Let me start by saying that publications are usually evaluated not only according to their journal, but also according to the times they have been cited and to the impact they have had, which is a bit harder to gauge and a less objective metric. There are some cases where (at least where I work) the committee requires candidates to select a small-ish number of publications that they deem as the most important (5-12), and these are then read and carefully evaluated individually.

Regarding journals, the answer, as often happens, pretty much depends on the field. In many communities, the impact factor (IF) is surely important, but there are also other (often intangible) factors that come into play.

If many fields, the journals at the very top are few and well known (often Science, Nature and a few others). Papers published in these journals are usually considered to be the top of the cream. For all the other journals, the way they are considered by single scientists or committees is a combination of IF and of these people's own background.

For instance, I work in a pretty multidisciplinary field (in between physics, chemistry and materials science). Some journals are more chemistry- and materials-science-related, and these tend to have higher impact factors than their physics counterparts. As a result, I often find myself publishing in journals that, according to their IF, would be very good from a physicist perspective (>10). However, in the physics community these are regarded way lower than other physics-only journals that have a long history of publishing exceptionally important papers. A notable example is Physical Review Letters, which has published many famous papers like the original papers on the Higgs' Boson or the first detection of gravitational waves and has an IF of ~ 8.8 or PNAS, which is widely known and has an IF of ~ 9.5. I can tell you that, for many physicists, a paper published in PRL is valued higher than a paper published in a materials science journal with an IF of, say, 15 (everything else, such as the number of citations, being the same). I believe that in other communities the attitude is probably very similar: journals that are well known and have a long history will be ranked high, regardless of their IF.


The fundamental reason for friction is that these are commercially licensed resources, and so the licensors have a strong motive to ensure that only people who've paid for it in some way have access to them. Without that requirement, there'd be no reason to throw up the barriers.

The exact ways in which this friction manifests vary a lot - my understanding is that different access methods can be preferred in different places. I'll try and be general here, and explain what's currently used.

There are two basic methods for authorisation.

Site verification.
Individual verification.

The first of these involves identifying that you, the user, are coming from a site which has access. This is pretty trivial if you are on-campus and that campus has a defined IP range - "oh, they're coming from 1.2.3.4, they must be at Wherever University, let them in". In these cases, it can be completely seamless - in fact, so seamless that one real problem is that users can believe the resources are public, and get frustrated when they go home and they're not there! It also allows for 'walk-in' access - many licenses explicitly provide that if you're physically using the library, even as a visitor, you can access these databases. I am guessing from your post that you normally use this approach.

The second, individual verification, relies on each user having a signin to the database. This can be an enormous headache for both institutions and users, especially when you have multiple systems you need to sign in to. IP authentication is thus more popular.

However, IP verification breaks down if your institution shares its IP ranges with someone else (this is more common outside the West). If two institutions have a shared IP range, there's no practical way to provide access to users from one but block them from the other. If most of a country shares an IP range... you can see where this is going.

A similar problem arises if you are at an institution that uses IP authentication and you go somewhere else - perhaps you're at a conference, perhaps you're working from home, but either way you're not on the right network. One approach to get around this is to provide a VPN system, which drives all your traffic back through the "right" IPs. This is a hassle for users (and for the provider), and may not always be available. Another approach is to use a proxy server, but this is again something of a hassle for users. Both can lead to long network delays, and you have the associated problems of actually getting into the VPN/proxy server.

A common approach is to fall back on individual authentication. Most major databases offer optional individual logins, which let you save papers, set your viewing preferences, etc. These can be repurposed as logins which 'remember' that you have access rights, and let you use the service when away from your home network. They'll usually stop providing access after a while (a few weeks or months?) if you haven't signed in to it from your home network at some point, in order to prevent them remaining active forever. However, this still has the too-many-names problem of individual verification - no-one wants to juggle a ScienceDirect account and a JSTOR account and a Lexis account etc etc etc.

The best solution to this is to use an identity management/single sign-on system. The most common of these at the moment (less common in the US, I believe) is Shibboleth. Shibboleth provides a single login screen for all participating services. A user selects their home institution, is taken to a page there, signs in (or is automatically authenticated), and returns to the database service with authorised access. If done effectively, this can even completely replace IP authentication - you can do the necessary authentication for people on a local network automatically.

In theory, a system like Shibboleth should reduce friction dramatically - it can provide a standard sign-on system for all databases, and only require a single username/password which the user already knows (usually because it gets them into their email...). Compare to, eg, the ubiquitous "sign in with Facebook/Twitter/Google" buttons on web services. However, the problem is that each individual provider service has to set it up. The big databases like ScienceDirect or JSTOR are usually happy to do this, but small journals or databases - especially if the majority of their customers are happy with IP authentication - may not be willing to go to the effort of setting it up.

In an ideal world, we'd all be standardising on something like this. Unfortunately, there's a lot of people who all have to pull in the same direction for it to happen, and what is most convenient for publishers is not always what's most convenient for libraries or for users.


Are personality clashes with other faculty a valid reason to deny tenure

In practice, "collegiality" is often a consideration in tenure decisions, whether or not it is a factor identified in the university policy on tenure and promotion.

The American Association of University Professors (AAUP) has come out with a statement against the use of collegiality as a an explicit factor in tenure decisions:

http://www.aaup.org/report/collegiality-criterion-faculty-evaluation/

However, this report also makes it clear that a faculty member who is hostile to the other faculty in his/her department would typically not be doing an adequate job in service and teaching, because working with colleagues in these areas is a necessary part of the job.

Thus "We're not granting tenure to John because no one likes him" wouldn't be a good reason, while "We're not granting tenure to John because he doesn't work productively in departmental committees" would be a reason to deny tenure.

As a practical matter, if the tenured faculty in the department don't like you and don't want you to get tenure, they'll probably find an excuse to deny you tenure.  Any tenure track faculty member would be well advised to get along with the other faculty in the department.


Professor Job Prospects for PhD in Computer Science vs Computational Neuroscience?

I will share my own results from my research as I am on the same boat (Torn between Bioinformatics/CS). From looking at profiles of recently appointed faculty across institutions, it certainly seems easier to get a position if you are a CS graduate.
Due to higher volumes of CS PhD's, most end up going in industry or doing post-docs for 1-2 yrs before getting a faculty position. Whereas grads from other disciplines (Computational neuroscience/bioinformatics) usually end up doing post-docs for a bit longer and I have rarely seen a recent faculty appointment in these areas without a post-doc.
All reasons aside, It will greatly depend on your research/publications and to some degree the institution and your supervisor.


Are journal back covers, inside covers (i.e. not front covers) worth the cost?

I would assume your question can not be answered without a personal perspective - what makes it "worth the cost"? Someone liking it? Two more people reading your paper? An invitation as invited speaker? 2 million [insert a currency of your choice] of additional funding per year?

To be a bit more serious: I would check how the pages are included in the digital version of the journal. Most readers do not read the journal but go to the website and pick specific articles. If the images are not shown, very little people will notice them.


What is a good amount of time to wait to check up on a recommender after the initial request?

I would definitely not contact him until the week before the week he said he could get to the recommendation letter. Anything earlier could just lead to the same answer as before. I wouldn't stress it too much, however. My recommenders this year submitted their letters within the last two weeks of the deadline. One of them submitted it two days before the Thanksgiving break (at the end of which, some applications were already due).


Reworking a Homework Project to Publish as Research

Chances are your plan is fine. You created the piece of work, and you weren't funded, so there's nobody else that can claim that as his or her intellectual property. Still, I would suggest working with an academic over this - probably the person who set the homework problem. If there's a potential issue with your plan, he is likely to know; further, he can offer you critical comments to get your work up to scratch (writing a literature review is quite different from a homework assignment), and if he's willing to add his name to the paper that adds a lot of credibility to it. He might even be able to suggest a journal for you.

As for affiliation, yes, you list the university you were at since that's where you did most of the work.


Do statements giving background about a problem require proper citation?

I describe the problem in almost exactly the same way as some earlier papers.

If your description of the problem is based on the description in another paper, then you have to cite that paper. If your description is not based on another paper, but is such a standard thing, obvious to any expert in the field, that you have naturally written it in a similar way to other papers, then the following applies:

Statements like

  this is a problem that has challenged mathematicians for over half a century

or

  the computability of the matrix, given only partial spectral data quickly becomes intractable in higher dimensions

can benefit from citation(s). Not necessarily to avoid plagiarism - if you don't include citations, you're probably not misleading anyone into thinking it's an original contribution - but to support the statements with evidence.

Statements giving background about a problem often benefit from citations  because without evidence, the reader might not be convinced of the truth of the statement. (Or, even if we know our audience will agree with the statement, we sometimes cite evidence to show that we know the evidence.)

To some degree, this depends on conventions in your field, though.

In some fields, statements like the ones above would typically be supported by citations to a handful of papers that either directly support the statement with evidence, or show that other experts in the field agree with this statement and have made similar statements themselves.
In other fields, the standard is to only cite things you really use, and in that case you probably wouldn't cite anything in this situation.

You can look for some high-quality published papers on topics similar to yours to get a sense of what the convention is in your field. If in doubt: cite.


Is use of multiple bibliographies, especially with annotations, in a thesis, accepted?

I think the answer to your question is very dependent on your subject and the culture of that research area.  In my area, math, I've never seen an annotated bibliography as part of the thesis.  I've probably only looked at 15 or 20 theses, but I've never seen one.  In other areas (humanities and social sciences?), I suspect such a bibliography is more par for the course.


I applied for one program, but I still want to apply for other schools

It is absolutely accepted - and usually strongly suggested - that a student apply to multiple programs for grad school. Strong programs tend to be "competitive", which is a way of saying that not everyone who applies will get a spot so you aren't guaranteed to get in just because you applied. The amount suggested varies, but I've not heard anyone suggest less than 5-6, and some suggest more like a dozen (especially if some of those are departments with a very small admissions rate). So there is nothing unusual about you want to apply than more than one - you definitely should!

Reference writers usually write one letter, then make only small modifications depending on what program you apply to. I know it can feel weird to ask someone to take time for you in this way, but it's part of the job and part of what they agreed to when they agreed to write a letter for you. Be appropriately grateful, but do not hesitate to apply to a program you'd like to be able to attend for this reason. Any sensible person writing a recommendation letter wants you to get in somewhere you are excited to go, and would very much enjoy hearing a positive result for you, and are generally happy to do their part - even if it does take them a little extra time to submit letters to a few extra places.


Can I still pursue a research career after a possibly lengthy break?

Please contact the dean of graduate studies at the department that accepted you and describe your situation.  Various creative approaches to this problem may be possible.  For example, if the first stage of your degree program involves coursework to prepare for some qualifying exams, it may be possible for you to take some of these courses at a university closer to home, with careful planning, and direct communication between the two departments.
If you are not already working with a counselor or therapist, I suggest that you find someone you like to get started with.  When going through a family upheaval this can be helpful.  Also, in the safety of the counseling relationship, you may gradually become comfortable about exploring different ways of balancing supporting your family and pursuing your own personal growth.  Sometimes the stress of the situation one is living through at the moment makes it difficult to see all possible options.


The editor doesn't respond after accepting the manuscript

You should write to the editor and tell him what you have told us.  Really your concrete problem is that your correspondence has not been returned so you don't know what's going on.  Maybe everything is proceeding as it should, maybe it isn't, but you need a reply.

  Could editor reject my manuscript after acceptance?

Why do you even ask?  Are you worried that the editor thought, "No, hang on, I don't want to publish this paper after all.  Let's not publish it, never contact the author again, and hope for the best"?!?  That's just totally loopy, unprofessional behavior.  In this big, bad world of ours, anything could happen, but the chance of this happening to you -- provided only that you are dealing with a partway reputable, professional journal (essentially: not a journal that you learned about via a spammy, semi-literate email) -- is negligibly small.

Just get back in contact with the editor ASAP and take it from there.  Be polite, but be persistent.  Give the editor a week or two to reply.  I honestly expect that he will.  If not, write to the editor-in-chief / managing editor / some other members of the editorial board.  You'll hear back from someone.  Again, don't assume that something has gone terribly wrong, and certainly don't worry that your polite, professional behavior will jeopardize the future of your paper.


Emailing professor for help with (non class related) project

I want to do an analysis involving computational fluid dynamics (CFD)...and I would like to reach out to [a professor] to ask for suggestions on learning more about using CFD, and hopefully discuss it with them to get feedback on this particular project.

As mentioned already, "Visit in office hours or make an appointment." Once you have demonstrated your abilities to the professor, you'll be in a stronger position to:

  get involved in this professor’s research

Although you won't express "both of [your] requests at once," you can present both of your requests in a short time frame. If this isn't an option, then start by discussing CFD and mention that you'd be interested in working with the professor at the end.

  Would it be more effective to only request some guidance on the project?

If you ask for both at the same time, then the professor mightn't know your strengths. Whereas, asking later lets you demonstrate yourself first.

  Would it come across rude asking for guidance as well as ask to get involved in their research?

It isn't rude. You can ask for guidance and the professor can say "no." You can offer to be involved in their research and they can again say "no."


Why do I see research being republished in Springer?

I don't know what book you're looking at, but it could be a reprint volume. These are, as their name indicates, collections of reprinted works. They are usually reprinted works of some famous person (example), or they might be works which the editor of the volume has decided are worth including (example).
These books will usually make it quite clear the works contained are reprints though, so there should be no confusion over the date the original work was published.


difference between symposium and workshop?

By your description it seems like the main or the principal track(s) of the conference are the symposium(s) and that the workshops are sided events. So, typically, workshops are smaller, more focused on a given subject or theme within a larger research field. The symposium is, typically, wider with several subjects being contemplated within a research field. For example, a conference in Software Engineering (wider) can have a workshop on Model-driven Software Engineering (specific).

So, usually, it is more easier to be accepted in a workshop, if and only if, your contribution is really focused on the subject of it. For the main track, it is typically more complicated because there should be clear contributions to the state of art in an area of study, with well-stated results and more detailed research.


How to choose references for postdoc application?

I think, what really matters is the quality of the reference letter. As you mentioned that both the persons that you have chosen other than your mentor are highly active and are happy with your work, so getting a good recommendation letter from them would be very fine then getting a bad recommendation from a noble laureate.  Position really doesn't matter as long as you get a good recommendation.  Make sure that the person you have chosen as a recommender gives you really a good one.

  Does any personal account matter while considering a recommendation or a generic-looking letter does fine?

A well-written letter on an official notepad would be fine, having all the necessary details of your recommender with the phone number and email id.


How to set the threshold below which students get a failing grade in a university-level course?

My classes are typically curved to the median.  To grade, I first set what I think should be the median grade, based on my assessment of the class as a whole.  Then one half of a standard deviation away from the median is one half-letter grade (e.g. if the standard deviation is 10 raw points out of 100, then 5 points would move an A- to a B+).

Using this scale, an F is simply someone who is a certain number of standard deviations below the median.

Several points:

I explain my general scheme to students on the first day of class,
    so that expectations are clear up front. There is some wriggle room
    at the letter grade borders.
I typically look for clean breaks
    between student performers (i.e. if one cluster is 2 points above
    another cluster, then it makes sense to separate their grades).


Is it appropriate to use an Independent Study as a mechanism to get projects built?

Universities and individual departments have criteria for allowable independent study courses. One of the reasons is exactly the scenario you outline. In my department, approval will depend on whether there is "academic value" for the student. Academic value, however, is subject to interpretation.

By all means, inquire with colleagues, department chair, etc. to find out the relevant criteria for you. Of course the student should feel that the project is worthwhile for them, or you won't get anyone signing up. Students will prefer paid positions, all else equal. As you know, it is routine at research universities for students to be paid as researchers, to do the research that becomes part of their thesis. You have to offer more value, or accept a lower ability student.


In the US, if you are conducting a survey or certain type of interview, you need to have it approved (or declared exempt) by your campus IRB committee. This body will regulate what you need to disclose, and will also approve the wording of any cover letter.

In a written context, putting the cover letter on school letterhead should convey that the project is academic.

In an interview, you would likely state that you are a PhD student at UNIVERSITY and are working on a dissertation related to X to convey that your project is an academic one.


Must one use the © symbol on a book's copyright page when using a CC license?

Is it necessary to say copyright on the "copyright" page when using a Creative Commons (CC) license?

It's not "necessary" but it is a good idea. This communicates the information that there is a copyright holder for the work and the copyright holder is licensing the copyright under the terms of the CC license. Using the CC license does not negate the existence of a copyright on the work; in fact, it is only by virtue of having a copyright on a work in the first place that you can license it to others under the CC license if you so wish.

In most jurisdictions (Berne convention), copyright is "automatic" and it is not required to claim a copyright in any particular form. However, people who might otherwise use your work as permitted by the CC license may be put off if your legalese is missing or unconventional.


Referee access to a not-yet-public URL cited in a paper?

First, I think you are worrying too much. Second, I think it is bad form on the part of the authors. If the material on the website is critical for the paper, it needs to be provided in an archival form that the journal can keep track of. I would evaluate it based on what you have been given.


Can I correct a mistake that the reviewers didn't spot in a paper that has not been accepted yet?

YES.  The responsibility for correctness of the paper is yours not the reviewers’.  The reviewers may help you find errors, but that is secondary to their main function: recommending to the editor whether to publish.


Is it my responsibility to refute misinformation in social situations?

I think you should say more, but definitely don't respond all the time, and definitely don't be too harsh all the time.

It's not black and white, and you have to judge every time if it's worth it, if it's your place to say something and if anybody benefits from you saying it.

Compare it too remarks about looks. You'd tell a friend he should wear another color, you'd tell a colleague that his sweater is inside out, you'd tell a stranger on the elevator that a label is sticking out, but internet remarks about how Britney looks nowadays are completely useless.


Is it reasonable to apply for (postdoc) positions early?

My recommendation is first that you don't worry too much about it, but I think there is an important exception: if you are applying using MathJobs, then you should apply once you have your documents ready, hopefully at least a couple of days before the deadline.  In particular, you should not wait for your references to add their letters if that is the only thing you're waiting for.  Those will show up when they are available, but it's much better for someone to see your application is there without all the letters, than for you to get lost right in the avalanche when everybody else submits right at the deadline.  Similarly, you can update your CV, so there's no reason to wait in hope of another paper to getting accepted.


If a reference/book authored by your professor contains typos, how should you react?

For the textbook I've written, I appreciate any feedback, including typos, misformed sentences, vague formulations and of course errors. Some points to consider (partly contained in the other answers):

Wait until you have a reasonable list or, e. g., until a chapter is over, the whole book, or the course.
Check if there is some errata available somewhere. Some authors maintain an errata on their webpage, sometimes the publisher hosts this, for some lecture notes I have a blog post. Only send the points that are not already in the errata.
There is no need to ask if such a list would be welcome. I guess it is safe to assume that this is the case (but others seem to disagree - see the comment below).
For other feedback than errors and typos (e. g.  feedback for formulations or the organization of the book) be prepared that your comments may not be taken into account for various reasons.

Oh, and for the lecture notes I reward bonus points for every mistake spotted and submitted by a student.


Here is what got me through Undergrad:

Sit in the front row, even if you stick out like a sore thumb.
Write down everything the professor says by hand. Don't type it out, just write.
Focus on one subject at a time. If writing a paper, just write that paper for a couple of days.
Turn off your phone. If you don't need a laptop for the class, don't bring it.
A spiral notebook helps you focus more than a binder. Loose pages are the enemy.
Avoid scheduling classes in the evening or around times where you would rather be doing something else.


Plagiarism: quotation from videos course or conference

According to your question, you're "tak[ing] some of the phrases" from the videos. If you do not cite them, then you are guilty of plagiarism, since you are presenting the ideas and words of others as your own, which is essentially the definition of plagiarism. It doesn't matter that the text isn't written out. Stealing someone's oral statements is just as bad.


Are Master's becoming required for USA PhD programs?

At least in my field (mathematics), every US PhD program I know of accepts students with a bachelor's degree.  I see no sign of this changing.


How to write PIs asking for PhD position?

When drafting your email, keep in mind that PhD advisors get tons of request like this. Your request has to stand out in order to have a chance of success. Most email requests are pretty generic, simply asking for a position, with some generic praise of the advisor's reputation, and a CV attached.

In order to stand out from the mass, the most important thing is probably that you do your research. What topic is the advisor working on? How does your background fit in there? Make it clear what you think you can contribute to the advisor's work. Try to get all this across as concisely as possible, maybe three or four sentences, at most. By all means, avoid being generic.

Surely you will have to put some time into it, but it will increase your chances of being considered dramatically. Better to send out fewer but well targeted emails than masses of generic requests.

If you get no response in spite of your request being well crafted, you can try following up once, after a week or so, but not more often.

EDIT: "Doing your research" does not mean writing a research proposal, but finding out what the PI works on and putting your skills and interests in this context. Most of the time the info on their website is sufficient, you don't have to read every single one of their papers.


Teaching Loads by Field at Research Universities

There is no standard load; it depends widely on the department, the number of students enrolled, the available number of faculty, and so on.

Moreover, in some departments, it is possible to fundraise your way out of commitments. For instance, if you bring in X dollars in overhead, you can "buy" out of teaching a class for a semester.

In addition, stating that a load is "1-and-1" can mean different things. In the department where I did my graduate work, professors now co-teach one class per semester, and sometimes offer an elective course on top of that 1-and-1 load.


Can I include the completion of Udacity and Coursera classes I have attended in an academic CV?

No.  Specific coursework (whether formal or informal, online or in-person) does not belong in an academic CV.


Is it common that marker TA make the marking scheme instead of the professor?

This might vary by country, but in the US, if the graders are undergraduates--which shouldn't be the case for midterms--then I would say that it's unusual to allow them to decide on the grading scheme. If the graders are grad students, it's quite common. At many schools even first-year grad students are the instructor of record for a course.


Should I publish as sole author and do everything or invite coauthors so that I mostly just do the programming and benchmarking?

I had discussion with several well-known professors with experience (30+ years in research) about this sort of thing, how did they list authorship in their early papers where they were the less well known authors. I started publishing only several years ago, so I will give their opinion (which I agree with I should add). Their response was the same across the board: the person who did most of the work they ought simply list themselves as first author when writing the paper and if the coauthors ask them about it, then they just discuss their concern with their coauthors honestly. If your coauthors are real scientists (regardless of whether they are more well known than you), and if your claim is true, they will agree with you.

If your coauthors are administrators mostly, and it's convention in your field and location, that they are added to your paper and listed ahead of you, consider working elsewhere, otherwise the problem cannot be solved in that environment.

There is another option: publish with them according to whatever convention is appropriate, and if you did not get listed as first author when you did actually most of the work, then at the same time also extend the work (>40% different material) on your own and publish a second paper in another journal as single author, covering both new and old material. (This is how you also find out who the major contributing author was on a particular work, where there are both team and individual papers at once.)

The first solution minimizes opportunity cost; the last solution requires more time and hassle for you, but you don't forgo anything academically, only some time writing a second paper and doing a bit more work.


My paper was too revolutionary - reviewers at a top journal rejected it "by simply reading the title". What now?

You don't say what your field is.  I think you would get a better answer if you did, as cultural norms differ.  My answer is from the perspective of a pure mathematician.

The first thing I want to say is that, given absolutely no specific technical information about your situation, your post gives me the impression that your work is most likely not correct.  Or to be more precise: it is an empirical fact that most papers which claim to completely revolutionize a field turn out to be incorrect, so from a probabilistic perspective anyone who says that is most likely not to be correct -- and this by the way is an attitude that you need to be aware of and take into account.  What I really mean is that the way you describe your work makes me think it is more likely to be incorrect than if you had just said "I believe I have done work of the highest level of importance in my field, but I have not been able to publish it.  What should I do?"

But rather than picking apart your post to reveal why I got that impression, let me concentrate on directly answering your questions.

  And is rejecting a paper because it is too good even a valid reason?

Obviously not.  Not only is this an invalid reason, it is a reason that does not make any sense and thus is never given.  And it was not given to you.  If you really think your paper might have been rejected because it was too good, you need to have a long talk with your mentors about how academia works.

  So what should I do now?

My advice you to you is to talk to your advisor once more to make sure you've correctly understood what he told you to do.  If you have, then I'm sorry to say that I think you may need to find a new advisor -- or at least a new mentor to help you out here.  The advice as reported sounds terrible.

  I must add here, as my advisor congratulated me and hugged me on this great discovery, he was skeptical of my paper being published because it is simply too outstanding to be true.

Please remember to choose your language carefully in academic discussions.  Did your advisor really say "it is simply too outstanding to be true"?  If so, he is saying that he does not believe your work is correct, and somehow that most important message has been lost.  You are acting as if he said "it is simply too outstanding to be published in a top journal", which doesn't make sense.

  And big journals who receive thousands of paper each day will most likely reject it in quickness, and this paper needs to be read with a lot of thought and concentration to be believed.

It would be very helpful to know what your field is here.  In my field (mathematics) there are no journals which receive thousands of papers a day.  Moreover most papers which are submitted to top journals are read with a lot of thought and concentration -- in fact, the very top journal in my field, Annals of Mathematics, is a bit notorious for keeping (correct!) papers for more than a year before rejecting them after a careful evaluation.

Of course if your paper does something revolutionary and the arguments are difficult and technical, the burden is on you to present them as clearly as you possibly can, and also to make sure that your paper does not have any superficial flaws that would invite an early rejection.  The question which has been suggested as a duplicate of this one has many good answers giving advice about this issue.  Let me add that it sounds like it has arisen for you:

  As I contacted the reviewer, I was told that he and others "rejected it by simply reading the title".

(Again, please choose language carefully: do you really mean the "reviewer" or the "editor"?) Rejecting a paper simply by reading its title would be inappropriate and unprofessional.  Even if the title is terrible or worse, one should read at least a little farther to confirm the initial impression.  I have to say that I am skeptical that the editor at the top journal in your field told you this.  Could you confirm that this is exactly what happened?  (FYI, exhibiting a terrible title that you didn't use didn't convince me that your title was adequate.)

  He advised that I should submit it to a lesser known journal whose reviewers he is great friends with, so that he'll tell him to take a good thoughtful look at it. He assured me that my paper would be accepted there. However, I might have naively not considered this and simply went for the biggest journal out of extolment.

This sounds like very bad advice.  (Again I assume by "reviewers" you mean "editors".) If your advisor really thought your paper was correct and revolutionary, he should be helping you publish it in a top journal, not a journal in which he can arrange to have his influence exerted.  It is really inappropriate for him to ensure that your paper will be accepted: again, how does he know it is correct?  But I see a germ of something valuable: if he has colleagues or contacts that can give your work the attention it deserves, why don't you ask him to send your paper, as a manuscript, to those people?

In general the way that you try to publish a truly revolutionary paper is not exactly the same as a run-of-the-mill one.  Namely, as I said at the beginning, the better a result you claim the more likely it is incorrect (no matter who you are).  Everyone knows this.  So -- and here I may be talking more specifically about my own field, which has a vibrant preprint culture -- you can make your life a lot easier by circulating your revolutionary paper as a preprint, giving talks / going to conferences / visiting various experts and so forth.  If you can't convince any top person in the field that your work is correct, how will you publish it -- and more importantly, so what if you do publish it?  Conversely if you can convince several worldwide experts in the area that what you've done is correct, then the path to publication becomes a lot smoother.

Good luck.


When giving a seminar talk, should I sit or stand?

I personally find that sit vs. stand strongly depends on the degree of formality and interactivity of a presentation.

When the presenter stands, it signals a strong differential between the roles of presenter and audience (who sit).  This generally creates a much more formal atmosphere and means that the audience will not contribute to the discussion except to ask occasional questions.
When the presenter sits, it signals a more equal discussion environment, where it just happens that the presenter is the one who is structuring the discussion and/or controlling the slides.  I almost never see this except in the most informal sorts of meetings within a project or group, but in such meetings (e.g., coordination of a project team) it is very common.

For the specific case that you give, of a department seminar, I would strongly advise standing.  The reason for this is that, even if it is a fairly intimate and informal group, a strong motivation for the organization of such seminars is to give you practice for more formal talks.  You may find it more comfortable to be sitting but this is a good opportunity to practice and find ways to be comfortable when standing as well.

Two caveats to all of this:

If a person has a medical condition, they should take whatever position the medical condition encourages.  I've stood and walked around at the back of a talk when my back was having issues; nobody expects Steven Hawking to stand and speak.  If the condition is not obvious, you may wish to inform the audience so they know not to misinterpret your position.
If you are giving a presentation remotely, the position that you are in generally does not matter, as a well-adjusted camera will typically only pick up your head and shoulders.


What does "Awaiting Assignment to Batch" mean?

First, congratulations!!
"Awaiting Assignment to Batch" is part of the accepted workflow. Once accepted, some journals have a set of tasks that a manuscript goes through. One of the steps available (and being used here) is batching and sending of the manuscript to the journals production service. It will wait until a predetermined condition (so many ready to go, or a regular timed interval), then be added to a large zip file (along with others in the "batch"), and sent to the production server.
Hope this helps!
NOTE: I am am employee of ScholarOne, but my opinions and answers are only my own.


Apply for assistant/associate professor at same institution as postdoc?

It's not common to stay at the same university after doing a postdoc.  When you do a postdoc somewhere, you can certainly apply for a faculty position there afterwards, the same as anyone else, and you might get it.  The fact that the department is familiar with you and your work could be a modest advantage, but there may be disadvantages as well.  For example, the university already has someone in your general area, namely your postdoctoral supervisor, so they may feel less need to hire you as well.

Without some special reason to think otherwise, the chances of being hired at this university are probably roughly the same as they would have been had you done a postdoc somewhere else.  That generally means they're low.  In most cases, you can't just pick a university to focus your attention on and hope to get a faculty job there.  Even if you're qualified, many other applicants will be as well, and some may be even more so.  Of course you may be exceptionally accomplished, or in a hot field in which recruiting is very difficult.  If that's the case, then you may be in a strong position to stay, but otherwise it will take a lot of luck.

Another way to look at it is by counting.  Most major research universities hire a lot more postdocs than faculty members.  (An average faculty member will supervise quite a few postdocs over the years, but the university isn't growing exponentially.)  Probably most of the postdocs would like to stay, but there just aren't enough faculty positions to hire them, even if nobody were hired from outside.  In other words, it's the same argument as for why most graduate students can't expect to find faculty positions at institutions comparable to the one they graduated from.


Data Set Definition , Where to Place (Introduction, Material and Methods)?

There is no universally-agreed way to do it. I usually place the information about the datasets under the experiments section, before reporting the results. Also, I prefer to present parameters about the datasets (e.g., number of features, number of samples) in a table. If many datasets are used, and there are some points that needs to be clarified, I would create a subsection for the datasets under the experiments section.


How should I plan my course schedule given that my wife is due to give birth during the semester?

Yes, I would say that at the beginning of the course. In my case that was received positively, and when the day came they were very flexible in handling any schedule changes (much more so than students normally are).

I would also discuss this early on with your collegues. In my case they were very willing to help out (people are much less irreplacable as we like to think we are...)

This is definately something to discuss with HR, as there may be all kinds of policies and programs that you never heard of and could really help you balance your new family life with your work (as a colleage told me: however you will measure it, your life will change significantly (We both teach statistics), and he was right)


Is it unethical to give a gift to my professor who might potentially write me a LOR?

Your first sentence tells us that you are still a student in the institution where these professors teach.  If you are currently in classes with any of these professors, or there is any possibility that you will be in their classes in the future, do not offer a gift, either prior to a request for an LOR or as a thank-you for having written one.

Giving anything of value to someone who will assign a grade is almost certain to make the professor uncomfortable and, although very unlikely, could cause the professor a great deal of difficulty.

Finally, consider that writing letters of recommendation is part of a professor's job.  You shouldn't think of doing anything that will seem like compensation for a professor having done the professor's job.

The things I value most from students for whom I've written LORs are notes telling me that they've been admitted and thanking me for my part in making that happen.  A particularly nice one was written on a postcard depicting the former student's new university.

Keep the goodies or share them with fellow students.  Send the professors a nice note after you've graduated and been admitted to graduate school.


Making sense of U.S. assist. prof. salaries: gross vs net, 9 vs. 12 months

In the United States, the "academic year" consists of the 9 months that comprise the fall and spring semesters. This is the period during which you are formally employed by the university and receive a salary. These 9 months also define what salary you are essentially guaranteed. However, it is possible that you will also get a salary for the remaining 3 months; for example, if you have grants from a funding agency or from industry, or if your department runs a summer program and you teach during these months. You can inquire with the head of the department that made you an offer whether they run a summer teaching program, and what your chances would be to get an assignment to teach. In other words, your salary may be up to 4/3 of the nominal, academic year salary, but that is not guaranteed.

How much of this money ends up in your pocket depends on a number of factors that are hard to estimate without knowing more:

You can look up the Federal tax rate for this income. If you're single, I would think that you have to estimate a tax rate somewhere in the 20-25% range on your total salary, including the 6.2% social security tax. But it may be significantly less if you have family and your spouse is not working.
Some but not all states (and in some cases, cities) have a state income tax. You can also look that up. Many states use a flat percentage of your income, typically somewhere in the 4-8% range. I don't know whether that includes deductions for dependents.
Retirement: Most universities have switched to a 401(k) system where you get no benefits from the university after retiring and both you and the university instead pays into an account over the time of your employment from which you can later draw money in retirement. Depending on university and state, you will have to expect to pay 6-10% of your total income into this account.
Health insurance: If your health insurance has to cover only yourself, then you can expect that your employer picks up all or almost all of the cost. On the other hand, if you have family that needs to be insured, then you have to expect that your share of health insurance will be in the range of $500 per month (for only a spouse) or larger (if you have children).

So if you add all of this together, if you start with $100k per year, you'll end up with maybe $100k-25%-5%-8%=$62k in your pocket if you're single, plus or minus several thousand dollars. But it may be quite different if you had family, depending on the state you're employed in, and any number of other factors.


Is physics taught using phrases that are too easily misinterpreted, and can this be improved?

Yes, this is a real issue and yes, we are obligated as a community to address it because we ourselves are the source of so many of the misconceptions and errors we so often complain about. The higher the level, the greater the accountability should be, but frequently isn't.

There are nearly innumerable examples of faulty language all throughout the physics literature and physics textbook at all levels. I will list some here. Before doing so, I also want to point out that science, ALL science, is based on progressively sophisticated models. Each new level of sophistication brings deeper understanding, and the process never ends. It's okay to use simplistic models and accompanying simplistic language as long as we warn the listener that in simplifying things, we're introducing errors that will be addressed in the more sophisticated models. We frequently neglect this warning.

  "Vectors are quantities that have magnitude and direction."

It is not the case that every quantity that has a magnitude and direction is a vector (e.g. finite rotations). There are also different kinds of vectors, and unfortunately this is rarely mentioned in introductory courses.

  "Vector components are scalars."

Well, not always. Components can be vectors as well. In fact, what we call scalar components are really pseudoscalars because of their behavior under coordinate inversion.

  "Energy is the capacity to do work."

This is a model of meaningless circularity if ever there were one.

  "The potential energy of the ball..."

A single entity cannot have potential energy assigned to it. Potential energy is a property of a system.

  "Energy or momentum flows..."

Neither is a concrete physical substance so they can't flow. What we really should say is that we treat them mathematically as though they flow.

  "Charging a capacitor..."

Charge is a fundamental property of matter, and yet we routinely use it as both a noun and a verb, which is a huge potential source of confusion. When we use it as a verb, we really mean and should say "accumulating" because that's the physical process we're trying to describe. "Charging a capacitor" simply means "accumulating charge on the capacitor". Actually, upon deeper thought, it amounts to a "redistribution of charge creating the appearance of accumulation of charge on the capacitor." Sometimes more words enhance the meaning.

  "Electricity is..."

I can think of the following words used by students to complete this thought: charge, current, potential difference, electric force, power. Electricity is really a meaningless word used as a substitute for lack of understanding of the concepts behind all those other words. If you mean power, then use the word power. If you mean current, then use the word current.

  "Newton's third law says two objects exert equal and opposite forces on each other."

This directly contradicts the definition of force as a vector because two vectors cannot be equal if they have different directions. The term "equal and opposite" is inherently self-contradictory.

  "Dot products and cross products are two ways of multiplying vectors."

These are very different from students' conceptions of multiplication. Dot products require both multiplication and addition (and sometimes subtraction). Cross products also require more than trivial multiplication. We shouldn't use the simplistic "multiplying" UNLESS we warn students that we're redefining what "multiplying" means.

  "Moving clocks run slow. Moving rods contract."

These are very misleading. Time dilation and length contraction are nothing more than consequences of measurement from different frames.

  "Time..."

This problem took too much time. (time as a quantifiable concept)
Distance is the product of speed and time. (time as a duration)
What time is it? (time as a clock reading)
Six times three is eighteen. (times as repeated addition)
Please time the oscillations of this pendulum. (time as a verb)
That was a very timely remark. (time as an adverb)
Here is a time-dependent function. (time as an adjective)

These are a few from introductory and intermediate physics. Perhaps we should create a community wiki of more examples from advanced physics.


Can we add articles downloaded from Sci-Hub to a meta-analysis study?

If you disclose that you downloaded it from Sci-Hub, one cannot rule out that you will suffer legal consequences one day (alongside, perhaps, social punishments based on moral grounds). But given the almost non-existence of a legal enforcement against the individual use of this 'pirate', I find it unlikely.
To be on the safe side, you should simply not disclose the source from which you downloaded that publication. Mention it, discuss it, cite it, but do so without telling the reader how you acquired the PDF. This would be too much detail anyway.
(Yes, a meta-analysis would do good to disclose how it came to include certain studies, but it does not have to tell the reader in minute detail how you downloaded each study's PDF.)


Should funding be listed under "distinctions and honours" on a PhD application?

Typically, when you put together a C.V., there is a place for listing the funding that you have obtained, and these would go in that section (unless they are primarily about the honor and secondarily about the money, in which case they would go in the funding section).

For the application, if there is nowhere to list these types of funding, then I would list them in this "distinctions and honors" section.  These are significant pieces of your history, and should be listed somewhere in your application, and if this is the best fit, well, why not there?


How to handle repeated references in footnotes?

Generally speaking, you should use whichever style sheet your publication venue asks you to use. Different styles have different ways to handle this.

As an example, the following are two common ways to deal with repeated references in footnotes:

Use "op. cit." to refer to the prior reference by the same author.
Use "supra X", "supra note X", to refer to a prior footnote, where X is the number of the footnote. This is relatively common in law. You can also provide different page numbers by using "supra note X, at Y" where Y is the page number.


Suggestions for making the most out of a set graduate school program?

For graduate programs with this kind of structure, there is usually an expectation that your core courses (algebra and analysis) will be your main focus for the first year.  So you should not necessarily expect to have much extra time to spend on other topics during that year, nor will the program be expecting you to do so.

If you find that you are able to handle those courses pretty easily and have a significant amount of extra time and energy, then you could consider:

studying additional topics on your own
enrolling in other courses, if there are some that don't have the core courses as prerequisite
approaching an individual professor in an area of your interest about a reading course or independent study

But if not then don't worry about it.  There will be plenty of time after your first year to explore other areas of math, and having a thorough grounding in core areas will make that exploration much more productive.


In this case, I would do the following first. Go to your present admin/PI and let them know what you have said here and ask them what would happen if they don't get the grant. Is there the possibility that you can be kept on with other funding, or is it absolutely dependent on the grant?

If you are valued enough where you are, it is just possible that they can make some arrangement to keep you. "I'd rather stay, but it seems uncertain, and I have this other offer. What can be done?"

I think it is probably worth asking the question.

But if it isn't possible to make an accommodation, then you need to decide how much risk you are willing to accept. That is personal. It would depend on the likelihood of other options, of course.


Funding is from TA - What to put for funding acknowledgment

A TA doesn't directly fund your research. It funds you, personally and allows you to be a student. Your research hasn't been funded specifically other than the fact that you may have an office, etc. There is probably a tuition waiver, which is a sort of general funding.
You could list the department and university generally as you suggest. You could probably also list "none", but the department might be the better option.


If you think you are on the edge of being annoying, then it might be better to wait. But, you don't have to wait passively. See what other, backup options you might have with other professors and start a conversation there. Be a bit tentative with them, of course.

And, if he is negligent about responding, note that he might also be negligent about giving you the guidance you need. So, other options are worth a look.

But, it is also possible that he is just a last-minute procrastinator sort of person, so be prepared to spring into action if you get a favorable response.


I had the same experience with arxiv and it took only 1-2 days after they change my paper track. However, they mentioned it may take up to several days. The arxiv helps says

  On Hold

  Your submission was identified by arXiv administrators or moderators
  as needing further attention.

  Submissions may be put on hold for a variety of reasons, ranging from
  questions about proper classification, pending moderator approval,
  presentation issues, copyrighted PDF, etc., to editorial concerns.
  Most of these do not require any further input from the submitter and
  will be dealt with in due course. arXiv urges submitters to be
  patient. Due to the large volume of submissions, it may take several
  days before a resolution is reached.

  Note that oversize submissions are automatically put on hold, and this
  is one particular circumstance in which submitters should follow up
  with arXiv administrators.

  Submissions in this status will not expire. Authors must not create a
  new submission with the same content when a pending submission is on
  hold.

  Please be sure to include the submission identifier of the form
  submit/NNNNNNN when contacting arXiv administrators.

wait for few more days and send them an email. They are quick in response.


Medical school admissions vs. STEM PhD admissions in the United States

This may have changed but we studied cartels in college and the American Medical Association (AMA) was called a cartel by my professor.

In the US the AMA not only sanctions the medical schools but puts a count on how many students can be accepted. Since there are a limited number of slots competition is more fierce.

There is no external body limiting STEM or other graduate school departments.

STEM and other PhD can get grants as they are producing a product (thesis) that can be (and often is) sponsored.

In medical school the only product is medical training for the student. There is little to no incentive to sponsor a medical degree.


Is it worth/okay to write an email to a grad school I'm waiting on in an attempt to strengthen my position as an applicant?

I think David's comment sums it up well:

  Emailing the admissions office will almost certainly do nothing. Emailing a professor you'd like to work with could be useful[.]

Regardless, emailing is a complete shot in the dark -- the more likely possibility is your email is ignored. But it depends on how you write the email, and how impressive the additional internship is.

For best results, I would not phrase it as a way to boost your application, but rather just an email to say "hi" and introduce yourself, and ask about the status of your application. But then you can find a way to throw in the additional qualification somewhere.


Should I try to re-invent the wheel while doing research?

I don’t think this approach is feasible for the following reason:

Theoretical research (and any other research for that matter) takes much more time to perform than to understand.
For example, if you have sufficient mathematical background knowledge, I am pretty confident that a few hours suffice for me to make you fully appreciate and understand the entire (theoretical) research I did in the last year, such that the only difference between you and me would be that I have more experience with thinking in these my terms.
I am not very familiar with the history of quantum mechanics, but I am pretty confident that writing down the axioms was the result of quite some hard thinking, conceptualising, and a considerable amount of experience.

If this weren’t the case, it would be impossible to advance a field beyond what can be done from scratch in a lifetime.
Rather, it is an ongoing challenge for science to improve didactics, programmes, etc. to bring new people to the forefront of a field within a reasonable amount of time, such that they can advance this front – standing on the shoulders of giants.
As a sidenote, take a look at some really old mathematics textbooks to feel how didactics has marched on and how important that is.

That being said, trying to do some things from scratch at times can be a helpful exercise that yields a deeper understanding of the matter and trains your field-specific problem-solving skills.
But mind that this should be only as an exercise – you do not want to do this all the time.

Finally note that (at least in the fields I am familiar with), most theoretical research is not about coming up with a new theory, new axioms, or similar, but working out the consequences of existing theories.
If you can come up with a new, useful theory, that’s great, but chances are that this will only happen after you gained a considerable amount of experience with the existing theories and doing theoretical work in general.

As a complete sidenote: Doing a PhD without a supervisor experienced in your respective subject is usually not a good idea.


Complaining about an ISI journal's unreasonable behavior

First, to quickly address your explicit question in boldface, here's the official words from Thomson Reuters regarding their journal selection process for Web of Science and annual review:

http://wokinfo.com/essays/journal-selection-process/

While they apparently take timeliness and peer review very seriously, my impression is that a single instance of slow external review is not a strong enough reason to remove a journal. As this recent blog post on Nature shows, they do ban journals rather aggressively when they feel necessary. But those dropped journals are serious offenders of abuse and are clearly hurting Thomson Reuters' business.

Every researcher experiences unfair rejection in some way or another once in a while. I understand that it is very unfortunate that this has happened at a very early stage of your career. But this seems to be a lost cause at this point. And if you are sure that it was unjustifiable and if you do want to take some action, the best you could do seems to be let Editor in Chief know exactly what happened by writing a letter from an objective viewpoint in polite language and in sober tone and ask them to consider what they might be able to do to improve contributor experience. If you do not receive a satisfactory reply from them, you might consider reporting everything to the publisher that owns the journal.

But before you take any action, you should ask opinions from experienced researchers in your fields, such as your advisor. This is very important because different fields have different cultures in academia.

I assume that you are enrolled in a Ph.D. program in mathematics; I saw your post on MathOverflow. If this is the case, you might want to take a look at the most recent yearly report by American Mathematical Society on how long it typically takes for a paper to get accepted:

http://www.ams.org/notices/201210/rtx121001473p.pdf

As you can see, the median time from submission to final acceptance varies greatly from journal to journal. You might want to notice how it takes a long time to get your paper reviewed by some of the most respected mathematics journals. For instance, Annals of Mathematics, which is arguably the most prestigious journal in mathematics, takes 24 months on average for review. The Memoirs of American Mathematical Society averagely takes more than 18 months from submission to acceptance. Granted that the practice of these journals is more of an exception than the norm, two years of review is certainly not unheard of in mathematics. So, while I tend to believe that your paper could have been reviewed much more quickly because a typical paper certainly does not require two years, it is impossible for us to tell if it was unjust or not without more context.

As for the priority issue you brought up, if it is in mathematics, I must say that you should not be surprised if you do not receive much sympathy. Reading your post, it appears that you did not make your preprint available to other members of the mathematics community before or soon after submission. Because mathematics has a much longer review process than other fields, it is quite common and, I think, very important to disseminate your results as soon as possible by, for example, uploading your preprint on arXiv or directly sending it through email to people you are sure will be interested. In fact, some journals explicitly encourage authors to upload their preprints on arXiv upon submission.

With that said, I understand that arXiv and other means of "pre-publication" are not for everyone. In mathematics, for example, one Fields Medalist mentions unpopularity of arXiv among East Asian authors he noticed during his little experiment on arXiv usage. As someone who was born and raised in Japan and received a Ph.D. from a Japanese university, I know how people may have their own valid reasons not to make their preprint public. You may have some strong belief or policy regarding science publication models as well. I din not use arXiv when I was a graduate student in Japan, either. However, you should not complain when someone "beats you to it" when you could prevent it by following the normal practice in the community.

Now, if you managed to read this wall of text this much, that means that you are the good kind of person who can stay calm and be in control of yourself in a tough situation. And, obviously, you have good math skills with which you proved new theorems worth publishing. So, if there is one thing I am sure of, it is that you have been heading in the right direction as a graduate student.

If you feel like the journal caused an unnecessary delay or "gap year" of some sort to your career, I guess you're right. But personally I try not to overthink, and try to think it's just another unavoidable glitch that often gets us out of the blue in our lives. (Notice the word "try." I fail very often.) You know, there are so many horror stories like yours out there in mathematics... (And never ask why I've been doing a postdoc for so many years!) It sucks for sure. But probably the best you can do now is talk to your advisor, who is there to give you advice anyway, and get back to your math life as soon as possible to prove more theorems. Good luck!


What are some options for a graduate student abandoned by Ph. D advisor?

There are two questions to answer:

  If you got another project from this advisor, would you stay?
  If you got the opportunity to switch advisors, would you leave?

If you are willing to stick with this advisor, you should bring up your dissatisfaction—and perhaps suggest a plan of action to "migrate" to another topic. (Can you, for instance, use the methodology on a different problem where it might be more successful?)

If that isn't an option—and to be honest, I suspect it isn't—you should work as aggressively as you can to find a new advisor and a new research topic, while if possible staying under the radar. You don't want to create a situation before you have somebody firmly in your corner who's willing to support you.


Graduate Program Director Congratulating Me on Failing Comprehensive

No one writes these letters "by hand," but rather cuts-and-pastes names to avoid writing the same thing dozens of times. It seems extremely likely to me that this person copied a standard "I'm pleased to relay ...", used to tell students they passed, into the letter telling you you failed, and then didn't notice this. There isn't anything else in the letter that seems at all disagreeable. Seeking legal recourse, etc., without even finding out whether this is a typo seems like a severe over-reaction.


Not sure if a postdoc is for me. Terrible at quantitative methods

First of all, happy to hear you're doing better. Many people go through times in their academic career where they feel like utter frauds, it's unfortunately common.

To your question - I think the key point here is to be absolutely honest with any potential employer. Tell them your strengths and weaknesses and they will make the call on whether you will be a valuable addition to their group. If you tell someone that you would not be comfortable running quantitative analysis and rather focus on something else, and they take you, it would be unreasonable of them to later demand that you run quantitative analysis.

Similarly, if someone is willing to take you under the requirement that you learn these skills on the fly, you need to make a very honest assessment of your own capability to do so. If you can - go for it; if you feel like it'll be too much, politely decline and let them know that you're probably not the best fit for the position.

Good luck!


Reneging a postdoctoral offer from Canada due to Canadian work permit delays

Whether this specific Canadian professor would understand we, of course, cannot tell. Yet people tend to be understanding of delays due to bureaucratic visa issues, or things just not working out - especially if you communicate this clearly. I would suggest reaching out to that professor, laying out the situation and seeing if anything can be done. Perhaps they're willing to delay your start by a year, perhaps not. What you don't want to happen is the professor reaching out to you a month from now, asking when you're planning to show up, and you having to respond that actually you started a completely different position.

A sidenote is that you'd probably not be legally bound to a one-year commitment in the US, but I think you're right in not wanting to burn those bridges before they're even built.


How should I approach a professor whose class I'm taking for advice regarding a project I'm working on?

Ask and find out.

That way you will know instead of just thinking about it. Either it will be no or you will get the advice you seek.


Is it acceptable to say that a reviewer's concern is not going to be addressed because then the paper would be too long?

This is the kind of thing you ask the editor about. "If I include this philosopher's view, the manuscript's length will increase by roughly 40%. Are you sure?" If the editor says yes, you're in the clear - they are clearly going to waive the word limit. If the editor says nevermind, you're also in the clear - even if the reviewer objects, the editor's on your side and can overrule the reviewer's objections if the reviewer recommends reject.


Providing a novel tool is not necessarily novel per se and even with a novel tool you still might not qualify for the editorial line of the journal. But I can't say really with this information only

A - Usually reviewers do not have even knowledge of all the papers in a journal or conference. That means that if they rejected you for that, it's that the same reviewer reviewed both papers. Moreover, they should not have any ground to favor one tool over the other, since they are both unaware of the other, and they are both new. It usually is a good thing when 2 tools come out at the same time in the same journal, because it usually leads to a comparison paper :p
B - Other tool couldn't cite you since your paper was rejected. Maybe given them the website, but that's a gray area i think.
C - As a rule of thumb i don't give up on a paper I think it is interesting. If your tool is better than the other, then compare it in a paper (maybe conference rather than journal). If your tool is worse and you want to improve it, do so and be better, then compare it. If you don't really care, and only have a bruised ego from the rejection (yes, i know, it hurts...), you can give it up. But I still would say, don't, because there is always room for improvement.


Is it a good idea to publish a complete open-access solutions manual to accompany my open-access textbook?

Consider a compromise: Even numbered problems have solutions provided, odd numbered problems do not. Make sure each important point and degree of difficulty is covered by both.

An instructor setting homework would base it on odd numbered problems.

An independent student, or one that wants more practice e.g. before an exam, would use the even numbered problems.


Could getting an MS in CS be bad for my career?

One recurring issue I've seen in folks considering a CS M.S. or Ph.D. is a belief that the advanced degree will qualify them to employers as some sort of "super-programmer". This is generally not the case, and I think it's where folks get the notion that an advanced degree can hurt your job prospects. In my experience very few companies are interested in hiring folks with advanced degrees for jobs that can be handled far more cheaply by someone with no degree, but a lot of experience.

Where an advanced degree becomes helpful is in domain knowledge. Somebody with a C.S. Ph.D. may or may not be a decent web site developer, but there is supposed to be some (tiny) area of CS where they know as much as anybody on the planet. If they can find a company that needs that particular bit of knowledge (or something closely related), they have a good shot at a well paying job.

Once you have an advanced degree you shouldn't be looking for "programming" jobs, you should be looking for jobs as an expert in a topic like machine learning, compiler code generation, agile methodology, high-availability databases, etc. etc. There aren't as many of these jobs as there are "programmer" jobs, but there is also a lot less competition for them. Lots of excellent programmers are self-taught, but not so many experts in convex optimization.


What can I do after giving GRE and TOEFL exams?

How should I know which universities should I apply for?

As JeffE mentioned in his comment, you should start by asking your professors, and others at your school what they suggest.  It sounds like you've already been given good guidance to shoot for a range of schools, but you should avoid simply picking from a list and do some serious research into the type of place where you believe you will want to study.

  There are so many good universities in US that it confuses me. What are the parameters that I should be considering while deciding where to apply?

I would start by looking at the web pages of schools you are considering, and seeing what kinds of research the professors are working on. You may find that this is overwhelming, but I think you'll start to find some places that interest you.  I actually began my search by explicitly thinking about where in the country I didn't want to live for five years, and then went from there (not necessarily the best method, but it gave me some limits to the search).

  I don't want to just randomly apply and get rejected. Is there a way to know it before hand - what things a particular university would be looking for in an applicant?

This is dependent on the departments you apply to, but in general (and this has been answered many times on this site): schools are looking for an indication that you have the potential to do quality research.  The best way to demonstrate this is by having research experience and by having one or more publications under your belt. Letters of recommendation are extremely important, and grades are important, but I would say grades serve as more of a barrier rather than an indicator (i.e., lots of people have the grades, but not all have the other factors that make good candidates).

  Most of the people have suggested me to select 2 ambitious, 3 moderate and 2 safe universities.

This is a good start.  Some might suggest adding more schools (you never know), but this does get expensive and if you are relatively confident you will get into the "safe" schools and believe you will be happy working there, then you're probably on the right track.  Bear in mind that all PhD programs worth the degree do turn away qualified candidates.

  I am referring to this list for all my analysis. But its difficult to know the standards that I should use to decide what an ambitiuos university is. I mean should I consider the top 10 or the top 30 universities as ambitious.

This does depend on your situation, and it's almost impossible to give an answer strictly for your situation.  If you have peer reviewed publications and get outstanding letters of recommendation, you have a good shot at some top universities.  But no one is guaranteed to get into any top-10 program, so don't be surprised if you don't get accepted even as an outstanding candidate.  Again, it comes down to doing some research and talking to people about individual programs.


The correct answer is not to wait until two days before the deadline to check in on your co-author's progress. Presumably this is no longer an option.

If the section is not necessary, take it out. If it is necessary, you and your non-tardy co-authors can try to get together and do it together before the final deadline.

You should certainly tell the tardy co-author what you plan to do (I mean the collective "you," as in you and your other co-authors).

If the tardy co-author's contribution doesn't make it in before the final deadline, then his name won't go on it either.

Note that if this was a paper being submitted for publication, e.g. a conference submission, and not for school, you would likely just miss this deadline entirely and have to wait to submit to another conference.


Is the adoption of IS0 9000 principles, or even actual ISO certification very common in universities?

I know of one university which is ISO 9001 certified.  Most universities are not.  I have not been able to discern any benefit to the certification.  I am not aware of any "science effort" that is certified.


Using Wikipedia definitions in research paper

I would recommend that you do not use Wikipedia definitions---they're good as a starting point for informing yourself, but aren't generally considered reliable enough to be citable literature.

Instead, follow the references provided on the Wikipedia page to back up those definitions, and you should be able to find a more primary-source document that is appropriate to take definitions from and to formally cite.


Will they send offer letter within 15th April

There is certainly a possibility that you will get moved from the wait list to acceptance before April 15th, but there is absolutely no guarantee or requirement of further contact. By "possibility", I mean this happens to students every year and it isn't particularly unusual - but I also mean that this only happens to a minority of students, and is hard to predict due to the nature of statistics and small numbers per program. Some programs might admit 2 students and both admitted students accept, while others might admit 20 yet go 2+ full rounds of wait list contacts before admission decisions are officially finished.

The general advice in the US is that you are safe to wait until close to that April 15th deadline for acceptance if you are not certain that's where you want to go, even if you are just holding out to see if any wait listed programs might accept you. Waiting past that deadline is risky unless you request and obtain an extension, as programs are well within their rights to rescind their offers and move on to their own wait list after the dead line.


Is it possible to become a research assistant just after b.tech?

Yes.

First be admitted to graduate school.

Then convince a professor to hire you.


Everybody cheats, administration does not care, what to do?

Unfortunately, in this kind of situation, it might be best for your friend to look around for a different educational institution.  It is all very well to say "just stay strong and don't cheat", and of course she definitely should not cheat, but it is still demoralising to work in an environment that systematically incentivises bad behaviour and punishes good behaviour.  Particularly given that her relative standing and future opportunities are being harmed by being compared to a substantial number of students who cheat, it would be good to look around for other places she can go.
Now, if there is no escape from this school (i.e., if your friend has no opportunity to go somewhere else) then I would suggest she try to set herself apart from the other students by doing some kind of extra-curricular project that cannot be faked.  If she can use her coursework knowledge to create some valuable project that she can exhibit to show her skills (e.g., writing a good paper on a topic, building a working go-cart, creating a diorama of how a smelting plant works, etc.) then she will have something to show recruiters for later schools so that she can demonstrate her knowledge and ability.


How should one advertise a program if it doesn't lead to jobs?

If the basic degree is still Physics with a bit of astro tacked on I don't see the problem. Even pure Astrophysics degrees usually follow all the core physics classes before specialising.

For example, my Astrophysics degree is probably about 75% identical to my pure Physics counterparts, so as long as students make potential employers aware of this, they should be just as employable as a Physics graduate.

As a side note, perhaps students should be encouraged to study what they actually find interesting, not what will get them a job. They are likely to perform better if they enjoy the material, and with better grades and an enthusiasm for their degree, the jobs will come.


How much does a publisher charge authors if they want to make their book open access?

For SpringerOpen to publish an open access book, author fees vary according to page length, where 525 words = 1 page, and costs start about €7,000.

One option to publish a book for free would be to self-publish it using the open-source, free Open Monograph Press software.


What are the pros and cons of being a volunteer editor for ACM XRDS?

While I don't know ACM XRDS in particular, in general the pros and cons of service of this type as a student are:

Pros:

You will get to know the journal publication process well, which will help you with publishing your own work.
You will get to know your field more broadly, and likely pick up interesting networking connections.
You will get to affect (slightly) the scientific dialogue.
You will get a nice bullet-point on your CV.

Cons:

It might be a lot of work, and thus might detract from your efforts on classes, research, other projects, or having a life outside of research.
You might discover that you hate the work, and be faced with a decision of sticking it out or quitting.

The likelihood of the cons applying depends very strongly on the particular journal, so I would recommend emailing a couple of the current editors to ask how much work it is and how much they are enjoying it.


I am highly suspicious that a big name in a field would make up a bunch of one line reviews for a submission. You should have definite proof and should think long and hard about how irrefutable your proof is before proceeding further. Bringing this up will reflect extremely poorly upon you  and your co-authors if you turn out to be wrong.

That being said, if you believe that you have proof of foul play, you should raise the issue with the editor-in-chief or whoever is higher up the totem pole. If you turn out to be correct, someone should inform the editor's school or place of employment about the academic misconduct.

If you'd like to take a more cautious path, you can email the editor-in-chief and ask if there was a reason all of your reviews were so short and if they had any suggestions for avoiding this in the future. You'll side-step the direct accusation while bringing the reviews to their attention.


Why professors spend most of their time to write proposals than doing research?

I'm a bit puzzled by the word "hidden," since I don't think the answer is at all hidden -- in fact, I often discuss this with my students. Why spend lots of time writing proposals?

(1) It's expensive to run a lab! At least in the U.S., a graduate student typically costs ~$50k/year, which includes tuition and overhead costs that the student doesn't see. Postdocs are ~$100k/year. Equipment and supplies are not cheap. The sum of all this is a lot of money.

(2) For a variety of reasons, it's hard to get money. The success rates for proposals at NIH or NSF are around 10-20%, meaning that most proposals don't get funded. Certainly more than 20% of proposals are very good -- at least based on my experience on grant review panels. Writing a proposal that's at least very good takes a lot of work. Writing N such proposals so that enough get funded to keep one's lab afloat takes an even larger amount of work.


Can I write a thesis or paper without my school's support?

Can I just write and submit a paper to a conference?

Yes, absolutely anyone can write and submit papers.  It's difficult to do a good job on your first attempt if you don't have any guidance from a mentor, but it's not impossible.

  I'm a Master's student, and I'd like to write a thesis, but my grade's don't qualify me (you need at least a 3.75/4.0 GPA). Can I just go ahead and write on?

Nobody can stop you from writing something, but it won't be a thesis.  You'll lack supervision from an advisor, which will make it much harder to do a good job, and even if you manage to do a good job the department will not accept it as a thesis.  (Bureaucracies don't work that way, plus working with an advisor is considered a crucial part of the process.)


Most graduate schools in the U.S. follow a policy that accepted candidates are not required to make a decision until a set date agreed upon by the schools (April 15th, I believe).  This means you can (and should) take as much time to make your decision as you need.  It sounds like you do need to make your decision earlier than that deadline (but it might be worth finding out if the other schools do follow that policy and simply asked you to make a decision earlier), so contacting the other schools is probably a good idea.

Remember, however, you are making a decision that will at the very least directly affect the next four to six years of your life, who you work and collaborate with, future contacts, where you live, and what your future employment prospects are!  So, I'll reiterate: take the time you need, and get as much information as you can if you are up against a hard deadline.


What topics should go in the thesis Appendix?

If the methods that you are considering including in the appendix were necessary to arrive at your final results, then they certainly aren't "off topic". Without knowing your field of study or your topic of research, it's hard to give a more direct answer than that.

I'm in the social sciences, and we often include mathematical proofs in our appendices in order to save space in the main text (as well as not distract from the substance). Nonetheless, given the importance of transparency, we include our proofs for review by others.


How to properly cite when using most of the text verbatim

It isn't plagiarism if you don't represent it as your own work. If it is cited, it isn't plagiarism. However, copying complete articles is fraught and comes up against copyright restrictions which can result in either legal action or lawsuit. You should talk to someone locally about what is allowed and what is not. Librarians are good at that as is the legal department, if available, at your institution. As to how to cite, either of your options seems fine. They both indicate that you are quoting, not just paraphrasing.

Just be sure you are covered or willing to take the risk of possible censure.

Contacting the article's author may give you additional guidance and possibly permission.


How to negotiate a salary in Norway/Scandinavian countries?

I'm a PhD student, born and raised in Denmark. I have not applied for jobs in Norway, but have done some teaching in Norway and had a few interactions with Norwegian academics.

The Norwegians will appreciate humbleness, good manners and honesty. In the culture, it is very acceptable to care for your family.
In all communications in particular, good manners is key.

My recommended approach: Be humble and grateful for their offer, state all the reasons why you really want to work with them, then, without overdoing this (remain humble) state all the reasons that you are valuable. Then, proceed with honesty: state that you want to be at their workplace, how much you want to get paid, that you have some experience and that you need some funding to support your family.

Wish you luck!


Can my degree be revoked if my relationship with my advisor sours post-defense?

Once a degree has been conferred, it is exceedingly difficult to retract at without clear evidence of misconduct. Having a souring of relations with your advisor definitely does not rise to the level where you should have to worry about your degree being revoked. It is definitely worth mending your relationship with your former advisor just on professional grounds, but the "safety" of your degree shouldn't be one of them.


How do I reconcile with a vindictive professor, or at least protect my grade?

Without knowing the professor, my bet is that you - unfortunately - will have little possibility mending your relationship with him. Maybe he is a believer in second chances, but judging from your description, I doubt it.

The first thing you need is a reality check - are you really being treated unfairly. You need to get a hold of some more senior students or friendly faculty members, it could either be at your own university or in an online community. Show them your graded coursework and the syllabus, and have them asses whether you are actually being treated unfairly. If you get down marked by 80 % or more, it should be obvious.

If you are, then your should contact your local dean immediately. Let him or her know the full story, it is their job to listen and deal with these things. Make it clear that you would like to just get this over with as easy as possible, but you don't feel safe taking the exam with this particular professor. If you are lucky, they have a procedure ready for these things. When you approach the dean, stay descriptive, and don't feel like you have to fight for your right. It should not matter, but unfortunately it does.

Make up your mind in advance whether or not you would be ok with transferring to another course. Even though it may slow you down a bit - or force you to read faster - it may be your best option.

When all this is done and over, just stay clear of that professor, and you should be ok. If I should guess, I would say that unless this is a very young professor, this is not the first occurrence of such a situation, and the professor will have a 'rumor', even among his political connections. You should be very unlucky if this comes back to bite you, and it would also be very unlikely that the professor would actually go out of his way to harm you.


Erratum or corrigendum on arXiv too? Should the authors lists match?

#1 is best: use arXiv's "replace" option to upload a new v2 with the same arXiv: id, which has the corrections incorporated into the paper.  The arXiv preprint has its own life, independent from that of the published paper, and this makes the preprint as useful and convenient as possible - people following the arXiv id or URL for the original preprint will get the corrected version automatically.

In the comments field, I would put something like "incorporates published corrigendum".  If the corrigendum has its own DOI, I would include it in the comment as well.  (And while you're at it, make sure you've included the DOI of the paper itself in the appropriate arXiv field.)

Keep the authors field unchanged.  People don't really need to know which authors actually wrote the mistake or the correction, so long as all of them accept responsibility and approve the correction.  (Unless there are special circumstances - e.g. the correction is itself a major scientific advance, or the "mistake" was something like data fraud and the guilty party needs to be outed, in which cases you could consider adding a note within the paper itself.)

Note that the original v1 will continue to be available for those who click it explicitly, so anyone who really wants to see the history or compare the versions can do so.


Should I change my undergraduate thesis topic because of travel issues?

Some thoughts:

Can you collect oral histories without travelling to the US? For example, you can do interviews through Skype or work with a research assistant to collect some of the oral histories for you?
Why are you fixated on collecting oral histories? It seems to me that, in this case, the research question may be answered through some other means of data collection. For example, document analysis may be an alternative.
It seems to me like your equating travel (or at least presence in a country) with the feasibility of your research question. I'm not sure that's appropriate. What would you do if you can't get to NZ, say because of visa or cost issues? Select a third country? What happens if you can't get into that country? Select a fourth?
Why are you intent on a bilingual thesis? There are a number of great South American wine manufacturers -- Chile, for example -- where you might apply the same basic research question.

Good luck!


When should a faculty candidate notify schools about a competing offer?

I think it depends on the deadline the offering school gave you. If it's after you expect to hear from the other schools, maybe waiting will be OK. If it's before, then you may have to light a fire under the slower schools. Also, there's a big difference between being "notified that she is going to receive an offer from" the first school and actually receiving it. I wouldn't do anything until you have the first offer in hand (or email).


Is it expected that a part-time masters student publish before transferring to a PhD?

The expectation to publish does not depend on whether you are full-time, half-time or spare-time student, it is based on the general expectations on students in your field, department, or academic culture, or some combination. If a PhD thesis is a monograph then the main focus will be to complete such a thesis. this commonly does not preclude publishing as well. If you need to write a thesis that consists of published papers and manuscripts then that is what you need to do.

I doubt the advisor is the key player here although that person will be representative of what you can expect from your graduate school education in terms of expectations on your writing. So check what is written in the form of PhD these and you will know. Communicating your results will inevitably be required so some form of written result will be on the horizon.


Is it plagiarism to copy from the textbook and referencing properly but not using quotation marks?

Plagiarism is not a matter of quotation marks. The question is whether, when reading your homework, it is clear that the excerpts are not your own words but from some place else. You could also use an indentation for a paragraph, or put it all in italics. Quite often this is a matter of style guides or the preferences of the respective department or whoever is grading your work.

However, if you simply referenced a book, chapter or anything else at the beginning of a section and then started copy and pasting, at worst changing the order of paragraphs and mixing in your own words to connect passages, I'd have serious problems with that. Even if not reading your homework cover to cover (but let's say when opening a random page) it needs to be clear what is copied and what not and where copied passages are from. So yes, depending on how you have formatted and phrased the text, the omission of quotation marks may well be interpreted as plagiarism.

By the way, copying several paragraphs from any source will most likely not get you the best grade. Quote where necessary but focus on your own thougths and words and use the quotes to get your overall point across.


Explaining undergrad transfer on application to grad school

If there were no GPA problems at the first school, then there's nothing in that first transcript to look askance at; hence, no explanation needed.

However, the specific change you made, from engineering to pure math, might help your application.  Perhaps a small anecdote will help me explain why.

When I took my Calculus III (multivariate), it happened that my fellow students had no patience for proofs.  They were overwhelmingly engineering students. One of them became a self-appointed spokesman for the impatient majority, and would interrupt the instructor in the middle of a proof of a major theorem: "Excuse me, Ma'am, could you skip the proof, please, and go straight to the applications?"

Not all engineering students are like that; and to be fair, the large number of credit hours they are frequently expected to take per semester isn't conducive to stopping to smell the roses.

Conclusion: a brief mention in the essay or cover letter of your change of major from engineering to math might help your application.


How can a masters student compensate for lack of solid foundation in basic math and CS fundamentals?

That you realize this is good, but the appropriate approach depends on lots of individual factors.  The people who are likely to be able to give you the best advice are your professors/advisor.  They probably know best where you are at and what is most important for you to succeed in their program.  Also, informing them that you are aware of your deficiencies and are trying to make up for them should improve their opinions of you, and also make them more willing to help you succeed in the program.

That said, here are some things that can help: start tutoring or TAing for lower level math/CS classes (I first really understood eigenvectors when I was tutoring other students in linear algebra), going through texts on your own (exercises are the most important!), taking/sitting in on undergrad classes (some of our grad students with weak backgrounds do this), typing up your own notes on this fundamental material, finding people (students or faculty) you can ask specific questions.

Also: read up on the impostor syndrome (on wiki-p and here, say).  You may have it.