text:
Does an MD make a difference to a PhD application in bioengineering?
Does having an MD affect in any way, help or hurt, a PhD application to a top tier program (right after medical school and in the same field as the undergrad major--bioengineering, in my case)? Does doing or not doing a clinical residency matter to this either way?

Graduate schools are going to want students that will successfully complete their program. You will have to make a strong case for why the research experience afforded you by the PhD program is what you want to do - having an MD, you have a really tempting "out" with good job prospects and high pay versus careers where you will use the PhD. That doesn't necessarily hurt you, but you should be prepared to defend why you did not start a medical scientist training program (i.e., MD/PhD co-degree program) in the first place.

I am in a PhD program and we have students who are 2 years into their MD who have transferred (not MSTP-MD/PHD) to complete a PhD before they finish medical school.
The main components most schools look at are:
(1) Test scores - whether they accept your MCAT depends on the program, but having a strong GRE score is a great start.
(2) Research experience - this is the biggest make or break. If you can show that you know how to do hands on research, and even if you have a publication or abstract presented at a national conference, that weighs a lot.
(3) Grades - obviously there is some weight on your ability to successfully complete rigorous classes.
(4) Letters of recommendation
Will it help or hurt? This depends on how well you currently stand in components 1-3 that I mentioned above. If you have a very low GRE score, it may hurt you regardless of your other degree. Alternatively, if you have a very high score, it may help you because it proves you've been successful previously in a tough program.
The question you should be prepared for is why you want a PhD now that you have an MD. There are plenty of residency programs where you can have protected research time and gain experience in the lab. When interviewing, they will want to see that you have really considered dedicating another 4-6 years of your life to a PhD.
I do not think the residency matters, but I do not have experience with this. No students in my program have done residency yet.
Best of luck!


text:
On what factors is a dissertation approved
What are the factors that are considered when granting a PhD degree. For example, if a person has published excellent papers, but their dissertation is not perfect i.e. omissions and typos, would the committee consider it?
Also, what happens if they have good papers published, but the oral defense is not great.
People generally believe that if the dissertation advisors says OK, then everything works out. How true is that?
P.S. I am asking in the U.S.

In general, this depends on the process and rules of the university. In which country is this?

Although the exact process varies from university to university, the general form of the process in the United States is typically as follows:

The student needs to do work that makes a novel contribution to the sum of all human knowledge.  This is the universal part of the process, and the key thing that a Ph.D. really certifies that you are capable of.
The student, with guidance from the advisor writes up this work in a thesis document.  In some areas this is not-yet-published work, in others it is a summation of things already published.  In either case, it should be a complete and thorough presentation of the ideas and work.
Eventually the advisor and student are both satisfied, and the advisor judges that the student's work will pass external review.
External review is obtained from some combination of oral or public defense and input from other committee members.  Sometimes the defense is a serious part of the process, sometimes it is not; in either case, an advisor should never allow a student to stand for a defense unless they will pass.
The student satisfies any additional requirements imposed through the external review.  Sometimes this is just correcting typos, sometimes this is a lengthy period of additional research.  If it is the latter, then the advisor has generally screwed up.
Submit the final document for archive, and graduate.

Note that this process assumes some flexibility in the length of a Ph.D., which is typically the case in the US.  I know that in some other places, such as many institutions in Europe, there is often a shorter and fixed schedule.  I'm not sure how one deals with not being ready on time in that case...

It mostly depends on the university policy. Normally typoes are accepted to a certain extent as especially foreign students are not expected to manage the language perfectly.
Omissions on the other hand are a totally different thing. You have to omit many things anyway as they would not fit into the frame of your thesis. On the other handm if you omit something which is part of the area you are doing research on, then chances are high, that you are rejected - at least you will never get more than a "cum rite" and if you're satisfied with that, then I'd reconsider the whole doctorate-thing.

It greatly depends on the country and less so on the university. In general, it is true that a supervisor will not approve a thesis to be sent to the committee that he/she doesn't feel has a good chance of being accepted. Because doing so would not only reflect poorly on the supervisor, it also means more work for everyone involved.
In general, things like language errors are not cause for rejection unless you make it really bad. The thesis is judged primarily on its scientific content. Note that in some fields, you can create a thesis by simply making each published paper into a chapter and adding an introduction and conclusion. This allows for all of the critical parts of the thesis to be completed and reviewed beforehand.
The importance of the oral defense depends on the country. In my country, the Netherlands, the oral defense is practically irrelevant for most people. While in theory you can fail, as long as you keep talking, you will pass. It's mostly a show for friends and family. But in other countries the oral defense has more weight

Well, of course it is only dissertations in the sciences which are judged on their scientific content.

source: Stack Exchange

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

sort: votes


text:
Different CV/Resume for US Universities
I want to submit my CV/Resume to universities for MS in CS. I have learnt web designing and development along with other programming languages learnt in undergraduation.
I used to prepare 2 resumes, one for web development companies and other for software companies and I would submit suitable one.
Now can I do something creative and submit a CV that looks something like this? http://www.smashingmagazine.com/images/design-cv-resume/sarah_parmenter.pdf
Will the universities not consider if I do something like this? or do I need to submit normal 2 page resume?

Your link does not work ("403 Forbidden").

Sorry about that. It's working on my end. Nevertheless here is the link to the article http://www.smashingmagazine.com/2009/04/01/10-handy-tips-for-web-design-cvs-and-resumes/ Please refer to the 5th image (Yellow) that I am talking about.

Ew.  Just... ew.  No.

Unless you're specifically applying for a MS in graphic design, your CV should, first and foremost, show off your academic and research accomplishments, not your graphic design skills.
Keep it simple.   Creativity is fine; good typography is great; but emphasize the content.  The fourth image on that page (with the blue dot) is much more suitable.
Good design is invisible.  A bright yellow background is not invisible.  Therefore....

I would write about my academic and research accomplishments first but that was just to give you an overview of how my resume might look like. Do you suggest to go with that format or a simple 2 page black and white resume?

@user1395787 Try the ModernCV package for LaTeX for a good, "pre-baked" CV format. The way to make yourself stand out is through what's written, not how it is presented. As JeffE says, good design is invisible. The reader should be able to look at the document as a whole and think "huh, this one looks quite nice...", but have difficulty picking exactly which element stands out to them. I think it's unusual (depending on the country you're applying to) to include a photo, your DOB, and marital status. If such personal information is not expected, do not include it.

@Moriarty: It's standard in Europe, but verboten in the U.S.

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


text:
What is proper etiquette for college students needing to leave the lecture room for any reason?
Like, if I needed to use the bathroom or blow my nose or take an urgent phone call, what should I do?

I, for one, have no idea what playing the trumpet means. The first two are rather different situations. So I can't even begin to imagine what you intend with your third example.

Voting to close, so that the OP can freely "play his trumpet" by himself.

@WillieWong: I have no idea what is meant, either; I am trying to find out on English SE.

@gnometorule: Please read my linked English SE question meant to settle the question. What you imply is one of the guesses I had considered there, as well. That notwithstanding, the shape of a trumpet requires tremendous abstraction.

I am from Taiwan. "Play the trumpet" does mean something to me (in an un-speak-able manner on this site). Unless you are from Taiwan, I don't think what you mean by it is the same as what I think it is. Please confirm. Thanks. BTW, I won't say it either here or on English SE).

@scaaahu: While I will respect your decision not to explain this yourself, I find it entirely unhelpful from a language learner's perspective.

@O.R.Mapper I was hoping the OP would respond to my comment above. Obviously, he hasn't. It's really a bad thing. I am afraid I would get an offensive(or rude) flag if I said it here. Please pardon me.

@scaaahu: It's ok. I still think if StackExchange removes a bit of information for offensiveness on English SE when it is explaining an (offensive as it may be) expression in the respective language, SE (and many language learning sites that impose bans on language just as well) are completely missing the mark, but I will have one of my Taiwanese friends elucidate me in a private conversation and then decide whether to post the answer as an (unconfirmed) suggestion on my question (and possibly add it here, which doesn't have trumpets).

@scaaahu: Either, my imagination is lacking, or I actually don't find it overly profane (at least compared to some other items on the WP page I linked to) ;) Thanks for the explanations, though; you've provided all that is necessary :)

@O.R.Mapper I was thinking of sending a link here, but then I gave up later because I am not sure if it was what the OP meant. That's why I asked the OP in the comment in the first place. I'll stop here. Hopefully you'll get some answers off-line.

@O.R.Mapper I saw your updated question on English. Glad to know you figured it out. More info here. There is a movie You Are the Apple of My Eye made in Taiwan in 2011. It is a very popular movie in the Chinese world. In the movie, there is a famous scene (please see "One day, ..." at the end of the first paragraph of Plot section of that Wiki page). This scene is why I guess the OP was referring to that word you mentioned on English SE. I still don't know if I am right.

When I said "play the trumpet" I think I was talking about a need to blow a nose.

As this is no longer unclear, I am voting to reopen.

I believe that would vary from lecturer to lecturer. At my university, most of the faculties make such rules crystal clear at the beginning of the semester. Quoting the rule from one such class:

If you have any urgent work whatsoever like calls, dizziness or just
  don't want to sit in the lecture, walk out without interrupting anyone

While another faculty asked us to switch off phones and forget anything that is outside the lecture room unless it can't for half an hour.
But in general, if it is really important you may just politely interrupt the faculty indicating you have an urgent call and you would like to attend. In case you have some other commitment for which you may only attend a portion of the lecture, I believe informing the faculty at the beginning would be the best option so that you may just indicate to him when you leave without disturbing the momentum of rest of your batchmates.  (I don't think bathroom breaks come under such category since you already have breaks between lectures for those :) )

+1 If you are not suffering from the symptoms of food poisoning or similar, you probably should not leave lecture just to go to the bathroom. If you are suffering from the symptoms, I would prefer it if you just go as fast as you can and not stop by to explain. // I also 100% agree with the fact that if you are anticipating a possible important phone call, best to let the lecturer know ahead of the time.

+1. leave quietly and unobtrusively.  If it is a small class, and you know in advance that you will leave, then you can tell the instructor before class.

It probably depends upon the size of the class too.  A 3 person graduate class is more intimate, so ask to be excused.  A 100 person lecture hall, just get up and go with as little noise and distraction as possible.  @WillieWong, I suffer from IBD and there are many extremely legitimate reasons a student may need to leave a class and a bathroom break IS one of these.  Also note that I don't consider most phone calls legitimate (I make exceptions for health and welfare of loved ones though).

@Jim2B: if I have a student with a chronic medical condition like yours, I would much prefer if the student let me know way in the beginning of the class that "it's not you, it's me."

In other words: If it is something that can be anticipated and explained, anticipate and explain it before hand. (1) This means you will not have to waste my class time to explain yourself, and (2) you won't be seen as impolite by me. On the other hand, if it is a true emergency: just go, and maybe explain later in an e-mail or something.

Fair enough.  I'm now in the working world and this is what I do with my co-workers.  Let them know of the condition and that I may need to "cut & run" on short notice.


text:
Should I inform my thesis adviser about current situation
I had unofficially agreed to start working on my thesis during September, with no concrete date being mentioned.
However there are two factors which might delay this date:

Me not being available due to travelling until the end of the month
I don't feel confident about the programming task that has to be done during the thesis, so I want to take a little bit more time to work on some exercises

The problem is that in case that I go there, they might request me to sign for the official thesis registration, which then will impose the deadline when I have to be completely done with all the thesis stuff. I don't want to do this, before being confident that I can proceed easily with the programming, because otherwise the period that I will spend doing some extra programming exercises will be eating from timeslot limited with the deadline.
My question is, should I inform the adviser about these developments, or should I shut up until I come back (and use another 10 days to do some extra exercises) and then go to his office and talk about the official thesis start?
Which situation would reflect best on me? I'm afraid I am causing too much communication overhead unnecessarily and somehow not respecting the time-frames I have agreed myself.
Reason to go to the advisor: I have already verbally promised that I will be around once September comes
Reason not to go: They may require me to sign the official thesis start.

10 days in 3/4 years make a very small difference regarding learning. Doing some exercises is good, but you will only truly learn when you get to the real stuff.

As a rule of thumb, if you tell someone you'll be doing stuff with them at time X, and then change your mind, let them know!
More specifically, I would recommend an email such as:
"Dear Advisor,
we had planned for me to start my thesis in September, but because of REASONS I'll only be able to start on October. I apologize bla bla
In the meantime, I'm planning to do EXERCISES. Please let me know if you have any other suggestions on how to prepare."
I don't see a point in telling this to your advisor in person anyway, and this should keep you safe from being made to sign stuff.

+1 Although this is good advice, the answer by the advisor could still be NO.

@Alexandros in which case, not showing up would have been worse.

This depends a lot on the personal stance of the advisor. Does he or she readily accommodate wishes by students, especially if they are comparably insignificant (delaying the start date by some 10 days) and seldom (it's not a perfect start to bring such an issue up right at the beginning of the thesis already, but if you don't come up with such requests every week, that may be fine).
I would definitely suggest contacting the advisor, as just ignoring him or her and disappearing for some 10 days does certainly not make a good initial impression.
As for the "danger" of being made to sign the start, I am not sure as to how realistic that is, given that you have concrete reasons (physical absence while travelling) for a (rather limited, less than two weeks!) delay - and I think it is unlikely the department or the advisor could be eager to force students that do not feel ready into starting their thesis (and thus provoke bad results). One issue might be that they have a certain rule concerning the maximum duration of preparation time before the official start, but if that is the case, that is all the more reason to talk to your advisor.
Beside just telling the advisor about your wish for a slight delay, I suggest you go see him or her in person, as just writing an e-mail may express a rather lackadaisical attitude towards your thesis. At least, you could write an e-mail to the advisor, utter your wish to slightly delay the official start, and express that you're ready for a meeting where you can discuss that in detail. That should make it clear that you're not willing to sign the official start yet.
One extra thing you might do to make your advisor extra-receptive about your request is being concrete about what you want to do in the additional ten days. Do not just mention "some extra programming exercises", but provide a concrete link or book title (or whatever else) that denotes a set of exercises you are planning to work through. Convey to your advisor that you really care, and that you don't just want 10 more days for idling, but that you have a concrete plan in mind, based upon which those 10 days would realistically make any difference concerning your current worries.

As a side-note, if we abstract your question to what you asked in the title, "Should I inform my thesis adviser about current situation?", the answer should invariably be an unanimous YES.

The last paragraph deserves an upvote on its own.


text:
After emailing a professor and getting no response from him, how long should I wait before sending a second email?
From time to time, I come across this problem: I send an email to a professor asking him about something (e.g., making an appointment to ask his opinion on something) and I do not hear back from the professor. In this case, how long is the reasonable amount of time for me to resend a similar email?


text:
How does an early career researcher gain a high citation count?
In my field of research (wireless networks ) I know of one researcher who is just 33 years old and has more than 1300 citations on Google-Scholar. How is this possible when he is so young? What are the best methods to gain more academic citations and attention from other researchers for one's work?
I think there are some parameters like this:

Contributing to open source project(s)
Working with other top researchers
Working on new field,  like new standard, etc .
Warm welcome to another researcher and willingness to help them.

Are these accurate? What other factors influence a high citation count at a relatively young age?

Citation counts vary dramatically between fields so this question isn't really answerable in its current state.

While those kind of numbers are in the upper portion of the bell curve, they are not actually all that unusual.  Three likely scenarios for somebody to have 1000+ citations early in their career:

One "super paper" that hit a hot topic with exactly the right idea at exactly the right time and did the scientific equivalent of going viral.
Doing very good work as part of a highly productive group that a lot of people are paying attention to, and thus ending up with a number of well-cited papers.
Leading an intellectual break-out into a new area of work, which many others become interested in.

It's great for somebody to have a good start to their career like this, but you shouldn't spend too much time worrying about it or comparing citation numbers: that way lies madness and brain-dead administrative metrics.

While this answer is 100% correct, it underestimates the fact that there are certain individuals that are so extremely and unusually talented that can produce a significant body of work within an inch of a time that the rest of us would require.

@Alexandros Sure, but that's much rarer than the cases I mention, I believe.

@jakebeal "Doing very good work as part of a highly productive group that a lot of people are paying attention to, and thus ending up with a number of well-cited papers." how many times tell you thanks for that advise

Another slightly self-congratulatory point of information: I am 36 and recently passed 1000 citations myself, and do not consider myself particularly unusual...


text:
How can I get a list of citations for a DoI or PubMed ID?
I'd like to be able to submit a DoI or PubMed ID and find all the papers that cited that paper.
In other words, I need a publicly-available citation graph database that covers papers in PubMed.
The bottom comment on this question refers to a publicly-available citation graph: How do I get a citation dataset with full text articles in PDF format? but does not give any details of where it can be found.
Does anyone know of any such citation databases?
UPDATE: To be clear, I really need a database - not a service like Google Scholar - because I want to do it programmatically for many hundreds of thousands of articles.

Quick and dirty version: Google Scholar
Type-in the DOI and read the citation count on the field "Cited by". Google Scholar does not filter for quality, so the citation count will include self-published papers, fake publications, etc. Expect some noise.
Better version: Web of Science
Ask your institution's librarian how you can access the Web of Science database and how to use it to retrieve the data that you need. That might require you to walk in daylight to the physical location of your library. Many survived that journey.

Web of Science is generally a good choice but it can sometimes be too narrow in what it includes- many quite reputable publication venues (particularly conference proceedings) are not indexed in Web of Science.  Furthermore, this coverage varies across disciplines so that it is not appropriate to compare publications in different disciplines based on Web of Science citation counts.

Thanks. I know about these services, but I really meant "how do I do this programmatically for 100,000 articles" :) I've updated the question to make that clearer.

@Richard Web of Science provides downloadable data (that is in part why libraries subscribe to it), usually in the form of spreadsheets. That would suit your purpose.

Thank you @CapeCode! I'll look into whether this data is downloadable programmatically or only on an individual-article basis.

@Richard You might want to look into whether you also have access to Scopus - many institutions pay for both. Scopus is a little broader\less selective & the interface may be easier for what you're trying to do.

@Andrew great advice, thank you. Scopus seems to have a RESTful API (WoS is SOAP) which would certainly be nicer to work with!

The graph you are looking for is not easy to get and therefore probably not publicly available for free.  Certain firms have specialized in making this data available (e.g. Thomson Reuters "Web of Science, Google Scholar).  To protect their asset it seems likely that they will not let you download their databases or query it in such large quantities.
In a way, their business model depends on making this hard to access, for if you could download the whole database, you could offer the same service for a lower price.
Maybe even their terms of use forbid too unstructured or too large queries.

This is not an answer to the question but possibly a comment on my answer. 2. the business model depends on how they gather the information and compile it, not giving away your product for free is the basic of every viable commercial company. 3. Anybody is free to start a business of collecting article metrics, serious competition will be welcome by the consumers (our institutions).

I addressed this in a revision of the answer. 2) The question is: What is the product.  Google Scholar is free to use so in a way they are giving that data away for free. 3) Sure, but how is that relevant?

Obtaining a license for working with a full local copy / download of WoS is possible (though redistribution is not for understandable reasons...).

As for doing this programmatically, there are two options. Daniele Rotolo has written an R-script (MedlineR) that will allow to download Web of Science (WoS) information from PMIDs, if your institution provides IP-access to WoS. See: http://www.ncbi.nlm.nih.gov/pubmed/15284107
However, there are some issues with this program - it occassionally crashes after fetching ≈1,000 records.
The other (better) option requires your institution to subscribe to Thomson Reuters Web Services Expanded, which will allow you to use a SOAP API to search WoS and download relevant fields. This also includes cited reference searches. If you can confirm that your institution has such an access, I will be glad to share my own (simple) PHP SOAP call for matching PMID against WoS accession numbers (UT).

There are two services that you can use to get this information. The DataCite GraphQL API (if you are a tech person) or DataCite Search. With the caveat that most of the citations come from an approach that uses persistent identifiers. That is the all the citations need to have been explicitly stated by the authors of the dataset or the publication.
Example: https://commons.datacite.org/doi.org/10.5281/zenodo.3731977
One can also embed citations counter for a DOI in any webpage using the Data Metrics Badge (it includes usage metrics besides citations).
edit: Full disclosure, I work at DataCite as a developer.

I know of two freely available datasets which might be interesting for you:

the Microsoft Academic Graph, a very broad dataset that should contain a decent proportion of PubMed
the CORE dataset, which should contain PubMed Central

For both of them, expect some noise in the extracted citations.

Europe PMC provides a freely available citation graph for papers indexed in PubMed (I work for Europe PMC). You can access it programmatically using citation module of the Articles RESTful API.

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


text:
What are the differences between Peer Reviewed Journals and Refereed Journals?
I would be interested to know the differences between peer reviewed journals and refereed journals in these aspects:

Conditions for the acceptance of papers for publications.
The time length of paper stage after submission.
Amount payable by authors.

They mean the exact same thing.

To expand on Yuichiro Fujiwara's comment, "peer review" and "refereeing" are exact synonyms, and no differences at all are implied by the names.  For historical reasons, some fields are more likely to use one term than the other (for example, mathematicians talk more often about refereeing than peer review).  Publishing practices also differ between fields in other ways, such as the length of the reviewing process.  There might be a weak correlation with the use of terms like peer review and refereeing, since both issues are heavily influenced by which field you are looking at.  However, I'd bet that any correlations are small, and in any case this is not a productive way to investigate journal differences (since knowing the field would tell you enormously more than just knowing which term the journal uses for peer review).

thank you very much for your answer, pleas look this answer  :Dear Rafik
Academic Research Journals are Peer Reviewed Journals. It is not a Refreed Journal.
It is not a Spam. So don't afraid to publish in this Journal. It is a developing Journal. So the amount is costlier.
So if you send money you can get Journal Copy. Nothing to Worry.
If you have any other doubts please feel free to share.
Are you a Doctorate in Mathematics?
Please reply me. i will give some other oppertunities.
With Regards
Dr.S.Lakshmi

this message directed to me from editor in chief .

@user51189 when an editor-in-chief sends you a semi-literate email like that, go somewhere else. And when a publisher is on Beall's list of predatory publishers, as "Academic Research Journals" is, go somewhere else.

@EnergyNumbers that's actually a different "Academic Research Journals" from the one the OP is referring to.

@user51189 Dr. S. Lakshmi is the Nigerian prince of academic publishing.

@Energynumber : pleas check this link "online submission and pleas tel me if it's a predatory publishers :http://academicresearchjournals.com/journal-detail.php?journals_id=37,

@ Davidmh : he is found in editoriel boared as editor in chief of this journal:http://academicresearchjournals.com/journal-detail.php?journals_id=37,

@user51189 Any journal that publishes this rubbish and claims to be high quality and peer-reviewed is, well... neither of those things to put it kindly. Ask your advisor if you're trying to decide where to publish, and stick to the popular and well-reputed journals in your field. It's usually pretty easy to spot predatory journals just by reading a few papers of the "research" they publish.

@user51189 That email made my day.

@Moriarty: Oh, that one's not so bad.  How about this gem from one of its sister journals, in which it is proved that it is possible, given only the length of one side of a right triangle, to determine the lengths of the other two sides?

I could be mistaken, but the correlation that I believed to exist was that refereeing was common in fields where works where fully self contained. E.g. with mathematics you do not need to additional research to (in)validate a work, as long as the steps are correct the conclusion is correct. Contrast this to a field like medicine where you would need to redo all the experiments as well to truly 'referee' a result, whilst peer review 'simply' means somebody went over your work and gauged it's reliability.
Now, I could well be mistaken and it's definitely not a clear cut line, but that seemed to be the general trend I observed. Then again, I don't know that great a number of fields that use the term 'refereed' over 'peer-reviewed' in the first place, so I could well be mistaken.


text:
Want to form independent research group outside university, while working?
I have just concluded my Master's degree. I am interested in doing independent research  (publish some surveys on topic, create a few basic software prototypes). I am looking forward to form a pseudo-research group/online-space on internet, where I can find serious people for collaboration, to improve my odds for phd.
1) Ideal way of achieving this? Registering the domain name / advertising on job portals in order to scout for people with similar interests?

You are talking about software propotypes. Is your research in Computer Science?

Yes , computer science.

You need to find people that will share your research interests. To get them interested, you first have to offer something. Let's talk software prototypes.

Publish your (possibly beta version, possibly not-very-product-quality) software prototype so that other people could download it.
Publish documentation so that those people could use it after they download it.
Arrange a mailing list / forum so that people could suggest improvements after they use your software.
Possibly, make it open-source so that people could make the said improvements themselves.

Having some prototype to touch, explore and work on will, based on my experience, bond your newborn community more than just discussions. It is important to have something tangible before you start scouting for people.
Also, it may be easier to find people for your project offline. Talk to people of your age and interests in your local university (even if you are not affiliated), in computer science conferences and enthusiasts meetings (there might be some in your area).
The advice above is based on my personal experience of involving people into collaboration and inspired by this article.


text:
How important is the time it takes to graduate?
In some countries (e.g. Greece) there is no penalty if you fail a course. You can simply try again next time. Also, there is no limit to the amount of time it takes to get a degree.
I am a good student who works hard and tries his best to get good grades.
Unfortunately, on my 1st semester some very bad things happened and I passed no courses for 3 semesters. I will explain this in my essay.
Is it reasonable for me to expect to be accepted by top US/UK universities for a Masters in Computer Science given that I get high grades, but I take 5-6 years instead of 4 to get my degree?

In an answer to this question, user JeffE states: "Nobody cares how long you took to graduate. There is no advantage to graduating early, and there is no disadvantage to graduating late."

As a fellow Greek (who finished his undergraduate many years ago), I know that the average time for finishing a 4-year degree is 5 years for those who actually start from the beginning. Passing no course for 3 semesters, means you already need 6-7 years to graduate.... (continued)

....This "Is it reasonable for me to expect to be accepted by top US/UK universities" should be first replaced with "Will I be able to actually get the degree?" and then "Will I be able to actually get the degree with at least a 7.5/10?", since this average (or better) is a cutoff point not just for the best schools in USA (several question here state that a GPA 3/4 in the USA is the bare minimum) but any school.

@Alexandros: I see your points. Fact is, if I decide to do something I try my very best to do it, unless things out of my control happen. I am also aware of the average time to finish, but keep in mind those students are living a "more relaxed" student life. I am planning to work hard to finish in 5-6 years.

@MadJack Is that analogy fair? JeffE later states 'It is extremely common for students to take more than four years to get an undergraduate degree, especially if they change majors, as you are effectively doing.
' --> I'm assuming that that is relevant to JeffE saying 'no'.

@BCLC Well, I linked to both JeffE's answer and the question, so I guess it is up to the reader to draw their own conclusion.

to answer your first question and then comment on a statement:
Personally I graduated from both High School, and my first B.S early. There's not advantage or disadvantage when another school (or even the school you attend) looks at your record to decide if you can enter the program. There isn't a disadvantage to graduating late either. The rate of students who graduate (In the U.S) has dropped the past years for a few reasons:
1). Financial issues.
2). Work & school at the same time limits the amount of courses you can take at one time.
3). Single-course to graduate students (there's no formal name for this so I'll explain). Some students take 1-2 courses a semester and may even skip a semester or two. They do this to keep educating themselves and eventually earn a degree without having to stress over taking 4-6 courses at once.
You mentioned failing courses because of personal reasons. Normally when this happen's grades are seen to drop and the student either drops out or get's back in the school motion and grades rise. You mentioned failing courses for 3 semesters which could look bad (granted I don't know what caused the issue in the first place). Be ready to talk about it in person and in your essay because it's unusually for someone who is failing semesters to continue to attend.


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Submitting ACM Conference papers to ArXiv
I'm a little confused. The ACM Author Rights and Publishing Policy states:

ACM authors hold the right to post copies of their own peer-reviewed accepted ACM works on any non-commercial repository or aggregation that does not duplicate ACM tables of contents, i.e., whose patterns of links do not substantially duplicate an ACM-copyrighted volume or issue. Non-commercial repositories are here understood as repositories owned by non-profit organizations that do not charge a fee for accessing deposited articles and that do not sell advertising or otherwise profit from serving articles.

However, the ACM Fair Access site states:

Can I publish the published version of my publication on arXiv?
      No. An ACM author cannot grant arXiv.org or any other publisher rights to distribute their works that have been published by ACM.

SHERPA/Romeo shows ACM as being a "Green Publisher", which would support the case that I can upload to ArXiv.
Dissem.in states that I can upload pre- or postprints under certain circumstances, but does not explicitly mention Arxiv, positively or negatively.
So, what is it? Can I submit a paper I published with an ACM Conference (ACM WiSec, if that makes a difference) to ArXiv or not? As I understand it, ArXiv is a non-profit, so it would fit the terms of the publishing policy. Or is this related to the rights you have to grant ArXiv upon submission?
If I can only publish a specific version of the paper, which one?

This is a matter of obsolete documentation.
The current version of the "ACM Author Rights and Publishing Policy" you linked to is v9, last revised in 1/2016. This version says that authors have the right to:

Post the Accepted Version of the Work on (1) the Author's home page, (2) the Owner's institutional repository, (3) any repository legally mandated by an agency funding the research on which the Work is based, and (4) any non-commercial repository or aggregation that does not duplicate ACM tables of contents, i.e., whose patterns of links do not substantially duplicate an ACM-copyrighted volume or issue. Non-commercial repositories are here understood as repositories owned by non-profit organizations that do not charge a fee for accessing deposited articles and that do not sell advertising or otherwise profit from serving articles.

(emphasis mine.)
The previous version, v9 with a 5/2015 last revision date, only gave authors the right to

Post the Accepted Version of the Work on (1) the Author's home page, (2) the Owner's institutional repository, or (3) any repository legally mandated by an agency funding the research on which the Work is based.

The Fair Access FAQ page is from before January 2016, and reflects the old policy.
The current policy as of January 2016 does allow the accepted version of the work to be posted on "any non-commercial repository or aggregation that does not duplicate ACM tables of contents" such as arXiv.
malexmave confirms after contacting ACM:

FAQ was indeed outdated. Posting the peer-reviewed / accepted version to ArXiv and other non-commercial repositories is fine (but not the final version). Policy change does not apply retroactively, only to new papers under the new policy.

Interesting. Do you by any chance know if this applies retroactively to conferences from before that change?

Now I am confused, only two days ago we signed an ACM copyright transfer agreement with the following terms: "(iii) Post the Accepted Version of the Work on (1) the Authors home page, (2) the Owner's institutional repository, or (3) any repository legally mandated by an agency funding the research on which the Work is based." There was no point (4) there? Have you seen the new terms in use in some ACM conferences already?

(In any case I deleted my answer as it was based on the old terms.)

@JukkaSuomela I'm not at all surprised that the copyright transfer form hasn't been updated.  However, it does say on it, "ACM authors retain all proprietary rights other than copyright including a set of “Retained Rights” stated on the Form.  (Also see the ACM Copyright Policy, §2.4, §2.5 and the Permissions Policy, §3 for further details)." (emphasis mine) The list of retained rights on the form need not be comprehensive.

@malexmave I don't know the answer to that.

@ff524 Okay, I guess I'll have to contact the ACM, then. I'll leave this question open until then and will update you and accept your answer once the ACM gives a definitive statement. Thanks!

@ff524 results are in. FAQ was indeed outdated. Posting the peer-reviewed / accepted version to ArXiv and other non-commercial repositories is fine (but not the final version). Policy change does not apply retroactively, only to new papers under the new policy. Feel free to add this to your answer so it isn't buried in the comments, I'll accept it now either way.

How does this go hand-in-hand with Supplementary Material? I am assuming the final version doesn't have the Supplementary Material with it. So the final version  + revisions + Supp Material is allowed on ArXiv?

@malexmave Sorry if this is obvious, but what exactly is the "peer-reviewed" / "accepted" version? In particular, am I allowed to put a post-print on arxiv, i.e., including the final edits after receiving peer review feedback but without ACM branding etc.?

The ACM offers guidelines for Prior Publication and Simultaneous Submissions.  Information there (from April 2018) extends this answer if the paper is a technical report prior to submission or under review as opposed to being already accepted. The guidelines state

Issuing the paper as a technical report, posting the paper on a web site, or presenting the paper at a workshop or conference that does not publish formally reviewed proceedings does not disqualify it from appearing in an ACM publication.

I assume for the case that the manuscript is not yet submitted or still under review, arXiv would count as "issuing the paper as a technical report, posting the paper on a web site."
I understand the following: Overall, ACM usually allows researchers to archive their manuscripts prior to submission, during review, and after peer-review/acceptance as long as the manuscript is not equal to the official ACM publication and, after publication, contains a corresponding link to this official (i.e. formally reviewed) publication.
Please, let me know if this is incorrect. Some philosophical background on why publishers should be less restrictive anyway.


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Is it better to publish a few papers in one journal, or one paper each in several (equally good) journals?
Suppose there are several journals with the same impact factor.
Is it better to submit my papers to one of them or each time I finished a manuscript it is better to submit to an equally good journal that I have not published in yet.
I am early in my career and I already published two papers in the same journal and I am going to finish my third paper, which potentially can be published in the same journal as my previous two papers.

I find it hard to see any distinction.

What matters is what is in the papers, not what the papers are in.

What David said.  In fact, what is in the papers is more important than the impact factors of the journals.

Are we to assume that these journals have the exact same scope, that none of them tens to publish more papers on your topic than the others, and that the journals are otherwise equally appealing to you?

While I cannot state authoritatively that this is the case for all disciples, it is my experience that it does not matter.  Equally prestigious journals have equal prestige.  Moreover, while the reputations of the journals you publish in is certainly not irrelevant to your future career prospects, you should expect your work to be evaluated at a deeper level than just looking at journal names and citation counts.
If you want to pursue a research career, the people who will be considering hiring you are going to want to know about the substance and significance of your work.  What journals you publish in may be relatively low down on the list of things that they look at.  Hiring committees want to see clear explanations of why your work matters from your reference letter writers; and the committee members likely will read some of your publications for themselves and draw their own conclusions about the quality of your work.
For reference, when I was a post-doc, I published the vast majority of my papers in a single highly-regarded journal, and it was never an issue when I was looking for permanent faculty positions.  I do not think the issue of having too many publications in a single journal has ever come up in the search committees that I have been on either.

Is there a risk that a single, reputable journal will fail?

In general, it doesn't matter a lot, especially if you have more than a few publications.
However, if you work in a field with a number of sub-disciplines and different audiences, which journals you publish in says something about your specialization.
Say, you are a political scientist and have only published three papers so far. Those papers analyzed the implementation of different environmental policy instruments on different levels of government (regional, national, European, international). With this overlapping topic you could have published some or all of your papers in an environmental policy journal, in an European integration journal, in a regulation-focused journal, or in an international relations journal, etc.
If, for some reason, you published all three in, say, Environmental Policy and Governance, this will brand you as environmental policy specialist. But perhaps you would rather like to be seen as European integration scholar, as a comparative politics researcher, or as someone with a broad profile. This is a strategic decision that you have to make especially at the beginning of your career, with a view to the jobs you are planning to apply for.
So the answer to your question depends on your career trajectory and on which profile you want to build.

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


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How does ORCID work?
Will the ORCID appear in the article people write? I could not find an article in which ORCID was included. Can somebody point out some examples if there are any?

I don't remember seeing ORCID ID in research papers, but I have seen it in several CVs. Perhaps, the reason is that journals' style guides do not allow or support that. In regard to ORCID ID's use, you can use just a numeric form or generate a QR code for CV, papers, poster labels, website and other "marketing" purposes.

If it does not appear in the article, then how the article written by the person is linked to this ID?
If it would appear in the article then by searching it people could have easily find the profile of the author.

Papers, authored and co-authored by a person, are supposed to be listed (currently, AFAIK, manually) in the relevant section(s) of the person's ORCID profile, which uniquely identifies researcher via the corresponding ORCID ID. That one-way linkage, while not ideal, is, at least, better than no linkage at all.

I've recently seen journals starting to put the ORCID in the actual papers. Here's an example pdf.

"ORCID ID" is one more item in the list that contains "AC current", "ICBM missile," "ATM machine", and "PIN number".

@AleksandrBlekh. How doe this uniquely identifies the author? If I put another person's article in my profile, who has the same name as I have, then how can the ORCID know I am cheating? ORCID ID must be in the article itself or linked to the article to make this identification possible. Maybe, when I add an article, ORCID asks the publisher for the ORCID ID authors sent during papaer submission and then compare that with the ORCID ID of the person trying to put the article in the profile.

@yashar Requiring ORCIDs in the source paper would make it impossible to build a complete record for anyone who began publishing before this was standard. Yes, this means you can indeed cheat by claiming other people's papers - the system is not intended to guard against abusive behaviour.

@Andrew What would it be the benefit of ORCID then?

@AndreasBlass from orcid.org: "you may only register for an ORCID iD for yourself". So, writing "ORCID iD" is correct. "ORCID" should be pronounced like "orchid", the flower, so it's not too redundant phonetically speaking.

@pintoch I was aware that ORCID itself does what I'm complaining about, but I decided to complain anyway.  "PIN number" isn't too redundant phonetically either, but I complain about that too.

@AndreasBlass OK, but still it there are differences between the organization running ORCID ("ORCID"), a profile on that system ("ORCID record"), and its identifier ("ORCID iD").

@yashar The benefit is what it always was - identification. It's not intended to be an absolute legal guarantee of identity, just a way to easily distinguish two people with similar names.

ORCID identifiers do not mean much when you write them on the first page of a paper. Humans usually prefer to see affiliations or email addresses, because they carry more meaning.
However, ORCID iDs are very useful when they are included in the metadata associated with the article. This helps search engines and research information systems identify the authors the paper. As this metadata is rarely shown directly to users, it is not so easy to observe ORCID iDs in the wild. Here are a few examples:

Some papers registered on CrossRef or DataCite have ORCID iDs associated with their authors. For instance, you can search for the papers associated with 0000-0001-5556-6616.
Some repositories also store ORCID iDs, such as Zenodo: for instance, this paper has an id in its metadata.
Some research information systems such as Dissemin display ORCID identified authors with the ORCID logo, as in this example.

Europe PMC have been displaying it on the site since 2013.  Nature also started in 2013 - click on Chen Dong's name in this article and you'll see his ORCID ID.  There are plenty of other examples out there, Springer, Wiley etc etc.
ORCID adoption by journals is increasing day by day.  Most major journals now accept it upon submission. Many of the big publishers are on the board.   Many funders ask for it.  Wellcome mandates it.
Some publishers display ORCID IDs on their article pages or author pages, others have not yet got round to it.  Even if they are not yet displaying it on their article pages, the ID is often propagated to Crossref or Datacite via DOI metadata.  This helps discoverability and disambiguation and also allows for auto updating of ORCID records.


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Using leaked proprietary information in scientific paper
I am working on a project in the area of IT security where we are analyzing a proprietary embedded system. While researching the system, we came across a confidential data sheet that was made publically available by a third party without the consent of the manufacturer of the system. The datasheet is marked confidential and usually only given out after an NDA is signed. It describes an outdated version of the system we are analyzing, but is partially relevant, as some parts of the system have not changed since then.
Is it ethical / acceptable to use and reference this resource in a paper?
"Related Work": this and this question ask about citing documents that aren't widely available (while my document can be found by anyone using Google, and none of the involved researchers have signed any NDAs).
Edit: To add some additional information that I added spread over a few comments:

The datasheet in question describes the security protocols used by an older version of a popular embedded security chip, current versions of which are being used in payment and access control systems
The manufacturer is aware that the data sheet has been leaked and is not happy about it, but has not gotten the datasheet removed from the third-party servers where it is located for the past two years. The reasons for this are unclear
The data is confidential (as in private-sector NDA-confidential), but not classified in a government sense.
The company has already stated that they would prefer if we did not publish based on this document, but that they would not be taking any legal action if we did, as long as all information was factually correct.

One thing to consider: you probably cannot include the data in the paper, and the document could be taken down because of the NDA issues.

@NickS In this specific case, the document has staid up for multiple years, so either the vendor (who is aware of it) is not pursuing it, or they can't get a legal handle on it. But yes, in general, that is definitely a consideration.

I am not a lawyer, but...ask a lawyer. Depending on where you are the legal implications may differ significantly. You may bear no legal responsibility at all, though that doesn't answer the question of how this would be received within the research community. There are questions invoked about reliability and trustworthiness of what you've found that are completely independent of ethics and legality. They're purely scientific problems.

Have you contemplated contacting the company? It's possible that the data for an old system may no longer be access controlled.

@David I talked to the company to disclose a vulnerability we found. They confirmed that they were aware of the existence of the leak and not happy about it, but that it was generally not officially "declassified" (in parenthesis since it is not government-classified, but private-sector-confidential). They appearently did not take any (effective) action to get the document offline, as it is still widely available.

Ignoring the ethical issues, publishing this information is just plain illegal, unless the company gives you explicit permission to publish it. Trying to "get a document offline" from the web is next to impossible, since there is no way to track down all the copies that have been made, but taking effective legal action against a print publisher is very much easier!

@alephzero Publishing the whole document may very well be illegal, but I'd be interested in how a legal case about using the underlying information in a published paper and citing the datasheet would look like - is there any precedent you are aware of? For what it's worth, the company has already (grudgingly) stated that they would not take legal action against us if we use the data in this specific case, they only requested we run the paper by them first for fact checking.

You say that this involves "security protocols...used in payment and access control systems" and that you've found at least one vulnerability.  If these systems are used by people outside the company and those vulnerabilities aren't public, the users have a right to know about them, at which point releasing the information may be morally required.  (Although in such case you should give the company time to fix the vulnerability before public release, per Responsible Disclosure (which is admittedly more complicated for hardware than it is for software)).  Arguments can be made both ways.

In journalism, the distinction to publish is usually made based on if the information in question was offered unsolicited, and without any stipulations: it came in "over the transom". Unsolicited so that you couldn't have suggested or implied in any way to a source that "it would be nice if I had this", and without any stipulations (i.e. "you must publish this") to avoid blackmail concerns.

Now I am no lawyer, but this is not primarily an ethical question but I would suspect that in many legislations it could be a legal question. You don't want to accidentally be accused for say, industrial espionage.

Sounds like you have found an interesting source and are considering the moral implications of using it. What I will say is based purely on personal opinion and probably what I would do unless instructed otherwise.
Leaks are a fact of life. With the proliferation of digital material they are commonplace. Look at Wikileaks, the Snowden revelations etc. Once material has become public there is - fortunately or unfortunately - no going back, regardless of how that information became public. It is the responsibility of the owner/creator of the material to ensure it says secure.
Dissemination of such material could be highly fruitful - but think of it this way - will your publishing research based on the material be ultimately constructive or destructive? Will it benefit just you or the wider world? Who is it really advantageous for? If the answer is just you, I would probably withhold your research based on it. If it has wider ramifications of great import, go with it. Also consider the reasons why it is confidential. Who does it serve - who does it protect? Was the confidentially because of financial reasons, incomplete research, company policy, or 'national security'?
There is a heavy moral tinge to this question, and you may have to do some soul-searching. But ultimately, if it serves the wider discipline in a positive way, and such servitude grossly outweighs the few individuals who it would ire, I would use it, as long as there are no legal implications for yourself [unlikely since a third party leaked it, but you can never be too careful].

@andorian If these results would save people's lives, then yes, I would publish them. Obtaining the results as you suggest is obviously unethical, and I would make that clear too, but withholding information that can save lives is even worse.

@andorian: I didn't think we'd get to Godwin's law so quickly. You really think using data leaked from a company is comparable to using data from Nazi human torture?

Why are we suddenly positing "but what if it saves lives?"  This makes the entire exercise hyperbole. I'm rather certain the OP found nothing of the sort.  It's not even in same city as the ballpark.

@zibadawatimmy: It's "IT security" for an "embedded system". The kind of thing that could affect lives. Not saying it's necessarily happening here but it's a hell of a lot less of a stretch than data from Nazi torture.

To give some context about the data in this specific case: It's a data sheet that defines how a certain embedded chip with security functionality behaves, and how to communicate with it. We are looking at the security of the protocols that are defined in there. More up-to-date versions of the chip are used in access control and payment systems, among other things.

@andorian why not? lives of unfortunate tested people were already lost at that point and nothing will fix it. But the information might help everyone else in the future.

I'm glad I'm not in your situation.  It's tricky.  While I can't really offer the ethics of scientific publication for this situation, a journalist, which is a constitutionally protected entity in the US, would probably publish after soliciting comment from the company.
You, however, would probably be sued, as would your university.  If I were in your situation, I would probably consult university counsel, and abide by whatever they tell me to do.  If the school won't cover my back, I wouldn't want to assume the personal liability.
I suppose another way to look at it is by how important the matter is.  Is it worth the s***storm you're likely to find yourself in?

Have you asked the editor of the journal?  They might be unwilling to publish your paper because of the risk of being sued by the company that had its proprietary material leaked.  They might also argue that the source shouldn't be cited because it might disappear at any time and wasn't really "published."

The usual method is to find a paper or publication, use it's contents, and cite it properly. Maybe not in this case, but just consider your position if you publish your paper quoting this leaked material, and the company that allegedly produced the leaked material denies that they produced any of this material. That's not good news for your paper.

If the company who had the document leaked said that they would prefer not publishing based on the leaked data, it means that it can be harmful for them.
So you are chosing between your benefit and their benefit. If you chose to publish it may be legal but less moral.
Maybe you can convince them to co-author the paper, given that the harm has already been done for them, and it puts them in a better light. If that does not work, you could see if they agree to review your paper and you can acknowledge them.
Basically, I think it's fair to take any action that would avoid doing more damage to the company with the leaked document.


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Reproducing work of others - name them as conflicts of interest?
We are currently reproducing several papers in a specific sub-field of computer science under different experimental conditions. When we submit the paper, we will be required to declare people who may have conflicts of interest. Most of the original authors of the papers we are reproducing are aware that we are doing this work.
Should we declare the authors of the original papers that we are reproducing as conflicts of interest?
Arguments in favor:

Reviews may not be blind, as they know we are doing the work (review is double-blind)
We may be "stepping on some toes" by showing that their results do not hold up when reproduced under more realistic circumstances. Conversely, as Wrzlprmft notes, we may be biasing others in favor of accepting, if we show their results to be correct.

Arguments against:

They are best suited as reviewers. If we name all of them as conflicts of interest, we will have excluded more or less every expert in the field, thus making it much less likely that we will get a reviewer familiar with the field

Is there an established guideline for this kind of situation (in CS or other fields)?

I don't know about general guidelines, but since the pros and cons are both reasonable, I would delegate this issue to the journal's editor.
You could mention it in the letter to the editor (and even list your pros and cons) but leave the decision to them.

Your reasons for declaring conflicts of interest are valid, so I would suggest not worrying yourself over the rest. It's the journal's responsibility to find reviewers. In any case, I don't think any journal is obligated to choose reviewers based on the authors' perceived conflict of interest. These are usually only suggestions solicited.
By not declaring some authors and declaring others, you would be guilty of partiality and possible malpractice. By not declaring any, while you know they exist, you might be doing something unethical.
In summary, save yourself worry, go ahead and declare all authors involved in the study.


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Requiring specific licensing for optional coursework - is it OK?
To gain extra credit for a course I lead, students can share their notes from a lecture which we intend to use as starting point to develop a better (free) learning material than just sharing slides from the lectures. To this end we explicitly asked the students to share their notes under a Creative Commons license.
At this point I have second thoughts whether this is completely OK ethically/legally. I would intuitively think that requiring students to waive some of their rights as authors would be problematic if the assignment was necessary to complete the course. Doing so for optional extra credit (which then lowers their point limit for the final exam) seems less problematic, but I am not sure this is actually a good enough distinction. Thanks for any notes/feedback.
I should also note that using student's work to build educational material is likely already allowed due to our country's laws (Czechia, EU) on intellectual property where work created to obtain academic credentials is explicitly allowed to be be "used by the academic institution for its internal needs and for educational purposes", no permission from the author required. CC licensing is still a step further, though.

While I am a big proponent of CC-licenses, you should in any case think about offering an alternative, in particular one that does not require attribution. Learning from mistakes is a very important thing, but if you want to use a student's answer to show how something is not done, then it might not be the best idea to do so under a license that requires you to identify the author by name every time you mention it.

@mlk: Under version 4 of the CC licenses, the author can not only waive attribution, but can affirmatively demand that attribution be removed, even if the work has not been modified. Licensees are required to comply with such a demand or they forfeit the right to use the work at all.

It’s definitely not okay (as you yourself concluded) to require students to waive legal rights as a necessary element of the course grade. Extra credit is a bit more of a gray area, but I’d still tend to think it’s not a great idea. See this earlier discussion.

You should definitely consult a corporate lawyer at your academic institution for a definitive answer, but I will offer my thoughts.
First, the excerpt that you quoted does not seem to apply to the situation that you are asking about: "work created to obtain academic credentials is explicitly allowed to be 'used by the academic institution for its internal needs and for educational purposes'". Licensing work under Creative Commons goes far beyond internal use.
Second, I do not think students should ever be forced to give up their copyright or the freedom to exercise their copyright. (Licensing under Creative Commons would mean that the students forego their freedom to exercise some of their copyright privileges.) Offering extra credit is not directly forcing the students but it is definitely pressuring them by compelling them to forego some of their rights in exchange for free credit. I would consider this unethical.
For some background, I am on my institution's research ethics board, and we would definitely not permit a similar situation in a research context. Even though your situation is not a research context, it is similar in that students are being offered extra credit for something which they might otherwise consider to not be in their best interest.
My institution's research ethics board takes a creative approach to research ethics, by which I mean that we try our best to help researchers to design ethical research rather simply saying no to proposals. Along those lines, here is my proposal for something that might work better:
I propose that you offer extra credit to all students who are willing to share their notes and you let the matter of Creative Commons licensing be completely optional. For students who decline the Creative Commons license, you give them the credit but do not incorporate their work in what is publicly shared with the rest. However, you should take the time to educate the students on the benefits of such licensing. In particular, highlight that Creative Commons licensing requires people to cite the work when used, and so this would give the students visibility and appreciation. (However, you must be responsible to also inform them of the implications of the irrevocable release of their work.) If you do this, you would probably find that most students would willingly choose the Creative Commons license.

Greatly appreciated. Agree that the law does not allow me to assume CC license or anything like it, edited the question to make it obvious that this is not the point of the question. I am quite sure I could share the notes with other students even if not CC licensed (still, explicitly asking is reasonable).

The operative word for me is "ask". To my mind, there's nothing wrong with asking students to do this. But I agree that tying grades to this request is problematic. This no longer makes it a free choice. And presumably part of the point of this exercise is to encourage students in future to share their work freely for the benefit of others. This point is in my opinion, somewhat undermined if they feel coerced to do it in order to get a better grade.
In my opinion, a better way of doing this would be that the extra credit is only tied to sharing the notes with you. You can attach to this a request to licence the notes under CC but the grade should not be dependent on that. I suspect most students will happily do so.

Thanks for the feedback! To clarify and broaden the applicability of the answer: would you apply the same reasoning for extra credit that is tied to making a contribution to Wiki/open source project/...? One varaint we considered was to tie the points to people sharing the notes on a local country-wide wiki-like server for lecture notes, but then decided to keep more options open...

@MartinModrák I think this may also be a bad idea without proper consideration. Aside from the ethical issues already raised, Wikipedia has guidance about such assignments https://en.wikipedia.org/wiki/Wikipedia:Student_assignments . There is a perverse incentive when exchanging edits for marks which can lead students doing more harm than good. Same will apply to eg open source projects. So again, I'd advise the assignment should have the option of adding to wikipedia, but base marks on a version which doesn't need to be licenced as CC.

Your question essentially amounts to: "is it ok to sell extra credit to students?" You are offering them marks if they give you something with intrinsic value: the rights to use their notes.
It is probably the case that the monetary value involved is very low, but the principle remains. Would you have problems giving extra credit to students in exchange for buying a coffee and delivering it to your office? Or to those who paid you €5?
Edited to add: Discussion in the comments led me to appreciate something that I think is important here. The proposed 'extra credit' task here (publish your notes with a given license) has minimal educational value for the student concerned. This is in marked contrast to alternatives such as "write a Wikipedia article" or "contribute to an open-source software project", where concrete learning outcomes can be identified: e.g. consolidation of knowledge, communication skills, coding experience, etc. In those cases, extra credit is (or at least can be argued to be) given for demonstrating the ability to apply knowledge in 'the real world'. In the OP's case, the credit is simply offered as an inducement to act in a certain way.

Are you sure this is a good reference class? Consider a different scenario: giving extra credit for writing a Wikipedia article or contributing to an existing open source projects. I'd think that would be quite OK. My use case IMHO lies between "giving credits for valueable" and the Wiki/Github case, but is IMHO closer to the latter (though as others have argued my use is still likely problematic in a way asking for Wiki/Github contribution isn't).

@MartinModrák I think there is a distinction: Wikipedia/Github are well-established as resources used by the worldwide community, and any benefit to the instructor is very marginal. Moreover, there is clear educational value to the student in (e.g.) gaining experience as an open-source contributor. In your case there seems to be little educational benefit associated with the extra credit (unless you are arguing it encourages them to take better notes), but the instructor "gets out of" doing the work required to prepare good course materials.

@MartinModrák I think it's also relevant that with Wiki/Github students can understand how their work will be used before deciding whether they want to participate. However, as I understand it you want to use their notes to build something new.

Mostly agree. The reason why I think the comparison to wiki is relevant is that contributing the lecture notes to local country-wide wiki-like site for lecture notes  is an explicitly encouraged option to fulfill the requirements for extra credit. The site enforces a CC license. So I don't think I can be making the situation substantially worse from an ethical point of view by also allowing students to just send the notes to me by email.

The principle is the same for wiki articles etc. The TA is getting something he values and giving extra marks for it.  That something is outside the course work and outside the usual method of evaluating performance in the class. Whether it's a coffee or a donation to the Home for Indignant Cats does not change the principle.


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Citations in a Paper After the Whole Quotation is Shown
Say I have a quotation that is written at the top of my page something like this:

Abook
Robert Contor was always an odd fellow, but when the neighbors discovered his secret, everything changed. (p. 12)

Then, in my paragraph, I reference the quotation like this:

In Abook, it says that Robert Contor's life changed irreversibly after "the neighbors discovered his secret". This shows that .......

To be fully correct and not even have to worry about plagiarism and incorrect citations, do I have to include:

(Abook Leauthor p. 12)

or something like that? Can I legitimately get away with not adding the inline citations after every quotation, even though it is obvious what I'm citing? Does this apply in general when it is fairly obvious where the quotation came from?
Thanks a lot in advance. All responses are greatly appreciated!

Are you talking about other books in that area of the text? Personally, as a reader, I find quite tedious when people write "(Smith 1994) said this. And (Smith 1994) continued saying. (Smith 1994) finishes pointing out that..."

I'd look for some form of "short citation" format in whatever style you are using. E.g. the first time around give the full citation, and later on the short one. Another technique would be to cite once, and then just go "As Leauthor says, ...", or even just try to keep all this together. If it is a long discussion, you might even dedicate a (sub)section to this, using sectioning to have it hang together.
In LaTeX/BibTeX I use the plain citation style, which gives a unintrusive [42] only. But that is major surgery...

You should cite every source of information not just text within a publishable content.
Just rephrasing the sentence from the book doesn't mean you didn't refer the book. If the content you referred is included in the book, then you must cite the relevant book too.
Another word of advice: Citing a material doesn't permit you to reproduce its content as it is in the original source. So, in general you ought to rephrase all of information you cite. Exceptions are for equations and quotations.

The quote looks fiction, so I think this is a literary analysis piece, and the point here is not talking about Robert Contor, but asserting that this is what the book says.

If you are in MLA format, it should always be cited. You would have to cite it as
(Author Last Name pg.#)
for example,
(Smith 7)


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One student grading other students' assignments in the same course?
In the US, can a student who is already enrolled in a course grade homework assignments of all other students in the same course (but not actually accessing and changing academic records)? Is it legal and compatible with academic integrity?
Two of several issues that I'm concerned about are:
1. He has not actually done his own homework (because homework submissions are not recorded).
2. By comparing my paper with other students I wasn't able to observer a consistency in grading. Actually initially I found who has graded our homeworks based on a pattern of inconsistency in grading and also inappropriate comments on my paper.
However the professor rejects my concerns by stating that he has overseen and reviewed everything himself.
In this page from USC.edu it is stated that "Please note that it is not possible for you to be both a student and a TA within the same course. Federal law [FERPA] and University policy both specifically prohibit students enrolled in a class from being able to modify their own grades or to view or modify the grades of other students enrolled in that same class." However as pointed out by Bob Brown, Supreme Court allowed in-class peer-grading.

Is the grading student a member of your cohort? I could imagine a PhD student being an expert in a topic and taking the course for the easy credits.

@Davidmh He is a master student, I refused his request to involve in his cheating/plagiarism last semester.

A student grading other students in the same course is unusual, but certainly not illegal.  As to whether it is inappropriate, I would consider two cases:

Sometimes professors ask all students to do part of the "teaching" responsibilities for a course, whether that be lecturing, grading, creating course notes, etc.  The theory of this is that it forces a deeper engagement with the material, and may help prepare further skills.  When grading or similar is done by a student or other students for a pedagogical reason like this, I see no problem, as long as the professor takes into account the potential for quality variation.
If an individual student is simultaneously a class member and a TA/grader, that is much more unusual, and generally a bad idea.  In this case, the pedagogical value of having all students engaged with the process is not there to balance the expected decrease in grading accuracy and quality.  There may be certain unusual circumstances where it is appropriate, and a professor can, in fact, organize things to compensate for the issues that you raise, but in general I would be highly dubious about this practice.

Thanks, however generally it is illegal, see my update. But there has been some exceptional court decisions about peer-grading.

The Supreme Court disagrees with you.  See Owasso Independent School District v. Falvo: https://www.law.cornell.edu/supct/html/00-1073.ZO.html

I was aware of that, that's why I asked it here. The problem is that details are different, in our case it was neither peer-grading nor for learning purpose. And we didn't know who had graded until I figure out based on inappropriate comments on my paper.

The differences in detail don't matter.  The Supremes said a grade is not a "record" under FERPA until it is recorded and maintained by the institution.  As Jake Beal has written, such a practice is highly dubious, but it is clearly not illegal in the United States, so you need to get over that part.

@BobBrown Ok, what's your idea about academic integrity?

between jakebeal, bob brown and your edit, you seem to have much of the first part of your question addressed. I would add though, an addressing of the second part about academic integrity. It would seem that from your description, it is more a case of a single student performing this grading, rather than a pedagogical exercise in which all can partake. I also get your sense of frustration at a seeming lack of response from the professor. So what to do?
It seems (from Bob Brown's link) that it is not illegal. If your institution has a policy in place however, (based on the page to which you linked), regardless of what the law of the land says and what justification the university provides for their policy, their policy is their policy. If they say what is happening in your class shouldn't be happening, then it shouldn't be happening. If there's no official opposition, then your only recourse is to make a case based on the personal discomfort you feel about having your assessments, whether official or not, being prepared/(gossiped over? shared?) by a peer. And I don't at all mean to minimize it, if that's what you're feeling.
You mentioned a couple of things, including grading inconsistencies and inappropriate comments. These are potentially more serious, particularly with regard to academic integrity (what happens to these grades? recorded? even if not, you won't be helped in learning if the feedback is not consistent/constructive). As the professor has said he is reviewing this grader's work, he is then also responsible for what this person does. Depending on the severity, it may be something that needs to be taken to a higher power, depending on how strongly you feel something wrong is happening. If you do go that route, you might also want to be sure to stick to inependently verifiable observations (eg. you can get your hands on those other papers to demonstrate these inconsistencies, and unless you can prove he's not doing his homework, it might come across as a petulant accusation to just throw that out). Be aware though, that for the former, getting your hands on the papers of others, may itself weaken any argument about discomfort in marks being shared.

Actually, students also learn when they evaluate others' writing and it also helps to improve the feeling of integrity and responsibility. Do not worry to much about the grade since you can always ask to see your paper. If he says he reviews the paper there is no problem.

I have compared my paper with other students, grading was not consistent. Also see my update.

The thing is, as long as the names are blanked out it suits the law

It's not even necessary to conceal the names.  See Falvo; there's a link in my earlier comment.


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Chosing a suitable Ph.D. program in Mathematics
I am new to this webboard so I am not sure if I can ask this questions here (I am sorry if it is not suitable).
I am currently pursuing a MS degree in Pure Mathematics in a university in America. In a half year time, I will earn the MS degree, and I would like to continue to Ph.D. program. The thing is, for almost two years I spent time at this university, I had a really hard time. I believe that the math program here is quite strong, and I feel that my academic background is not suitable to stay here any longer. So I am trying to find another university to attend Ph.D. program.
To be more precise, I think that I am interested in Number Theory (might be either algebraic or analytic) and Analysis (Real analysis). I also can do relatively good in Algebra. So what I am looking for is a suitable university with relatively decent program in number thoery or analysis (or algebra).
The suitability here I suppose that I mean the program is not too intensive. I do not want to go to the best 50 math graduate school since I know that my academic insight does not that good. I am looking for a university with acceptable Ph.D. math program with relatively easier qualification requirements. I am not sure how to select universities which match my requirement. It is also hard to ask for suggestion for choosing a less intensive Ph.D. program to my advisor. (Most of the time, people are looking for a good best-25-math-grad school. So there is almost no information about a decent or relatively lower math Ph.d. program. That why I decide to ask it here)
If anyone experienced my situation or can suggest what I should do, please leave the advice below.
If you need more specific information in order to give more helpful advice, please mention it.

I am confused. Number theory is the queen of Mathematics and yet you want to find a relatively lower PhD program to study it. Why?

I mean I want to find a NEW University to attend Ph.D. program. My point is that I would like to find a new university that appropriate for me. My research interest is Number theory or analysis. I think research interest is one of important factors for choosing university.

The main reason I need to find a new university is because the deficiency in my academic background. I think that different universities have different expectation for Ph.D. and also different in standard of academic work. I find that my current university has too high expectation that I do not wish to continue studying here. It is too intense and serious.

I notice that my topic is somehow not appropriate to this stack. Can anyone please recommend where I should post this question or how should I fix my question to fit this acedemia stack ?

Your question is about seeking recommendations or lists of individual universities. That's why it's put on hold. If you change it to explaining why you look for those universities and asking about how to look for them, you might have chance to get the question re-opened - my opinion.

I would simply get a list of the Group II and Group III universities in America (such as here), and then visit their web pages, and then make notes on faculty members who appear to do work you're interested in, perhaps writing to some of them personally. For example, I taught for several years at one of the Group III schools listed under "Not Ranked by the 1995 NRC Study", and among the faculty is someone relatively well known in the study of small gaps in primes who could easily supervise research in analytic number theory.

There is a new proposal in Area 51 that may be a better forum for addressing this question: http://area51.stackexchange.com/proposals/97164/graduate-school-admissions-individual-assessment