Is it normal for an academic conference to ask for a revised abstract before paper acceptance?

Having been on the other side of similar transactions, what I suspect is going on is that they think your submission is not up to their standards (of quality / focus / formatting / whatever), but that they think it is salvageable and are trying to work with you to help make it acceptable.


Planning for physics PhD apps - Classes vs research?

Research experience and track record is more important than courses you have taken.  You will very likely be required to take Jackson E&M for the PhD program.  You might be required to repeat it if you took it before, depending on the program's rules.  Keep in mind that classes you take (or research you perform) after you apply for the PhD program usually do not change your admissions decision.

In sum, I recommend postponing the E&M course.


How many hours per day do I need to work to become a very good PhD student?

Uri Alon has a lot to say on this subject. See from 6:00 onwards in this video, the whole of this video, and the first 2 or 3 minutes of this video (they are all from one talk broken into separate videos).

The way he once described it to me is this: According to the parento principle, you get 80% of the benefit for the the first 20% of the effort. But productivity doesn't just keep increasing if you work more.  If you do 0 work, you will fail. If you work 100% of the time you will also fail, because you will die. Thus there must be a curve with a peak in between 0% and 100%. Because its a peak there will be two x values (time spent) that give each y value (productivity): working slightly less that the optimal time will give you the same amount of productivity as being slightly to the right.

Thus it is always better to be slightly to the left of the peak as you get the same productivity with less effort. Where that peak is will be different for different people, and you will have to find your own peak, but many people stop working harder when they realize that putting more effort in is making things worst rather than better, and thus are on the right of the curve.

The other reason for being on the left is that if you are on the left of the curve, you wll have to reserves to give a little extra for a short term boost when its needed.

I don't know where your peak is, but for many people its probably at 40 hours or less a week. Remember this is actually time doing your work, not just being present in the office.  Just make sure you are working for those hours you think you are working, and you are taking proper time off in the hours you are not.


How to search for articles from a specific journal in Google Scholar when the journal name is a subset of other journal names (e.g., Science)?

Like Google, Google Scholar seems to support boolean operators. So one way to solve the problem would be to use "-source:[string]" (note the minus sign) to exclude by hand journals with names containing "[string]". This may take a few iterations of trial and error before you get only the results you want, and can of course also be used in conjunction with the "site:" qualifier to narrow things down further. E.g.

coffee source:"physical review" -source:"physical review letters"

Generally speaking, boolean searching is a powerful technique, and one that a lot of people seem to be unaware of.


What are the important factors I must consider while applying to a CS program for an MS after majoring as a mechanical engineer in my undergrad?

Overall, your MS in ME will be viewed positively when you apply for MS in CS with Machine Learning specialization.  What will matter most are how many computer science courses you have taken (and grades you received) and how many relevant math classes you have taken -- calculus, probability & statistics, linear algebra, numerical methods, optimization.  The project work you have done in simulations could be very relevant and helpful, too, if the software you wrote was something more than procedural programming or deterministic simulation.

In your Statement of Purpose, it would be to your advantage to make a strong link between your ME education and work experience and your goals in CS-ML.  Are there applications or problems that arise in ME that you want to address with ML methods? Are there particular methods of optimization or classification that you've encountered in ME that you want to explore further in other settings?

Regarding what schools to which you might apply: I would suggest that you aim at CS departments that are part of an institution with a strong "engineering" culture or focus.  In the US there are many colleges, universities, and institutes that have an engineering focus, including the Polytechnics, Case Western Reserve, Harvey Mudd, Carnegie-Mellon, and many others.  In contrast, the CS departments at Yale, Harvard, etc. have less orientation toward engineering.


Is using academic writing services for a thesis considered plagiarism? Can they write in an original fashion?

There's a big difference between paying someone to proof read your thesis (generally acceptable, and sometimes encouraged) and paying someone to write original material from scratch (plagiarism).

The way your question is worded (and from one of the comments about getting someone to "edit and write the thesis") it sounds like you are asking whether if you pay someone to write part of your thesis, will they do it well enough that it wont be detected by plagiarism software (e.g., the idea that people who write paid essays just copy and paste huge chunks from Wikipedia and random journal articles). My apologies if this is not what you are asking. But to state the obvious point, paying someone to write your thesis and contribute intellectually is plagiarism and unethical whether they do it in a rigorous or a sloppy way. It is plagiarism, because you are not acknowledging the source of the intellectual effort.

Surely if you are paying someone merely to refine your expression, phrasing and give general guidance on structuring, then there is minimal risk of plagiarism.


Is a journal based on extending Wikipedia articles feasible?

There are already three journals very similar to this idea:

WikiJournal of Medicine
WikiJournal of Science
WikiJournal of Humanities

There is even a UserGroup in which these are operated.


Forward-citation chasing: Is there a formal study for what I'm doing?

There is no name for it that I'm aware of.  It's how one uses the literature correctly.  You search backwards until you find the seminal papers, and then you search forwards, and then repeat until you retire.

It's much easier now than it used to be.  As recently as the '80s, the only way to do this was to find a library with a complete multi-year set of the Scientific Citation Index and grind it through.  Now, even google scholar just lets you click a button and find all the papers that cited the paper of interest.


Which tables should be put in the appendix?

I like to think of appendices (or supporting information, which is the same thing for a journal paper) in terms of the narrative structure of a text. The main text should contain everything that makes up the "story" of the work.  In it, a reader who basically trusts that your methods are sound should find everything that they need to understand the work.

There are often, however, places where it is important to show your work, but that are not particularly interesting.  If they are lengthy enough that they start feeling like a major detour in the flow of the narrative, then they are a good candidate for moving to an appendix.

Some examples from my own recent papers:

Theorem and proof sketch in main text, boring exhaustive proof with lots of slightly different cases in appendix.
Graph summarizing results plus an example of result detail in main text, all the rest of the results in appendix.
Data from method presented in main text, data showing that plausible alternatives didn't work in appendix.
Intuitive description of method and key mathematical concepts in main text, exhaustive mathematical details in appendix.

Exactly where to draw the line is somewhat subjective, but fortunately doesn't matter all that much unless you are dealing with format or length restrictions.


Co-author keeps delaying crucial part of paper

I have been on both sides of that situation, so I know how frustrated you must feel.

However, the reality is that the number of "collaborative" research that fizzle out and never get finished due to lack of interest, willingness to actually do something, or time is a lot more than it should be. I could give you multiple stories from my experiences but I won't bore you with the details. Let's just say that there are over a hundred hours of my time sleeping in various people's desks and email accounts that will never come to fruition.

Your collaborator may simply be busy, or the worst case scenario is that he isn't able to actually deliver on what he promised and is stalling because they are embarrassed and/or don't want to admit to it (I've had this happen). Regardless of the reason, this is not a good situation, for both you and your collaborator.

Face-to-face and/or heart-to-heart conversations have resolved such situations (in one way or another) for me, but I can't say that it works for everyone. Still, it wouldn't hurt to try. Just let them understand you simply want to know whether the project is still alive or it's time for you to either find other ways to get the project finished or simply move on.


Asking my supervisor to be frank and give feedback

It seems that you are overthinking this. You say she is like a friend. Neither a friend, nor an advisor, has any incentive to lead you into traps. Accept it if she praises your work. Perhaps you are on the right track after all.

But we can all improve at the margins, at least. If you have specific doubts about particular things that you do, or write, ask about just those things and listen to the answers. Perhaps there are suggestions for improvement in there that aren't criticisms, but just pointers to better ways to do or say things.

But, your note almost sounds like you are soliciting negative feedback.

I'm pretty sure that if a friend and advisor saw you going down the wrong road you would be told that. Otherwise she is wasting her own time as well as yours. That doesn't seem like a reasonable action for an advisor.

After all, if you finish and go on to a brilliant career it reflects well on her also. Relax.


How formal should I be when sending an email to the University's staff?

From a US perspective, I think the most important thing is politeness and clarity. "Official" contractions should be fine, as long as the writing is otherwise grammatical. ("You're" is fine, while "ur" should be avoided like the plague.) (There is a slight possibility that this differs at some very formal British universities(???) but it should be fine at any U.S. university.)
I would steer clear of jokes by email, since you haven't met them before and the communication is across a language (and culture?) barrier.
When I email people I don't know who work in staff positions, I keep in mind that they're busy and often deal with demanding people or people who are upset. I usually try to keep the "polite" parts of the email at the beginning and end, so the other parts are clear in the middle.

Good morning,
As a prospective graduate student [from country or university, if relevant to question], I have a few questions about enrolling in the English department that I hope you may be able to help me with. If there's a better person to contact about these questions, I'd really appreciate it if you could direct me to them. [If it's a question about funding or visas, e.g., it's quite possible they would probably have to refer you to another office.]

...
...

[Possible additional clarification about what you have already tried, e.g. "I saw on the department web page that all applicants must have taken an introductory British literature course (link to that webpage), but it did not specify whether courses taught in another language ('English Romantic Poetry in Translation') or about specific areas (like 'Irish Literature' and 'Indian Literature: Colonial Era' would qualify)."]
[If you're attaching any files, have a really good reason, and explain them here. E.g. "In case it helps answer the question, I am attaching the descriptions of the British literature courses I took, with my own translation of the descriptions from [my language]. The original versions are online at [link], [link], and [link]."]
Thank you for your time. Please let me know if you need any additional information or clarification.
Thank you very much,
Your name


How to politely reject a professor's request for work that I was recommended for?

"While normally as a graduate I should be very thankful and jump on this, I simply cannot do the work asked due to time and I believe there would be a more suitable candidate for the work."

That is more or less exactly what you should say. Express your gratitude to Professor A. If you have a major academic obligation taking up your time, like comprehensive exams or something, mention that. Do NOT CC the candidates you have in mind, but do mention to Professor B that you can recommend someone else who you think would be a good fit.


My professor is rigging data and plagiarizing. What can I do?

Your backing off reaction is the appropriate one: cease any form of association with him right away.

The description of your first-hand witnessing of him fabricating data is more than enough to ascertain his academic dishonesty. You don't need to know about nanotechnology to know that manually modifying data to make it pass a statistical test is idiotic and fraudulent. Also, experts in that field will assume the data are real when conducting peer review, so it's not something they can easily detect without repeating the (alleged) experiments.

His 'results' are unwanted. By publishing bogus science he makes people lose time and money, he's robbing legitimate researchers of their funding, he is adding noise that masks the signal. If you can afford to report his behavior please, do it. Depending on where this story takes place, you might lose a variable number of feathers in his striking back, but at the end of the day he is the one who is wrong.

Taking direct action to publicly expose his fraudulent behavior is risky for you, especially since he is your hierarchical superior. But, when he will get caught (because he will), if it is apparent that you were aware of his wrongdoings and still accepted co-authorship or credit for his publications, his bad reputation is going to stain your career. If you fail to prove your claim, it's your career that will be at risk. So, proceed with caution. Note that it is ethically perfectly fine to report scientific wrongdoings anonymously.

Make sure that all institutional reporting routes are inefficient before bringing the issue to another level. It is not clear in your post if you actually tried or if you just assume 'they won't listen to you'.
Since you provided the content of at least one paper, and know about its fake nature, if he submits the paper despite your protests, notifying the editor is a thing you could do. Editors will take you very seriously in reputable journals.
You can also take part (anonymously if relevant) in a post-publication comment on his papers, on websites like pubpeer.com or retractionwatch.com.


Will US graduate schools accept me retaking a GRE subject test in the spring?

A poor test score is not disqualifying if the rest of your application is strong.

However, an April test date will not work for admission next fall. The reason for this is that the US admissions cycle requires acceptance decisions around mid-April. Since the test is in mid-April, and scores won't be available until mid-May, they would have to accept you "blind," without knowing what your scores would be. So you're essentially "stuck" with the scores you have, at least for admission for the upcoming fall semester.


What's the purpose of writing one's academic biography in the third person?

When I wrote a biography of myself, it was because someone in administration asked me to so they could put it into a prospectus, where there would be lots of biographies in a row all in the same editorial voice.

It was specifically required to be in the third person for that reason: all the profiles are presented as though they have been written by the omniscient author of the document. It wasn't written that way because I wanted it to be, but for an actual purpose.

Once written, that biography went on file and was put everywhere that needed one. That includes the university website, future grant applications, other advertising material, commendations for students, reports, papers, and sundry other places. Sometimes I copy it there, and sometimes it happens without my even being involved (sometimes without any actual person being involved!).

In particular, it's useful to put it up front on a public website so that collaborators can easily just copy accurate pre-written text in when they need to provide a profile of me for one of their own purposes.

There are places that I've written a first-person biography, which is generally a lot shorter. Those are places that are 1) in my voice, and 2) where it was worth the fuss of rewriting something tailored to the situation. In general, and particularly for things published by the university, my "official" biography just goes back in again, because it's there, it's been edited, and it's comprehensive enough.


Can I pursue a PhD while working as an Accounting Instructor/Lecturer?

There are many fields—including accounting—which offer “adjunct” positions which allow professionals to give lectures while not having full PhD qualifications necessary to be a professor. They’re usually advertised as “adjunct” or “contract” positions. But it’s also true that in many disciplines, such instructor positions are given to graduate students. It’s largely a question of how financing in the given program is handled.


When shall one write a mathematical expression as a separate line in a paper/Ph.D. thesis?

In the areas in which I work, there are no formal rules and it is left up to the author when to separate an equation and when to embed it in the text.  When I am writing, I find that there are three fairly straightforward principles that work well for me in determining whether an equation (or other mathematical statement) deserves its own line or can be inline with the text:

Will I need to refer to the equation elsewhere?  If so, it needs its own line, and equation numbering as well.
Is it more than ~1/3 of a line long?  Anything so long that it is likely to get broken across lines and otherwise be a typographical mess should be pulled out onto its own line.  Numbering is not required.
Do I want the reader to "pause" and contemplate the equation, or do I want it to "flow" as part of the sentence encompassing it?

This last needs a little bit more explanation... let's elaborate on one of the examples from the original question.  If I write the sentence this way:

  We know that the identity a^2+b^2=c^2 holds true if the system is in condition X.

then the equation should be inline, because the sentence is really about condition X, rather than about the equation.  If, on the other hand, the reader's attention should be directed to the equation, then it is better to use something like the following form, with the equation on its own line:

  We know that if the system is in condition X, then the following identity holds:

    a^2+b^2=c^2

Note: these principles reduce to a similar effect as the style guide given by @silvado


How to revise/resubmit a rejected article taking an unorthodox view

I certainly can't speak for all reviewers, and what I'm saying might be true only for me, but when I review a paper, I try to ask myself three questions: is it interesting for the venue? is it correct? is it improving the state-of-the-art? I need to be convinced that all answers are "yes", and the burden of convincing me is on the authors.

A problem I've seen with some papers is that they focus mostly on showing the correctness of their approach, and at first glance, it seems to be the case with the paper you're describing.  Showing the interest of the approach is tricky, because often the authors are convinced it's interesting (otherwise, they probably wouldn't work on it), and they to think that everybody else understand why it's interesting. Similarly, explaining why it's improving the state-of-the-art might be tricky, especially for novel approaches, but it's necessary to explain why other approaches won't work. You have the right to write: "To the best of our knowledge, this approach has never been used to tackle this particular issue", but then, as a reviewer, I need to be convinced that your knowledge is good enough to make this kind of claim.

Basically, in your situation, what you need is a compelling example (e.g., a situation/use-case where your approach is either the only viable one, or where you can show with experiments or formal proofs that yours is better than others). If you can focus on that point, then you can probably resubmit it to the same journal, but it's possible that you will get some of the same reviewers you had the first time.

Another solution could be to publish the paper first as a technical report (e.g., on arXiv), try to submit it a short version without the proofs and technical details to a specialised workshop, where maybe you can get interesting feedback from the community (for instance, some recent related work), and then use that feedback to improve the paper.


Finding graduate program with large number of high quality peers

Yes, in the US, start with the list you link to. A lot of them are large State funded universities and they have large faculties and most of them cover most fields. But to narrow it to a single field you need to do some research yourself.

They will all have websites listing faculty by department. Some of them also list graduate students. Find departments with a fairly large number of members and then narrow it further by looking at the sub fields and, especially, the recent papers that the faculty has published. But, unless your desired field of study is very esoteric, most large R1 universities and even some R2 places will serve you well. Smaller places can be excellent, but they may also be a bit spotty in the research fields they are able to support well.


Writing a recommendation letter for a senior colleague

The fact you are more junior does not mean you can't write a helpful letter.

Write a letter that describes what you observed, e.g., in his lectures and in his interactions with students and colleagues, and in his research.  Try to be specific.  Instead of simply saying he was a great lecturer, describe the techniques you observed, e.g., that he mixed PowerPoint and whiteboard effectively, answered students' questions really well, how he's mentored and taught you, etc.

After you've outlined the facts that might support it, offer your opinion, that this is an individual who would be perfect for the position.

I'm a lecturer in CS at University of Michigan.  I've written lots of LORs for both students and colleagues.  They're very formulaic.  You can do this.


Is this a legitimate excuse for missing an exam?

Rather than having to think about what is a legitimate excuse or not, I routinely give make-ups to anyone who misses a quiz or exam. Yes, it is explicitly assumed that they are operating with knowledge of what was on the quiz or exam that was given, so the situation is somewhat different, and the nature of the make-up is consequently somewhat different. I explain this at the beginning of the course. One might worry that there'd be too many people trying to game the system, but it seemed not so.

(I think it is not reasonable to demand that people who are sick get a note from their doctor... if it's something like a severe cold, say, because the wisest and most socially reasonable thing to do is stay home in bed, not travel to a clinic... Also, I do like to cultivate the atmosphere that I am willing to believe students' excuses, rather than have the default be skepticism about their honesty.)


Writing Sample Topics: Applying for History Phd

In my limited, but certainly present*, experience with history departments, your writing sample wont be used as a negative indication of language abilities. Your statement of interest and and language test/coursework proof will be noted, but if you have no Portuguese in your sample they are unlikely to notice. Your interests sound like a natural progression and they do not expect to see undergraduate work that directly relates to your proposed topic. If you're worried about it, sit a formal Portuguese test of some kind and report that on your cv.

*before grad school I was the secretary of a history department in the usa and managed admissions admin for it.


Is informing your advisor about a community cause considered unprofessional?

I don’t think that there is a norm for this kind of interaction, and I think that’s a good thing. Some people will be interested in talking about it with you, others will not. It wildly depends on who your advisor is and what they care about.

It sounds like the issues you’re talking about are issues that are in vogue in the US, a country you aren’t from and potentially have never visited. I would leverage that as a way to talk about it with your professor. Ask the professor about it casually. Say that you have been reading a newspaper or blog or something, that you heard about this political issue in America, and that you were interested in getting his perspective on it. Presumably you don’t know a lot of Americans, and it’s natural to ask one who you already have an established relationship with about it.

Bringing it up in casual conversation is a lot better than email, in my mind. There’s less of a chance for the message to get lost, and I know plenty of academics for whom that’s a major factor.


How do I reassure myself that I am a worthy candidate for a tenure-track position, when department would likely have interviewed me even if I wasn't?

There are two things worth keeping in mind. First, while it might be the case that the committee is "forced" to interview a female candidate, it might not. You have no actual evidence in either case, and though it's tempting to assume the worst, there's no reason to, and there's absolutely nothing to gain by thinking the search committee doesn't want you there. So: spend your mental energy working on your talk, your research plans, etc.

Second, even if it is the case that the committee wouldn't be interviewing you if left to itself, the interview is in many respects a "blank slate" -- an opportunity for candidates to impress potential colleagues beyond what's evident on paper, and (of course) for candidates to fall flat and perform terribly. I've been on enough search committees to assure you that several of your fellow interviewees will do terribly, and that conversely it is not uncommon for committee members to say "I wasn't really in favor of bringing X to campus, but now having interacted with him/her, I'm glad we did."

This is all, I suppose, a long-winded way of saying "worry less, and always do your best!"


Can PhD students turn down teaching assistantships?

Turning down a teaching assistant position in your position is probably a very poor idea.

The renumeration for working as a TA normally covers both the a stipend and your graduate tuition.  If you do not have some other form of support (research assistantship or fellowship), you will have to pay your own way entirely.  This is normally financially prohibitive, although there are sometimes exceptions.

Moreover, some doctoral programs (such as my own) actually require that students spend a certain time working as TAs.  The teaching is considered a part of their professional training.  So even students who might have other ways of funding their entire graduate education may have to spend a certain amount of time teaching.


My transcripts are not an accurate indication of my academic ability

The lack of an official advisor is most unlikely to be of any benefit as an excuse for not doing well in classwork. Presumably you have a common core of classes in your major, and you'd better have a good explanation for any significant deficits in those courses. The lack of an advisor might have led to poor course choices in electives, but you could have ended up taking the same courses even if you had had an advisor. Moreover, your advisor didn't take your classes for you; he didn't do your homework or take your tests or complete your projects for you. Ultimately, you are responsible for your performance as a student.


What do you do if your PhD advisor tells to publish your work alone without his name?

Consider the possibility that you are seeing things emotionally rather than rationally. Additionally, you should critically reflect whether your expectations of the operational principles of doing a PhD are realistic. Based on the little information you provide, it appears that your supervisor is doing a fairly good job. He is answering questions and helping you out in your work. In a nutshell, this is the kind of support you should expect.

It is per se not your supervisor's job to "include you in his papers". This has almost certainly nothing to do with him being "ashamed" of you. Authorship in papers is not a courtesy that is, or should not, be granted based on friendship, but due to intellectual contributions. If you are not contributing to these papers, why would your supervisor add you to the author list?

Of course you could ask the question why your supervisor is not inviting you to help with his papers. This may be because your expertise is not necessary for the papers (which is not the same as that he does not respect you!), or maybe the papers have developed from a longer ongoing collaboration. You should not fault your supervisor for not warping his projects just so that you can fit in them somehow.

  What does this mean? How to handle such a situation?

It means that he wants you to be an independent researcher, as you should be. Why do you think there is something to handle, other than to heed his advice and look into publishing your own papers?

In many disciplines, it is fairly common that PhD students are expected to publish their own research without their supervisors. Have you actually attempted to do so? Have you talked to your supervisor in what capacity (helping with experiments and arguments, structuring and presentation, reviewing drafts?) he would be willing and able to help should you go ahead and publish your own work?


Should I send follow-up email one week after post-doc interview if interviewer said they will make decision in "week or two"?

No. Do not do that. You will receive an e-mail one way or another when the PI makes the decision.


When is it appropriate for a post-doc/grad student to be the senior author?

In my field (Computer Science), I usually assume that the first author and/or the "corresponding author" is the one who "did most of the work" and the last author is the one who secured the funding to do said work.  In some cases the latter does not exist (e.g., if a publication is not funded by a research grant/contract) or these are both the same person.  In my opinion and experience, the author with the greatest technical contribution should be the corresponding author.  This is because most inquiries to the corresponding author will be technical in nature.  If I were interested in contacting the authors of a paper for a non-technical reason (e.g., an inquiry to team for a competitive proposal) and I were unfamiliar with the authors (which is unlikely), then I would do a quick Internet search to determine if any of the authors are advisors of the others and contact the most senior one in terms of academic rank.

Therefore, I think it is perfectly appropriate and even desirable for whomever provided the greatest technical contribution to be the senior author.  This may vary by discipline and/or country, however.


Competitiveness and Success Caliber in Academia

No, it's not too late, my former spouse finished a doctorate when over 40 and had a great career afterwards.

But you seem to have an odd view of academia, especially when you write about "competitiveness". That seems to imply that for me to "win" you need to "lose". A zero sum game. It ain't like that, and making it like that will only harm your chances of success.

Academics normally work for personal success. They want to do good work. They strive to extend what is known in their field. But one of the best tools for that is cooperation, not competition. There is no reason for me to think that I'm better or worse than you if I'm doing what I like and produce valid results - perhaps with your help. Or you produce good results with mine.

In fact, many people rise to the "top" in academia for purely random reasons. They choose to work in a field they find interesting. But at the same time, many others, seeing the history, choose to do the same. The field becomes "hot" and so some of its practitioners are seen as hot as well. But it was just chance in many ways.

But the really big breakthroughs have often/usually been the result of teamwork. The fact that many breakthroughs in computing came out of Bell Labs was due to the close association it provided among good people. Those people reinforced one another's ideas in a synergistic way.

My advice is to do what you love. And find others to work with you to achieve success. It can be great success or not, but if life is rewarding it is worth it. You don't have to "beat" anyone.

Also, prominence is a mixed blessing/curse. You will get asked to do more than you want to do. You will give yourself an ulcer if you don't learn to relax. Your personal life may come under a microscope. If it comes naturally you will be able to handle the pressure as it develops, but if you are overly competitive you will find few allies. Relax. Focus on the science, not the success.


PhD Dissertation Introduction: What to call section on thesis structure/overview?

Personally, I wouldn't worry about subtlety in titles.  People who read your thesis are not looking for subtlety, but for information, and particularly from the overview section.  Just call it "Overview" or "Outline" and don't worry about it.


What to do if a peer-reviewed journal took so much time to review your paper?

Generally Editor takes decision on a Manuscript based on minimum two reviewers comments. So one possible reason is the required reviews are not completed yet. Followings are few points which are responsible for it.

Editor has contacted many suitable and potential reviewers, but at least two of them has not agreed to act as a reviewer of your manuscript.
Minimum two reviewers have agreed, but one or both of them are delaying to submit their comments
Sometimes, editor does not satisfy with the one or both reviewers comments, so again he/she send your manuscript to another reviewers.

So there are many things are in behind. But most of the journals generally takes 2-4 months for the first decision and some journal takes more than 6 months and some even more than 1 year depending on above situations..  So if you are in hurry to get this publication and can't wait more, then you may request to the Editor for a final decision at the earliest possible, otherwise you are going to withdraw your manuscript. Since there are number of suitable journal available, so you will definitely find another one.


I am a professor in a top ten math dept. in the US.  I have sat on admissions committees for many years, and talked to colleagues at other top tier institutions about admissions.

First: admissions is not done by a "bureacracy", or "officers".  It is done by some subset of the math dept. faculty, who read the applications, including the letters, the GRE scores, the transcripts, and the essay, and then rank order them.

Second: To get to a top institution, high GRE scores are essential.  These don't guarantee admission by any means, but if someone can't get high scores on this exam, it calls into question their understanding of all the basic undergrad math they've learnt.   It's true that different schools (and different faculty members, even at a given school) place different weights on this exam, but doing well on it is something you have some control over in the admissions process (by preparing well), so it makes sense to do so.

Your GPA in your math courses is also very important.  Presumably you are doing your best in your courses, and getting as high a GPA as possible.  So there is no real magic to this; you just have to work hard at learning math.

Third: Assuming that your GPA and GRE scores put you in the ball-park of being a credible candidate for admission, people will read your letters carefully.  So you want to get letter writers who can write about your achievements and abilities in as much detail as possible.

Fourth: No-one expects undergrads to have done real research; REU experience certainly helps, but one main reason for this is that it provides a way to meet professors who may get to know you quite well, and so can (hopefully) write a strong letter for you.

Fifth: Graduate courses certainly help, if your grade in them is good and meaningful.  It is often the case that undergrads in grad courses will be given somewhat inflated grades out of sympathy on the part of the instructor.  This makes sense from the point of view of not destroying someone's GPA because they took a challenging class, but an admissions committee will look for evidence that the undergrad really did master the material in the grad classes they have taken.  One way to show this is to have the instructor of the graduate class write a (hopefully positive) letter.

Again, different schools have different expectations about what incoming students will know.  At the absolute top places (Harvard, Princeton) essentially all the incoming students will know essentially all the material in basic graduate courses (measure theory and functional analysis, basic algebraic topology, basic commutative algebra, and so on).  At other places this is not the case, but most incoming students at most top schools will be familiar with a reasonable percentage of what would be regarded as basic graduate math.

Sixth:
In terms of preparation for grad school, writing a senior thesis is great.  It teaches you about a topic in much more depth than you would normally investigate it, normally leads to learning some grad level math, and also again builds a closer connection with a professor (your advisor) who can then hopefully write a good letter for you.   And at a more fundamental level, since mathematicians spend most of their time writing about mathematics, this is pretty good preparation for that.

As far as applications to grad school go (rather than as preparation for succeeding in graduate school, where as I've said it's great), my sense is that the real pay-off for writing a senior thesis is the letter from the advisor.

Since this is a bit harder to quantify than entries on a transcript, often students are advised to take grad classes rather than write a senior thesis (if this option exists).  I can see why this advice is given, but I do think writing a senior thesis (if you put your heart into it) is an invaluable mathematical experience.

A related option is to do independent study on a topic with a faculty member. Again, from the pragmatic point of view this doesn't do much for your transcript, but the benefits for your mathematical education are similar to those of writing a senior thesis, if you have a good advisor and take the independent study seriously.

Finally: Remember that there are lots graduate schools in mathematics.  What I've written above more-or-less reflects admissions experience at top ten institutions, but obviously there are many more very good math programs out there, and they are not all as competitive as the top ten.

So overall, the most sensible thing to do is to work on learning as much math as you can as well as you can, and interacting with your professors enough that they know what you're learning and can write about it.  I think the only things that are really worth thinking about in terms of "gaming" the admissions process are attending an REU or doing independent study or writing a senior thesis, something that gives you a chance to interact with a professor, and a specific topic, in more depth; and making sure you study well for the GRE before you take it.


What warrants acknowledgement or citation in a dissertation?

Citing in this case is unnecessary. An acknowledgement would be gracious, but also not strictly necessary. My personal inclination would be to do it if their explanation led to some insight on my part.
But "Thanks to JDoe for their insights into Theorem 35 of Gauss", or whatever, is, as I say, gracious.
It is even less necessary if the person's job is to teach you stuff.


Is it possible to sit in a class without registering it?

In the US, as far as I'm aware, the term you're looking for is "auditing" a class. You'll need to check your school's policy for this, as they vary.

For example, here's the audit policy for The University of Texas at Austin, which requires filling out a form, getting permission from the professor and there being space available in the class. But, when you're auditing, you only go to lectures, you don't participate in discussions or do any of the actual coursework.

This is pretty similar for other schools I've looked at but, as noted, you'll need to check your specific university's policy for it. Hopefully knowing the term will help.

For huge classes with 100+ students, you may be able to get in the unofficial way but for smaller classes of 10-30, the professor will probably notice that there's someone extra in the class, particularly if there aren't enough seats in the room.


Effective ways of organising one's time during a sabbatical

I work remotely as an academic editor and writer, and have done so for 5 years. The transition from full-time employment to part-time remote work was interesting. I tended to work all the time without leaving much room for self care. What we do in our jobs, we tend to do when our boundaries are relaxed.

I often have large blocks of free time. My productivity suffers (I have personal writing and creative projects) when I don't organize myself well. After years of fine tuning, I have a system that works well for me.

I discovered and addressed three issues:

I am effective for only about 5 hours a day. Anything more and the quality and efficiency of my work suffers; moreover, my physical and mental well-being declines. Accordingly, I work 2.5 hours (with a 5 min break) then take a large chunk of time to play; then I work 2.5 more hours (with a 5 minute break). I find that during play time, I often have creative insights.
Unless I schedule in fitness, fun, and socializing I am likely to waste my time with unhealthy (Netflix) activity. In your case, you might spend your whole time writing 4 articles! That is quite a hefty commitment and your sabbatical time likely should include time for pondering life's meaning and reading the stack of books that is piling up.
Get up when the sun rises and go to bed soon after it sets. I've done all combinations of working all night, playing all night and everything in between. I feel the best when I follow the sun. When I was in Orkney the nights were 4.5 hours long and it was enough sleep for me though I usually sleep 7-8 hours a night. I don't understand it, but there it is.

Although there are many options the productivity tool I found most effective is bullet journaling. It is simple and quick and there's no software involved (although you could buy some if you want to). I create a daily plan bar https://bulletjournal.com/blogs/bulletjournalist/daily-plan-bar

and I also have a weekly plan
https://bulletjournal.com/blogs/bulletjournalist/top-5-bujo-ideas-in-2016

And I never beat myself up for varying from the plan if something more enjoyable arises.

Have a great 6 months.


There is a finite number of universities in Finland. Disregard universities of applied sciences (ammattikorkeakoulu); they are teaching institutues with some R&D and do not offer PhD positions. Wikipedia contains a list of proper universities: https://en.wikipedia.org/wiki/List_of_universities_in_Finland . I recommend starting with technical universities, including Aalto university.

Go through those universities and check if they have faculty in relevant areas. Follow the open position announcements in all of them. Apply when you find something relevant.

Also, you should contact relevant faculty and ask them about possibilities and vacancies. If your university has contacts to Finland, use those.

I recommend starting to apply when you know you will receive your master's thesis soon.

Recruitment is university-dependent. There might be two open calls, one ending around now (maybe has ended already) and before new year, or there might be open calls whenever there is funding. I do not know if it is possible to hire a PhD student without an open call; I would assume yes, but this might very well be university-specific.

There is typically an online form that you fill. It asks for studies, employment history, and maybe language skills and publications (if any) and so forth. There is typically room for a freeform application or motivation. Attach CV, maybe list of publications, maybe a cover letter or letter of motivation etc. I would not expect anyone to ask for letters of recommendation, but they might ask for people who can recommend you. I would mention such people in the CV.

On CV (no photo included, typically): http://www.tenk.fi/en/template-researchers-curriculum-vitae , http://www.aka.fi/en/funding/how-to-apply/appendices-required/curriculum-vitae-guidelines/ . These are guidelines for making a general academic CV. Leave off the empty categories.

Most PhD students get paid reasonable, but not large, wages. The program is typically four years with 60 ECTS credits of coursework. Some are funded entirely or partially by grant money they bring in themselves. I cannot give specific advice on grants; please ask someone you would like to study under.

Random vocabulary:

PhD student: jatko-opiskelija, tohtoriopiskelija, tohtorikoulutettava
grant: apuraha
university: yliopisto

Educated people and young people usually speak English, but I would still recommend learning at least a little bit of Finnish. It sends (a weakish) signal of commitment and interest if you can write on your CV that you know or are learning basics of Finnish, and will certainly make life and navigation easier.


I cannot graduate from high school because the school is closed. Can I still start college or university?

Ask them.
You mentioned that they accepted you already. Only they can tell you whether the admission process is affected by the recent events and whether they're willing to accomodate last minute changes to your academic schedule.


When I was a grad student, I mounted a 1x2 meters glass plane in front of a white wall at my place. It was great for scribbling stuff and for large drawings. I also developed the habit of drawing on the glass doors at my previous lab, because the closest whiteboard was in another room.

The big advantage: glass is very smooth, you will never have stains accumulating like on a white board. No matter how zealous you or the cleaning staff is, white boards are a bit porous and the material deteriorates with time (UV radiations, etc.) and becomes even more porous, making it harder to clean up.
For the same reasons, if you inadvertently use a permanent marker instead of a white board marker, it's easy to clean it up. Finally, existing glass structures also provide large surfaces for drawing.

The disadvantages: lighting (back lighting, shadows, etc.) can impede reading what you wrote. It helps if the glass is placed immediately in front of a white wall. Also, the cleaning staff might erase your brilliant ideas overnight because they were instructed to clean all windows.


What might be very impressive is if you would be willing to apply as a special student.

This might be a good “backdoor” way to get into a top 10 university.

I worked in the office of graduate admissions at Harvard university:

Most do not realize that applying as a special student is just as competitive as applying as a degree seeking student, but in many cases you do not have to take the GRE

Here is the answer I gave to another person on this forum:

https://academia.stackexchange.com/a/61120/123306


Didn't attend field-specific conferences during my PhD; how much of a disadvantage is it?

People skills can be very important for an academic. We teach, we advise and guide students, we interact with colleagues. In lab sciences we often have to work closely with others. Collaboration, even in such fields as math, is very important today. Moreover, people will tend to ignore your ideas if you don't learn how to present them enthusiastically.

However, that doesn't close you out if you are introverted. Even if you are very introverted. People skills are just that: skills. They can be learned and practiced. Many of the people you meet who have good people skills are actually introverted.

I've mentioned how introverts can interact effectively in public in answer to other questions here, for example.

Treat people skills just like any other skills that you need to learn. Start out slow, if necessary, but practice. Play the role of a confident somewhat extroverted person, even if you aren't.

This answer was provided for an earlier version of the question that was quite focused on effective strategies for introverts in academia.


Repeating abbreviation in body text if already in chapter/section title

Just my opinion, but normally I wouldn't include the abbreviation in a title or chapter heading. Instead, I would introduce the abbreviation in "normal" text. So in your example, I would change the heading to

  Chapter 4 - Results of Differential Scanning Calorimetry

but leave the rest as you have it.

An exception would be if this is a well-known abbreviation, so common that people tend to forget what it stands for. In this case, not including it might actually be confusing. For example, if a heading mentions "Internet protocol address", it might take me a split second to realise you're talking about an IP address!


What does "Reviews Completed" mean one week post-submission?

Yes, it's a bad sign. If a review is completed that quickly the odds are the reviewer recommended a quick rejection. There's also a small chance the reviewer said something like "I can't understand this paper's English" in which case you might still receive a revise decision. However it's also possible that the editor invited multiple reviewers of which only the first has submitted, so it might be a while longer to a decision. If the other reviews are more positive, you might also get a revise decision.

Human error here is unlikely. The editorial management systems I've seen automatically update the status only when reviews are submitted. If the editor's making a decision without reviewers, the status never shows 'reviews complete'; it goes straight to 'decision in progress'.


Time between Viva (minor corrections) and the letter

The process of getting the official papers for a Ph.D. degree can last for months following the oral examination, depending on the university's policies and procedures.

That said, most universities are aware of the need for Ph.D. recipients to start jobs before the "official" Ph.D. degree is sent out, and there's usually a mechanism in place to issue a document stating that the oral examination has been passed and that the candidate is done except for the formal procedures required. Such paperwork is usually provided at an administrative level higher than the professor advising the Ph.D. candidate. You should consult with the graduate advisor of your department for guidance on who to contact.


Asking for a letter of recommendation from a professor who's witnessed my breakdown

I've had students ask me for letters with some wording along the lines of "if you feel you can write me a strong letter."  From what you've said, it makes sense asking him for a letter, but you might consider this approach:

First let him know that you're interested in this program and see what he thinks about it.  If he's very supportive of the idea, then you should have nothing to worry about asking for a letter.  If he's not, you could ask for other suggestions.  (And even if he thinks it's a good idea, he may suggest some other other opportunities as well.)


When Does "Adapting" An Image Go Too Far?

If this is for a book, rather than for a paper, you have another option. Many book publishers will give you a certain budget for paying royalties on figures and such. Another alternative, if you are to receive royalties from book sales is to have the publisher pay any fees up front and charge it against your future earnings on the book. The former is preferable, of course. But book publishers expect to have to pay for some things such as cover pictures and some internal figures.

I doubt that this is an option for any journal, however.


Should academics allow student to submit a possibly flawed paper?

In my opinion, since you aren't the supervisor, it's not your role to stop the student from publishing.  If you are an expert in the subject of the publication and you don't think it's strong, you should advise them not to publish and explain why, but that's as far as you should go.

However, you "let him put [your] name on the paper" -- a paper which, by your own admission, you don't know much about!  Regardless of whether the co-author is a student, and regardless of the quality of the paper, the behavior you're describing is wrong.  In my field, it's actually forbidden by at least one of our professional societies:

  All the authors listed for a paper . . . must have made a significant contribution to its content.

This is generally construed as meaning you should have done a significant part of the research and a significant part of the writing.

Now, violating this rule for a paper that you don't even have a high opinion of seems not only unethical but foolish.

I realize this is a harsh-sounding answer, but you have posted the question anonymously so I hope you don't mind me being frank.


Is it possible to find out how one was nominated for Sigma Xi and is this organization worth joining?

The likeliest answer is that one or more of your professors nominated you. I don't think they nominate a lot of people, so you are highly thought of by some, at least. I've been a member since approximately forever. It is worth a line in your CV, at least.

But if you are at a large university and interested, generally, in scholarly pursuits, it is worth joining as some chapters have periodic meetings at which you can connect with other people in other areas. This can be interesting and stimulating, much like Sherry Hour after Dinner at British universities. But it can also lead to collaboration. Many Nobel laureates are members.

I don't see any reason not to accept the invitation.


Are separate essays in a single volume (on a single subject) considered "the same source"?

We could argue whether this is technically this is or isn't "the same source".
More productive is to ask, "could relying strongly on multiple essays in the same edited volume be putting blinders on your thinking?", and the answer is yes.
The use of multiple, genuinely independent sources ensures you have had to engage with different perspectives on a topic: different framings of the issues; differences in terminology, methodology, conclusions/implications. If there are schisms, you are likely to have stumbled across them.
In a single edited volume, the editor is likely to have -- deliberately or accidentally -- chosen authors with the same perspectives, and therefore biases. In fact, the individual essays may well have been edited to uniformize their framing, teminology, etc. Now, in some cases the editor may have carefully reached out to include differing voices. But very often not, and you have no way of knowing unless you've looked elsewhere.
All of these things taken together mean that though it may look (from the number of different names) that you're taking a broad look at the topic, it is fairly likely to have been curated enough that this is not truly the case.


Almost certainly the best information you'll find is from the AMS Annual Survey: http://www.ams.org/profession/data/annual-survey/annual-survey.  I don't know that it will answer all your questions (in particular, it's mostly focused on newly graduating Ph.D.'s; it doesn't track where people end up after postdocs), but if the data isn't in there, probably nobody has it.


Difference between transactions and journal

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

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

In this historical usage, it is synonymous to proceedings, i.e. it is a published report of a conference or a set of meetings. Many learned societies have transactions: Philosophical Transactions of the Royal Society, Transactions of the Faraday Society, Transactions of the AMS, etc.. Some other institutions use the term “proceedings”, e.g. Proceedings of the National Academy of Science.

These transactions or proceedings were separate from journals, which do not have to coincide with a conference or meeting. However, with time the customs changed, and many of these reputable publishing venues became independent from actual meetings or conferences. But, because they were reputable (and famous is some cases), the name remained.


How does earning a Masters in Iceland differ from the US?

In Europe, to be admitted to a Master's program, there are normally quite formal requirements.  In particular, you need a Bachelor in a to-be-defined field.  If your Bachelor is from another university, or in your case even another country, someone will have to approve its equivalence.  That's usually not the professor's role (though their support might help to convince the relevant offices of the relevance of your background).

I would recommend to first contact the University's International Office, introduce to them what Bachelor you have from what university, to ask them what the procedure would be for you to enroll in the Master course.

In Europe, a Master degree is typically one or two years including course work and a small (~6 months) research project.  You don't need to decide on the research project at time of enrollment, rather when you are already enrolled you can contact professors with ideas, or the professors may suggest ideas already.  Details vary.


Do they really mean "in all areas" and "will continue to be accepted until..." in Computer Science faculty opening ads in the US?

As to the research area, whether they really mean that any research area will be considered is impossible to know from the ad.  Sometimes the search committee really is open to a broad range of areas; other times, there is really so strong a preference for one particular area that people from outside area have essentially no chance.  I have served on search committees of both types; although the relevant verbiage in the ad was the same in either case, in one case, a majority of the committee was committed to hiring somebody from a very narrow area.

As to the deadline statement, I think that is pretty much always meant seriously.  The statements is there so that the committee does not have any possible obligation to not consider applications that are not completed until after the deadline.  There's no practical reason for the committee not to consider applications that come in a little late, and in my experience, slightly late applications have always been given full consideration.

By "slightly late," I mean a couple weeks. Actual review of the applications by the committee typically doesn't start until that long after the due date. (That's particularly true if the due date is early, falling during the winter break or earlier.) The latest application that I can recall getting full consideration was completed about a month late, but at that point things are probably getting dicey. And (just like in graduate admissions) committee members are likely to be more flexible about the dates of recommendation letters than the package put together by the job applicant.


When should we repeat a statement of a theorem before proof in a paper?

Unless, you are facing a particular nasty page limit, those few lines spent repeating the theorem should not be a concern to you. Thus, the only concern you should have is what benefits the reader. Here, redundancy is not bad as such, but only if it annoys the reader and wastes their time. Therefore, you have to compromise between the following:

Readers whom the redundant information helps. In most cases, you have to expect that readers have not memorised the entire theorem yet, and this is clearly information that is relevant to reading the proof. Of course, readers can flip back to the theorem, but that’s a major annoyance (even if you can put the pages next to each other).

Even if the theorem equals the title of your paper and is something like:

  Every frasmotic contrafibularity is a compunctuous pericobobulation.

and you spend the entirety of the space between first stating the theorem and proving it with talking about the four terms involved, you cannot expect the reader to remember that, e.g., Theorem 2 was this titular theorem. Even if you refer to it as titular theorem, readers may need more time to understand this than to read the short theorem again.
Readers who are annoyed by the repetition. – In the situation you describe, I would expect that only very few readers do not need the theorem repeated to them. If the formatting is any reasonable, those should notice very quickly that you are restating the theorem so they can skip it.

Therefore, in most cases (including the one you describe), I would conclude that for the average reader the usefulness of restating the theorem outweighs the annoyance.


What are the pros and cons of submitting to a Preprint server?

The classical answer for that is:
Pro: More people are able to read your work, they are able to read it earlier, you will most likely reach more readers.
Contra: It might not always be beneficial to publish too soon, e.g. if your paper is just an introduction to a big, ongoing project, you might not want too many people to suddenly start working on the same project and maybe publish important results before you do. Furthermore, some journals might not allow it, so check that first.

Whenever such questions come up, there is always a little debate about whether or not it is good to upload to preprint archives. The base line of these discussions can be summarized as "Both sides have good arguments and things might strongly differ between different fields." Thus, you need to decide for yourself if you want to do it or not.


If a professor analyzed my work, does the university own my idea?

This is a good question for the legal department at your university. At the university where I teach, there is a standard software license agreement form that I sign with students to basically ensure that software is owned by everyone at the end of the class. But your university will likely have its own rules and policies. If you have your own attorney, you can work with the university to modify such agreements.


What to do if my university does not offer any advanced math courses?

It is very unlikely that your university will start giving full-fledged advanced math courses at one person's request. However, there are multiple things you could try instead. I suggest discussing these with your program supervisor. (or whoever you can best talk to about your course program)

Take a single course at another university

It might be possible to follow a course at another university without enrolling there. Advanced mathematics courses tend to be highly specialized, so it is not uncommon that a single university is unable to provide a diverse program of advanced math courses. For this reason, some universities have programs to 'share' their advanced math courses. (see e.g. the Mastermath program in the Netherlands)

It is possible that your university does not have such arrangements with other universities, but you may be able to make arrangements for yourself.

Guided self-study

While self-study is an option, feedback from a teacher is be very useful when learning. You could ask a faculty member at your university whether they would be willing to have a short weekly meeting where you can ask them questions and they look at your progress. An additional advantage of this is that while you will not have this 'course' listed on your diploma, you can mention it during applications, as there is someone who can 'verify' that you have learned this topic.

There may be no faculty at your university that can or is willing to help you here, but they probably know someone at another university who would. It never hurts to ask around.

Research project

Since you mention you want to do research, consider approaching someone to do an undergraduate research project. This may not work out due to a lack of pre-knowledge, but as there is usually an expectation that some self-study is required, you might be able to find a project that fits.


How would a small liberal arts college view a PhD from Germany or the UK? Factors other than teaching ops?

It's hard to get a job teaching in America unless you do the degree in America. This is because so much of getting an academic job, especially at a small teaching college is going to depend upon personal connections.

Think about it from their point of view. The hiring committee wants somebody who is a good scholar, a good teacher, and a good citizen of the department (in some order, which factors are more important differ from school to school). It's really hard to evaluate somebody in depth along all three of those axes. It's even harder when you have a pile of three or four hundred applications for one job. So you use shortcuts.

One quick shortcut is no Ph.D. in hand, or a Ph.D. from a place that has a bad reputation. That cuts your pile to 200 or so applications. Then you look and see who doesn't have any good publications or presentations. Now you're down to 100 or so candidates, all of whom are very strong, but you're only going to be able to interview about 20 or so. So the next thing you look at is letters of recommendation. The way you get from that pile of 100 to the pile of 20 is by having letters of recommendation from people that members of the search committee have heard of. There's a chance that they've heard of your famous german mentor, but there's an even better chance that they haven't. Take two scholars X and Y of equal ability, but where X is an American and Y is a German. Let X and Y have equally good publication records and so on, it's still far more likely that the search committee has heard of X than that they've heard of Y, because they've got to conferences with X and heard X's papers and been impressed by him over drinks, etc. This matters hugely in terms of getting hired in the ultra competitive world of academic hiring, and so doing a degree abroad is always going to handicap you.

The only exception I can think of are Oxford and Cambridge. American scholars tend to know the names of those folks, and those two universities have such a strong reputation that you might not get penalized in this way having the degree from them. Everywhere else is a danger zone.


Do I need a PhD in mathematics if my goal is to teach at the undergraduate level?

At least in the US, if you want to teach calculus, differential equations, and linear algebra, and are also willing to teach lower-level stuff (e.g., algebra stuff like quadratic equations and trigonometry) you can likely do that at a community college, which means you might not need a PhD. If you really want to teach abstract algebra and real analysis you probably could not do that at a community college, which means you'd probably need a PhD.


Coming from an unknown university, is it possible to publish a good research paper in a good journal?

Yes, it is possible. The institution doesn't matter. The advisor doesn't matter. What matters is the content (and correctness) of the paper, along with a judgement about its "novelty". Those judgements will be made by reviewers and editors, independent of where the paper originates.
Good writing helps, of course.


Is it right to cite a retracted research article?

Dissenting View: You Absolutely Can Cite a Retracted Paper
Research is about telling the truth about facts of reality.  You can cite any fact of reality you want if it is relevant to your research; if someone says something, you can report that they said it.  You can cite a published academic paper; you can cite a newspaper article; you can cite a letter; you can cite a Post-It note or a tweet; you can cite that thing your neighbour said to you over the back fence when he got really drunk that time.
Generally researchers cite claims/information from academic papers as a source of authoritative information that has been through the process of peer review.  However, there is certainly no rule that confines academics from citing information from other sources, including sources that have not been through peer review, or have been through it, but have later been retracted.  There are many cases where it might be useful to cite a paper that has been retracted.  There may be cases where you want to cite something from a retracted paper, where the part you are citing is undisputed, and the cause of the retraction had nothing to do with the part you are citing.  There may be cases where you want to cite a claim that has been retracted, but you still think the claim is relevant despite its retraction.  There may even be cases where you want to cite a retracted paper because you want to talk specifically about it having been retracted (e.g., if you are doing research on how often and why academic papers in some field are retracted).
Now, if you cite a retracted paper, it is proper practice to disclose to your reader that it is a retracted paper, and this should be done in your bibliography where you list the citation details, and should probably also be done in your main body text (e.g., Johnson 2011 - retracted).  If you are citing something from the paper that is a reason for the retraction, you should make it clear to your reader that you are citing a claim that has been retracted (and hence has not passed peer review).
The notion that retraction of a paper precludes you from citing it has several obvious absurdities.  First, it would make research on retracted publications extremely awkward, if not impossible.  Secondly, it would implicitly require that other sources of material that have not passed peer-review could also not be cited.  Thirdly, it is tantamount to claiming that writers/editors have the prerogative to preclude you from reporting what they have written.  If a politician says something scandalous, and then says "retracted!" does that mean you're not allowed to report it in your research?


Talking about career plans given short supply of academic jobs?

I guess you mean you are applying for a government fellowship to fund your graduate studies, and the government agency asks about your career plans on the application form.  My experience in the US is that many students don't really know what they want to do before entering a PhD program.  My impression from some countries where you are required to have a master's first is that most people at the master's level don't know what they want to do coming in (or at least their advisors don't know), but that people who start PhD programs at least think they want to do research.  The point is that unless someone shows real mathematical maturity in their application, I wouldn't put too much weight on what they say their career goals are when applying to a US-type combined master's + PhD program (and I guess you are talking about the US), as these goals often change anyway.

Anyway, I think you should state your plans as clearly and as honestly as you can, so if there are a couple of things you're interested in, you can mention them both, but you probably don't need to go into back-up scenarios if things don't work out with your current goals.  I expect they mean to ask: "what do you want to do?" rather than "give a strategy for your career that is achievable with a 95% chance of success."  Moreover, I don't think the job market is really that bleak in pure math in academia, as long as you are not set on anything too specific (see, e.g., https://academia.stackexchange.com/a/44187/19607), so I don't think something like "staying in academia" is that unrealistic as "getting an endowed chair at MIT" would be.

In addition, since it seems like you're not too sure what the program is looking for, I suggest you read through the selection criteria, which are mostly likely available somewhere in the application guide.


Scanned detailed comments for a paper review

I think it really comes down to the editor. You should first ask the editor of the journal if there is any issue and then think if your handwriting is clear enough. Hoewver, please keep in mind that scanned copies cannot be copy - pasted. You could return a pdf or Word version of the paper with annotated comments, either on the side or baloons (Adobe Acrobat and Adobe Reader allow for that and I find it very useful when finalising a draft). This sounds to me like a more convenient solution that a scanned copy.
I would like to stress that, despite your good intentions, the full responsibility of presentation and language falls on the authors, not the referee. A paper is not just about content but also sound presentation and communication of ideas.


How to answer a professor asking "what your masters work is about?" when my thesis is not in English?

I think that you should send the professor your thesis, pointing out the obvious that it is not in English.  Perhaps they actually know the language or have a trusted student or postdoc who does?

You should also offer to send an English summary and/or any papers that you have written related to the subject in English.


Is it fair to withhold test and assignment memorandums at tertiary educational institutes?

There may be many reasons why no feedback is given; complexity of the undertaking, legal issues, organisation etc. However, not promoting students thinking for themselves, as reason, simply does not make sense. Of course, students need feedback. Assuming, however, you got feedback during the course, the feedback from the assessment is not really central anymore.


Turning down an accepted tenure track for a better one?

Because of the way the academic schedule works, if you accept a job you are expected to go to that job for an entire academic year.  This is different from other kinds of jobs where hiring happens all year round.  As a part of this, you are expected to withdraw your other applications when you accept a position.  Anything else will usually be seen as unethical behavior by most people.  This can get complicated in some corner cases (eg you take a temporary job but then get offered a permanent job, where the usual ethical move is to delay the start of the permanent job for a year, but often there’s no hard feelings if you just drop the temporary one, especially if you’re nice about it), but it’s the standard ethical rule.


Filling "Educational Status" in GRE subject test application form

If you've already completes a full year of study toward a master's degree, I'd lean towards "second-year graduate student." However, frankly I don't think schools pay a whole lot of attention to what label you use. They're much more interested in the recency and the results of the test.


Asking for reversing my decision after declining a PhD offer

I suggest you contact the department, minimizing overly personal details - but basically outlining that the life situation that caused you to decline their offer changed unexpectedly, and you would like to know if it would be possible to attend after all.

It is basically down to: 1) no, spot is no longer available or they can't extend/re-extend the offer, but you can probably reapply next year, no guarantees; 2) sure, that is possible, 3) it depends, they will ask additional questions or want to talk to you more before rendering a decision.

If you are professional in the communication then it will not cause everyone to look down on you, all reasonable people know life situations can change unexpectedly. It really isn't that big of a deal, they can either help or they can't/won't.

As for who to contact, I would tend to suggest whoever contacted you with the offer and/or the person who you contacted to decline. As for what to emphasize, I'd just keep it simple and relate it most directly to why you declined in the first place, but try not to over-explain. Perhaps you just realized that there are ways to mitigate being away from family that you had not considered, or that you will have other family you can visit, or just that you'll end up having to be away from some parts of your family regardless so you'd rather persue something you are passionate about rather than stick with the familiar - etc. A sentence or two is probably all you need to include in the first contact - the situation has changed and you just want to see if attending would still be an option.

The only other thing you should be clear about is that you are in a position to accept such an offer from A - i.e., you have not already accepted a mutually-exclusive offer from another US graduate school, as that will tend to create additional bureaucratic resistance (such as needing a statement from the other school, etc.).

It might be an option, or it just might not, but so long as you act reasonably (maybe have an especially rational friend read your email before you send it to make sure you keep it short and professional) there is no long time harm in asking. Life happens - good luck, regardless!


I printed my PhD thesis and one of the image graphics came out as a black square and I sent copies yesterday to the reviewrs

These things can happen with printing services. This is why you always get a test print, which you check thoroughly. You did get that, right? And you did check it, right? If so, then you probably have a good case against the printing service, to get them to print replacement copies free of charge.
But this does not help you right now. Yes, it will be an issue for the committee if several figures in your thesis are not legible. What you can do is to write an email to your committee members explaining the situation. Attach a pdf of your thesis - which you have double checked to be correct - and promise to send them replacement copies once they arrive.
And before you send the replacement copies, you make damn sure that all the graphics display as it should.


Graduate Program - Re-application etiquette?

This can be subtle and depends on the schools. In particular, it might depend on the size of the institution and on how many people apply each year. It may well be that no one remembers an earlier application (large school) or that they do.

I can't recommend which of the following might be best in any given situation, but consider, at least, the following.

One strategy is just to strengthen your application in all ways that you can and apply just as if you never had done so. Of course, you may need to also account properly for the intervening year. This strategy has you not mentioning the prior history with the institution. Stress your strengths and your likelihood of success in your application and have letters of recommendation that support that idea.

But, in an opposite case, if you think you need to address the fact that you were denied entry, then, I think, you should also speak about what is different not. What has changed from a year ago, not just what is good, now. I worry that if you go too far with this it sounds like begging. But don't just mention it unless you also explicitly give the evidence that supports why they should make a different judgement this year.

If you want to contact the prior committee for information about what failed you in the past, you may get a response or not. But make it distinct from the new application itself. It may be that it was nothing more than the fact that the competition was (and remains) fierce for graduate admissions in some places. This varies by field and by time, of course.

But you can probably get a lot of information about what went wrong last time from your current professors, without even contacting the other institutions directly. Find a trusted professor and show him or her any rejection letters you got along with the material you used to support the application, especially letters of intent and statement of purpose documents. They have been through this, and may be involved, themselves, in such decisions at the current institution and can, perhaps, see how things will be read and interpreted.


Why would a professor assign more grades to a presentation than a report in a software engineering subject?

Presentations generally involve a discussion with the panel, questions from the audience, and even heated debates.  Papers present the research and can absolutely give an impression of the knowledge of the writer, however, it can be easy to hide behind a paper.  You can't hide in a presentation.  It becomes quickly, and sometimes painfully, obvious in a presentation when the researcher has not fully developed their work.

Also, very few people will take the time to read the paper, but there's a good chance that quite a few people will attend the presentation.  How well you present your work will reflect the quality of the work in the eyes of the audience.  It might be outstanding research, but if you can't present it well and your message is lost, the work will be shrugged off.


A PI gave me 2 days to accept his offer after I mentioned I still have another interview. Is this normal?

This means one of two things:

The PI has a certain set of needs right now and wants them met. Your needs are irrelevant. This will be the case for the duration of your employment - they'll be a decent boss until they need something and then that thing will be more important than anything you've got going on. This is a reasonably common PI mindset and most of them will respond to pushback - if you're assertive and can manage their expectations and needs this could be an ok fit for you.

The PI is cynically abusive to staff. This is a test. They want anyone assertive to get filtered out at this stage, because you'd just quit later in the face of abuse anyway. This is a shibboleth to identify postdocs who can be used and discarded. There is no way to make this job work for you. This PI is rarer but tends to be hiring a lot (for obvious reasons) and so you'll see them more than you would expect on the job market.

It's better to not work for either kind of PI if you can avoid it.


Shortlisting criteria for an oversubscribed course: first-come-first-served vs grade point and classroom diversity

The main problems with doing something unusual are that it is unfamiliar to your students, which could cause consternation if they feel they didn't receive enough info about how to get into your class, especially if it caused problems with their graduation plans.
At universities I'm familiar with, registration is allowed for grad students first, followed by seniors, then juniors, down the line. It would be really unfortunate to choose a third-year for the last spot and force a senior to take another year or semester because they couldn't get into your class because they had incomplete information.
"Instructor discretion" sounds like a recipe for mishandling individual qualifications, whether you want to talk about inherent bias or lack of information (GPA seems far too coarse for this).
A couple of simple ways to address your problem:

Split grad students into a separate grad student class that meets at the same time with the undergrads.
If you can in your registration system, reserve spots for non-seniors (common at universities I'm familiar with). While within-year, it would still be first-come-first-served, you would achieve your goal of having both third- and fourth-years.

Finally, I think having an application system would be OK, but it needs to be handled transparently and early so students can plan their schedule; i.e. your application is due early enough so that you can select your students before the earliest registration date. Ideally, you should have a second person help you evaluate. This also lets you ask for cover letters and CVs. You should be clear you are reserving, say, 10 spots for third-years. Then, you just lock registration and give codes to the students whom you selected.


What services would you recommend to ship belongings to graduate school beforehand?

When I moved coast-to-coast for graduate school, I used

UPS for my personal belongings (e.g., clothes, beddings...etc)
USPS Media Mail for my books and CD's
Southwest Airlines free check-in bags (they allowed up to three pieces back then)

PS: I didn't have any furniture to ship.

If there's stuff you won't need for grad school, send them home until you settle down somewhere with a permanent residence. It'll be cumbersome and costly to haul them around the country.

As for storage, I contacted the department secretary and asked if they could store a few boxes for me (and they kindly agreed). You may also write to fellow grad students in your department and ask if they could receive your boxes for you and store them in their office.

Hope this helps!


Navigating the Thorny Issue of Receiving Job Offers While in a PhD Program

As an advisor, I want students to be up front about what their long term goals are. If a student is not interested in an academic career, I'll take that into account when I decide to work with them. Part of that calculus is the concern that the student might jump ship part way through.

It sounds like you've been up front and honest about your intentions with your advisor at every step of the way. Your advisor will probably be disappointed, but they will not likely be surprised. I don't think you owe it to them to stay and that seems like a bad reason to stay doing something other than what you want to do with your life. Your own time is simply too valuable and your advisor should respect that.


Is a computational scientist/engineer a viable professional goal?

Computational science is more of a mode of work than an actual career path—using modeling and mathematical techniques to solve problems in engineering, medicine, finance, and other disciplines. Almost all computational scientists have an area of emphasis within that field (as you mentioned, computational imaging engineer or computational biologist). You can move within areas relatively closely related, but making larger leaps may be more difficult: a computational fluid mechanics expert cannot quickly be substituted for someone working in bioinformatics, and vice versa.


Is pregnancy a valid explanation of a weak academic performance?

I'm going to side-step this question by simply saying: in PhD admissions, grades are not nearly as important as one might think.  Far more important are 1. your letters of recommendation and 2. tangible evidence that you are capable of being creative and productive in a research environment (e.g., class projects, publications if you have them, etc.).  One semester of bad grades is not going to kill your application, especially if the rest of your grades are strong.

Some even broader advice is: draw attention to the good rather than the bad.  Compare the two statements:

(A) "Despite my poor performance in area X, I believe that I am still a strong candidate for the program in (your field of study)."
(B) "My strong performance in area Y demonstrates that I am well prepared for a research career in (your field of study)."

Both statements communicate the same idea ("I am qualified"), but (B) draws attention to the good, whereas (A) draws attention to the bad.  Don't draw attention to the bad.  If people think something is bad, they'll think it's bad no matter what you say about it.  Get them focused on the good stuff instead.


Are online-only sister journals simply a way to generate revenue?

Can it be both?  In the cases I am familiar with, these online-only journals serve primarily to publish marginal papers.  These are papers that are of fairly limited interest, but they still have some value, and it would be a shame if they were not published somewhere.  At the same time, they provide an additional revenue stream for the journal.  The net result is that the journal makes extra money and manages to publish more material, with limited additional costs to themselves.

I have experience with one of these journals, myself.  A co-author (who needed one more paper for tenure) picked the journal, which was advertised as considering only the correctness, not the importance, of work as a criteria for publication.  However, the referees were much harsher than they ought to have been, based on the journal's stated policies.  The referees took whether the work was significant quite seriously, even though, in theory, they should not.  So the result was quite a rigorous review process, which forced us to improve the paper.  The journal got a sum of money, and a worthwhile paper was added to the literature, so both goals were met.


How will study as a non-degree student affect my graduate admissions chances later?

Will the non-degree option help my chances at being accepted to university A's MS program?

No.

Will the non-degree option hurt my chances at being accepted to university B's PhD program?

No.

Will they need to know about the non-degree if I'm eventually accepted to the degree option?

Do well in the course and then you'll be proud to share the transcript with them.


Mastering in the same field as my Bachelors

I would say it all depends on where you want to go. Of course, you may not yet be 100% sure yet. I was in a similar situation a few years ago. Here are a few things right off my head that may help you decide:

You probably did a Bachelor thesis or some kind of final work for your undergraduate. What was the closest field to the topic of your thesis? Human Resource Management in general or, say, something more specific like Employee Stress Performance (I just made that up, not sure if that is a valid subfield of HRM)?. Did you like it? Would you have liked a different topic in another subfield better?
What are fields related to HRM? Is it hard to switch from one to the other? Would one require you to learn difficult skills or acquire knowledge in disciplines considered to be difficult (for example math or computing)?. Would you like to acquire those? Would it be beneficial to acquire those skills, even if ending up working in a different field?
Do you have an idol in your field? Some guy who wrote a book about HRM that you like? Your supervisor? Check their CV's and career path? Did they study HRM for a Master's or do they have a very diversified path? Or ask one of your professors for advice.

Finally, a recommendation: why not wait a year or so and work in your field? Probably you would see much clearer which study would be most beneficial, if you'd like continue to study and you would also have had contact to people who'd just have finished their Master's and could give you some more feedback.


What should I do about my supervisor's high demand?

Do you feel that the demand of my supervisor is too much?

I work in theoretical mathematics.  In that field, a requirement of four publications in journals of impact factor greater than 2 would stop more than 99% of students from getting a PhD thesis.  (I got my PhD in 2003 and am now a tenured, "full" professor.  If I'm not mistaken, I have zero publications in journals of impact factor greater than 2....but in my field we do not speak of impact factors when we talk about journal quality.)

The above paragraph is there only to tell you where I'm coming from.  In fact I do not understand the logic behind such a requirement -- in particular, I don't see where the number four is coming from, and if I wanted to impose high standards on my students I would do it in terms of the quality of their work rather than the quantity.  But I can't say that the demand is too much, since I am not in your field, am probably not in your country or university, and I am not working with your supervisor.  Whether it is too much is mostly up to the two of you to decide, along with other members of your committee and subject to the rules of your program and university.

  Is it even possible to produce 4 more journal paper in the next 3 years?

It is certainly possible for someone.  I would be willing to bet at any reasonable odds that there are students in computational biology who have this many publications in this amount of time.  I urge you to look in the literature of your field and see when, where and how often this occurs.

Perhaps you mean to ask whether it is possible for you.  That's a really good question, though of course we are not in a position to answer it.

  Is it possible to bargain the count of paper down to 3 instead of 4? If so, how should I do it?

The language of "bargaining" is not very apt, but: yes, you should certainly discuss the situation with your advisor sooner rather than later.  Your advisor is setting what I think we can agree is an unusually high bar -- you mention that other students in your institute have gotten their PhD with a single paper, and he is asking for four papers.  Note though that you said that that's what he wants.  Many thesis advisors have high expectations for their students and try to push them to do their best work.  (And the others are not very good advisors, in my opinion.)  However, (i) what you want your student to do, (ii) the least they need to do to graduate and (iii) what they actually end up doing are three different things: wildly different, sometimes.   Here you seem to be assuming (i) and (ii) are the same.  I think that they probably are not, but they could be in your situation.  The only way to find out is to ask.

Here are my specific recommendations:

Step 1: Do your research.  Find out the publication records of students in your area.  In particular, look at all the students who have gotten PhDs in computational biology in your institute and under your advisor.  Then pick a few other institutions for comparison, including at least one that would be regarded as better.  How often is it that students have four publications in IF > 2 journals before they graduate?  If this happens only a small percentage of the time and/or if it almost never happens at your institute or with other students of your advisor, that's a strong clue that the constraints you've been given are aspirational...or ought to be.

Step 2: Have a serious conversation with your advisor.  Show him the research you've done in Step 1 -- not confrontationally, but so that both of you will be working with the same facts. Then show him a plan of the work that you will do and the papers that you will have published by a certain time.  This plan should be serious but realistic: you should be able to defend the amount of time you'll spend at any stage.  Your plan should include a specific time that you want to graduate.  If your plan shows you with three papers for sure and very iffy on the fourth, bring that up explicitly with your advisor.

I think it is likely that you will find that your advisor is flexible on the requirements and appreciative of the thought you've put into your future.  However, it is also possible that he is absolutely intransigent and insists on more papers than you think you can reasonably write in the allotted time.  Well, if that is the case, far better to have that information now rather than three years later!  If you have it now, you have plenty of time to figure out how to respond to it.


Do academicians routinely face discrimination in industry job searches?

I think of a PhD as "vocational education for researchers", not as the "highest level of education". So if a company is looking for a researcher then a PhD should be an advantage, but if a company is looking for a "spreadsheet jockey" as in your example then there is a mismatch between the education and the job and a company should take that into account.

On top of that there are large cultural differences between companies and universities. Such differences can lead to frictions, and if you can hire someone without such frictions then that will be an argument.


What are the implications of the whole class failing an exam?

Your question is about the consequences for the lecturer, but you've asked in comments what you should do.

In the UK, if it's felt that noone has reached the required standard then noone will pass. The basic paradigm is that everyone is measure against a standard, unlike in North America where it's more about measuring students against the others in the class. Still, it would not be a popular move to fail a whole class. What the effect on the lecturer would be will depend on their position, and what the uni is like.

Given it's two days from the exam, and I'm guessing it's in maths or similar, I think you should start memorising. The pass mark is 40% (usually), and with high homework scores you can pass with slightly less than that. You're more likely to convince someone you deserve to pass if you can show you've understood the basic ideas of the topic. Make sure you can reproduce the key definitions and theorems, and have at least an intuitive understanding on the methods of proof appropriate to what you are doing.