

@Alexandros Yes of course I keep all the information to myself, it's very valuable and one day I'll become rich thanks to it.

not about academia. at best, about one field thereof.

@keshlam I have no idea why you believe this isn't about academia.

It's no more about academia than any other data-mining, linguistics or philosophy question would be. And it's a "please do a literature search for me" question, which is generally considered bad form unless the OP explains what efforts they've already made to answer the question themselves. I'm willing to be outvoted, but if so I don't understand which rules are actually in effect.

@keshlam Well it's about academic research.

To the best of my knowledge, this isn't about academia as defined for this area. Ymmv.

-1 because this question pertains to, "The content of your research, rather than the process of doing research". In particular, since you don't intend to share what you find except for some sort of personal gain, I don't believe that this can be construed as a contribution to the forum. Everyone has vague, half-baked ideas. The correct way to pursue them is by talking to colleagues/mentors and/or getting a research assistant.

@Moriarty, I disagree on hoping it happens often. It would mean sloppy work of the authors. On the other hand, it would be nice if such claims get really followed up, if only for the sake of historical accuracy.

Isn't this what reviewers are supposed to check? Even if the author uses "to the best of my knowledge" as a euphemism for "I can't be bothered to spend more than five minutes at finding out", the referees are supposed to judge (and be able to judge!) the originality of the work. Hence in reviewed papers I would assume a high probability that the approach truly is original.

To the best of my knowledge, it is unlikely anyone has done the gruelling work of trawling through the literature, looking for such statements, and then doing the detailed work of finding out if the claim was true.
On the other hand, if I state such, you'd have to prove I did have prior knowledge to refute my statement. In itself, that could come close to an accusation of plagiarism in the context you cite. Or at least of sloppy checking of previous work.


text:
What books, biographies or survival guides are helpful for women in engineering in academia?
Recently, I was giving a small informal talk in a local college. The audience comprised of engineers and my talk was based on current research in engineering. One of the girls asked about the position of women in academia. I answered that stating that academia was like just another field for women but now that I think of it, it might not be entirely true.
I thought that perhaps I could refer interested female student to resources explaining any gender specific aspects of academic life. I've read 2 books "Surviving your Stupid Stupid Decision" and "What you came for." Both were books to read before PhD to discuss common problems and their solutions presented as a preparatory handbook or survival guide. I am looking for something similar, but specifically addressing the aspect of gender in academia. I don't have a specific question in mind. A cursory Amazon search failed to yield any fruitful results.
I'd like to find resources applicable to female students:

Engineering in North America but maybe even Europe. These students showed some statistics of bias within academia.
Interested in joining faculty positions or industrial labs.

Are there books, biographies, or survival guides for women in academia?

Something about this question doesn't seem right. It's at once too broad (What field are you trying to enter? What country do you live in?) and not answerable (What's your goal as an academic? Why would you think that gender should affect it?). You stated question of just asking for books doesn't address a problem, it's you asking us to provide the answer you already thought of (namely, read a book). I suggest reformulating the question so it explicitly asks the questions you hope to find answers to in a book.

I disagree with @eykanal; the question is both focused and answerable.  And the mere fact that this site has so few (publicly) female users is evidence that academic gender issues are very real.

FWIW, as much as I'm a fan of it, "Surviving your Stupid Stupid Decision to go to Grad School" is really for entertainment value more than anything else - though unofficially, it does of course contain many nuggets of truth.

@JeffE There are few publicly females users in many in fact most places on the internet. For example youtube comments almost never feature females users. This is more a problem of the internet in general not only in academy.

About a month ago, MIT published their most recent Report on the Status of Women Faculty in Science and Engineering, following up on previous reports from 1999 and 2002.  It's not exactly a "survival guide"—it's written for existing faculty and administrators more than for prospective academics—but it does clearly describe several barriers to gender inequality, both past and present.  The National Academies published a similar report in 2006.
Even more recently, Nancy Hopkins (one of the authors of the MIT reports) gave a fascinating talk about MIT's efforts to attract and retain female faculty.
(Hopefully someone else will suggest something more useful for prospective academics.)

Update: One of my female colleagues sent me the following reply, which I'm posting with her permission.  (I'll delete this update if she decides to post an answer herself.)

My more recent reading has focused more on survival with children in
  academia, which is not quite the same thing.  However, some of the
  issues might be the same.  Two good books are Mama,
  PhD and Motherhood: the Elephant in the
  Library,
  both of which are essay-based, with women sharing their stories.  Both
  are available on Amazon, and are quite good.
Some of the best survival guides these days are the blogs - there are
  a bunch of good ones which provided sanity and good advice along the
  way.  My two favorite aren't active anymore, but their archives are
  nice, and there are plenty of good ones still active:

http://scienceblogs.com/sciencewoman/
http://scienceblogs.com/seejanecompute/
http://science-professor.blogspot.com/

There are tons of research papers on the issue, but to be honest, at
  least for me, those tend to be more depressing than helpful.  For
  example, an interesting (but outdated) one:
  http://people.mills.edu/spertus/Gender/EKNU.html There was a recent
  article that retention is going better among faculty (except in math,
  which surprised me):
  http://www.sciencemag.org/content/335/6070/864.abstract

That MIT report is very interesting. One point of note... the report lists (page 5, bottom) that "...mentorship by women faculty members is tied to the stereotype that women will be sympathetic mentors because of their gender." Personally, the harshest—and simultaneously most useful—member of my committee was a female psychology professor. Definitely no sympathy from her at any point, merely professionally-given recognition (and reproach) when and where appropriate.

Here are two blogs that academics might enjoy:

Female Computer Scientist - Especially, read the archives, starting from the beginning and moving forward, for a perspective from a graduate student who later went on to a professor position.  Lots of great advice for men and women alike.
Female Science Professor - Worth reading, and with a sense of humor.  Written from the perspective of a mid-career science professor.  Probably more likely to be of interest to faculty than grad students, but for faculty, you may find some of her writing spot-on.

I certainly found some of the stuff there helpful.  I don't know if it will help women in the position you mentioned, except perhaps to feel a sense that others have gone through this and that it is possible to remain a sane, productive person despite the hurdles.

What advice would you give men wanting to do the same things?
That advice that you would give them, you give to women.
It'd be quite foolish to give women different advice and expect them to have realistic expectations and not set them up to fail, unless you feel that women aren't as competent and need to have their hands held, which would be wildly sexist.
Chances are high that if you direct them to a source that's "for women," it will more than likely ensure a negative outlook about their future coworkers and employment.
Engineering is engineering. Gender need not apply.

I would give the same advice to anyone asking about the position of women in academia, regardless of the gender of the asker. That advice would be "Educate yourself about the reality of women in academia by reading the research and/or blogs describing personal experiences (both positive and negative)", as JeffE and DW suggest.

@Jackson: The experience of women in academia is (currently) fundamentally not the same as that of men. For example, men don't have to choose between work and maternity leave. Assuming that all advice for men apply to women—or that women don't have special challenges that men don't face—is overly simplistic.

@aeismail You example is actually country-specific, but the general point is of course good.

Maternity leave? Isn't that common sense and way too situational? Let alone that completely depends on the country, the company, what your profession is, how many hours you work, whether or not you want children, whether or not you have a man/partner, etc., you might as well give advice about menstrual cycles and how to bathe. It's weird watching people claim women are equal with men, but then claiming that they need all of this common sense knowledge because they need to read feminist blogs about maternity leave. Non sequitur to say the least.


text:
New author, independent research, scope of publishing
I have done my masters in Computer Science, but did not receive much support in the masters program to get the final project published. I am presently working as a software developer in the industry while also trying to perform independent research on a few topics which I have in mind when out of the office.
I have recently completed some research ad derived new method for data clustering based on a heuristic which is novel idea as far as I can tell. I have shown it to work better with respect to only one metric with a few other algorithms which is of the closest type.
I have been allowed to use my employer's organization address and email for correspondence, but my organization has told that there should be a disclaimer that my organization has nothing to do with this research. If I do not use this address, I need to give my current address. I am not sure if I can give my university address at this point, as the entire research was done after I graduated. At the university I had access to journal subscriptions for which appropriate acknowledgments are given.
Previously I have not published any peer-reviewed work anywhere and I am the only author of this manuscript. I am not sure how shall I proceed. Submitting to journal such as Elsevier will be single blind, and as I am trying to publish as a new independent author, will my submission be subject to biases based on my lack of previous publications? Or shall I go for a conference with double blind review process? Also the 7 ~ 10 page mark for conference is difficult to maintain without removing vital components.
Some information about the work. The work was not complex, but is unique and it is shown to work on several well known data-sets. The main topic is data clustering.
How should I proceed with publication?

Edit:
Adding information in reply to @Nahkk's comment.
I have no previous academic experience. I have shown this to one professor from a different research interest domain because none of the professors from the paper's domain were interested in this topic, surprisingly. I have also asked for suggestion from a person working in this field. One of them suggests to try for a journal and another suggests a conference first, then work and improve the algorithm do exhaustive tests and then go for a journal later.

Some further information would be helpful. Do you have previous academic publishing experience? Additionally have you shown this work to professors or others researching in the field for feedback?

I think there are many questions here;
Independent Publishing? It is possible to publish your work as an independent researcher.  see this question "Does one need to be affiliated with a university to publish papers?". For further confirmation, I would suggest to directly contact the responsible personnel of the conference or journal.
Forums(Journal vs Conference)?  Journals are usually assumed to be of high standard. However, this might not be true always.Some conferences have equal or higher standard than journals; they only accept high quality works. However, you should be able to find many conferences with a track record of accepting publications with varying qualities.
How to find the quality of a forum? If you want to find out the quality of a forum, check their previous publications and try judging their quality. You can also look for people who have published there, if they are expert in your field then it could be a high quality journal or conference.
What forum suits my work? You know the quality of your work therefore aiming for forums inline with the quality of your work will save you a lot of time.
Otherwise, you can discuss with an expert (a professor or researcher in academia) who knows the forums and their qualities. If they can read your work that would make it easy to find the matching forum.
These are just my suggestions, rest you know what is best for you. Good luck!

You can try any of the options, and see what result occurs.
As a thought experiment, try submitting your paper to a journal of French historical literature.  It will be rejected because (I am guessing) the paper has nothing to do with French historical literature, but it may also be rejected because it doesn't have French in it, or pay enough respect to history, or be written in an appropriate style used to criticize literature in an academic fashion.
More to your case, I would be surprised if, even after reading other papers and attempting to imitate their style, you were able to get your paper accepted at first try to a creditable journal without a large amount of outside coaching, because of issues even more subtle than I mention in the thought experiment above.  The advice mentioned in the comments of working on the result to make it more robust and applicable and introducing it to many other people sounds like the right tack to me.  In this fashion you will encounter the people who may be interested in your result, and have the experience to share with you on how to best present it, and help you raise its chances for being accepted by a journal.
Since you don't have these experiences yet, you need to depend on the experiences of others or earn it on your own.
Of course, you can try submitting it to a journal first anyway, and see what feedback you get.  That is a less gentle but still valid way of gaining experience in these matters.
(If you try the longer and more laborious route of introducing it to several people, I recommend leveraging the effort by researching these people and seeing if they can help you in other ways.  With the right preparation, intent, and eye toward future goals, such as recommendation letters accompanying future grant proposals, the "extra" labor in taking this route may turn out to save a lot of work in the long run.)


text:
Weird changes to status of paper
Last november I submitted a paper to a journal. I have been tracking the status of the review rather regularly (quite obsessively actually) and I have noticed that 3 weeks ago it went from awaiting AE decision back to reviewer assignment. After a couple of days, it went to reviewer selection. Now, it has gone back to reviewer assignment yet again.
I find this quite curious and if anyone has any idea what could be going on, please share it here! I suspect there's a conflict of opinion initially and then the third reviewer rejected reviewing so now they are back to finding a third reviewer? Any help is appreciated.

Probably best to simply not obsess so much. Work on other things and let the journal process happen, unless the process begins to take an unusually long time for your field in which case see other Q&A here for how to proceed. See also https://academia.stackexchange.com/questions/55665/what-does-the-typical-workflow-of-a-journal-look-like

Yeh I shouldn't haha :)

Just chill, hit the gym, go for a walk. Nothing you can do about it anyway. Fingers crossed :-)

Nobody except the editor in charge of the paper can possibly know. We can all -- and you can -- speculate what the editor may have been doing, but none of us will actually know. If you must know what is going on, write to the editor. If you are only curious but do not need to know, then practice patience and wait for the outcome.

excellent advice about practicing patience haha :)

Your explanation of a conflict in reviewer opinions is certainly possible. Also possible is that the reviews weren't very good: perhaps some of them are superficial, perhaps the reviewer said "I can review X portion of the paper but not Y portion", etc.

thats a good shout!

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


text:
How to teach students to ask good questions in seminars?
My university has a course called "Technical Communication" that aims to teach undergraduate math and computer science students (usually sophomores and juniors) how to give good talks. We have lots of great materials for teaching them how to speak clearly, how to engage with the audience, how to construct a technical talk, how to make good slides, etc. We also bring in external speakers so that students can see how professionals do it.
I'd like to add a bit to the course teaching students how to ask good questions when attending seminar talks. I have my own technique for coming up with and keeping track of questions I want to ask speakers, but I'd prefer to have some article or chapter on this topic that I can share with the students.
Can someone please recommend such a reference?
I very much like the advice in this Academic.SE question, but asking students to read that thread feels a bit informal. I'm hoping for a source with similar advice but written with an audience of students in mind (ideally, a pdf I can give them to read, like a book chapter).

Could you expand on your end goal? For example, are you trying to address students not asking (or only rarely asking) questions in seminars, or that they are asking "bad" questions? The former may have a lot of contributing factors beyond knowledge of how to ask a good question, see e.g. Students and postdocs not asking questions, Should I be worried that I don't have ideas of questions to ask during seminars?.

@Anyon Mostly the former, but both are important. I ask lots of questions in seminars (or one-on-one to speakers after) and this has generally been a very good thing for my research and for my career. My advisor was the same way. I constantly hear good things about other mathematicians known for asking good questions in talks. I suspect this is a teachable skill. I think most of our students are shy, but this can be overcome. Both of the links you shared have good tips, and I commented on a few I liked. I'm still hoping for a more formal reference (if I can't locate one, I'll write it myself)

Expanding: I want my students to be active listeners, to think about where the speaker might be going next, to think of other ways the speaker could have proceeded, etc. I want them writing down questions as they pop up, and knowing when to ask (eg, sometimes you ask your neighbor, clarifying notation is good to ask right away, but "why did you do it this way?" might be best for the end of the talk). All talks are aimed at exactly these students (not at the faculty) but often no students ask questions. Having lunch with the speaker before might help (that's what we did when I was an undergrad)

This is somehwat off-topic - but as the question just popped up at the frontpage I had a look ad the "great materials" you linked. I think it's nice to have such a collection of common mistakes during talks. I can't refrain from pointing out, though, that "Don't use a chalkboard [because] [t]he physical act of writing will take up too much valuable time. [...] Computer presentation programs can convey large amounts of material quickly and efficiently" ranks very highly on the list of the worst advice that one can possibly give - and the sample video illustrates perfectly why:

One might use a chalkboard or slides for various different reasons, but the very moment one decides for slides rather than a chalkboard in order to "save time" and "convey more material", the talk is already lost. In the sample video, everybody in the audience who doesn't already know very well what a group is, will have forgotten the definition at the very moment the slide is switched, thus turning the remaining 14 minutes of this 15 minutes talk into a waste of time.

I'm not sure whether you have any influence on the material presented there - but in case that you have, it might be worthwhile to remove advice that is extremely likely to make talks worse rather than better.

Show them good and bad stackoverflow questions :D

Can you please clarify what you consider good questions?

@MichaelGreinecker This is the context of seminar talks. A good question is one where the speaker or other audience members think to themselves "that's a good question." It's not a good question if it displays a deep lack of understanding of what the seminar talk was about, and makes people cringe. For questions asked while a professor is teaching, it's an entirely different definitions and then I might be more inclined to feel that there are (almost) no bad questions.

@MichaelGreinecker is there a point of your comments?

@DavidWhite Yes. One can ask questions with the goal of being better able to follow the presentation. One can ask questions to help other audience members to follow the presentations. One can ask questions to make it less awkward for others to ask questions. There are many other goals for asking questions than seeking the external validation of others, and often different goals are in conflict.

Based on what I've seen at department seminars I've attended, we can't reliably teach full professors how to ask good questions.  (Yes, that is a scathing, caustic statement, but borne of experience.  I think the large majority of ones I've attended had a professor ask what I considered to be a stupid, often seminar-diverting question.  Informal polls of my peers indicate I was not alone in my opinion.  So maybe point out the plentiful bad examples in private later.)

This isn't really an answer to the question in the body of your post, but it is an anecdotal answer to the question in the title of your post. (And it's too long to be a comment.)
In short, I'm not sure that reading an article is really going to teach students how to ask good questions. In my experience, the most important thing is to (1) ask lots of questions and (2) listen to questions that other people ask. I have found that over the years of asking questions and listening to other people's questions at seminars (and elsewhere), my sense of "good questions" has gradually improved.
I think what you really want to teach is: how do you learn to ask questions? As you know, this is an essential skill for mathematics in general. I don't know a good answer to this version of the question, but here's something that stuck with me personally.
As an undergrad, I took a second-semester algebra course taught by a geometric group theorist. It was an awesome course that got me hooked on the subject. Around midterms, he scheduled a meeting with each student to check on their progress. During our meeting, he told me something along the lines of:

"You're doing great on the assignments and exams, but you're missing the point. You need to ask questions. You take these courses to learn how to be a mathematician, and mathematics starts with asking questions."

I learned a lot of great math in that class, but this lesson has paid off even more.

Poin one in my opinion is not that right. "Ask lots of questions", doesn't make the environment the good, it might halt the talk or it might disturb other audiences. Every individual should ask at most 2-3 questions during a single talk atleast from the content if not precise.

Certainly not all questions should be asked to the speaker during the talk. You can also ask your neighbors, save questions for directly after the talk, or during the seminar dinner, or a week later via email when you still can't figure out the answer. A large percentage of questions that I ask, I only ask to myself. But I still think it is essential to ask lots of questions.

I'll also say that as a speaker, I would much rather have lots of questions during a talk than a relatively silent audience. This is just a personal preference, but I tend to learn more from my talks and receive better feedback from the audience when there has been substantial back-and-forth.


text:
Can I sue my university for allowing me to take classes at the same time (schedule conflict)?
I took a class that started at 5:30. Another class I was taking started the same time. Can I get a refund or sue for this, as there should have been a message not letting me complete my schedule because of the conflict?

Why not check the times yourself when you enrolled and avoid a conflict?

Maybe this is regional, but I'm confused - any institution I've ever been involved with had a drop/add period at least in the first few weeks. Have you just asked your institutions registrar about changing your schedule? Example policy I found on a quick google: https://graduate.lclark.edu/offices/registrar/forms_and_resources/late_add_drop/ (this will vary by institution, there is no universal policy)

In my alma mater you would be automatically dropped from both of them, for failing to check the schedules. You may or may not get a notification before you show up for the final exam.

Can I sue my university for allowing me to take classes at the same time? Yes, of course you can. In the US and most other countries I'm familiar with, anybody can sue anyone, for any reason. Now, whether you can successfully sue, that is a different question...

Just a sidenote: Where I am from, people sometimes take lectures with some overlap because they do not learn from lectures anyway. So unless your presence is obligatory for all classes, it even makes sense for the system to allow you to do this.

At the schools I've been at, courses scheduled at the same time also have their final exams at the same time. This even if you skip lectures, you might be in for a world of hurt later.

This sounds like a typical case of "I made a mistake, now I want to sue someone for it."

No, that sounds like something that you should be responsible for avoiding yourself.  It might be nice if the school kept better track of this kind of thing for you, but it is ultimately your responsibility to know what you are enrolling in and paying for.  You might be able to get some kind of tuition refund, if you are really polite and persistent, but even that is quite unlikely.  A successful lawsuit is simply not going to happen.

if you sue:

You have a low probability of winning
Your "damages" and the amount of money to be won, seem low
You will likely have lawyer's fees and other cost of litigation
You will waste your time and focus
Your relationship with the university will be damaged
Your reputation will likely be damaged

I hope that list helps.


text:
How to approach professor about potential paper?
Earlier in my undergrad I co-authored a paper with one of my professors. Initially it was supposed to be just a class project, but on his suggestion I did some more work and went with it at a student conference and then with substantial help from his part we managed to further expand the topic and write an article which has been published on a (small) national journal.
A few months ago I took part in a problem solving contest for undergrads. Among the problems there was one which was quite interesting, basically made out of two parts. I got the highest score on the problem, but barely did any work on the second part. I tried looking in the literature and while there are many references about the general concept, nothing about the specific version presented on the contest (I should point out that there is nothing trivial about it, i.e. the solution and the implications are different from anything I found so far). This seems like a nice opportunity for a paper, and I think I could actually get it solved with some additional help. I was thinking about proposing this to the professor that was my co-author on my first paper, but I’m not really sure how to approach him, as the synopsis for the first one was totally different from this case. To make matters more complicated, we got some money out of the first paper (not much and it was his initiative to apply for the prize), and I also received a scientific performance scholarship for it, and I don’t want him to feel/think that I’m trying to do research for the sake of money.
So, how should I formulate my e-mail in order to make him understand that I see an opportunity for an article but without seeming like I’m desperate?

"I don’t want him to feel/think that I’m trying to do research for the sake of money" this is literally what professors have made a career out of, I wouldn't worry about it.

I think you're overthinking this.
I can't imagine any professor thinking you are desperate or just want money out of this. In fact, I would expect a professor to be excited to get an email from a student that has taken the initiative to start a project and reaches out to see if they are interested in collaborating.
You really have nothing to lose here. Professors are generally eager to publish. Send an email!

I don't understand why your professor might think that you are desperate just because you want to collaborate with him. He was a co-author of your previous paper which is why you should contact him without any hesitation. The fact that you actually got some money out of the first paper should encourage your professor to collaborate with you again. He probably gets e-mails of people he doesn't even know, who want to collaborate with him. Use your personal connection to your advantage! Your fear of him thinking that you are doing research for the sake of money is unfounded. For some people scholarships like the one you got are the only option to earn a degree because they don't have the financial resources to go to college otherwise.
If you want to increase the chance of your professor collaborating with you, make sure you are prepared to show him how far you have got and where you need his insight. Professors don't really have that much time at their hands and if you show him that investing his time is worth it he will support you. Send him an e-mail in which you tell him about the topic and kindly ask for a meeting to talk about it.
Good luck!


text:
What are some useful workflows for keeping track of interesting but not immediatly relevant books/articles?
I read lots of academic literature to stay up on my field (law). The articles fall into one of three categories:

immediately relevant;
clearly irrelevant or of low quality; or
very interesting, and may prove useful in some future, as-yet-unimagined research project, but not immediately relevant.

My question is: what is the best way of managing articles in category 3—i.e., taking notes on them, organizing those notes, and then periodically revisiting them? The issue is that I have limited time and so taking detailed notes on all of the interesting articles that I read isn’t an option. However, I want to absorb them in sufficient depth such that, at some point in the future, I can recall that I read them, that they may now be useful to my current research project, and that I should revisit and re-read them.
I’m less interesting in specific software/tools, but rather in an overall workflow/approach. Many thanks.

C Wright Mills, the famous sociologist, would periodically dump out the contents of a whole file drawer, on purpose, onto the floor of his office.  As he cleaned up, he found himself making new connections and getting ideas for new directions.

Hah! That's awesome.

Here are two approaches that work for me. The first is a way to capture the essence of documents that are "very interesting, and may prove useful in some future, as-yet-imagined research project, but not immediately relevant". The second is a way to quickly capture the details of documents and prioritize how soon you revisit them to read in more detail.
First, you can use tagging in your reference manager to summarize the documents. I use endnote. In the research notes section of endnote I put tags to characterize the reference. For example, I will tag the method (e.g., experiment), theory (e.g., motivation) and so on where relevant. Where possible I will also link the record to a specific paper, for example by tagging it as RP1 (RP1 = research paper 1). I separate tags using semi-colons. When it is a paper that I think I will need to read in the future, I will put VIP, or to read. I might also write a note (which I put in notes section of the reference record) of why it is important to read the paper. All of the above means that I can easily find papers with certain tags in the future, as well as use this meta knowledge to quickly determine which papers are relevant on certain topics - without having to actually reread them to find out.
Second, you can also put it somewhere in a list. I use a prioritised to-do list including an an Eisenhower grid, in evernote.

To do today
1.
2.
3.
To Do Asap:
1.

To think about
1.
In my case I have 7 lists in my evernote document. As shown in figure 1 above 2 of these are at the top of the Eisenhower grid: To do today and To do asap. Four of them are within the box: High importance/High urgency, High importance/low urgency; Low importance/High urgency; Low importance/Low urgency. I have one below the box called: To think about. If I find a useful paper I will add it to one of these list so that I can find it at some point in the future. Of course the list I chose to add it to will be a function of its relevance.


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Advisor wants me to send manuscript to a potentially shady journal
I have a paper that has never been submitted elsewhere. Now my advisor thinks that this Elsevier journal called Chaos, Solitons and Fractals (CSF) is a good fit. A cursory search shows that this journal has had a history of misconduct involving the chief editor. When I brought this up, my advisor told me that this happened over ten years ago and the journal seemed to be doing okay after the relaunch. He tells me that his peer had a good experience with them and peer review seemed to be at work.
Obviously, I don’t want to argue over things like this with my advisor. After all my paper might not even get published there. But I am also worried about ruining the credibility of my work given the reputation of this journal. Should I go with it? Is it okay to publish in a journal with such a history?

Can people change? If they can then can journals change? Perhaps your advisor knows more than you.

If Max Tegmark can publish there, you can publish there, too...

It’s always hard to assess at a single option in isolation — what are the alternative options?  Are there other journals where your paper would be a good fit, in either your or your advisor’s judgement?  You will be able to make a much better case to your advisor if you can propose an alternative — “Journal XYZ seems a good fit too; it’s slightly lower-impact than CSF, but avoids the danger of getting tainted by memories of CSF’s scandals, so I’d prefer to submit there” is a much more constructive suggestion than just “I don’t want to submit to CSF.”

Ignoring the simple fact that you are arguing with your advisor, why not choose three to six journals in that field which are respected, and ask their submissions editors?
You don't need to give your real name or get specific about your project, but you could simply share exactly what you've already Posted.

Why not? A quick look at the controversy indicates that the disagreements were entirely around the editor-in-chief publishing his own papers in the journal, papers which were lightly reviewed + indulged in a lot of self-citation. This means:

It's only the editor-in-chief's papers that are affected; none of the papers by other authors published in the journal are;
Once the editor-in-chief changed, it's no longer a problem.

So even if the editor-in-chief was in the wrong (which is not certain), it should be fine for you to publish there.
If it still concerns you, note that Clarivate Analytics / Web of science still has the journal indexed, i.e. they think the journal still meets their standards, and it has an impact factor of (as of time of writing) 3.064 which is good for the field.

The controversy was not entirely around those papers being published: the point is that those papers had a high amount of self-citations, and as a result CSF gained a disproportionate impact factor. This is mentioned here and here. What might still be true is that the journal has a place where it does not belong in ratings, and a reputation acquired with fraud.

it has an impact factor of ... 3.064 --- Interestingly, Annals of Mathematics has an impact factor of 3.027, and its reputation is light years higher. However, I do believe CSF has been OK since the controversy with the former editor-in-chief. I suspect the impact factor "paradox" is due to the fact that CSF publishes many papers not purely devoted to mathematics, which skews the values upward, as such papers tend to get cited more widely and sooner than mathematics papers. And maybe, as @Federico Poloni suggests, the former issues also play a role.

@DaveLRenfro Annals of Mathematics is not in the same field. CSF is in three categories: "Physics, interdisciplinary", "Mathematics, interdisciplinary applications" and "Physics, mathematical". Annals is simply in "Mathematics". Further its impact factor is 4.165, not 3.027.

@DaveLRenfro also impact factors are calculated using only the past two years' data only. There should be no impact from the controversial issues anymore.

@Allure Sure, but impact factor is a rich-get-richer reputation system: journals with a high impact factor attract better articles, which in turn push the impact factor. Would CSF have the same impact factor today without everything that happened 10 years ago?

I don't know to what extent the journal has recovered its reputation (I was aware of the  controversy, but it's not remotely in my area). However, a good place to look is the Scimago journal rankings, which gives you quite a lot of information. In particular, looking at the graph of "cites per doc" vs "external cites", you can see that the steep rise in citations during the period 2003-09 was largely driven by an increase in internal citations. These dropped off completely in 2010, and in recent years there has been a rise in citations driven almost entirely by external citations. That looks to me like a sign of a journal which is strengthening its reputation.
But, as others have said in comments, the best course is to discuss it further with your supervisor, who is likely to have more specific insights into how it is currently regarded in your field.


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Becoming a referee if authoring mostly in large collaborations
As we all know, in the average academic field a researcher who authored relevant papers in a field, may be asked to serve as journal referee. Relevance is typically judged by his contribution to the field - the number and quality of his/her papers (h-index) as metric for expertise, and direct submission to that journal as a metric of understanding publication dynamics and relevance for the journal.
But how does this work in large collaborations (hundreds or more) where authors are listed alphabetically, every author sign all papers (making h-index useless) and the paper submission is not performed by the key author(s) but rather handed over to a committee?

Being asked to be a reviewer means that people think your scientific opinion is likely to be valuable.
Authoring papers in an area is only one of several ways to be noticed in this way (and, in my experience, not the best way). Other ways of being noticed include:

letting people in your professional network know that you are interested in reviewing papers
asking your supervisors to delegate sub-reviews to you
participating in conferences and workshops
organizing scientific events
giving seminars or other talks

In most areas, there is always a need for more prompt, thorough, and constructive reviewers. Thus, if you are at an appropriate point in your career to begin reviewing (e.g., at least a senior graduate student or postdoc), then people who know you will likely be interested to start delegating work to you as soon as you express interest, and performing a few good reviews will start more and more people looking your way to provide input, as your reputation spreads through the network.

This seems more of a generic "how reviewers get selected" sort of answer, and not so much concerned with the particular realities of papers with massive author lists (in the hundreds).  Are you trying to say that in your experience these are treated exactly the same?

@zibadawatimmy  I am saying that my judgement of somebody's potential as a reviewer has little to do with their position on author lists, whether those lists are big or small.


text:
Can I publish a paper with new proof but the same result?
I found a better proof for a theorem than a proof from a published paper. Is it possible for me to publish my proof with the same theorem citing that paper?

Yes, but watch the venue. There might be different journals/conferences which are interested in new results vs new proofs for old results. Or it might be the same ones.

You can publish virtually anything, whether you should is another matter.

@JeffE This site isn't a place for you to advertise for your own publications. Have some shame, jeez.

Here is an example. Does your proof have "an unusually elegant and polished character"?

Related: https://simplicityalgorithms.wixsite.com/sosa

As Google Scholar would put it: about 54,200 results say "yes".

Cough Wiles /cough Actually there are three different "proofs" for Fermats last theorum and many failed ones. Ironically Iwasawa theory was the catalyst for Wiles's second and successful proof.
There's a fourth unpublished one in the works, apparently some guy in the US (IIRC) is claiming to have one but its 24 pages long!
The actual core proof is still only one A4 though.

I would read the introduction to Gowers' paper "A new proof.." to see a beautiful example of how one justifies publishing the third known proof to an old theorem.

It may not be possible to publish it in a well known journal. Depends on how much better the proof is and how interesting the theorem is.

@AsianHornet I'm not sure which proofs you're talking about. Wiles's first proof wasn't a proof: that's why he had to produce another (or, rather, fill in the gaps). I don't know who this "some guy in the US" is but there have been hundreds of people over the centuries who've claimed to have a proof that fits in a few pages. Such claims aren't notable and mostly aren't credible.

In 1948, Selberg and Erdos found an elementary proof for the prime number theorem (proven using complex analysis by de la Vallée-Poussin in 1896), a discovery definitely worth a publication.

Gowers' paper "A new proof of Szemerédi's theorem" can be found at https://pdfs.semanticscholar.org/3e47/e427a64759a41e54dd60c27e5663068886ca.pdf

You can publish anything interesting.
There are instance where a new proof of a new theorem is not interesting. There are also cases where a better exposition of the existing proof is interesting.

Keep in mind that interesting isn't something the author should solely judge for themselves. Seek opinions of others before getting invested. If you are interested it's good. If you can't convince anyone else to be interested you need to work on solving that problem. Better mousetraps only sell themselves once people know they're better.

Why wouldn't it be? This is somewhat common. To cite just one example, Dilworth's Theorem (about antichains in a partially ordered set) originally had a somewhat involved proof when it was first published in 1950. Since then there have been a number of papers published with titles like "A Proof of Dilworth's Chain Decomposition Theorem" (that one by Fred Galvin), with many of these papers being widely cited in their own right. The one by Galvin is a masterpiece of mathematical elegance.
The crucial question is if you can convince the referees that your proof is both sufficiently new and sufficiently better and/or interesting so as to warrant publication.

To give some more famous examples of theorems with multiple proofs published: the fundamental theorem of algebra, the prime number theorem, quadratic reciprocity, ...

In computer science, Hopcroft's algorithm for DFA minimization has been the subject of many papers, some of which are just new presentations (not even new proofs).

@Kimball, the Pythagorean Theorem (370+ proofs and counting).

@Mark Yes, I thought about mentioning the Pythagorean theorem too, but then I couldn't recall if I'd seen proofs published in research journals, or just books/recreational periodicals.

Sure. People publish new proofs of old results all the time. I've done it twice, myself.
Publishability, as with any paper, depends on how much you can get people to care about your new proof. If the result itself isn't very significant, your proof will need to be a big improvement; for a more significant result, it might be enough to improve one of the steps. People will probably care more if your proof is shorter, simpler, requires less material from outside the field (or, conversely, establishes links with other areas), leads to a stronger result, etc.
Be careful that your new proof isn't circular. If Smith proves that every widget has an even number of facets and Jones extends this to prove that the number of facets is actually a multiple of six, you don't get to publish A Short Proof of Smith's Theorem that simply points out that every multiple of six is even.

As several people already mentioned, the prime number theorem is a great example:

No elementary proof of the prime number theorem is known, and one may
  ask whether it is reasonable to expect one. Now we know that the
  theorem is roughly equivalent to a theorem about an analytic function,
  the theorem that Riemann’s zeta function has no roots on a certain
  line. A proof of such a theorem, not fundamentally dependent on the
  theory of functions, seems to me extraordinarily unlikely. It is rash
  to assert that a mathematical theorem cannot be proved in a particular
  way; but one thing seems quite clear. We have certain views about the
  logic of the theory; we think that some theorems, as we say ‘lie deep’
  and others nearer to the surface. If anyone produces an elementary
  proof of the prime number theorem, he will show that these views are
  wrong, that the subject does not hang together in the way we have
  supposed, and that it is time for the books to be cast aside and for
  the theory to be rewritten.” - Hardy, 1921

Then, Erdös and Selberg gave a non-complex-analysis proof in 1948,
see history of this problem here.

OK, but "Paul Erdős managed to do it" doesn't really help us mere mortals. A simple existence proof doesn't really tell us much.

@DavidRicherby: Well, in my field, algebraic combinatorics, there is the saying that you can prove EVERYTHING twice - first with representation theory, and then with purely combinatorial means.
There are several open problems that are of this form, (usually positivity results), where some quantity is proven to be positive, but lacks a combinatorial proof of this fact.

That's a much better example, IMO.

Apart from the trivial answer, yes, I would like to highlight a few points before submitting new proof for an existing theorem to a publishing venue.

It depends on where you are submitting it. Certain peer-reviewed journals might not welcome proofs for established theorems.
It mainly depends on the subject or discipline of concern. It is much more common to see alternate proofs in venues of mathematics and physics than in computer science.
It depends on whether the new proof is theoretical or practical in nature. Unless the theorem is not practically proved before, referees of reputable technical publications might not readily accept application papers of existing theorems.
The new proof ought not to be a trivial simplification of an existing proof. Otherwise, it would become an exposition paper than a research paper. This again comes down to the perception of the reviewer and the publisher.

Having stated above, you could technically publish anything new as long as you believe it benefits a wide scientific community.


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Publishing and Self-Archiving
Recently I had a paper accepted by a major journal in discrete mathematics. Now the paper is going through the final stages of publication. The publisher sent me a link in which I have to specify the access policy for the paper. I can choose to either pay a fee (which I won't), and make my paper publicly available from the publisher website, or I can choose to self-archive, and
then make my paper publicly available after a period of 24 months of embargo.
More precisely, the text for the self-archiving is the following:

I wish to self-archive my accepted author manucript , which is my draft
      version of the article and which may include any author-incorporated
      changes from the peer review process. I can post this author manuscript
      on my institutional or subject-orientated repository immediately for
      internal use and make it publicly available after a journal specific
      embargo period has expired.

The problem is that I have already posted the revised version of my paper at arxiv much before receiving this access form from the publisher. So I have some questions concerning this paragraph.

The paragraph says that I can post the manuscript at a subject-oriented repository immediately for internal use. As mentioned before I already posted it to arxiv, which I think can be considered as a subject-oriented repository. Is that allowed? What do they mean by internal use?
What do they mean about making the manuscript publicly available after the embargo? I have a link at my homepage pointing to the arxiv page. Is this considered to be publicly available?
What is the difference between posting it to a repository and making it public?
Can I get in trouble if they find the link to the paper at my homepage?

Did you tell the journal that your manuscript was already available on arxiv upon submission? I hope you did...

You should also check the policies of the body that funded this work.  Some will pay for open access (in fact some require that you take the paid open access option, and make funds available through your institution).

@CapeCode: Public distribution of preprints---either on the arxiv or personal websites---is common bordering on universal in mathematics.  There's no need to report it to a journal, because the journal should assume that's the case.

@Henry So I've heard, but I'd thought a journal that has en embargo policiy would surely care about whether it's already online before submission.

@CapeCode: They might care, but they don't need to be told, because the answer is "yes, of course it is".

@Henry So... they accept papers even though they know it violates their policy? I'm not saying it's a bad thing, it just sound inconsistent.

@CapeCode: Most publishers have adjusted their policies to accommodate reality (as other people have pointed out, publishing on the arxiv does not violate Elsevier's embargo policy).  But even before those policies were changed to explicitly accommodate the arxiv and distribution on school websites, there was a tacit understanding that the journals wouldn't try to use their copyright to interfere with the practice.

The text you quote is from Elsevier, and their policy on hosting articles says that "arXiv and RePEc can update a preprint immediately with the accepted manuscript and a DOI link to the formal publication" (while the embargo period applies only to other organizations), so you haven't violated the agreement in updating the arXiv posting.  You can add the DOI via the arXiv's journal reference feature once it is available.

Thanks. It is indeed from elsevier.  The copyright page indeeds specify that one can share the paper scholarly. (http://www.elsevier.com/about/company-information/policies/copyright) and there is a precise definition of what they mean by sharing at the homepage ( http://www.elsevier.com/about/company-information/policies/sharing)

I can post this author manuscript on my institutional or subject-orientated repository immediately for internal use […]

[…]
The paragraph says that I can post the manuscript at a subject-oriented repository immediately for internal use. As mentioned before I already posted it to arxiv, which I think can be considered as a subject-oriented repository. Is that allowed? What do they mean by internal use?

This respective sentence is not very well phrased and probably misphrased. “Subject-orientated repository” sounds very much like ArXiv but contradicts “internal use” (unless they have a very wide definition of internal). Having a “subject-orientated repository“ for “internal use” would have to be institutional and thus already be covered without adding “subject-orientated repository“.
To be sure you should check other information by the publisher, in particular the copyright agreement (or similar) you probably agreed to already. Sherpa/Romeo may also help. If all that fails, you need to (and should) ask the publisher to clarify this.
If needed to guess, I would say that that line originally read “I can post this author manuscript on my institutional immediately for internal use” and then somebody inserted “or subject-orientated repository”.

What do they mean about making the manuscript publicly available after the embargo? I have a link at my homepage pointing to the arxiv page. Is this considered to be publicly available?

The ArXiv is already publically available, linking it does not change this. Making publically available means exactly that, so, e.g., it would cover putting the manuscript directly on your homepage.

What is the difference between posting it to a repository and making it public?

A repository may be not public. For example, our group has its own private paper repository.

Can I get in trouble if they find the link to the paper at my homepage?

If they find out about your ArXiv publication only that way, perhaps. But given that the ArXiv is public and easily searchable, that’s very unlikely.
What you can get in trouble for is publishing the paper on ArXiv. However, if the journal is general open to ArXiv publishing (see the first point), it is unlikely that they only allow it after they published the paper themselves. Again, what you should do is to take a look into the copyright agreement and similar and what they say about prior publication on public repositories and ask them if the information is unclear.

As stated by others in the comment section, it may also depend on your funding agency.  In Canada, for instance, NSERC requires the manuscript be freely available within 12 months of publication, using a repository and/or the journal itself (http://www.science.gc.ca/eic/site/063.nsf/eng/h_F6765465.html?OpenDocument).

As a general reference tool, there is an attempt to collect all the different policies centrally such that you may search by your paper's DOI and get the information you need about legally sharing it: https://shareyourpaper.org/
Typically (for me) it's been the final author versions that I'm allowed to share, which I then go on to share with ShareYourPaper and also post on my ResearchGate, etc.
As with the comment about about ArXiv, there is also growing acceptance and promotion of preprint servers by major journals, e.g. on recently submitting a paper to the Royal Society of Chemistry (RSC), the process concluded by encouraging me to head on over to https://chemrxiv.org/ and upload all my materials there, too.


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How to increase my chance for being admitted to a PhD if my MSc is in a different topic?
I have a MSc degree in Computer Science from a well known university, but the problem is that my degree is, for example in Computer Graphics. Now I would like to study PhD in computer Science, but related to another topic such as Green Computing.
How I can convince the admission committee or the Professor in charge of the research group that I can be a good student in his group?
One friend told me that one important thing is the motivation letter others about the research proposal (which for me is somewhat not so clear, because for what I know one do a research proposal only when one is inside a group)
Any help will be valuable? I have applied to a lot of PhD positions and the frustration is getting higher with each rejection.

Turn that into a positive by saying that you would like to broaden yourself and learn about a different area. Professors usually like to have some variety in their research groups: having people of different backgrounds around you can be very useful when you're trying to think outside of the box to solve a problem.

The linked question asks only if this is possible, not how best to increase chances of acceptance in this situation.

The change of topic should not be a serious problem as long as you have a solid CS background.  What is more likely the problem is your choice of new topic, and whether the schools where you are applying have faculty working in green computing.
For PhD programs, your best bet is to send a targeted and well-informed letter to professors working in the field that interests you.  I cannot stress the well-informed part enough - this is more than just looking at the faculty member's web page.  Read some of his/her papers, think up of suggested research directions or potential improvements of the research.  Demonstrate an ability to understand the professor's research and provide novel and meaningful ideas.

I doubt anyone will care about your master's degree field, because many top programs don't require a master's for admission. As long as you have a solid background and a good record you should be fine.