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Editor says "the paper will not be acceptable within a reasonable number of revisions": is it worth appealing the rejection?
Given the editor's comments reported below, is it worth appealing this rejection or one should submit to another journal?

At the rate of improvement that has occurred over the last revision,
  the paper will not be acceptable within a reasonable number of
  revisions. Consequently, your paper is being declined. The reviewer
  comments are very helpful and should assist you to prepare the paper
  for consideration in another journal. Reviewers' comments on your work
  have now been received. You will see that they are advising against
  publication of your work. Therefore I must reject it. For your
  guidance, I append the reviewers' comments below. Thank you for giving
  us the opportunity to consider your work.

Move on to another journal. There is no reason to appeal a rejection, particularly when the reviewers and the editor agree on the rejection of your manuscript.

My calculation is only with regard to the time required in a re submission.

The editor seems to be basing it on a delay in submitting the first revision and of course reviewers comments to the first revision . If he does allow a second submission ( I will necessarily need to include atleast edits for those comments I feel are valid for this or any other journal but hope to save time given the familarity of existing reviewrs

A reject is a reject. Reject != major revision. There is nothing more to discuss with this journal or this editor

I don't think the problem is a delay in submitting the first revision; it sounds to me as if the problem is the quality of the first revision.  Specifically, the editor seems to say that the first revision produced so little improvement in the paper that, if further revisions produce equally little improvement, then an unreasonable number of revisions would be needed to bring the paper up to publishable quality.

I agree partially but rate indicates both time and the quantum of revision.

I am infering a second revision which is not minor is unlikely in a top tier high impact journal /

The way that I am reading this, the editor is not happy with how things went, and that may include parts of your correspondence with him.

rate indicates both time and the quantum of revision — The intended meaning is clearly the latter, because the sentence ends with "...a reasonable number of revisions", not "...a reasonable amount of time."

Appeals are usually intended to be pursued when you think there was a serious procedural problem with the way your paper was handled, resulting in a decision that was not properly based on your paper's content.  Some examples I might think of:

Reviewers were not qualified to judge the paper, or their reports were of extremely low quality (suggesting they may not have read the paper or given it serious consideration)
Editor or reviewers have a conflict of interest
Editor or reviewers show evidence of bias or prejudice against the author
Other unprofessional behavior on the part of editors or reviewers

None of that seems to apply here (unless there is something you haven't mentioned).  It sounds like the reviewers read your initial submission and said it wasn't acceptable for publication as it was; it needed significant revision.  You made some revisions but they are not satisfied.  So you still don't have a version which they consider suitable for publication.  If the editor thought it was worth the time to keep revising it, he could let you do that, but he doesn't.  So your paper is rejected.
It sounds to me like this decision was properly made based on the reviewer's opinion of the paper's content, with which the editor concurs.  You may disagree with that opinion, but simple disagreement isn't grounds for appeal - you'd have to show the editor and/or reviewers did something objectively wrong.
So submit to another journal.  But first, go through the reviewers' comments carefully, and make the changes you feel are appropriate.  They might need to be extensive.  Reading between the lines, it sounds like the reviewers didn't think that your revision did a good enough job of addressing their concerns, so maybe you need to think more carefully about what they said.  The reviewers for the new journal may well have the same concerns.

Does it make sense to  ask the editor's suggestion regarding which journal to target for re submission.( Given his suggestion for submitting to other journal) This is a high impact top tier journal

@dEEPAK: I don't think so.  Finding the right journal for your paper is your job, not his.  If he had a specific journal to suggest, he would have already mentioned it.


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How do I look up grant information of PIs in Germany?
I know NIH allows you to look up grant information of PIs in the United States. Is there a similar website in Germany (DFG?) that allows you to see grants information of PIs?
Also if someone knows of a similar website in Sweden?
Thank you!

You can find DFG-funded projects on their website via the DFG GEPRIS tool. This only shows the DFG funded projects, for other projects the PI might be involved in, you should check the websites of the respective funding agencies (e.g. CORDIS for those funded by the EU).

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How can our department solicit more (good) PhD applications?
Our department is awesome. But every year, I think: "why aren't we getting more awesome applicants? They could be super happy here, and we could do a great job of jump-starting their careers."
Well, this year, I am on the PhD admissions committee.
What can I do to improve the quality of our applicant pool?  Of course I realize reputation is a big component, but that is a long-term game (and we are already quite well-ranked by USN&WR I don't think that's the core issue here). I'm wondering more about short-term, actionable, guerilla mercenary acts I can execute in the next few months.
If you have participated in grad admissions at your university, what (if anything) helped you get more quality applications?
For reference I'm in North America, in the sciences.

What sort of university is it? What specific science if I can ask?

See How to improve graduate student recruitment at a small, good, but non-elite department? and How can a researcher in his early career attract good PhD students?

Avoid answering questions in comments.  5/8 of the comments above this one are attempts at answers.

Echoing Andrew's question, could you share the field of the department?  I ask because there are a few specific places to look for students in certain fields, like http://www.physicsgre.com/

Are you simply looking to get a few more great applicants,  a bunch of good applicants along with some "bad" applicants, or not as many "bad" applicants?

You could kill two birds with one stone and target underrepresented groups.  Make connections with undergraduate student organizations of color.  Invite undergrads taking junior level classes in your department to meet with your committee at a barbecue to talk about what they have found most helpful in terms of supporting their academic success.  If you ask the question that way, you may get some helpful constructive feedback, without actually inviting them to kvetch.
Make sure your department has an effective community outreach program to K-12 students, and ask them to target underrepresented groups in your town or city.  Word will spread.
Co-sponsor, with the engineering department, and a student organization, a showing of the film "Underwater Dreams".  Better yet, invite the people involved in making the film to your showing, for a panel discussion after the movie.
Make sure your faculty members' webpages are clear and inviting.
Recruit some peer advisors and give them some online profiles.  Make sure the peer advisors have a quick way to get answers from the members of your committee in case there's something they can't answer.
I don't know if women are an underrepresented group in your field, but even if they aren't, make sure you have all the features that make a department women-friendly.
With respect to the GRE comment -- I don't have an opinion about this suggestion, but at least try to come up with an admissions policy that looks at the whole person, and make that policy clear to potential applicants.  A public statement along the lines of "we encourage returning students to apply" is a helpful clue to women who have taken a child rearing break.
Make sure you have an undergrad and grad student prize in your department, for example best poster, best thesis, and really celebrate the winners.  Feature different student bios on your department website on a rotating basis.
Get some funding for some upper level undergrads to go along to a conference.  Set up peer mentoring to make connections between students of different levels.
Make sure there are fun things for students to do together in free time, e.g. soccer or volleyball or Eurogames or whatever your department's students enjoy doing.
Really nice administrative support personnel can do a lot to make a department attractive to students.  (For example, "if you have any trouble getting registered for a class you need, let me know".)
Sorry if that was a bit disorganized -- hope these ideas get you thinking.

Do note that attracting underrepresented students is only one thing. If they are going to succeed, they need a department that is accepting, inclusive, and supportive. It will take effort across the department to make this happen and not have an environment/community that drives out those underrepresented persons.

@user2943160 - very well said.  You could turn this into a question and an answer, and they would add a lot to the site.

Welcome back, @aparente001 (+1)

Of course there's no guarantee that people from the 'underrepresented' groups are all going to be good applicants. You might get 100 'underrepresented' applicants and find that only 10 of them are of the quality you're hoping for. Also I'd be worred that targetting the 'underrepresented' groups would put off people from other groups or even the 'underrepresented' groups themselves. I know of a few people who get seriously fed up with being asked to attend science events just so people can tick boxes saying "yes, we got people from X minority here".

You have to specialize. If you can do that, you will be the first choice of those interested in your area of specialization, so the best ones will come.
Today's globalization has created "winner takes it all" markets, and the education market is not so different. In this style of market, the top players get many times more customers than second-tier players, second-tier players do much better than third-tier players, and so on. The differences between the tiers are huge, and each place in the first few tiers of the global market is already occupied. The competition is ferocious.
So currently, you are getting two types of student: A) Those for whom you are accidentally special, e.g. they live in your city and don't want to move, and B) those who dreamed to get into Harvard. A will contain the usual mix of brilliant and average students, while from B, Harvard picked all the chocolate chips from the cookie.
The solution is that you become top player by getting into a niche which has been overlooked. It may be completely new, or it may have 1-2 players which are in it accidentally, so you can beat them easily. Suddenly, you'll start getting applications from C), the students who dream of being in that niche. Not only did you open yourself to a new set of students, but those who know early on what they know, and find out which university offers it, tend to be the best. This is a set of self-selected people who are motivated and effective.
The good thing is that, once your core excellence area builds you a reputation, it rubs off on the whole department. If you are a computer science department and become the place to study formal verification methods, many future students will not hear specifically about the formal verification methods, or know what they are. They will have simply heard that there are good people vying for admission at your department, and conclude that they want to go there too.
You asked for short-term tactics, and I'm talking about reputation. But you can certainly start now short-term. The thing to do is to pick your niche right now, and recast your PR material to support it. Maybe even try to make some lightweight changes to teaching to support the new orientation, such as changing the names of existing courses to better show how they are connected to the niche you are going to claim.
By the way, the currently most upvoted answer - attract minorities - is also going in this direction. It suggests that you occupy a social niche, instead of a discipline-based niche. The good thing is that you don't have to choose, you can do both in parallel.
I realize that any good intentions in this direction are likely to get mired in politics and stopped at many levels, so this won't succeed in many cases, unless championed by somebody with sufficient power. This doesn't mean that the answer is wrong, just that it is difficult to do it right.

One method that my department has found to be quite effective
is to make outreach visits to universities.
We have relationships with professors in departments related to our own,
and these professors will often promote or recommend students to our department.
In addition,
colleagues from my department will make visits to other departments.
During these visits, my colleagues will give a short research talk
as well as talk about our department to the audience,
which is mostly undergraduate students in their second or third years.
Given that quite a few of the PhD students admitted to our department
have applied to our department because of these visits,
I would argue that this outreach program has been quite successful.

I think this is a good idea. Our program is successful in getting great people from a few particular universities which have good training for BA/MA students but no PhD program. Although we don't do specific on-campus outreach there, the professors recommend our department to their best students, and we typically admit at least one per year. I suppose, in a way, the students are acting as our "outreach committee" too, as they have good experiences here and are likely to tell their friends one year younger.

I'd recommend speaking with your marketing department/office, as it's a question of reaching the right market/audience for your department's subject area and standing.
I have worked on a new PhD programme previously, and we attracted very large number of excellent students; however, very few of them were anywhere near the subject specialism of the core academics available to supervise, so we struggled to recruit.
To remedy this, we went back to the drawing board and thought about 1) who is our ideal student, 2) what are our strengths (eg research activities, access to labs etc), 3) what are our weaknesses (what might turn off a potential student) and 4) what are our competitors other threats.
We also thought about in detail the kinds of subjects that we were able to supervise and came up with a succinct summary of these.  And got some funding for a specific topic to shout about too.
In terms of raw tactics, addressing the points above, we did the following:

Mail campaigns to relevant academic discussion groups (JISC and
ListServ) - to those who accept course announcements.
Updating website to specify subject area requirements.
Leaflets/bookmarks advertising the programme that academics can give
to prospective students they bump into at conferences etc.

There's no fancy trickery.  Provided that there actually are people out there that are interested and able to study at doctoral level with your department (which is always worth research - avoid confirmation bias!), then it is only a matter of reaching them.
One tip: keep it short and sweet, don't bury the key information in superlative text.  They will base their decision to come to you on the information you provide to them, not in how you dress it up!
EDIT: I will also add, we targeted 'in-house' MSc programmes that we felt could produce good candidates as well and set up an informal pathway from one to the other.

As I applied to graduate school (in North America in the sciences) I felt some hesitation applying to the top programs in my field because I was afraid I wasn't the caliber of student they were looking for.  This hesitation arose despite my professors being very confident that I was indeed the caliber of student the top programs were looking for.  I then decided to apply to many of the top programs in my field (not just because they were the top programs, but because there were specific aspects of the program/department that were attractive to me) and got accepted at most of them.  I am now attending the program that was my top choice of the programs I applied to and enjoying, as you put it, a great jump-start to my career.
This high acceptance rate I had came as a surprise to me (though not to my professors).  I think that's a key aspect for an answer to your question.
I still often wonder if I actually belong in the excellent program I am enrolled in, as do the majority of my classmates (if not all).  This is impostor syndrome, where high-achieving individuals feel like they don't belong in the circles to which their achievements have brought them.  Impostor syndrome affected me as I was applying to graduate school.  I almost didn't apply to the great programs that I was eventually accepted to because I did not feel like I belonged in such programs, although obviously the admissions committees felt different.  I still don't know how I snuck in.
I believe the great reputation that a top program has may discourage otherwise qualified students from applying to such a program, precisely because of impostor syndrome and related feelings.  Students gets scared away, thinking they have no chance of getting into a program when in fact they are very qualified.
If you could somehow modify the reputation of your department so that it doesn't seem unachievable to qualified students, I believe you'll get a better applicant pool.  This goes for all top programs, not just yours in particular.

Some suggestions moved from comments (if you have an urge to answer this question in a comment, please write an answer, or edit this answer and add your comment here instead. Comments are not for answers.):

Forgo GRE scores and the like (and make it known). That would have gotten me applying, and it is a huge financial investment. - Davidmh
A summer research program for undergraduates is a good way to build relationships with strong students. Depending on the field, the NSF has funding for this. - user37208
Exchange students with another Universities in different countries/regions might help. - Mikey Mike
If you teach courses, I would recommend showing excerpts of current research papers to your students and spending a bit of time explaining how they could get into research; maybe assign a literature survey for a class assignment in an undergrad course. As an undergrad I wanted to do research but I didn't realize I had access to journals, and I wasn't sure where to start. After a good course I got a taste of what research was like, and it made a big difference in my academic plans. – jrh
Generous scholarships. Pay people to come, and suddenly you need to weed them out and pick the best because there are too much. – Michael

Two suggestions:

Advertise on www.jobs.ac.uk and the academictransfer site in Europe.
Make a list of unis half a notch down from you and write to the professors telling them you are looking for students, should they have students they could recommend.

A less cheap suggestion --
Get funding.  In the UK it is almost unheard of to pay for research based degrees.  The expectation is that university gets the funding and pays itself fees and pays the student a tax-free amount that is quite livable.  In Europe, students are employees of the university and paid quite well.

I'll also give a few perspectives as a former applicant. First of all, a key aspect is the demeanour of faculty and PhD students, as they interact with undergraduates at other institutions. To be more specific:

As an undergrad I went to a few conferences. There I interacted with Professors from a diverse set of departments. Three of them recommended that I should apply to their department's PhD program and that I should e-mail them should I have any questions. I ended up applying to all three of these universities: Two of them I would never have applied at, one because it was relatively lowly ranked and the other because it originally seemed to be out of reach (tier 1).
In a similar spirit, I occasionally interacted with faculty or PhD students from other departments who left a very bad impression to me, e.g. being extremely arrogant. When I had to choose where to submit my applications (given time and money constraints), I avoided such departments.
Online media presence is also very important. I learned about many of the Professors whom I thought I would enjoy working with from their blog posts, online video lectures or even twitter activity. Such online presence really showcases the personality and style of individual faculty members, therefore being very informative. Note that the previous point also applies: Some blog posts I came across were extremely condescending and aggressively criticizing work from other labs. I did not apply to such labs.

Also, as others mentioned, one should  also try to avoid adding artificial barriers to applicants. For example, I applied as an international student and some universities required a certified "conversion" of grades on my degree to the GPA system. I avoided the hassle by not applying there.

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What things can I do as a job market candidate to gauge the internal political culture of a department that is hiring?
I am about to finish my phd and have been frustrated with the toxic politics and culture of my department.
During the job search, what are some specific things I can do to learn about the internal political environment of the hiring department?
I am not talking about their personal political beliefs, but instead the politics of how things are decided in the department, whether people respect each other, whether there are camps fighting for power, etc.
I want to avoid ending up in a department with similar political problems as the one I'm in now.

Related: How can I detect a toxic environment while on the interview circuit?

One measure of the politics within a department is the faculty member's attitude towards collaborations. When I was touring grad schools as a prospective PhD student I remember interviewing with a faculty member. I asked her if she collaborated with other faculty within the department or other departments. She answered dismissively and instead asked me why I was interested in asking such questions and why it mattered whether she was involved in collaborations. If you get such a response, or sense such attitudes, this might imply there is an unhealthy dose of hostility or competition between faculty within the department.

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Can a tenure-track job candidate infer any meaning from the response to an initial contact email?
I'm on the job market for tenure-track positions in mathematics in the US this application cycle. I was advised by various people to contact the people in the institutions that I would really like to go to, so I have just contacted 4-5 top institutions that I am planning to apply to.
In the usual job market desperation, I may try to decipher every word in their response (if they respond at all), so I am curious about if there is anything to be deciphered at all. I'm only a postdoc and I have not had emails of this sort, but I can see myself responding in various ways.
For example, for a complete no-name who has no chance in my school, maybe the kindest thing is just to thank them, ignore them, or just tell them that we're not hiring in their area.
Maybe if it's someone that looks like they have a shot, maybe I'd respond telling them that I'll read their applications carefully, or something along those lines. Or maybe I'll volunteer some extra information such as our intended area of hire (because those generally don't appear in job ads) or actually pass on the email to the hiring committee.
Or, do you just have a canned response that you send out to everyone who contacts you?
All of this is speculation, and I'm intentionally doing this before getting any response back, so that I don't go crazy over the responses.
Does what I say above have any similarities with the reality? Even a glimmer of hope from any of the responses will put my mind at ease, so I am hoping for many anecdotal stories from current/past faculty who have had to deal with emails of this sort, which I am sure they receive plenty of.

I feel we should add to our FAQ "Can X infer any meaning from the way how a response from Y about Z is worded?" - No"

Let me add a comment for your sanity.  Unless you're a superstar in the making (i.e. already have a substantial grant), given the information you have, your chance at any given job is at most 5% and more usually like 1%.  Other than an interview, no information you can get will substantially increase these odds.  You have to apply to lots of jobs and believe that probability works.  (Yes these probabilities are quite independent of each other.)  It's the number of reasonable shots you have that improves your chances, not the probability of any particular shot.

@AlexanderWoo The sane part of me agrees with most of the comments you made (along with the rest of the answers). I just want to say that the definition of a superstar is not equivalent to having a substantial grant. For example, most "superstars" are given an NSF postdoc fellowship, which prohibits them from applying for the actual NSF research grant (which is crazy competitive, and even some of the superstars who received multiple offers were rejected on their first application). I just felt the need to clarify in case other applicants read this and go into a panic attack :)

@xLeitix: or even more generally, "can any information whatever be conveyed by email?" - no, walk over there and talk to them ;-)

Don't stress out about the responses, since it's nearly impossible to get reliable information by reading between the lines.  The variation in how people might respond is enormous, and unless you really know the people involved it's hard to know what it means.  For example, suppose someone sends a friendly, encouraging reply.  Maybe it means you have a real shot at the job.  Maybe it means they think you have a real shot, but they could be totally wrong.  (Sometimes people on hiring committees have unrealistic beliefs about how everything will play out.)  Maybe it's just their personality and has nothing to do with your chances.  Maybe they are deliberately saying the same thing to everyone in order to avoid awkwardness.  If you don't know them pretty well, all you can do is guess.  Of course a standoffish reply is equally difficult to interpret.  The net effect is that you'll get replies that look like they may contain information, but you really won't know what, if anything, they mean.  It's best to resign yourself to this now, rather than spending a lot of time worrying over how to interpret replies and not actually learning anything valuable in the process.

Of course the voice of reason says this! In your personal experience, though, do you respond differently to different candidates?

@BMD I don't know about AM, but I do.  However you don't know how I'm responding to other applicants so you won't know if it's relatively more or less positive.  (That said, I try not to be misleading, but I also try to avoid being discouraging, and I'm sure some people misread my messages.)

@Kimball you're assuming that the applicants don't talk among themselves ;) I remember my last year at graduate school fondly, where things of this sort were all we talked about! But since I finally have some evidence of what I originally asked, do you mind sharing an example of an encouraging response or a negative response?

There is probably a small positive correlation between how encouraging e-mail responses are and how much of a chance you have. But there is also a large amount of random chance, depending on the personality of the responder. It can be maddening, and it is probably useless, to try to extract the signal from the noise.
Usually if you get specific information right away, it will be bad news. In particular, if your research interests are not a good match for whatever the search committee is looking for, you might be told immediately. Otherwise, I wouldn't recommend trying to read too much into the content (or presence or absence of these e-mails).
Good luck on your job search!

Things seem to have played out almost exactly as you predicted. Most people I contacted got back to me very quickly! Some of them told me that they're on the hiring committee (one of them is even the chair), most people told me that my area is one of the targeted areas of hire, and everyone that responded told me that they'll make sure that the hiring committee is aware of my application. All in all, nothing soul-crushing happened.

A few years ago, fresh out of PhD, I was hunting for a university job. I applied to a bunch of universities ranging from world's top to average/below average. I knew I didn't have a faintest chance to get a job at prestigious university, but I really enjoyed reading their responses:

Despite your excellent qualification, we regret to inform you that we
  hired another person, who was more suitable for this position...

Reading that would make me happy. They think I have an "excellent qualification"!
I think 99% of negative responses are standard and professionally tailored to incite positive emotions in spite of bad news. Like firing someone of Friday before Christmas.
All the positive responses I ever received/sent were as dry as they can get, loaded with specific and technical info.
With that being said, job hunting is a tremendously time consuming activity, like a full-time job. Trying to infer something from non-explicitly positive responses seems to be a waste of precious time. If the response seems neutral/unclear and you need to decide whether to agree to another job or not, then you should immediately ask them to clarify their response saying that you have a decision to make.

Don't infer anything from a return email, other than whether you get an invitation for a meeting/interview, or not. That's the first level of "screening" and that's all that can be reasonably done through email. Other than that, an email is no place to get even an "indication" of where you stand. It was sent by one contact person (out of many) who may not even be key decisionmaker.
During and after the interview/meeting, etc., you will probably be placed in one of three categories: 1) a "top" (tenure-track potential) candidate, 2) a marginal "borderline" candidate who will be made an offer with no guarantees, or 3) a non-candidate. Of course the third result is intellectually "easy" (if painful), so you'll want to distinguish between the first two. But the time to do that is after the interview.


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Masters Thesis: Self-containment
So I am currently writing my thesis in nanophysics (in particular, applications of nanomagnetism). My adviser and I had a few discussions about the inclusiveness (i.e., self-containment) of the material, quality of figures, etc. He does not seem to care about neither of these points, and just wants the thesis to be done so that 'I carry on with my research'...
I am now wondering:

Is it typical (or preferred) for the masters thesis to be rigor/self-contained, in terms of literature review? (I said masters only, because I assume it should typically be the case for a PhD dissertation - no?)

There is no such thing as a self-contained math exposition, unless you go all the way back to the axioms. When we write a proof, we always have a target readership in mind. We stop adding details at the point where the average reader would be completely convinced and could easily fill in the gaps. This holds true whether you are writing an article or a textbook; only the target audience changes. Writing proofs is human-to-human interaction; you ultimately have to convince your readers of the correctness of your assertions.

(writing proofs is human-to-human interaction -- and, probably, the only successful human interaction that we mathematicians are able of.) :p

The best advice I heard about this is: Write the thesis in the way you would like to have had it at hand when you started your thesis. Imagine yourself in a situation that you are a master's student and want to learn about the very topic of your actual thesis. What detail do you need? What background should you give? What literature should you refer to?
I often hear students say that their advisors do not really care about these issues, and indeed it's somehow true. As an advisor, you care much more about the content. This does not mean that the presentation does not matter, but it is not that much about what background you give, but how. Do you treat simple things at length but brush over more difficult things without proper reference? Do you provide proofs for standard facts but use advanced concepts without any argument?


text:
Is it okay to include a very long appendix (for MS thesis)?
I am currently doing my MS thesis and I have to include an appendix to describe a mathematical subject. However, I added extra details in that appendix and it is now too long.
My Prof. suggests I better not include it "at all", or if necessary just make it shorter (though he admits that it is very well written and referenced).
Is it unusual to include a very long appendix in a thesis?

My thesis is now 150 Pages; 20 pages are for that appendix.

This is probably not unusual, but extrapolating from my own behavior: the longer it is the less likely i read it (it is an appendix after all ..)

The only part of your situation that seems odd to me is an advisor recommending you remove 20 pages of well written math. That I cannot understand.

Just wait 'til you see a literature paper that includes a transcription ;-)  If the source text is long enough, the appendix can be several times longer than the thesis/dissertation itself.  But the big question is how necessary is it for people in the field to understand your work.  He might think it's not necessary.  If you really think it important, argue for it to go in the body (and maybe he'll settle for an appendix).

20 pages appendix on a 150 page thesis is not long at all.  150 page appendix on a 20 page thesis, now that would be long.  That's the ratio I've seen for some scientific proposals, where the format of the core proposal is so rigid that essentially all scientific information is in the appendices.

This does not sound unusual to me. Just ask yourself, is there a possibility that the reader would need this?
I have seen theses and dissertations with no appendices and some with over 50 pages of appendices. In my field, these are often filled with user study materials, source code, or raw data which can easily eat up many pages.
I don't see any harm done with being conservative and including everything. In this case, I have seen people list two versions of their thesis online, one with and one without the appendices.

Agreed: 20 pages on a 150 page thesis is quite a reasonable size.

From my knowledge, it is unusual, but you are missing the most important question: is everything you put there absolutely needed for any other person to understand the value of your work?And does removing any part of it decrease the value of your thesis? Try to see your thesis as an impartial, but knowledgeable person. If you answer these two questions, you will know what do do!
Edit: The number of pages of your appendix compared to your thesis is not much important. But I would like to let you know that my MSc thesis has 200 pages of which 50-60 are from several appendix
I hope I have helped you!
Thanks,
KingBaboon


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Do we have a citation ethics in science?
Citations matter! Everybody knows this and Google Scholar (or Publish or Perish) shows it. Over the last years, I met people with different citation "ethics": Supervisors and professors require students to cite their own papers, even if they don't really relate or if there is a paper which would be more appropriate to cite. Journal reviewers nicely recommend accepting the paper for publication if only more two or three references (paper from the reviewer) are included. And even when an author cites a paper, there is often the question if the "idea" is cited or a specific "result" etc. E.g. there is a study showing that wrong citations are often inherited in papers that cite the misspelled citation, which indicates that the author didn't really read or access the paper and cites it only because of its general reputation. Similar to the IEEE Code of Ethics or ACM Code of Ethics, is there any Citation Code of Ethics?

Welcome to Academia.SE! As currently written, this reads somewhat like a rant, but there's a good question hidden in here. You may find that the question will be better received and you'll get better answers if you make it more objective and simply ask the question directly.

Citations have only one practical purpose: indicating to your readers where they can find the published material on which you built the work that's described in your paper (methods you used, hypotheses that your work support or contradict, etc.).
Everything else is just more noise in an already too noisy signal.
Citations should not be used to show deference to senior researchers, to increase citation metrics of a person's supervisor, nor to "grease the palms" of reviewers or falsely infer relevance to a given journal. Please refrain from doing such things, they hurt science.

I certainly agree with this, but I think the OP is asking if there are tools for preventing this from happening (rather than whether they should). And sadly, there's no denying that it's extremely common place.

@CliffAB Yes, I would be interested in tools or measures, or ways to report it.


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The third letter of recommendation. Which one could strengthen my PhD application?
I will apply for the PhD GRA in the USA. It is focused on politics of my native country. Since graduating the university, I've been working in journalism and dealing with the same isssues. Does it make sense to get recommendation from my employer to prove my deep understanding of local specialities, if the first two answers are from academic community? As a third one I could also provide a strong recommendation letter from the foreign professor, whom I had met at the graduate conference. Then I assisted him for a short-term evaluation project (not academic one) in my own country (arranged interviews, organized travels etc) and did an interview with him as a journalist. Could this letter be better evaluated by admission committee?

I think both options are good. Personally, I'd slightly prefer the recommendation from your current employer, as they should be in a position to comment on a few things relevant to academia: that you write well, work independently, have initiative in solving problems, and good interpersonal skills.


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How to write publishable-quality math and science papers?
I've learned it a bit, through a thesis paper (not PhD-level), and from reading good papers in good journals.  But I'm interested in best practices, specifically the things to implement in my style of writing to get my work up to publishable quality (assuming that the content is good enough)?
Answers which summarize tips from available, useful resources are welcome.

I'm VTC as off-topic because it is (IMO) a shopping question, but I like the premise of the question and wish it didn't have to be off-topic.

OP: I edited your question so that it may be a better fit for this site. Please, check to make sure I have maintained the spirit of your question. If you don't like the edits, you can always revert back to the previous version, or you can further edit the question.

@MadJack I don't think your edit really changes anything about the question. It's still either a "gimme a long list of resources" or "write me a whole book's worth of answer" question and that's still not a good fit for the Stack Exchange format.

Two good primers specifically on the subject of mathematics, which is quite different from more empirical sciences in many of its conventions:

Paul Halmos’s How to write mathematics is a classic — still excellent, if slightly old-fashioned in some ways.
Terence Tao’s blog post On writing collects and summarises links to some excellent advice from himself and others.

A short but excellent reference is from the George Whitesides group at Harvard which is available in the public domain.
It goes from outline to draft to finished paper in a few informative pages.

I like the general ideas there, but as the OP specified math (and science) I need to point out that a lot of the advice there is actively poor for someone writing a paper in math, at least without someone to point out the ways in which it needs to be different.

Donald Erwin Knuth, Tracy Larrabee, and Paul Morris Adrian Roberts,
Mathematical Writing
Jerzy Trzeciak, Mathematical English Usage Dictionary, 2016
Jerzy Trzeciak, Writing Mathematical Papers in English - A Practical Guide, 2005
Three mistakes that people should stop making? 1. Worrying too much about formatting and not enough about content. 2. Worrying too much about formatting and not enough about content. 3. Worrying too much about formatting and not enough about content. (Source: Leslie Lamport, How (La)TeX changed the face of Mathematics.)

Steven G. Krantz's A Primer of Mathematical Writing, Second Edition is freely available on arxiv.


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First-authorship was taken by my Master's supervisor; how to strengthen my PhD application?
I have two papers in CS published during my Master's studies. The idea, the experiments and the writings were done all by myself, but my previous supervisor took the first-author place forcibly.
I am planning on applying to US PhD programs. My questions:

Generally speaking, will these publications still carry the same
  weight as if I were rightly listed as the first author?
Are there any general strategies I can use to maximize the impact that
  these publications will have on my acceptance?

@PeteL.Clark: I assume the OP is talking about PhD applications and has just mixed up the (admittedly complicated) distinction between the words college and university.  But clarification would be nice.

@PeteL.Clark Imperial College London is one of the top institutions to offer PhD programs.

@qsp: And in the US we have Dartmouth College.  But Pete is correct that in US English, the generic noun "college" usually refers to undergraduate institutions, or the undergraduate programs of a university.  I think that's clearly not what the OP means, however - probably just a simple language confusion.

@PeteL.Clark I mean the university admission... perhaps my poor English should be my primary obstacle :)

@PJ.Hades Please edit your question to clarify: Do you mean admission as an undergraduate or admission as a PhD student?

I have made some edits to the question with the hope that it will help the question be reopened. Please make sure that the edits maintain the spirit of your original question. If you don't like the edits, you can always rollback to an earlier version, or make additional edits.

(I assume here that you're talking about admission to PhD programs.)
I'm not in computer science, so I can't speak with authority.  We have a number of users here who are in US computer science departments and maybe one of them can step in.
However, I would think that first-author publications would not be essential for admission to good PhD programs in the US.  Keep in mind that in the US system, most students would enter a PhD program immediately after their undergraduate (bachelor's) degree, without doing a masters first.  These students would not necessarily have any publications at all.  The admission committee would expect somewhat more from a student with a masters, but I'd think any publications, first-author or not, would be a pretty good sign of your research ability and preparation to start a PhD.
Another thing to note is that recommendation letters are very important for admission to US PhD programs.  If your advisor writes you a letter which speaks highly of the work you did, that should help your application a lot.

Just cite them as they are, and let them stand. You can point out that "the following [1,2,3,4] resulted from my thesis...". Going out of your way to emphasize it was your work, and you should have been first author, or whatever, will just come across as petty.
[But then again, it is said university politics are so vicious because so little is at stake...]


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Should I mention in my personal statement that my poor performance in mathematics courses was due to the course delivery not being effective for me?
I have finished three years undergraduate course in maths in the UK and I am applying to do an MSc in maths.
The academic year was 26 weeks long and split into 2 semesters of equal length.
we had exams at the end of each semester.This is fine but in each module, we were also given one, in some cases 2, assignments from each module. This meant that we were being examined every 3 weeks.
I think that this is wrong and that when studying maths, people should be given the opportunity to learn at their own pace and that the onslaught of assignments does not help. I feel I could have done so much better with just having the single exams at the end of the semester because it takes me so long to get my head around mathematical concepts.
My question:

If I state this on my personal statement, would it work in my favour,
  or would it make me look really stupid, slow and someone who is
  disorganized?

Looking at the majority of courses for masters, they only have a single exam which should work in my favour.

"I think that this is wrong and that when studying maths, people should be given the opportunity to learn at their own pace and that the onslaught of assignments does not help". Personal opinions about how any subject should be taught are irrelevant to anyone else but you. Why do you expect that stating such an opinion would work in your favor?

" I feel I could have done so much better with just having the single exams at the end of the semester because it takes me so long to get my head around mathematical concepts." - you may want to consider relocating elsewhere. For instance, this is exactly the system I found in France (in 1999, things may have changed since then). I couldn't deal with it at all.

@StephanKolassa: yes, it's the same system we have in Italy: no homework (I give homework to my students but is optional and doesn't count for the exam) and just one final exam. It worked perfectly for me, I wouldn't have liked the "continuous" grading system.

Hmm, but what percentage do these module assignments count for?  In my experience they only count for a small amount e.g. %10-15, and the majority comes from the end of module exam.  The assignment questions are rehashed from the exercise sheets.  They are just to motivate you to spend a few hours with the exercises.  To be honest you might come across as making excuses.

Also I think that even MSc courses are starting to involve regular assessment, are you sure about "the majority of courses for masters [...] only have a single exam" ?

[Note:  I'm coming at this question as a professor in the American university system.  As such, there may be a few implicit assumptions below that don't quite apply to the UK system, for which I apologize in advance.]
The short answer is no;  putting something like this on your personal statement (at least the way you're framing it above) is likely to hurt you more than it will help you.  First, it cannot help but sound like a rationalization for poor performance;  you're essentially saying, "I got a D, but I'm sure if the course had been taught correctly I would have gotten an A."  The problem with a statement like this is that it's your word about a hypothetical course versus the actual grade that you earned in the real-live course.  An admissions committee is going to weigh the latter much, much more than the former.  Also, the way you're phrasing it could be read a moral judgment that you really don't want to be proclaiming in a statement like this.  (i.e., this method is "wrong", and it "should be done" a different way.)
The best way (in my opinion) to address poor grades in undergraduate courses is to frame them as learning experiences.  What did you learn about the way you work?  If you had to take the exact same course over again, what would you do differently?  What you want to do is to take responsibility for your failures, show self-awareness about your weaknesses, and demonstrate that you know how to work around them in tough situations.  These things are all signs of maturity, whereas a statement that effectively says "it wasn't my fault" is a bit lacking in that department.

Couldn't resist adding a relevant quote: "A man may fall many times, but he isn't a failure until he says somebody pushed him".


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Can a systematic review only review one article?
I got asked to review a systematic review in a peer-reviewed Pubmed-indexed journal. However, based on the author’s inclusion/exclusion criteria, they only review one article.
Isn't that peculiar? As a reviewer, how should I respond to this? Is this acceptable, only one article...?

What does it mean to review a review?

I'm not in a discipline where the concept of systematic reviews applies, so I'm willing to leave some room for doubt, but honestly... let's call a spade a spade here: a systematic review of only one review is simply absurd and it's hard to imagine how it can contribute meaningfully to scientific knowledge. So no, it is almost certainly not acceptable.

If it’s a systematic review, it is weird that there is only one article to include. However I think it could happen. After having applied inclusion criteria to all articles first retrieved, only one was left. I also think there’s a lesson out of this issue that the authors of the review should address.

Is it peculiar? Yes. How should you respond? Ask yourself if the "review" of only one paper adds anything meaningful to the literature on the subject. Perhaps the answer is 'yes' -- e.g. if the authors make a strong case that the subject is very under-explored, such that only one paper on it exists though many important questions exist to be answered. Or perhaps the answer is 'no.'

I think it depends very much on the exclusion criteria, and what the authors make of the single paper. For example, if it's just a review of that paper...it might not be particularly useful. However, many systematic reviews discuss the literature in the context of the field as a whole - is it surprising that this field only has one paper when a given exclusion criteria is applied? Is it possible the field is accidentally ignoring something because it's similar to something else?

If there are a considerable amount of other works which were excluded using the criteria, resulting in one included work, then I would expect a justification for the exclusion criteria (perhaps it was too extreme?).
If there are not a lot of other works in this field, I would expect a justification of why the authors conducted a systematic review in this particular field (as hinted by @Raghu Parthasarathy).
In any case, I would expect the author to clearly acknowledge and explain this odd situation somewhere in the paper.


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Can a graduate school dean prevent you from attending a class?
One of my professors is bullying me, so I filed a complaint with the Dean of the graduate school.  He said, "While the investigation is in progress, you are not to attend class."  He said that I was still responsible for passing the class and completing all assignments and taking all exams, but to not attend the class.  I have a midterm in a week and this week, the study guide is being handed out.  How I am suppose to pass this class?  If I fail, I will lose all of my financial aid and will not be able to continue my education.  I do not know what to do.  The Dean also told me not to discuss my situation with anyone except him and he meant that I cannot even discuss this situation with family and friends and not to have any contact with the professor, including email contact.  So, how do I turn in my papers?
Update: I had a friend go to class to pick up the study guide and the professor had absolutely no idea why I was not attending class. In other words, the Dean never spoke with him.

I don't necessarily recommend this, but you may want to review what your options are for withdrawing for the course (at my university, it still shows up on your transcript as a "withdrawal", but it does not impact your GPA or, generally, your financial aid). Beyond that, does your university have an ombudsperson you can go to seek advice?

Have you talked to the Dean of the department?

As a temporary measure, can you ask a classmate to share notes with you?

Check the complaints procedure policy, and talk to your student union. It seems to me highly unlikely that you would be forced into complete confidentiality on spoken basis alone, and be barred from classes, given you are in the US. A complaints procedure should not treat the one complaining as the problem, at least until it is shown to be a malicious complaint (and to some extent not even then).

I take it that the class you can't take is given by the professor in question? Were any constraints made on the professor? It seems incredibly unfair that the person who has made the complaint is treated in such a manner, this action would not encourage others to make complaints about staff.

Sure sounds like the Dean is not acting in your best interest.   For sure he cannot order you not to talk about this.  He is setting you up to fail the class.  If he had been proactive about getting you notes and study guide and hand the test into the Dean then maybe I could go along.  He is trowing you under the bus.

No matter what else you do, document everything. At a minimum, get the Dean's directive in writing/email, and write up notes of all your interactions that you can remember.

Depends on the administrative structure, but academic complaints are handled by the dept chairs/deans/provost and other issues are handled by "student affairs".   Check your institution's policies and procedures docs, they probably outline who to contact for whatever issue and what your responsibilities, etc. are.  Could be you've complained to the wrong person.

I wouldn't jump all the way to @Paparazzi's conclusion that you're being thrown under the bus, but given a Dean's responsibilities, a Dean won't necessarily act entirely in your best interest as they have other concerns. You definitely want to talk to someone who is unequivocally in a position to fight your corner and the Dean should not prohibit you from doing so.

If you do take @tonysdg's advice to withdraw from the class, be sure that the reduced course load will not change you from being a "full-time" to "part-time" student;  or if it does, that it will not affect your financial aid.  Your institution's financial aid office should be able to answer this question without knowing the details of why you're withdrawing.

@tonysdg As another pointed out, withdrawing from a course may transition one into part-time status and thus cause one to lose financial aid.  I once took an F in a course because withdrawing would have put me below 12 hours and I couldn't afford to pay back the semester's loans as I would have been required to do.  At my university there was a point in the semester before which a withdrawal would simply erase the course from your transcript (and drop one's enrollment hours), but after which it would be treated the same as an F toward GPA.

I thought getting an F affected financial aid too?

Having gone through something like this too, I can only advise that university officials take advantage of the fact that students don't know their rights and bully them into acting against their best interest.  Be informed.  If they tell you to do or not to do something, ask why and what the penalty is for disobeying.  You'll be surprised how often the answer is "Nothing".

Is the secrecy limited to the filed complaint, or did he specifically demand secrecy regarding everything, like not attending, needing notes and assignments, etc.?

It applied to everything.  He even told me not to seek help or discuss this with a third party.

@Shoshana: This is raising so many red flags for me it's not even funny. >95% chance you're being set up to get screwed over big time. Whether or not you should attend class depends on the particulars of your situation, but whether you can talk about it is not under question --
you have no confidentiality agreement with anybody. Do NOT fall for this nonsense.

The answer to the title question is, unfortunately, that the Dean of your graduate school is in a much better position to know whether he can prevent you from attending class than we are: we don't know what the school is, and we don't know any of the details of what sounds like an ugly situation.  This is not the sort of question that you can rely on the internet to answer.
Having said that, given only what you've said, the Dean's directive sounds outrageous.  A student's right to attend class should only be forfeited by serious negative behavior on the part of the student.  Reporting negative behavior of the instructor should not remotely qualify.  Moreover, a student who may not attend class should be withdrawn from the course...because the alternative does not make much sense.  In this case, if your withdrawal is necessary then you should be excused of any negative consequences of it.
I am at a loss to make any specific recommendations to you.  Frankly, as you depict it the Dean's behavior is so outrageous that I have to wonder about the further details of your story, including the nature of the bullying, but a sufficiently full accounting of your story would involve divulging too much personal information on the internet, so I am not fishing for more information here.  On the off chance that the Dean is simply behaving very strangely, it could not hurt to follow up with other university officials: e.g. your own academic advisor, an ombudsperson, the human resources department and/or the registrar.
Finally, 99% of the time, using the American legal system to resolve academic disputes is the wrong thing to do.  But (depending in part on the nature of the bullying) your case might be in the 1%.  Your issue -- namely that your institution is handling your allegations of interpersonal workplace misconduct in a way that seems inappropriately punitive to you -- is not an inherently academic one.  So you might look into exploring that further.
Good luck.
Added: @tonysdg's comment of looking into withdrawal is a good one.  I wouldn't only do this, but if withdrawing from the course saves you from failing and losing your financial aid, then it would give you some breathing room at least.

I agree if the student cannot attend class then they should be withdrawn from the class.  But an harassment compliant should not trigger that.  Good answer.

If the student's course load were to go below 12 credits, the financial aid is in jeopardy.  (I don't know if that would be the case here.)

First, I think it would be helpful to get to the bottom of why the dean is behaving this way.
One theory I can think of is that the dean may be intentionally putting obstacles in your path, perhaps hoping that you will drop the complaint and save him the headache of dealing with it. Perhaps he doesn’t believe your complaint, or is friends with the professor and wants to believe your complaint is false or exaggerated, or simply thinks protecting his institution’s interests requires him to automatically defend any faculty member and make life difficult for any student complaining against them.
Alternatively, he may be worried that the situation is so delicate that any interaction between you and the professor is risky and could lead to bad things happening to you, which would lead to more trouble for his institution, so such interaction must be avoided at all costs, and the only way to avoid it (other than removing the professor from teaching to class, which he may not feel comfortable/allowed to do while the accusations are still being investigated) is to instruct you not to attend class.
The first scenario, where the dean is actively opposing you out of spite or bad faith, is more problematic than the second, where his intentions may be decent but he has simply made a bad call. (Actually the decision to separate you from the professor may not be terrible given the situation, but he hasn’t thought out the implications of you not attending class - it is essential that he provide you with a way to mitigate the harm this would do to your studies.) But in any case I assume you have better insight into the dean’s motivations based on your interactions with him.
So what should you do? You need someone who knows the system and its rules and can advocate for you. Normally I would recommend going to someone from the administration, but here it’s the administration that is mistreating you. Fortunately, many institutions have third party groups and resources protecting students’ interests and/or offering impartial advice. Two I can think of are:

the university ombuds office/person
the student union

My suggestion is to go talk to one or both of those, tell them the details of the situation and ask for help.
The bottom line is that being told to successfully complete a class under a professor who is bullying you without being allowed to attend class does not sound to me like a reasonable or acceptable way to address a complaint by a student, so you are quite right to be concerned. Good luck!

An ombudsman shouldn't be protecting anyone's interests--they're supposed to be neutral. If the school has an ombudsman, they might be useful as intermediaries or to suggest ways to navigate the situation, but I don't think this student should discuss anything further with the school, directly or indirectly, without counsel. You can bet that the dean has consulted with the university's lawyers.

@Shoshana Preventing you from attending a required class you've paid for is arguably already retaliatory. Do you trust that they are acting in good faith or do you think they are planning to get rid of you as a problem? If it's the second, check your state's bar association website--there should be a directory there and many states have free or low-cost consultations. It takes time and effort to find a lawyer, so don't wait if you want to go that route.

@Elizabeth while getting legal representation is an option to consider and may be appropriate at some point, most conflicts students get into with their universities (including this one, in my opinion) don’t warrant doing that as a first resort. Can you explain why you think OP should hasten so much to get a lawyer before trying other options?

@Elizabeth you are correct about the ombuds office, thanks. Edited to clarify.

@Dan Grad students are already extremely vulnerable and (especially in light of the most recent edit) it looks to me like the dean has no intention of protecting the OP's interests against the university's. Better to get advice about protecting oneself early before the damage is done.

"First, I think it would be helpful to get to the bottom of why the dean is behaving this way." Well, yes, it would be, but...as a tenured faculty member, rarely am I confident that I've "gotten to the bottom" of why the higher administration behaves as they do.  To expect a student to be able to do this without substantial assistance seems rather unrealistic to me.

@Dan I'm wondering, completely nonrhetorically, why you think this situation is likely to have a positive outcome for the OP if left up to the dean?

@PeteL.Clark to clarify, that was just the introduction to my answer. I didn’t mean to suggest that OP should literally start by going on some sort of quest to understand the dean’s motivation, rather I was simply stating that it’s a useful thing to think about and discuss, as I did in the subsequent part of my answer.

@ElizabethHenning where in my answer do I give the impression that I’m suggesting “leaving things up to the dean”? I said no such thing. Quite the contrary: I advised OP to seek help and advice from allies who would be positioned to help her get assistance, in particular to address and hopefully mitigate the dean’s (apparently) hostile behavior. I did not propose getting a lawyer (personally I think that would be premature at this point), but neither did I advocate doing nothing.

OK, I should have said "university" instead of "dean."

@Shoshana I wish you the best of luck and sincerely hope that you can resolve your current difficulties. Unfortunately I see no foolproof recipe for you to overcome the hostility from your professor and dean. Hopefully the steps that I and others have suggested might prove of some use in this difficult situation.

@Shoshana While it certainly seems like the administration is not behaving in a way that is proper, you really do need to consider more carefully what is reasonable. Finding a new professor to teach a course based on a complaint that is still being investigated would not remotely be reasonable. And once a formal case has been initiated, it is quite common and reasonable to require the involved parties to not discuss the case with outsiders.

Talk to your parents and to your friends immediately. At the very least, you'll need a witness on your side the next time you speak with the dean. Of course, if you're afraid your parents or your friends would trigger a confrontation with the professor or if you're afraid that they'll make things worse, then choose appropriately. That being said, if you trust your family and friends, tell all of them. If someone in your family refers you a good lawyer, that's even better. If the dean is upset when you bring a family member/friend, or your own lawyer. Don't worry about it. If he's upset about that, he's definitely going to be super upset when he finds out that you're not going to back down and not make things convenient for him.
If you can't find a good lawyer through your family and friends network. Go to the nearest law library, do a Lexis-Nexus search on lawsuits against your University, against your particular school/department, and against you particular Professor or dean. If a law library with free Lexis-Nexus access is too far, just do a google search and look for news stories that reference lawsuits related to your school. Then, contact those lawyers that have sued your school. However, if this takes too long, or if you don't find a good lawyer that way, you can always go to the default step 3.
Call your local state bar association and ask for a referral. They should be able to tell you what kind of lawyer you need (I assume you'll need a lawyer that specializes in religious discrimination, but I could be wrong. I'm just a layman myself, I am not a lawyer). The first 30 minutes of a consultation are free. Do not get a lawyer who has graduated from your current university. Some alumni have strong social ties with their school. I know this is silly, but it's probably best to avoid alumni from your University, or avoid lawyers that have too many potential ties with your professor or your dean, whether academic ties or religious. Of course, if they've graduated from the same university and also sued their alma mater repeatedly, then that should be fine.

That being said, once you find a good lawyer who's not afraid to sue the school. His first instinct should not be to sue. His first instinct should be to call the dean and to find an amicable resolution to your problems.
Also, you may need to offer the deal to the dean that you'll never again contradict or correct publicly (or even privately) that professor if you can come to an agreement that guarantees that you will be treated with cordial indifference during class and treated fairly during exams and assignments, or that guarantees at least that your financial aid doesn't get affected by not having enough letter-graded units for the current term.
And by treated fairly during exams and assignments, I mean that another professor should take over the responsibility for grading your own assignments and exams. And that the original professor shouldn't try to introduce religious translations into his assignments and exam questions as a final way of getting back at you.
And finally, you should look at review sites for lecturers and find out if this professor or the dean have done anything similar to other students. Plus, you should put out feelers to your school friends to see if they might know someone who knows someone who was also mistreated by those two people.
Just keep this off from social media. If a social media campaign is needed, let your legal counsel decide if/when it's necessary and let him supervise it himself.

Go to the nearest law library, do a Lexis-Nexus search on lawsuits against your University, against your particular school/department, and against you particular Professor or Dean. This is good advice, but most law libraries not at state schools are not open to the public. However, the state and federal courthouses should have publicly accessible databases of cases.

My best guess given the very limited information that you've provided is that the dean is trying to CYA by preventing any contact between you and the professor to forestall any possibility that you might be able to file a retaliation lawsuit. You could go to the provost, but if this is the way things are done there it probably won't be much help.
Unless there's more information you've omittted, this sounds like a very hostile situation and they are on the defensive. Document absolutely every interaction with these people and get legal advice from someone who specializes in higher ed law before doing anything else. And do whatever you can to stay in good academic standing--that is the first thing hostile departments attack because it's very difficult for students to fight it.

CYA = cover your ass? cover his ass? something else?

Strictly talking, yes, a school can (and must) forbid access to an student in some very concrete situations: the student has a contagious illness; the student is making violent and public actions that prevents the normal behavior of the class; ... .
However, you say the ban has been triggered by a bullying complain from you. This is far, very far, from previous scenarios. You are the possible victim of a bad behavior from teacher, you can not be punished in any way.
Moreover, the ban to talk with any one is absolutely illegal. You have the right to talk with anyone, the right to find the best advice, etc.

What do your university's policy and procedures say?  They should be available online.  Unless they call for this, the dean's instructions smack of retaliation.
Retaliation is hard to prove.  I suggest a follow-up email to the dean. Here is some starting point text (even if you choose to follow this suggested strategy, you'd of course need to edit and make it your own):

Thank you very much for meeting with me yesterday.  I want to make sure I understood your instructions.  I was a bit nervous during our appointment and I'm not sure I took everything in properly.
When you said I should stop going to class, were you giving me that as a suggestion?  Or is that a required part of the grievance process?  Can you send me a copy of the university's grievance policy and procedures, so I can understand the process better?
I feel confused about the attendance part.  I want to do as well as I can in this class, and I feel that attending class is crucial for optimal learning.
If you're saying I must stop attending, then I'll need instructions on how to turn in homework and a delayed exam.  Also, I'll need an Incomplete, because the end of the semester is only x days away, and I'll have to do extra work on my own to make up for the missed classes.

Question: do you feel that the bullying was discriminatory?  In other words, do you think the professor singled you out because of something like  race, sex, color, religion, age, disability, protected veteran status, national or ethnic origin, sexual orientation, gender identity or expression, etc.?  And if your answer is yes, then comes a question that's at least as important: Do you have any convincing evidence?  If so, the route you chose might not be the optimal route; you might want to follow the university's civil rights grievance procedure instead.  (I strongly advise you to read your university's online documents about grievances of both types.  Do ask questions here and on campus if there are parts you don't understand.)
IMPORTANT
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How often are lectureship positions just for one year?
I am an adjunct instructor in English. I do not have a PhD and don't actually want one. What I really want is a full-time lectureship that would offer job stability. However, I was recently told that they are often offered for one year and then not offered the next year. I want to know if that is how things typically go, or if some full-time lectureships are renewed after the first year. A local public university offers full-time positions that come with tenure-like benefits after five years at the institution. What are the odds they will keep me around for four years and then not renew me so that they don't have to offer the job protection?
(Edit: This is the US, NYC to be exact.)

Which country are you talking about?

In the US, the way a university will look at full time lecturers may vary a lot, even between departments. Ask other lecturers how renewable the position is. It may be a set one or two year gig, and it may be effectively permanent so long as enrollment numbers are mostly consistent. At my university, after ten years, a lecturer becomes a senior lecturer and gets contracts of three years rather than one. I don't know of anyone being let go of right before the tenth year. Yay anecdata

We can't know what your university's plan is for you, but you can find out how long the other lecturers in the department you are considering have been there.
As a general rule (assuming that you are in the United States), lecturer positions at large universities are intended to be long term simply because (i) they are cheaper than tenure track faculty, (ii) the need to teach large introductory classes will not go away any time soon. Universities are not well served by having a revolving door for lecturers because a long-term employee carries a lot of experience that is necessary to be a successful teacher.

Although lecturers tend to hang around for a long time, and departments like to keep experienced lecturers around, there is usually no formal assurance of continued employment from year to year, even if the lecturer has been doing a good job.  If and when budget cuts force layoffs, "permanent" lecturers will typically be laid off after aprt time adjuncts but before tenured/tenure track faculty.

@BrianBorchers True, but I feel we academics are sometimes a bit hung up on tenure. Yes, not knowing 100% for sure that your job will exist in a year is worse than having tenure, but still equal or better job security than most regular jobs.

Correct. We promise our lectures one year's notice if they were to be laid off, and that increases to two years after a while (3 or 4 years) in the department. For all purposes, we treat them as permanents. I can only imagine that this is the case for all major universities.


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How to find a math conference accepting papers?
I have written a short math paper which may be suitable for a conference proceeding. However, I don't know how to find an appropriate (mathematical) conference  which accepting papers. Is there any suggestions?
Besides, do I have to actually attend the conference in order to make the paper accepted?
Thank you very much!

You will find that very few math conferences even publish proceedings, and as such, they do not accept papers but talks. In math (at least theoretical math), publishing is done in journals (and on arXiv. Remember to put the paper on arXiv).

The generic answer is ask your supervisor or colleagues. Your peers are the ones knowing which venues are appropriate or not.

In mathematics, you're very unlikely to find such a conference.  There are a few (the only one that springs to mind is FPSAC).  There are sometimes proceedings based on conferences, but typically those articles are solicited after the conference from the invited speakers.  The idea of taking submissions of papers before conferences and then judging whether they are appropriate for presentation at the conference is pretty foreign to mathematicians, and publishing in conference proceedings is much lower in prestige than in journals.
Thus, I recommend you submit to a journal instead.


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Can I publish research as "working paper" after journal submission?
I am aware that (at least in the field of economics) typically one first publishes their research as a working paper and later on submits to journals. (Where "later on" could be as short as the same day.)
In our case it so happened that a deadline was tight, and we have now submitted the article to a journal first. While we are waiting for a response from the journal, can we proceed to further prepare and publish our work as a working paper or would such a thing only be appropriate after learning of a negative response from the journal (i.e. only after our paper is no longer considered there)?

Downvoter, care to explain?

Most journal publishers have policies allowing you to release the manuscript that you have submitted to the journal (usually called the pre-print because it is pre-peer review) as long as you meet some requirements. Requirements vary by publisher, but commonly include only being able to put your manuscript on certain web sites and having to add a note to the manuscript saying it has been submitted to that journal.
You can find the policy that applies to the journal you've submitted to by searching for 'pre print policy' or similar on their website. You could also look at a website such as Sherpa Romeo, which act as a searchable database of different journals' policies.

That is of great help, thanks! While I was unable to find pre-print policies by searching, Sherpa Romeo did help. I will wait a bit more to see whether an answer specific to the field of economics comes along, nonetheless I am very keen to accept this answer for its general applicability.

Did you get any econ-specific answers? If not, would it be possible to accept this answer?


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Is it advisable to underline some key points in a statement of purpose?
I am an undergraduate student applying to grad schools this year.
I was recently told by my friend (who is already in a PhD program now) that I should consider underlining some key sentences in my SoP, and put them in bold font, since the admission committee most likely won't have the time to read every whole statement, and this would be a good way to catch their eyes on the key points I want to express. It can also expedite the reviewing process so in this sense it is also helpful to the admission committee.
I think this makes sense, but I am still a bit hesitant since I'm not sure if this would be viewed as a poor writing style. Would this be welcomed from the viewpoint of an admission committee?

Is there a word limit on your statement? If so, what is the limit?

@Nicholas Some does not mention the limit explicitly, but most others put it at around 1000 words.

Underlined and bold?  I think you should reconsider your friendship.

If it's your opinion that your readers won't have time to read your whole document, you might want to consider adding an executive summary at the top of your document. This would take the form of a short paragraph which essentially includes all the key phrases or sentences that you would otherwise have highlighted in bold font throughout your document.
If you make your summary pithy, punchy and exciting, you are more likely to entice your reader to read through the remainder of the document.
One might indeed say that highlighting key phrases throughout your summary is a touch lazy. I wrote a similar document and went through and highlighted key phrases, just as you are considering. Then I wrote an executive summary section as the first paragraph, reusing or paraphrasing the key points.  I removed the text formatting in the main text body, rewriting the phrases relating to the key points given in the summary to avoid repeating them word for word. To my mind, the result looked more professional and read much better.

Thank you Nicolas. My supervisor also advised me against underlining sentences, so I think your solution is the one I should go for.

No.  Never underline anything.  Underlining is left over from typewriters.  It instructs the typesetter to put things in italics.  Nowadays, you should put things in italics yourself.

I didn't know that underlining was supposed to indicate italicization. Interesting!


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Is research experience in a different field relevant for PhD application?
I am a economics major undergraduate student who will apply for grad schools in the coming semester. I think I have quite a strong research experience in mathematical statistics (asymptotic statistics to be specific), but, unfortunately, not much in economics itself. So I am curious if economics departments in graduate schools will care about my research experience in statistics?
Maybe a broader question is if grad schools care about applicants' research experience in a different (maybe even unrelated) field at all? I guess in my case statistics and economics are still quite correlated, but what about other more distant combinations of target departments and previous research experience?

While field-specific research experience is always the best kind, I think there is a role for good research experience in any related field. Close-by disciplines that share similar research methods and approaches will carry much more weight than something much further removed. (For instance, as a chemical engineer, I wouldn't put much stock in somebody doing sociology or clinical medical research, but somebody who had a background in research in applied mathematics or mechanical engineering would be potentially of interest.)
So, if you're going to go into an area of economics where your mathematical statistics background will be of benefit, I think that will (or at least should) be viewed favorably by an admissions committee.
That said, you will want to make sure that your research supervisor understands that you're applying to economics programs, and tailors her letter of recommendation accordingly. Also, if you have a lot of experience in a different field, you will need to make clear to the admissions committee why it is you want to pursue the new field.

A graduate program in any research field considers a variety of criteria for each applicant. The contents of a good application to graduate school have been addressed here before.
Most admissions committees look at several criteria, which are often weighted, but none weighted so high as to dominate the whole decision. A strong showing in one category can offset a weaker showing in another. Among them are:

Basic knowledge of the field: You demonstrate this by completing a Bachelor's Degree in the field or a related field, or presenting evidence that you will do so by the time you matriculate. For example, in your question you mention that you are majoring in economics and want to go to graduate school in economics. No conflicts there. If you were majoring in philosophy and wanted to pursue a Ph.D. in chemistry, you would be a harder sell. What constitutes a related field may vary, but I know that a B.S. in mathematics can get you into graduate programs in engineering.
Academic ability: You demonstrate this through your grades in your courses, especially those relevant to the graduate program you want to enroll in, and through your scores on whatever standardized tests the program asks you to take before you apply.
Research potential: You demonstrate this one of two ways. If you were lucky enough to publish your research as an undergraduate, then the committee can assess what you did directly. If not, then you need one or more letters of recommendation from someone who has supervised you in a research setting. The admissions committee wants evidence that you have certain qualities that make good researchers, regardless of discipline: curiosity, critical-thinking, creativity, strong work ethic, passion or drive, etc. A good research experience in another field is worth much more than a bad one in your own field.
Communications skills: You demonstrate these through your personal statement (or essay or letter) that you must write. Spelling and grammar errors or worse writing problems in this document are more damning than a bad letter of recommendation!
And as JeffE mentions in his answer to a related question: No Red Flags


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GRE: how important is it to get it in time?
I am student at a UK institution and looking to apply for a PhD programme in the USA. The application deadlines are nearing and I haven't taken the GRE general test yet. It seems that if I take the test at the first available date, the scores will arrive after most deadlines.
How important is it to have the GRE tests scores when applying to graduate programmes in the USA? Will not having it automatically have my application rejected?

The best thing to do is write the schools you are considering and ask -- great advice.  @PeterShor, could you please put this in an Answer?

Have you already signed up to take the GRE? If you have a scheduled exam date, I think you could add this information to your application, particularly if they have a remarks section. Something like, "I am scheduled to take the GRE on January 19, 2016" would be helpful information for the admissions office. It's generally better to furnish as much information as you can, and show you are serious about checking off all the squares.

Three things:

the application deadlines for you are several weeks earlier than the dates that decisions on the applications are made, so even if the scores arrive after the deadlines, they may still arrive in time to be taken into consideration.
different U.S. disciplines (and to a lesser extent, different departments in the same discipline) have radically different views on how much the GRE is worth. So the answer to your question really depends on what subject you're intending to study, which you haven't told us.
bureaucracy at some institutions may prevent your application from being considered, even if the faculty thinks the GRE is unimportant.

The best thing to do is write the schools you are considering and ask. You may have taken the GRE in time for some of them, and I expect others will consider your application even without the GRE.


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In the social sciences, does it make sense to embark on a longer-term project but write a dissertation on one part of it?
I realize this is field- and topic-specific but I'm hoping some of this is generalizable.
I'm in the social science side of information science and narrowing down dissertation topics. Some of what I'd like to do is frankly probably too ambitious for a dissertation, involving randomized control trials in the field (a developing country) that may take a while to get right. So I've thought of doing the dissertation as mixed-methods, based around interviews and surveys, but in such a way that it plants the seed of an RCT that will bear fruit after I write the actual dissertation.

Generally speaking, in the social sciences, does it make sense to embark on a longer-term project but write a dissertation on one part of it?
What external resources could help me figure out the trade-offs here? Obviously my adviser and committee will be the best resource, but it could also be helpful to network with people who have done something like this. Where would I find them?

Again, this may be so context-specific that it's hard to give useful general answers, and I can try to rephrase it in a more helpful way. But info science is a pretty small field, the part that deals with international development smaller still, so asking a question specific to that niche seems unlikely to benefit anyone else.

Have you discussed this with your supervisor?

Yes. He's generally supportive. He's a qualitative researcher so I don't know that he would be as knowledgeable about RCTs, but I have people on my committee who can fill that need.
How might I find resources outside of my own dept?

I have edited the title of your question to reflect the "generalizable" version. Since many people decide whether or not to read a question based on its title, I think the more general question title is likely to get more qualified people to read the rest of the question.

@ff524 what was the previous title!?

Research is rarely a one shot affair. Whatever you do you'll likely be building on later on, whether it was your original plan, or some offshoot you didn't even dream of initially. So I'd say you should be glad to have some plan for "after dissertation" now.

This is, in my mind, a fairly common way to actually do a dissertation, and if you're proposing extensive field work and I was on your committee, something I might actually insist on, for one reason alone:
Field-work is unreliable
So your data gets lost when a truck upends on some rural road. It turns out the place where you should be getting subjects who have X trait doesn't actually have anyone like that. You wanted to kick off something in rural Guinea in the summer of 2015, but you'd rather not get Ebola...
RCTs and field studies are long, they're hard, and they're expensive. Having a smaller part of it, whether it be a mixed-methods paper, preliminary data, theoretical work, etc. can help insulate you from some of the perils of that by making sure you at least have something to write about.
From my own experience, I embarked on a project that was way more ambitious than was really advisable for my dissertation, and as one mentor put it after I had finished 2-3 papers..."Cut and run. Finish stuff up for your postdoc or faculty position." Having created a larger project, having lots of data, etc., and having thought about your work in a larger context that you're already working on is, in my experience, a nice way to be able to articulate your future plans as a researcher on the job market.

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Choosing my name as an author when publishing a scientific paper, can I use my "unofficial" first name?
I have one official first name which appears on my ID card. I have another first name which friends call me by. Is it possible to use my unofficial first name and official family name to publish scientific papers? How can I prove to someone that I am one of the authors?

Deciding which name to use on your first publication is important. Once you make a decision, you need to keep it consistent. Changing the name later will create unnecessay problem for youself. Please see the question How to edit name on existing publications after a name change?.

The points about consistency are really important. Especially when searching online databases; some of them are not very intelligent when matching author names, and anything other than an exact match will not make it into the results. I've had trouble recently where one journal submitted author's names in Surname, First name format which the catalogue couldn't deal with.

Also, consider getting an ORCID ID. Many journals already include this in your name/affiliation information.

It depends on the field, and in particular on the venue in which you are publishing. It's possible that some journals and conferences might have policies about this, which would of course override anything you read here. But in general: nobody checks (or cares) whether the name you put on a published paper matches your official name. So if you use an informal variant of your name, e.g. if your name is "Stephen" but you publish as "Steve", nobody will bat an eyelid. If you use a nickname or publish under a pseudonym, it would be a little odd if the nickname is something that sounds very informal, but still, it probably won't cause problems.
What people do care about is building a record of your work, and putting a face to the name if they know your face. So you should (1) be consistent with the name you use to publish, and (2) make sure other people in the field know that it refers to you.

(1) and (2) in the last paragraph are very important. Thinking about name tags on conferences, it could be a hassle to get your "academic" name written there, if it is different from the official name stated e.g. on the credit card with which you pay the registration. That's why I'd recommend using your official name on publications.

That is a useful thing to consider, but in my experience most conferences ask for your name directly in their registration form, which they then use for their nametag printing. They don't use the name from the credit card for any purpose other than processing the payment. In fact it's possible, and even not uncommon, to use someone else's credit card entirely to pay for your conference registration.

Thanks. But, How someone can prove that he has written those articles?

You can't prove that you wrote something just by having the same name as the person who did write it, anyway!

@yashar about proving you wrote the papers, probably you won't write them alone, you are a person collaborating with some other people in a specific institution with an assigned and unique email address. The surname should do the rest. The email is more important for automatic tools to disambiguate as well. As a matter of fact, there are many (well, I found so far 6) guys out there writing papers with my name+surname. The name is not that important or useful for that.

I changed my name when publishing for a practical reason. My family name has a "comma below" letter which is hard to match when searching for author name. So I replaced it with regular letter. I authored/coauthored over 20 papers, got a PhD without any problems in proving that a certain paper is my paper. And some co-authors wrote my name with cedilla/comma below character. I think is harder to change the email address rather than the name.

The answer of David Z covers all important aspects regarding the name choice. In order to prove your authorship to someone, you would have to show correspondence letters with the publisher. You will typically receive several of those, the most important one being the acceptance letter stating that the publisher will publish your manuscript. If you show these to anybody, it should be sufficient proof that you are an author, especially if the address on the letter can be clearly linked to you.
Note that this is not just an issue with using pseudonyms. Anybody with a sufficiently common name will face exactly the same problem.

I have a legal (official) transliteration of my surname (family name) from the Greek alphabet to the Latin one on all my official documents. I consistently use for many years now another transliteration (just one letter difference) of my surname in all the publications I have produced until now. I have never had a problem with the name tag in my conference badge or the hotel reservation or paying the conference registration or anything. Nobody seems to care until now. The one and only exception was just one time that I needed to issue a travel visa for entering a country; in that case the embassy staff questioned me why my official surname did not match the invitation letter sent by the conference organizers to invite me to present in the conference. The visa was issued without any hassle in the end.