Writing to a reviewer to inform that one is not journal shopping?

I'll start with some remarks on the past events:

“the re-submission date was 10 days after I received the reviews” — If the reviewers had asked for large modifications, I am convinced you could have asked the editor to allow you more time to resubmit the manuscript (unless it was for a special issue).

“senior management […] forced me to resubmit to the same journal as is” — This is very wrong, and you should have said no (backed up with strong arguments, of course). Resubmitting the same manuscript, unmodified, to the same journal, is ethically borderline. Depending on the exact requirements for submission of the journal, and the information you gave to the editor, it may even be unethical (many journals ask “has this manuscript previously been submitted to this journal?” — if you say yes, the unmodified paper will be flat out rejected, if you say no, you are lying).

Now, regarding your questions:

“Should I ask […] the reasons for rejection?” — You can. I am guessing that the editor somehow didn't realize that it was a resubmission, if it took 2 months for it to get rejected. Thus, you probably got some new referee comments. However, if the editor didn't tell you… maybe the reviewers just flat out recommended rejection, with no comments.

“Should I explain him that I was not journal shopping and the situation was such that I had to resubmit the paper?” — I don't think so, and certainly not in these terms. There is not “situation such that I had to resubmit”: you resubmitted, and the blame of that bad decision lies with you. Pressure explains it, but it doesn't justify it.
If you want to contact the editor, I would do it very differently. Simply apologize to him for the bad decision, explain that it was done under pressure from your organization and you realized only afterwards that it was wrong. Say that you hope it won't be held against you in the future.

“I have now incorporated the suggested changes […] Should I now resubmit it to the same journal?” — I don't see why not… just make sure you carefully explain all the changes made in response to the reviewers, as a regular resubmission, and explain your earlier resubmission (apologize!).

To be honest, I don't think it will leave a bad stain to your name in the future: everybody makes mistakes, especially young researchers who don't yet understand fully the rules. Being honest and upfront in your future interactions with the editor should lead him to form a good opinion of you.


How do I phrase (in my thesis) that results in an important study are wrong?

I think you can be pretty straightforward, especially in a thesis.  Describe the experimental disagreement first (amount of it and number of measurements in your study versus the earlier work).  Next para, state that theoretical considerations also support your measurements versus the earlier study (~amount of difference and explication of the theory rationale).


How to self study effectively post graduation?

This is a great question and just the mere fact that you are posing it indicates that you are serious about your pursuit in academia. Many students simply study for exams or for specific minimal requirements. "True" learning however occurs when the person freely seeks out knowledge, not to pass some arbitrary exam but to learn more about a subject. It reminds me of the old quote attributed to Mark Twain (although some dispute this) "I have never let my schooling interfere with my education".

If you're studying for self-study, try to be structured about it. One way is to create a KWL chart - it's a system to organize your studies. You divide a piece of paper or a page on a notebook to three parts:

What I Know | 2. What I Want to know | 3. What I Learned

By doing this, you can chart out what knowledge you possess of the topic currently, identify which gaps you have in your knowledge and then finally summarize what you have learned after you finished your study session. It's a good way of keeping track of what you're learning and systematizing your thoughts.


As others have indicated, style guidelines have to be followed, regardless of whether the reasoning behind the rules is clear. However, this particular example often varies by geographic region. American English grammar always places periods and commas inside quotation marks, while British English grammar is "conditional" - that is, they include periods and commas inside quotes only if it is part of the quotation, not the larger sentence. This site has an example and a more detailed explanation.

http://www.quickanddirtytips.com/education/grammar/quotation-marks-with-periods-and-commas

Thus, it's possible that the style guide is based on American English grammar, while you have a different frame of reference and convention.


Has anyone ever written a paper and put your name on it?

Without knowing too many details of your situation, could you perhaps give the other author the benefit of the doubt? Cutting off all contact does seem harsh (unless you have other reasons) for what could simply be a misunderstanding.

I don't know the conventions of your field, but it seems in many science fields that authors are added if they contribute intellectual ideas on the research, not necessarily for doing the research. Other authors simply add support in some fashion, so get added. It is not uncommon to have many authors on a science paper. It does in fact get tricky because one can offend others by not including co-authors.

I'm of the opinion that it's probably better to include someone who contributed in some fashion than not include them. You could argue that this dilutes research and is a "pure research game", but honestly, one paper is not going to make or break anyone's career.

Could this author simply have been trying to extend kindness, or perhaps thought you had a bigger role in the research than you actually felt you did?


Undergrad GPA: Will a C affect grad program application?

The short answer is "yes". However, depending on the school you're applying at, they may use a holistic approach to your application, meaning the C could have a small negative impact. However, if it came down between you and another candidate and you're the one that has the C, the other candidate will most likely get accepted.


Can we add an acknowledgment to a paper after it has been published?

What stage is your paper at?

If your paper has been published: no, you cannot. It's too late. The electronic files have already been distributed and it's possible the hardcopy versions have been printed as well.

If your paper has been accepted but not published: you can, but hurry. Tell the editor/publisher you want to add an acknowledgements, and give them the exact text. Chances are they won't object. The earlier you do this the more convenient it'll be for the publisher. If you wait till after you've sent in author corrections, they might say it's too late.


Chances of getting into a PhD program (Physics) after an MS from another stream (Chemistry)

I'm going to guess that you should do fine. Of course, I'm not going to be on the admissions committee and every one has its own standards, so my prediction may mean little in any individual case.
But I think you have shown some diligence and some awareness of your needs. Changing fields early under the conditions you state seems like a positive thing (as opposed to failing out). You may need to explain a bit about the change in your SoP for any new program, but that should be easy enough.
Of course you will need to meet the entry requirements for any physics program you apply to. And the usual caveats about competition apply.


Whether to accept co-authorship for conference presentation after making only a small contribution?

My answer is based on experience in the field of applied mathematics.  I'm assuming (as stated in the question) that there is no written publication involved -- just a talk.
Don't worry about claiming unmerited credit
You have made some contribution.  Coauthorship on a conference presentation carries almost zero significance for purposes of evaluation.  It's not something you list on your CV, no matter how "early career" you are.  Usually, if you are not already well-known and the results are not earth-shattering, then nobody will even remember, five minutes after the talk, that you were a co-author.
When to insist on being removed
Obviously, coauthorship of the talk has some significance to you and to the presenter.  Since the presenter has already made it clear that he wishes to include you as coauthor, I would only insist on being taken off if:

The scientific work or the quality of the talk is so bad that you think it will reflect negatively on you; or
Your involvement is so minimal that you couldn't say anything interesting about the project (if asked by someone who attended the talk).

It doesn't sound like either of these conditions apply, so my advice is to let it go.


How should I deal with becoming discouraged as a graduate student?

The fact is research is hard. It appears to consist primarily of staring at a problem for days and days and days without getting anywhere. Sometimes, rarely, I do figure something out and that feels wonderful, but the overwhelming majority of my time appears to be spent banging my head against a mostly figurative wall.

Yes.  This.  And it wouldn't be so damn tempting if those bricks didn't wiggle just a little bit every time I slammed my forehead into them.  Sometimes I think my eyes must be playing tricks on me, what with the repeated cranial trauma and all.  But then I remember how good it felt the last time my head actually went through the wall, and so I keep plugging away.

I've found it extremely useful to have two or three walls to bang my head against at any given time.  Surprisingly, sometimes banging my head against one wall actually makes one of the other walls weaker.  But most walls prove considerably stronger than my head; so it's helpful to have options, so I don't feel so bad about walking away with some scalp intact.

If you're very lucky, one good smack on the bricks will actually bring the ceiling crashing around your ears.  That takes a long time to clean up, but sometimes the debris will knock down other walls for you.  And then you have a whole new set of even bigger walls to bang your head against!

  I find myself thinking along the lines of "Oh, if only someone actually smart were thinking about this problem they would have solved it in moments" and so on.

Do not listen to the Impostor Syndrome.  Everyone "actually smart" is hearing exactly the same voice in their head saying "Oh, if only someone who actually knew how to hit walls with their forehead hit this wall, it would come down like a stack of cards." when in fact the wall really is made of brick.

  Does it get better with time and experience?

Yes.  Eventually, you'll move from hoping that you'll be able to knock down a wall with your head someday, to being surprised at how often the walls you hit with your head actually fall, to finally believing that you really can knock down walls with your head sometimes.  (For me, the second transition happened some time after tenure.)

But your head will still hurt.


Knowing a lecturer from a previous course of study, would it have an impact?

Anybody who has taught and likes teaching knows that one of the biggest rewards is seeing your students grow.  From your description, it sounds like your only problems in your previous encounter were age-typical lack of focus and brattiness. If you are now a much more mature and polished student, then more likely than not, if the lecturer remembers you at all, it will be to your advantage when they compare with the kid they taught so many years ago.


Personal information (trivia) in the “about me” section of an academic webpage

So far, none of the other answers have mentioned Security.

Personal information, such as What is the name of your first pet, is used by many online account recovery mechanisms.

Many accounts have been hacked using such personal information:

  The following profile elements can be used to steal or misappropriate
  your identity:

  Full name (particularly your middle name)
  Date of birth (often required)
  Home town
  Relationship status
  School locations and graduation dates
  Pet names
  Other affiliations, interests and hobbies

...

  Best Practices

  Assuming you plan to be active in social media, minimize the use of personal information on your profiles that may be used for password
  verification or phishing attacks.
  Avoid listing the following information publicly: date of birth, hometown, home address, year of high school or college graduation,
  primary e-mail address.

Secrets, Lies, and Account Recovery:
Lessons from the Use of Personal Knowledge Questions at Google:

  Publicly available answers.

  Rabkin found that 16% of questions had answers routinely listed
  publicly in online social-networking profiles.

  Even if users keep data private on social networks, inference attacks
  enable approximating sensitive information from a user’s friends.

So think very carefully before publically exposing personal information.


Is the practice of lab members extensively citing each other's work looked down upon in academia?

It is only bad practice if the work is not particularly relevant, or if you cite your own group's papers instead of other relevant work.  The point of citations is to lead the reader to other related work necessary for some aspect of the paper (result, context, etc.).

That said, it is worth examining why those papers aren't getting cited.  Maybe nobody else is working in a sufficiently related area but it's critical background for the rest of what the lab is doing--then I wouldn't worry about it.  But if other people are working in the area (e.g. to the point that you might worry that if you take too long that someone else will publish the same results you're trying to get), it can be a sign that the results either aren't contributing to the field much, that the style of presentation isn't good enough for others to really understand what you're saying, or that the lab members aren't going to enough conferences to present.


Is it always bad if you continue to publish with your PhD advisor? What about the small country vs. big country bias?

Do good work and publish in high impact journals. As long as you're doing good work, then it really shouldn't matter who you are publishing with. I don't think I've ever read a paper from a small country and had a preconceived notion about the quality of the work. However, if your lab becomes well known for a research area then I think that's a benefit and not a hindrance.


There are only two possible options here.

Do nothing. Most probably, the professor never realized that you did not thank him for his supervision. He provided what was probably a good reference letter and you already thanked him after getting a job, so I suspect he does not have a bad opinion of you.
Clear up your mind by sending a polite email stating that you just realized you might not have thanked him for his participation in your master project. I do not think this would be awkward. I think any supervisor would be happy to receive such a message.

Both options are good.


What do principal investigators (PIs) look for in prospective post docs?

Postdocs have an absolutely critical and unique role in a research group.  They have more research potential than anyone else in academia, because they are both full time on research and yet experienced, not students.  They are also very expensive and a rare luxury that comes only with heavy investment from a funder or university.

The first thing I look for therefore is demonstrated proof that the candidate will take good advantage of the expensive opportunity they are being offered.  Forms of evidence:

existing publications
publications in prep.
letters of reference

These should show that the candidate has skills in what needs to be done, and the determination and internal motivation to be a successful academic.

The next thing I look for is evidence that the candidate is very likely to employ those skills in the area that I am funded for them to research.  This is done through open and frank conversations with the candidate about their research and career goals, what I need, what they need, where they intend to go next, etc.  A postdoc is at a critical time in their career, and everyone should know that they need to produce papers out of their PhD and that they may leave early if the right lifetime opportunity comes along.  I try to negotiate in advance about what research I absolutely need them to complete, what further I'd like them to complete, and to discuss writing and research schedules such that they can meet both of our needs and wants, preferably through some synergy (e.g. of the possible outcomes of this project, which would best suit both of our goals?)  I then try to agree a schedule about what research will be done when, what is the earliest date they'll start looking for their next position, when will they or we start writing the next grant or fellowship bid etc.

These negotiations give me not only a sense of how much I can expect us to accomplish if I make this hire, but also how well we can work together and how similarly we understand our responsibilities as academics.

Finally of course there is a luck element:  if there is more than one viable candidate, the one who seems likely to be the best fit wins.


Etiquette when unable to attend a conference

Just tell the convener that you will be unable to present due to unforeseen circumstances.  That is enough and will be understood — there can be many reasons and it won't be a first time.  He/she will be glad that you inform him/her at all — it happens all to often that people simply don't turn up without giving any information at all.  The convener shouldn't need a doctor's note.

That being said, is any co-author travelling to the conference, or perhaps a colleague familiar with your work?  If yes, you could ask one of them if they are willing to take over your presentation.  I've done this for colleagues and although I wasn't able to answer detailed questions from the audience, it's still beneficial both for me (visibility to experts in the field) and to the first author.


You are right that your paper may still be rejected, but you shouldn't worry too much.  The fact that the editor proposed a resubmission suggests that he/she sees real value in it.  As an editor, I can say that I would never waste time handling a submission again unless I thought there was a decent chance of acceptance.

Of course a decent chance is not 100%.  Acceptance conditional on minor revisions means the editor is confident the revisions can be completed straightforwardly, while major revisions are always more of a gamble.  They might just not work out in principle, or the authors might not be capable of pulling them off.  However, they are worth a try.

Turning down an offer to resubmit is usually a mistake.  It comes across as a sign of weakness, like you've decided your paper probably can't be fixed and you'd better just submit it somewhere less prestigious/demanding.

  Also, what is the difference between "reject and resubmit" and "major revision required"?

Sometimes there's no difference at all: there are fields in which "reject and resubmit" is just what majors revisions are always called.  Sometimes there's a difference, with reject and resubmit indicating a slightly less optimistic outlook (but still optimistic enough to be worth trying).

There are also borderline dishonest reasons some journals prefer reject and resubmit.  Splitting a single submission into two submissions can make the journal look good in two different ways.  Rejecting the initial submission decreases the journal's acceptance rate, which makes it look more selective.  (A journal that accepts every submission after an R&R can claim it technically has an acceptance rate of 50% rather than 100%.)  Furthermore, splitting the process in two decreases the average time from submission to a decision, which is another statistic authors care about.


Overlearn in undergraduate College - good or bad idea?

Having a good GPA is important; having a great GPA is not.  Assuming your GPA stays above a certain threshold (about 3.5), other factors like research experience are significantly more important, at least for admission to the best departments.

In particular, if you get a C in a distribution class because you spent "too much" time on that experiment you later published, nobody will even notice the C on your transcript.


How to improve graduate student recruitment at a small, good, but non-elite department?

All of the ideas that you've written down so far seem quite useful and reasonable, but I think that there is something important missing.  In particular, all of these are aimed at recruiting "generic" students rather than individual students.

Ph.D. recruitment is different than undergraduate recruitment because people choose their undergraduate institutions for so many random reasons, while they tend to be much more focused and "status-conscious" when looking for a doctoral program.  As such, rank matters a lot more for students... when they have no personal relationship.

As such, if you want top students to come to your department, you don't want them to be thinking, "I wonder if Nice University's grad program would be good for me," you want them thinking, "I really hope that I can do my graduate work with Professor Neato!"

There are at least two really good sources that I can think of for recruiting such students:

Your undergraduates: Because of the high variance in how people make their undergraduate choices, at least some really top students are likely to end up at pretty much any decent school.  If you can get those students involved in research as undergraduates, then they will know you and your research personally, and may well be inclined to continue with a cool program that they are already invested in rather than taking a blind leap into a big and possibly unfriendly place far away.
Close colleagues at other schools: Reaching beyond your own pool of students, your colleagues elsewhere are likely to have bright students that they may be looking for a good place for.  If they've got a top student who's just interested in generic stuff, then packing them off to an elite institution and hoping they'll find their way may be the right thing.  But if they think the person might be a good fit for your work on Frabjous Tulip Fractals, then they can refer them directly to you, and again a student may be much more interested in working with a specific professor who they can get to know and meet, particularly where that can improve their chances of admission.

I know of folks who are pursuing both these strategies with significant success.  Other approaches may work as well, such as international exchange programs.  The common theme, however, is to compete on the basis of your individual personal relationships, rather than as a generic institution.


Can the university you work for or study at protect your identity by listing you under a pseudonym?

This is commonly done in several types of cases:

by women who want to retain using their maiden name professionally while switching their legal name to their husbands
by students from countries who have taken a hostile stance towards the United States and who want to protect their extended families back in their home country
By foreigners with impossibly long (from an American standpoint) first or last names or who use non-mainstream variations on their name
By faculty who go by their middle names or nicknames not their formal first names
By aforementioned stalking victims

If you are at a large enough institution, they are prepared to handle these types of situations. My (large enough) institution has the following:

Fields in the university directory database that allow for 'nicknames' to take the place of names. Because all of our e-mails are firstname.lastname@myschool.edu, this allows for e-mails to arrive properly.
Flags in the university directory that particular information should not be publicly released. One can prevent the listing altogether if you choose.
The only other place where names would appear would be the faculty/staff/student website, which is under departmental control and easily changed.

One of the doctoral students that I work for is from one of the aforementioned hostile countries and you will not find any web presence for her on the departmental website.

This gets trickier when you are faculty, as students need to enroll in your courses and you need to publish. I would recommend in this case either a full legal name change or pushing your university/department to recognize a pseudonym. It helps greatly if you have a common last name and only need to modify your first name.


What is the usual process for forming a business partnership with a university lab?

How this gets arranged depends a lot on where the money is coming from.
If you are interested in working with a university on government-funded projects (or other third parties that act similar to government funders, e.g., research foundations), then it's pretty straight-forward.  For many such funding programs, companies are just as eligible as universities to bid as either a prime contractor or a subcontractor.  You thus form your research collaboration just as though you were both universities (or both companies, if you're more familiar with that) and bid jointly.  With a business involved, some programs will not be applicable (e.g., you are not "Young Faculty") but many others are specifically targeted to small businesses---SBIRs and STTRs, for example, are set-asides specifically designed to enable small-business R&D and partnerships with universities.  You'll need to figure out how to comply with government contracting rules and your contracts people and the university's contracts people will need to come to terms (every university has its own unique procedures), but this is a very normal and well-supported interaction.
If you want to fund the laboratory's research from your company's own funds, on the other hand, it may become a bit more difficult.  Universities are often well set up to handle this as well, but it more usually comes from large businesses rather than small businesses, and you are likely to find the arrangements much stickier, particularly regarding IP and publication control.  This is because you are a small business, and so the risks involved in taking your money are much more difficult for the university to predict and manage than the risks involved in taking money from a large company.  Still, if there is motivation on both sides, it's likely to be doable, and again, every university will have its own procedures.
In both cases, the right starting point is probably not money, but engaging the PI(s) you want to work with on an intellectual and scientific level.  The really good sort of people that you would probably like to work will will have many possible options available to them, and you're much more likely to get good results in this fashion rather than taking the chance that they may feel you're trying to "buy their science."  Once you've got intellectual buy-in, your primary PI contact will know the starting point in the university's contracting organization, who will in turn be able to hand off to others as needed to work out the contractual particulars of the deal.


Just because you have the additional digits, doesn't mean you should report them.

Accuracy and precision are extremely important concepts in the reporting of scientific data. Excessive precision, as you suggest, implies too much reliability in the accuracy of scientific data. For instance, someone turned in a report to me saying that a particular parameter was known to be:

  E = 1.3405987423423 GPa

If this were to be published in a paper, it could be rejected out of hand for incompetence, because the parameter E is often known only to one or two decimal places, let alone four.

In general, you need to make your reporting consistent with the assumptions and the accuracy of the measurement techniques. One way to figure this out is to note the accuracy of your measurement—what is the expected error in the measurement? If the error in your measurement technique is, for instance, plus or minus 1 global hectare, then by all means report it to the nearest hectare. If it's plus or minus 1000, though, reporting to the nearest hectare will look quite silly.

How do you deal with this? (I've actually had to do something like this before. Similar argument, but not exactly the same.) In this particular instance, engaging in a little hyperbole might be useful. Instead of reporting it to four significant digits, show him a version of the text that lists the data to the full precision you have available—something clearly ridiculous that reports things down to six or seven decimal places, if possible. Then, when he argues that what you're doing doesn't make sense, you can argue "what's the harm in reporting extra digits?" That should be enough to have your coauthor "see the light."


Advisor delaying response, proposing changes every now and then in last week, how to deal?

It is your PhD, not his!

While it is true that writing papers is hard work you really need to take some initiative here. You need to arrange the meetings and make sure things are done by the deadlines.

In all honesty he probably has more important things on his mind than your deadlines.


How does Google Scholar rank search results?

Here is what the about page says:

Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature.

Here is an academic article that attempted to deconstruct the ranking algorithm: Beel et al 2009, PDF
They suggest that two key factors were the citation count (more citations pushes the article higher up the search list) and the search term appearing in the title. They review a wide range of features.
Note that the article is 10 years old and the algorithm has presumably been updated over the years.
References

Beel, J., & Gipp, B. (2009, July). Google Scholar’s ranking algorithm: an introductory overview. In Proceedings of the 12th international conference on scientometrics and informetrics (ISSI’09) (Vol. 1, pp. 230-241).


Would a Russian specialist degree (diploma in dentistry) qualify me a for a master's program in Europe?

Different MSc programs have different requirements. Most MSc programs in Economic admit students with BSc (or equivalent degree) in Economics, or similar topic, such as Finance, Business, Mathematics, sometimes Management, etc.  Your Dentistry degree does not  fall in this category - it is not similar enough to what you want to study. Some MSc programs (called conversion degrees) will admit students with less relevant experience, but they are often run at less desirable Universities.
In principle, a specialist degree can be recognised as BSc or MSc depending on the international prestige of your University and the requirements of each particular University. There is no general rule on how a specialist degree must be converted into Bologna system degrees. However, in your case, this is less important, because as mentioned above, your Dentistry background is rather irrelevant to the Economy which you want to study.
UPD: In addition, this year many Universities in Europe prepare for a downfall in number of both local and international applications due to Covid19. It means that many programs will have to be more sympathetic to candidates with "borderline" profiles.  Many MSc programs are still open for applications and are more likely to issue offers this year, even to candidates who normally would not be admitted.


The review of one of the reviewers is basically a copy and paste from my paper. Should I care?

As you've described it, this sounds rather odd. Reviewers are under no obligation to accept a paper to review, so to accept one and then submit what sounds from your description like a complete cop-out is strange behaviour. It's also a bit odd for the editor to send you completely uninformative comments. It's possible that they genuinely did write a review, but that the text has been copied mistakenly, either by the reviewer or by the editor. It might therefore be worth sending a brief email to the editor to enquire about this review. Something along the lines of: "Thank you for consideration of our paper. In the copy that I received one of the reviews does not contain any comments, only text from our paper. I just wanted to double-check that the correct version has been sent through, in order to make sure that I can respond effectively to all of the reviewers." Be very polite, and make sure you phrase it as a request for clarification, rather than a complaint.

If it turns out it was their genuine review, you are of course allowed to care - it's a bit frustrating if one of the reviewers has not fulfilled their role properly. But it's not a big deal, and there's not much that you can or should do about it. Some journals only get comments from two reviewers anyway, so just think of it that way and ignore the third.


Possibly fraudulent journal: cite or not to cite?

The reasons these journals are called predatory is because they prey on unwary researchers looking for places to publish their work, tricking them into publishing with them rather than in legitimate places.  So just because a paper is in a predatory journal does not mean that it is necessarily bad work.

However, this paper still needs to be treated with greatly heightened suspicion: it should be assumed that it has not had any peer review, and that the authors are unfamiliar enough with the area and with the normal practices of science that they could be tricked by a predatory journal.  Alternately, they may have sent the work to the journal intentionally because they needed another line on their CV and knew the paper was not going to survive real peer review.

Thus, although such a paper might be legitimate, it is also very likely to be of low quality and may well even be fraudulent or simply nonsense.  It can also cause trouble for you if you cite it, as readers may think that you are not informed enough to tell the difference between real research and predatory crap.

I would thus suggest treating the paper like a random PDF found on the web: it might be usable as a primary source (e.g., like a newspaper opinion piece or a personal essay), or to point you for looking for similar information elsewhere.  If this information has only ever been published in this one paper in a fake journal, however, it should be considered to effectively not be published at all: the context in which it has been found casts so much doubt on its likelihood of being legitimate, and anything substantive will likely develop multiple real publications over time.


How should I approach the issue of students not writing their name and student number on an exam?

Y'all have never proctored or taken SATs?

Give only the answer sheets out first, and have students complete the important information before they even get the questions.

If you don't give the questions until students have filled out the relevant information on the answer sheet, they won't be able to ignore the answer sheets, in lieu of answering questions.

It may require a bit of a rethink as to the time available for the test (i.e. take five minutes away from testing and put it onto "administrivia"), but this might just be time well spent.

You could even incentivize students to arrive early to complete this task quickly by saying that the question packs will be given out as soon as all students have filled out their information; any student who shows up to class (up to five minutes) early will be given their answer sheet to fill out.  If all students have their answer sheets filled out by the time "##:##", the tests will be handed out then.  Anyone who shows up late will have to complete their information on the answer sheet at the front of the room before being given the questions.

Or, have part of the ID process be that students have to show you their IDs AND a completed information section on their answer sheet before they get the questions (or, maybe before they take their seats).

If it's an important step in the process, make sure it has a defined step in the process.

To forestall the comments I know are coming: Yeah, I know: Young adults should be able to follow directions.  OTOH, negative reinforcement doesn't have the learning results you think it does. Don't penalize students for a bad process.


Undergraduate thesis main author credit and prestige

I am not sure about undergraduate theses, but in graduate school the thesis is almost always (at least formally) an individual effort, and the student's name is the first and only name on the thesis itself. However, when that thesis is revised into a paper for submission to a conference or a journal, it is acceptable to acknowledge one's advisor (and possibly other committee members) as 2nd/3rd/etc. authors. In some cases where an advisor makes a more significant contribution than the student to the revised paper that is being submitted for publication (e.g. time/effort), their name can be first.

For undergraduate theses, I would guess that the students' names should appear first and advisor's name should appear last, if the thesis is not published but merely submitted to the university to fulfill the graduation requirements. However, when that thesis is revised for publication, the same rule as for graduate papers applies - if the advisor actually contributed more, their name can go first. Experienced, well respected faculty with tenure are not concerned with pushing their name, so more often than not they allow students to go ahead of them on the author list.

Finally, having your advisor go first on a revised thesis submitted to a conference or a journal may not be a bad idea, if your names are still on that paper. This still provides you acknowledgement for academic research and publication activity, so I would not worry too much if your name goes first or second or third.

It is an early effort in your research career, which will be superseded by more serious research work that you will do. Rather than straining your relationship with advisor, it may be wise to let it go and instead make sure that you remain on positive terms, as he/she may be writing recommendation letters for you... ;)

Good luck!


How should I interpret an almost-but-not-quite-alphabetical author list?

How should I interpret this authorship convention?

The first (non-alphabetic) authors are likely the main contributors in order of contribution significance as you guessed. Starting from the alphabetic ordering the authors would be those with lesser contributions (but equal to each other).

What fields is it used in, and to what purpose?

I do not know what fields this is specific to, but I would not be surprised if this is a common strategy for papers with many authors irrespective of the field. Ordering a long list of authors with equivalent contributions in some manner simply seems sensible and alphabetic ordering is a simple and common ordering scheme. Unless the publisher has a policy on how this should be handled, alphabetic ordering seems to be a simple go-to strategy.


Not citing code libraries used for paper

You have to clarify to yourself whether you "plug n'played" or did a real contribution. Hiding the contribution of others because it diminishes your own to a level where it's questionable were not only unethical in itself, it also would have the smell of plagiarism (because one would insinuate that one did all the work in the paper which is not cited by oneself).

You are very correct to be concerned about that. If your work is sufficiently good/substantial to be published, it is sufficiently good/substantial even if all external tools used are mentioned. That being said, you could, in the paper, make clear what your contribution is and why it is nontrivial.


Should I add the names or skip them altogether?

For many different reasons, you should always give credit/citation to those who have earned it. One type of reason is that your work depends on their work. Another type of reason is to recognize their prior work, even if your work does not necessarily depend on it. Another reason is to give indications to your audience about sources for further information...
EDIT: for situations where some people are doing critical work (such as diving...) but maybe not literally writing, although traditional "citation" does not quite work, I'd still want to make a point of saying something like "the work of <divers, by name> was critical to this study".


If you want an A+ then of course you could ask. Maybe he will consider the previous draft, maybe he won't; but it never hurts to ask.

You should be aware, though, that he is not obligated to give you points for it; it is completely your fault for forgetting to answer the questions. Therefore, don't demand points but ask nicely if there is any chance to consider the draft, you will have better chances this way.


Can I write a paper out of a simple idea?

I like papers about simple ideas. (I am writing one right now, hope others like it as well.) They are far easier to communicate and understand than complex ideas.

Then again, the question is why nobody else has thought about an idea if it is all that simple. In your specific example, the idea may not be workable, because people may simply delete the update SMS without replying to it. (And those that do answer may not be representative of your sample as a whole.)

So I would say that writing a paper about a simple idea is good, but it needs to meet the same conditions as any other paper: it needs to show that the idea actually works. An idea by itself is usually not worth an entire paper. Having the idea is often the easy part. Showing that it works is where the actual work happens.

So: Build your website for one city, let it run for six months, then write a paper about what you learned.

How to show that something "works" may well be the hard part. (For instance, in some parts of machine learning it is easy to "show" that a method is better than an established method by testing both on many datasets but then only reporting those on which the proposed method is superior.) Some journals/conferences/reviewers may be more stringent about what they consider proof that something "works". You may be able to get a publication out of a proof of concept by just building the website, without running it productively. Or by running it productively, but without assessing in some way whether the statistics collected by the website are actually more accurate than those collected in some other way. Look at what kinds of papers your target venue or community publishes, and let yourself be guided by that.

EDIT 2016-04-07, about that article based on a simple idea: it turns out that this simple idea (a randomized probability integral transform) was really good. So good, in fact, that multiple people had had the same idea previously, and at least partly independently of each other. Happily enough, a guru in the field pointed this out to me when I circulated a preprint and didn't savage me, but pointed out shortcomings of the rPIT and possible new lines of inquiry. The paper has just been published.

Bottom line: your simple idea may be good, but chances are that those ideas that are both simple and good have already been worked on.


How to physically handle hundreds and hundreds of papers

Some 20 years ago before all the electronics changed our ways of dealing with stuff, post and bank employees who had to deal with piles of paper (or banknotes) throughout day used a device which was essentially a piece of a wet sponge in a small bowl. They had this on the desk and whenever were about to touch paper, they would simply brush their fingers through it. Something like that could help you... To construct it, I would use a plastic travel-soap container and a small sponge for dishwashing.

Later edit: Indeed, this is what I had in mind.


At the age of 27 is it worth changing graduate schools and starting again?

There is no age limit for graduate studies. People are free to apply at whatever stage of life they choose, if they feel it's the right move for them.

As an example of this, a very good friend of mine was a social sciences major as an undergraduate, and worked in Washington, D.C., for a number of years before leaving politics and starting a PhD program in medical physics—and he did this in his mid-thirties. I've worked in the same department as other postdocs who made the career choice even later—they were in their early fifties!

So I would not look at your case as hopeless at all. If you find something else that inspires you, go for it.


Editor-in-chief sent an email to resubmit my manuscript

It means that you should resubmit the manuscript with figures separately, as it is probably stated somewhere in the journal's instructions for authors.

They probably cannot deal with the formatting otherwise, and depending on field and journal I would say that it is quite likely that your manuscript has not yet been reviewed, as stuff not living up to guidelines tends to go to the bottom of the pile.


Asking research committee about on-campus interview

I would wait for a few more days, actually. You don't want to seem too eager. If you are high on the list, you may still need to negotiate a few things, and it is better to be a bit calm about it. Let them come to you.

It is what it is, of course.

But if you have other decisions to make immediately, then you may need to ask now. Otherwise, patience is suggested.


Description of developed algorithm as part of method or result section?

The algorithm isn't part of the results. The results are what you learned from the project - the knowledge. In this case it would be the analysis of the performance on the specified problem. The algorithm is what you built to get the results, not the results themselves.

But with the current outline, it looks like you will have to put too much into the introduction. You need to describe, somewhere, the problem and current solutions and why you want a new algorithm. That seems like a lot for the intro. Likewise you need a conclusion putting the results in context.

Note that while most of your work may have been in developing the algorithm, that isn't the essence of your knowledge contribution. The essence is in why and how this was a good approach to a problem (properly quantified) in the first place.

For example, if I build a better garbage collector for, say, Ruby, the knowledge contribution is in how and why this approach is better than other GC systems, if, indeed, it is. But you can even get a thesis out of the work if you show that the approach, which seemed promising, in fact is worse, on some scale. It is the knowledge we require, not the software/algorithm.


Can being free of publication charge be an indication of being a non-predatory journal?

No. A journal that does not charge publication fees can still be a predatory journal.

Generally, the motivation for publishing a predatory journal is to make money. Since the product they create (the journal) is too low in quality for them to be able to sell subscriptions and earn revenue from readers, they often make money by collecting publication fees from authors.

However, predatory journals may also have reasons not to charge publication fees. For example, when starting out, they may offer publication free of charge in order to get authors to submit to them, so they can build up a publishing history to look more legitimate. As another example, an individual might start a fake journal so that he and some of his friends have somewhere to "publish" (for career advancement), and accept submissions from other authors without fee so as to make the journal appear legitimate.


I do not have direct experience with sabbaticals, however the professors I've known that have taken them have been explicitly sought out for the respective sabbatical at a particular institution (as a visiting professor), by colleagues that they personally know professionally (i.e., from being in the same field and interacting via conferences, collaborations, etc.).

In other words, it boils down to networking, and almost certainly doesn't come out of nowhere.  If a professor is planning a sabbatical, he or she will probably already have colleagues willing to host, or will start the process by calling up a colleague and pitching the idea.  I would gather that it isn't likely that there are too many successful cold-calls to departments that lead to sabbaticals.


This may vary from field to field, but in my experience (chemistry) it is always the case that you list your affiliation as the institution(s) where you performed your work; where appropriate, you can list more than one affiliation. In the case that an author's affiliation has changed since the work was performed, the convention is to add an additional "Currently at" or "Presently at" affiliation - your publisher would be able to give the details of how to do this for your article.

For an example of a publisher's take on this, see this excerpt from the ACS publications author guidelines:

  Institution Address: The author affiliation(s) listed should be the institution(s) where the work was conducted. If the present address of an author differs from that at which the work was done, that address should be given in an Author Information note


Expanding a bit on my comment: To find out the net (and gross) salary for any position at a German university (from administrative assistants up to and including the base salary of a full professor), you can use the online calculator at Öffentlicher Dienst.

It's in German only, but not that difficult to navigate. You need to know the following information (I'm not going down every branch, just the one you asked about):

For temporary positions (PhD, postdoc etc.), select TV-L ("Tarifvertrag-Länder", wage agreement of the states);  for permanent positions (lecturers, full professors), select Beamte (civil servant).
The state the university is located in (since every state has full independence in matters of science and education; this mostly affects civil servant positions). In particular, you need to select whether it's a former West or East German state.
The year you are interested in (the wage agreement is renegotiated somewhat frequently, so it might change even within a year).
The pay scale (Entgeltgruppe); PhD and postdoc positions are usually paid according to E13; senior postdocs with more responsibility such as lab management can be paid according to E14. Civil servant positions can be either A13 to A16 for lecturers (depending on administrative responsibilities) or W1 to W3 for (junior to full) professors.
The pay grade (Stufe): For some scales, you move up a grade after several years (used to be by age, now it's by time on the job). This is something you have to negotiate based on previous experience; for a starting PhD student usually only Stufe 1 makes sense. (For TV-L 13, you get bumped up to Stufe 2 in your second year and to Stufe 3 in your fourth year; if you continue on to do a postdoc, you can get up to Stufe 5; see http://oeffentlicher-dienst.info/tv-l/west/stufen.html.)
The additional pension scheme (Zusatzversorgung). This is basically the organization that keeps the money deducted from your gross salary to put into a pension fund. If you're in one of the western states, choose VBL, otherwise VBL-Ost.
The working time (Arbeitszeit) in percentage of a full (forty-odd hour) working week -- this is the important one for TV-L. PhD positions can be announced as everything from 50% to 100%; postdocs usually as 75% or 100%.  Your 66% is about par for the course (depending on the discipline); positions announced as 100% usually include teaching duties beside research.
The additional salary (monatliche Zulagen) is important for W2 and up, but very unusual for TV-L. In your case, leave it empty.
The tax class (Steuerklasse) makes the biggest difference in your net salary. If you're single and don't have another job, choose class I. If not, things can get messy -- I'll just refer you to the German wikipedia entry and wish you luck.
The church tax (Kirchensteuer) or tithe again depends on the state; if you're not registered with one of the officially recognized churches, select keine. (Otherwise it's slightly less than a tenth of the income tax, which comes out as slightly less than 1% of the gross salary).
The health insurance (Krankenkasse) depends on the scheme you're in -- it's either one of the public insurance companies ("gesetzliche Krankenversicherung"), in which case you pay a fixed percentage of your salary (which varies slightly with the company; currently it's around 15.5%) or a private insurance company ("private Krankenversicherung"), in which case you negotiate a personal contract with a certain monthly fee. If in doubt, leave the default (public insurance, current average percentage).

Putting in the information you listed (66% TV-L E13, single, no kids) and guessing the rest (western university, current wage agreement, no church affiliation, default insurance), I get an average monthly net salary of €1497.36 (according to the current -- at the time of this edit -- collective agreement for 2016).


GRE exams for those seeking a Masters in Computer Science

How well do you have to do on the GRE?  That depends entirely on how much weight the admissions committee gives to GRE scores.  Some universities may not really care.  Others may use GRE's as part of the screening process.  Universities have not adopted a universal policy as to how GRE scores should figure into admission decisions.
It doesn't matter if you are a CS major or any other major -- general principles of good study techniques for the GRE hold true for everybody.  If you are an independent learning who is self-motivated and skilled at structuring your own study, then you can probably just get some good test prep books.  If you need more structure, then you might benefit from paying for a course.


Why do principal investigators not hire grant writers?

Most research staff and many students are paid by grants, but most grant terms do not allow for you to pay for administrative staff or proposal writing time. So the funding has to come from the universities or departments. Most of them don't have the funds to hire a grant writer, though some do. I think most departments would rather have half the funding for another professor than a grant writer. I also think your estimate of the salary of a good grant writer in the sciences is off by large margin. The good ones, employed by institutes with large enough institutional budgets make as much as full-time researchers or professors.


How to search for one phrase in the title and a different phrase in the body of the paper in a single Google Scholar search?

You can use intitle: to search for phrases in the title (no space after the colon) and similarly you can use intext: to search in the body.

intitle:"meta analysis" intext:Alexandria


Data mining online course: does it go into my bibliography?

While you saw it first on this online course, that doesn't mean they are the correct citation. You can mention the URL, for instance, if you want to support it, but the citations should reference the original material OR some revised version (like a book, if the subject is somewhat  old).

Long story short: Want to cite a specific method? Search for the original article of the variation you are using and cite that. Is it something very common that is "textbook material"? Pick a good textbook and cite that.


Sharing set of exercises in a textbook (the morally right way?)

Consider switching to an open text books. Several are listed on pages such as this one.

Or, at the very least, assign problems from open textbooks so your students can do more problems.


Asking for a recommendation from a professor who I did bad in his courses

If they were genuinely bad grades, I would advise against using this professor. But a B+ is not "really" a bad grade, even though you might have done better.

Some professors are stricter than average, and a B+ from them is the equivalent of an A- or even an A from most others. This could well be the case here. One of my friends was told that he was in the "top 5" of his class. But there were only two A's, which explains his B+. If this is the case with you, this professor is in the best position to vouch for the quality of your work, and the fact that it would be worth an A elsewhere.

In your shoes, I would schedule a meeting with the professor to find out how he feels about your work, and about recommending you.  It could be that you were one of his best students that he'd recommend above most others (one student on another post reported being the "best student" in a class where he got the highest grade, 90%). On the other hand, he may think that you are "nothing special" in which case you should go another way.

Up to now, everything I've written is "speculation," so you need to find out what the "facts" are before making a decision.


Collaborative development of teaching materials and assessments

It's a wonderful idea.

In the spirit of start somewhere, how about:

Publish these teaching materials (pictures, notes and so on that you have developed to explain a particular concept) on a website of your own, and open it up to moderated comments.  Invite others to contribute guest posts.  You might want to include something like this: "You are free to use these materials in your own teaching, as long as you acknowledge the source."
Borrow liberally from this and create one or more Wikipedia articles.
Consider asking your university to videotape your lectures.
Write up a more scholarly version for publication in a journal.


Publishing paper using an open-source software

Yes, it is possible to publish a paper on model analysis. I would treat this like any other situation in which I wanted to use someone else's "data". Generally, it would be the owner of the data (in this case the developer of the model) that would do the analysis. In the absence of an analysis that I need (or want, or think would be interesting), I would contact the owner(s)/developer(s) and see if they have plans for a similar analysis or would like to collaborate.


I've been in a similar situation, and these are the things I took into consideration:

is it feasible to work on your thesis from abroad? Labwork would make that a lot harder, whereas computer simulations can also be done on a beach in Hawai.
do you have enough progress to finish the thesis rather independently? If so, I would try to write everything up and get it over with.
How easy is it to change advisors? I know it is possible at my institution, but not easy to get done due to the paperwork and the different boards involved. Plus, it often means a change in subject so you basically have to start all over again. Is it worth the effort?

My gut feeling tells me you best just put some elbow grease on, devote some time to your thesis and wrap it up. Take it from somebody who spent three years struggling to finish a thesis due to work: you want to get it over with so you can move on.

So what I would do, is:

write up a bit more, so you add some beef to your work.
roughly plan the rest of your work: when will the results be written out, when will the discussion be written out, still simulations to do? etc.
send an e-mail to your advisor explaining briefly that you had little time to work on the thesis due to personal reasons the past six months, but you want to finish the work in a timely manner. In a next paragraph, explain briefly where you're at now. Make sure to include briefly what you've done since you last contacted him. In a third paragraph, briefly give your planning and ask him whether he can agree on the feasibility of the planning.

You have to keep in mind:

supervisors often have more students. So big chance your supervisor doesn't remember the details of your thesis any more. That's why the brief summary is important.
supervisors like to see results. So if you show them effort, they often get more engaged in the discussion. A little initiative can go a long way, and showing initiative in your first contact mail is likely to get his attention.
a supervisors mailbox can get well over hundred emails in a day. They have little time, so keep it short. "Briefly" is the most important word in my answer ;-)

It might be possible that your mail get snowed under in your supervisor's mailbox. So if he didn't answer after a week, a gentle reminder mail -including the original information so he doesn't have to dive into his mailbox to find it - can do wonders.

Good luck with it!


If a reference is applying for the same position, are they obligated to inform you?

I am interpreting the question as: does someone who writes you a recommendation letter for academic position X and is themselves applying for academic position X have an obligation to inform you of this?

They certainly do not have a professional obligation.  By that I mean that there is no rule that requires it.  On the contrary a general principle of academic job processes is that when possible they should be kept confidential, so the information that someone is applying for academic jobs and if so what jobs need not be disclosed by them to anyone (except the institutions they apply to, obviously).

As usual, the question of ethical obligation is a bit more interesting.  In my opinion the answer is still generally no: in most circumstances there is no ethical obligation to disclose this information.

I should clarify that in my part of academia both job applications and reference letters are done in "carpet bombing" style: many people who are applying to one academic job are applying to twenty or more, more commonly fifty or more, and not so rarely one hundred or more.  Many of the letters are common to all 20, 50, or 100 jobs.  Thus if the writer happens to be applying for a position at one of the same institutions -- and let me say that whether someone is applying for "the same position" is sometimes well-defined and sometimes a bit nebulous; people of very differing levels of seniority can be treated very differently by hiring committees, and it is not uncommon that in that situation if one really does want to hire both people then one tries to do so and sometimes succeeds -- it is not necessarily a direct conflict of interest.  More specifically, I have occasionally seen an application by a letter writer for "the same position" that the letter writee has applied for, and the letter writer's application did not undercut their letter.

In my circle most letters of recommendation are general evaluations of the candidate that would be suitable across an entire range of institutions: they do not make a specific argument as to why Institution A should hire the candidate.  In fact, in my field (mathematics) we have an extremely convenient automated job applications site (called, reasonably enough, MathJobs), so when someone asks me for a recommendation I don't even know the full list of places in which that recommendation is being used.

I have written dozens of recommendation letters for academic jobs.  Exactly one was specifically targeted to one institution, the one job to which that person was applying.  If I had also been applying for the same job: yes, that would have been awkward and ethically problematic.

As above, I would say that the ethical problem occurs when you are writing a letter which is targeted to a specific institution and you know at the time of writing that you plan to apply for the same job.  Such a situation is the ne plus ultra of conflicts of interest, and the ethical thing to do would be to decline to write the recommendation for that institution.  It is not necessary to disclose why, but if one is willing to write other strong recommendation letters it would be good to say so.

Finally, let me say that one can largely avoid this issue by making sure that your recommenders are much more senior than you.  Thus, if you are applying for a postdoc position, have all your letter writers be on the tenure track.  If you are applying for an assistant professor position, have all your letter writers be tenured.  This turns out to be good advice anyway: senior people have more pull and, other things being equal or nearly equal, are the ones you want writing for you.


Not able to find peers to publish with. Will publishing alone affect the credibility of the paper?

Will submission of a paper with only my name on it affect the chances of the paper being accepted?

No.  Reputable journals do not intentionally make publication decisions based on who the author(s) are.

That said, getting feedback from colleagues can help you improve your work before you submit it.


Can a casual comparison of phenomena and assumptions based on it be presented in a journal/conference paper?

In comparison to the size of the universe, humans on earth are like bacteria on a speck of dirt. Much like in the animated movie "Horton hears a who"... There might be a civilization of creatures living on specks of dust that we see everyday.

I think the example you have chosen here is obscuring your real question. It's not clear that this example makes any scientific sense, so if I saw this in a computer science paper I would find it very strange and probably suggest that the authors delete it. But your real question is about some hypothetical opinion, not about the (scientifically indefensible) suggestion that there are entire worlds on specks of dirt.

So, to the question I think you wanted to ask: it is OK to write casual comparisons if the comparison is useful and illustrative. Not all arguments have to proceed with a hypothesis test or linear regression or something. Your job is to convince the reader of your hypothesis; the argument for that can be heuristic, philosophical, or on a totally meta level. If it's a compelling point of view and the reviewers buy that it is plausible, they will likely be happy with your paper.

  Observable Phenomenon: The universe is 92 billion light years in diameter. In comparison, the Earth is a mere 12742km in diameter, and the average human height is 1.7m and viruses can be just 20 nanometer in diameter.

  Our hypothesis: If the Earth could be assumed as a universe, it may very well be possible that there may be an entire civilization of creatures living on atoms or electrons.

Assuming that the "Observable Phenomenon" and "Our hypothesis" are replaced by something less ridiculous, this seems entirely fine. You are starting with some quantitative observations, and asking the reader to draw a conclusion about some hypothetically possible scenario.


What is the difference between Ph.D, D.Sc, D.Litt, etc.?

The meaning of these degrees vary by country. In some countries (especially in Europe), PhD is the "basic" degree. It's the one you get out of graduate school. D. Litt (aka. Doctor of Letters) and D.Sc (Doctor of Science) are the highest conferred degrees. You need sustained achievement at the top before these are awarded. Here's a quote from the Wikipedia article on D. Litt:

  The Litt.D. degree is awarded to candidates whose record of published work and research shows conspicuous ability and originality and constitutes a distinguished and sustained achievement. University committee and board approval is required, and candidates must provide documented mastery of a particular area or field. The degree may also be awarded honoris causa to such individuals as the university or the learned body in question deems worthy of this highest academic award.

D.Sc is similar, except it's for the sciences as opposed to social sciences. Again, see the Wikipedia article, except there're many non-European countries who take D.Sc to be effectively equivalent to PhD.


Why are cumulative tests typically weighted so high (U.S.)?

Cumulative tests show that you understand everything so far; they are meant to help students who perform poorly on the first exam, so they can do better on the second one, since they will have an idea of what to expect on the second one. It is uncommon when a student does worse from one test to the next.

Also, going back to projects, some professors don't value homework/projects as much because any student can copy / get help for their projects. Some professors I know would even give 100% for homework/projects just for turning them in, as they are meant for students to practice and learn by themselves. They are meant to help students prepare for tests. Because of this projects and homework are not a good (trusted) indicator of how a student is doing in a class.

By the looks on your grades, most likely you still don't know the topics of your class, if it was a more strict professor / class, just for failing the cumulative final, you would have failed the class as well, as this would be an indicator that you (maybe) cheated on your projects.

Cumulative tests are usually weighted high because in order to do the last topic you need to know the previous topics as well.


Vacation Days of Assistant Professor in Canada

How much vacation time an assistant professor gets is answered by the collective agreement in force at York U. According to a comment above, that's 4 weeks. These are days when you can do whatever you please.
Obviously, there are constraints regarding the time when you can take this vacation, as pointed out by some comments.

More importantly your question suggests that there's potentially vacation whenever there are no classes. So for one thing you may need the time between semesters to develop your teaching material, but also an Assistant Professor is not a teaching-only position, it's research/supervision + teaching + typically some admin duties.

Finally, note that in many Canadian Universities there is a summer term with classes going on between may and August. So you could very well end up teaching all year around; there's typically about 3 to 4 weeks between the end of classes for one term and the beginning of the next (and that time includes exams and marking).


Studying medicine after PhD in nuclear engineering

I don't see any conflict, actually. Nuclear medicine is a recognized specialty. Medical researchers often enough earn MDs as well as doctorates as it gives them more of an appreciation of the biological and clinical needs in medicine.
Moreover, it isn't necessary that a person have only one deep interest in life. Lots of doctors have other interests. Many are geeks and program computers "just for fun". Many are musicians, etc.
You might reach a stage, however, in which you need to choose, or at least emphasize, one interest over the other, so be prepared for that eventuality.
Since it isn't my field, I can't suggest an integrative path, but you might find one as you go along. Some medical practices are pretty crude, in fact and can benefit from the work of a researcher who can bring other ideas to bear.
Long road, though. Lots of sleeplessssss nights.


Is it too early to switch advisors if I just finished my first semester as a master's student?

Is it too early to switch advisors?

If there is evidence the advisor is not the right person for you, it's never too early.  It's clear from your question that you should switch.

  Is it too late to switch advisors?

It depends on the rules of your university, but in the first semester it is probably not too late.  Don't wait until it's too late.


Should a degree in an unrelated field be included in CV?

While there are some circumstances in which is it appropriate to use a "shortened" C.V. that does not include everything that you have done, I have never heard of a circumstance under which it is appropriate to omit a degree.  An irrelevant degree will not hurt how your C.V. is perceived, and if it is later discovered that you omitted a degree from your C.V., it may be considered suspicious or dishonest.  Furthermore, it may under some circumstances be considered a plus---you never know what kind of interesting cross-disciplinary connections somebody reading your C.V. might make in their head. I would thus advise you to include all of your degrees, even if some seem irrelevant to you.


Are papers entirely unrelated to my field going to hurt my chances in the future?

A legitimate scholarly publication can only help you (although it might not help much).  If you're really worried you can always just leave it off your cv.


How to grow as a researcher outside of research?

I would describe the areas you're concerned about as networking and service.

While neither of these are critical path for your ability to succeed as a researcher, they most certainly will make you more well-rounded and can help you in many ways, so they are definitely worthy of investing a small but significant fraction of your time and effort.

What I would advise you, however, is that there are more ways to do networking and service than taking a leadership role in organizing events.  There are many other types of role that you can ask to take on that can ease you more slowly into such organizations and roles, but which won't push you out of your comfort zone too quickly.  Two good directions that I would recommend are:

Secondary event organizing positions, such as web chair, publication chair (i.e., the person who turns accepted papers into proceedings), local arrangements chair, tutorials chair, publicity chair, etc.
Reviewing for journals and conferences (often starting as a "sub-reviewer" for your advisor or other professors you work closely with)

The professors that support you can likely help you get such opportunities, and from these "training wheels" positions you can start to establish yourself as a known contributor in your professional community and start getting more comfortable with more visible roles and more active forms of networking.


What is the best way to see if students understood?

I'm going to suggest that you are probably over-using lecture as a teaching technique. If that is the case, there is hardly any way to achieve the goals you set. Students don't learn something by hearing it once, or even twice. They learn by engaging with the material and that is impossible in the short term available in a lecture. At most, what you can elicit is a bit of ephemera from their short term memories. But that isn't learning. Let me suggest two techniques, but the first is, by far, the least effective.

Force the students to take extensive notes with paper and pencil. They can use full size sheets of paper, but should also each have a deck of index cards. Encourage/require the students to record on the index cards the three most important ideas from any given lecture (one idea per card). Take time periodically, if you like, but the end of the class period is likely enough, to ask them what were the most important three ideas. Students volunteer from their already prepared cards. You can accept or veto any idea. Do this every day. Also, encourage/require students to write questions on the cards and pass them to you periodically (this is your every 15 minute solution). Quickly sift through the questions and either answer them immediately or just incorporate them into what you do going forward. At the start of the next class, ask the question, what were the three most important ideas from the previous lecture. Again, volunteers can offer suggestions. Also, see my answer to a different, but related question at CSEducators
The above, still assumes that you use lecture primarily, but this is not an optimal teaching technique. Instead, you want to learn about and use a flipped classroom. A search for "flipped classroom" on this site will reveal a lot of discussion. I point you to an answer I gave for slightly younger students but which also applies here. I try, there, to outline the idea. But the key to it is that in a flipped classroom you use the face time to work with the students, rather than to perform for them. In a situation like this, you have no doubt about their understanding as you are involved directly in developing it.

Of these two techniques, the second is much more likely to be effective. In CS, it also gives you the opportunity to use pairing and group work so that the students can reinforce one another's learning, so that not every idea needs to come from you and so that you don't need to individually reinforce the learning of every student. Lots of wins can be achieved here.

Since it came up in a comment, let me add that one reason to dis-favor lecture as a primary teaching technique is that students have different "learning modalities" and lecturing disadvantages some students - those who are not primarily visual or aural learners. Active learning, combined with other things, is much more effective as it reinforces the learning immediately and drives it deeper into the brain's pathways. Every student is different and instructors should realize that most students are not like themselves unless they are doing doctoral level education.


How can I convince graduate students in China to not copy/paste from the Internet into their research papers?

OK, it's getting weird now. I thought this would be much less common in top 10s.

There's a simple path here: tell them plagiarized papers are not going to get published, or will be retracted in the future, and this will hinder their graduation & will create trouble for their advisor (+ advisor would lose face) if they insist on submitting such papers.

When your students (and everyone else) care only about the "pragmatic", give them "pragmatic" reasons! Chinese people generally do not like creating trouble/making others lose face, so that's a good path.

Convincing them that plagiarism is morally incorrect and not right would be harder, and students would likely not buy into that. But the pragmatic path gets the job done :-)

From the situation you described, I infer two things about your situation. Correct me if I am wrong:

The university you're at is likely not top-tier. I would be surprised if even the researchers at Tsinghua or Jiaoda (Shanghai Jiaotong University) engage in academically dishonest conduct frequently. I suppose you're likely at a local (provincial) university.
Your colleagues/students are mainly targeting domestic conferences/journals (and likely not the top ones). Otherwise they will surely know that academically dishonest practices will get their papers rejected.

If both are true, I'm afraid little could be done. You could try very hard to at least make your students not plagiarize, but this will probably have a very negative impact on future recruitment, and even your students are not going to 100% listen to you. The best option at hand is trying to move to another university (preferably in another country) if this bothers you (it would bother me for sure).

The ranty part: I decided to delete this, but just keep two key points.

Plagiarism is not dealt with seriously enough and people let it happen. Awareness of what constitutes plagiarism is low, but for reasonably experienced researchers this should be obvious. So, as you see, the problem is not that people don't know it is plagiarism; they likely do know, but they have no reason to care.
The quality of most domestic journals & conferences are questionable, so the problem is even more serious at this level (because not even the editors care).


Citing contemporaneous (interlaced?) preprints

Cite relevant literature
Since you have the option of adding a citation to a relevant source, you should do it. It improves the paper by making it a more useful reference, and comparing and contrasting the results might also be useful.
Priority
If relevant, use a phrase like "A very recent preprint A claims this and that.", or even, if your results are very similar and you really need to emphasize priority, "During peer review of this article a preprint A was published. The preprint...".


Can a university revoke my degree for not attending classes?

It is part of the cultural norms of American universities that your attendance or lack thereof is an issue for each individual course instructor to pursue or not pursue as they choose.  At my university the administration is involved precisely insofar as to have the following policy:

  Students are expected to attend classes regularly. A student who incurs an excessive number of absences may be withdrawn from a class at the discretion of a professor.

This states the situation well: the administration empowers the instructor to penalize the student for poor attendance, including withdrawing them from the course. Thus whether and how your lack of attendance in a course is problematic is between you and the instructor of that course.  You seem to be worried about attendance that is acceptable to the instructor -- more precisely, not resulting in failure or withdrawal -- but is somehow unacceptable to the university as a whole, since you write

  Despite this, would it be unprecedented for the university to claim I was in violation of an attendance policy anyway and revoke my degree? I'm worried the school may see this as an insult and retaliate.

In a word: yes, this would be completely unprecedented and moreover implausible.  First of all, how does the university even know about your attendance?  Even if they somehow found out (maybe you write an editorial in your school paper advocating attending class as little as possible?!?) it would widely be viewed as a violation of the instructor's rights to penalize you for lack of attendance when the instructor did not.  Finally, you speak of a degree being revoked which means that first you get it and then they take it away from you.  Degrees are only revoked for the grossest forms of academic misconduct.  It would be outrageous for a university to revoke a degree due to lack of attendance -- frankly, that would reflect very badly on them and would invite censure and possibly even legal action, as it seems manifestly unfair to conjure requirements retroactively.

Summing up: you should clear your attendance plans with each course instructor in advance.  To do otherwise is really not safe, as you can see that e.g. my university (which is not so far away from yours) empowers me to withdraw a student for sufficiently poor attendance.  If your attendance plan is okay with the instructor, it will be okay with everyone else too.


Mendeley - References in Bibliography that I did not insert (MS Word 2016 plugin)

I (kind of) solved the problem. I removed citations in earlier versions of the document and for some reason they were still being inserted into the bibliography. All cases were cases in which a there were multiple parenthetical citations. I deleted the entire set of citations and re-inserted them, and it's working again.


Does having a masters degree from a Chinese university have negative view for a PhD applicant in the United States?

I have some experience with Asian Universities, particularly Japanese.

First, take into account that having a Masters might boost a bit your application to PhD a bit, as long as you publish something over there. Also, if the profesor you are going with is unknown, it might not help you at all.

Second, many people think that studying abroad and traveling are similar things, when they are really not. You'll have to deal with the hardships of asian Academic culture, which are very different from the American ones.

You'll also have to deal with the hardships of life, be sure to know the language at least to communicate basic thoughts and deal with the fact that you might not like food there (Protip: Chinese American Food is somewhat different of real Chinese Food)

I would put more, but I would be edging on ranting, which I'm probably already are.


Two months to go on my masters programme and I want to drop out what should I do?

My heart goes out to you, it sounds like you're really unhappy with your current situation and feeling very conflicted.

It's hard to give someone advice on a topic like this because it's so personal so instead I'll give you a few of the questions that I might ask if we were able to sit down and have a chat about this.

What initially led you to apply into this masters? Is it your specific experience that is creating problems or is it that this masters does not align with your interests/goals?
What is the appeal of this job offer? Can you really see yourself doing that kind of work or is it that it represents a face-saving alternative to completing your masters?
What would have to change for you to be comfortable completing your program? Is it a change of dissertation topic? Is it extending by a term or a year to take the pressure off? Changing supervisors? All of the above?
Are there jobs that you want, now or in the future, that you can't have without this degree? How important are they to you?
Do you really hate your program/subject or do you hate the situation you are in?

Think on these on these until you hear back from your school and your potential employer. Once you have answers to them, take a break and step away from it for a little while; when you come back to it see if you still feel the same way about your answers or if your thoughts have changed.

There's no right or wrong way to do this - I personally trudged through a degree when I knew it wasn't right for me because I was so close to the finish line. Finishing that degree proved to me that I could see something through to completion (something I had always struggled with) but also kept me from finding my true path for another year. I'm still not sure what the right choice was, but I'm happy with where I am now.


What should I do with a workshop paper which is peer reviewed, but only available on the workshop website?

Works that appear in unpublished proceedings are not (generally) considered published, so such works can be submitted elsewhere, e.g., conferences with published proceedings, journals, etc. (Exceptions may arise if copyright was assigned, but workshops with unpublished proceedings shouldn't be asking for copyright.)


If there are two published versions of a paper, which one should I cite?

I favor acting in the following way:

If you've only read one of the versions, cite that one. God knows what's in the one you haven't read.
If you've read both versions:

if they are identical relative to the information you need, publication in a journal or proceedings volume takes precedence over (re)publication in a career collection (e.g., "Selected works of Jones"), which takes precedence over arxiv, which takes precedence over non-arxiv manuscripts.
if they are not identical relative to the information you need, cite whichever one contains the best version (where best probably needs to be decided on a case-by-case basis).


Endnotes of the sort you are suggesting would give the impression that you don't know how to write a teaching statement. In any document like this, you're trying to make a convincing case, which means knowing what to put in and what to leave out.


What is meaning of rolling deadline of grad school application in US?

When there is a "rolling deadline" of any kind there is usually a "date of full consideration", or at least the earliest date the program will begin reviewing applications. Then the program will review applications as they come in, extending offers daily/weekly.

The program will continue to accept applications until a final close day is reached, or until they have filled all their available seats - whichever comes first. This is on contrast to programs that do not view any applications of any kind until the application date has passed, and then all applications are reviewed at once.

If you apply early to such a program, you may still be declined/rejected. However if you wait until too late then indeed if all seats are taken and the program is closed then you miss out on being considered, regardless of how good an applicant you were.

In such a system you are generally best to get in your application as close to the first review date when applications open. In the job world this is analogous to job postings that list "until position is filled", and basically work the same way.


Is it possible to publish a simple result that refutes prior work in a leading journal? (without support from your advisor)

The answer is yes.

But you paper will have to meet the standards of the journals you're aiming at (that might include experimental data) and show a good understanding of the existing body of work. Especially if as you state your work contradicts a lot of the existing literature, the level of scrutiny will be high.

Now since you say you are quite early in your career it's possible that you are missing some aspects and that your work is not that controversial or that it is indeed just a technical quirk. In that case insisting in publishing it while ignoring your advisor's criticism will of course deteriorate your relationship and will probably mean you'all have to fined someone else to supervise you. But having it rejected will not affect your career negatively. Everyone gets paper rejected. Just make sure you don't make a habit of submitting work that claims to revolutionize the field but turn out to be wrong.

  I am [...] the most technical (mathematical) person in the lab

That might be true but it's very unlikely that everyone else in the field lacks the necessary mathematical skills to understand the issue.


Should / How do I include my school's GPA Scale in my CV / Application

I had the experience of sitting on a graduate admissions committee during my years in graduate school.  (This was at a "top-10" school in my field, though not a "top-5".)  In my experience, the raw GPA number was mainly used to make a "first cut" to weed out the fraction of applications that were almost certainly sub-par.  (Things like super-low GRE scores were also used at this stage as well.)    Once the applications got beyond this initial screening, committee members would read carefully through them;  and at this point, the raw GPA was put aside in favor of the more detailed grade information on the transcript.  Almost every transcript, especially those from US colleges or universities, had an explanation on the back about the system used to assign grades and calculate the GPA.  There's enough variety in the systems used by different institutions (even within the US—foreign institutions had even more variety) that I always had to read through this information to contextualize what I saw on the transcript.

Which is to say:  it's probably best to be honest about your GPA in the CV.  But if you don't mention it specifically, the committee members will almost certainly still be able to figure out that your school had a 4.3 scale;  and they almost certainly won't hold it against you for not mentioning it once they've figured it out.


Can I ask an author to send me his ebook?

Certainly you can ask. There is nothing wrong with that. If you explain a bit about your use and the restrictions you face it might make it more likely that the author might try to help you.

But the author might not be able to comply with your request due to contractual arrangements with the publisher (if any). So, you might get a reply that starts out "Sorry, but..."

On the other hand, I'm surprised that libraries don't have access. I would guess that if you take your request to the librarian him/herself, you might learn that copies of nearly everything can be borrowed. Librarians have a vast, legal, network of sources for academic/scientific works. Even my town library, which has no formal relationships, can find just about anything I need, though the sources are usually all in this country.

But there are no ethical issues about asking. Etiquette only requires politeness and being honest about your needs.


Can a department disallow a student-advisor pairing in order to distribute PhD students evenly among faculty?

Questions like this show the importance of understanding the perspective of faculty members.

Can a department tell a student and advisor not to work together? Who knows. It will come down to the department.

But it is much more likely the other faculty would try (in private) to convince a "greedy" faculty member not to accept so many students. Faculty have a longer perspective than students - students graduate in a few years, but tenured faculty usually stay at their institution far longer, with the same colleagues. So there is usually more risk for a faculty member who harms their relationship with their colleagues, compared to just turning down possible students.  There will always be new PhD students next year... At the same time, if a faculty member really wants to work with a particular student, no other faculty member is likely to want to "steal" the student.

What about the hypothetical situation from the question?

It would be extremely unusual for a department with 10 PhD students and 10 faculty to tell the 10 faculty that they each have to find one student, and none of them can take 2 students.
It would also be unusual for one faculty member of the 10 to work with all 10 students.

What happens in most cases is that the students naturally gravitate towards faculty they like, and faculty who don't feel they have enough students will make more effort to be friendly and reach out to possible students. If a faculty member doesn't want to work with a student, or a student doesn't want to work with a faculty member, they don't work together. In the end, the students all find mentors, although it may take some students more than one attempt.

The situation is different, of course, when students are required to select an advisor while applying to the university, because then there is no doubt who each student will work with.


May I mention in my CV that I am a reviewer for a journal if I co-refereed?

You can list reviewer activities on your CV, especially in an early stage of your career, see e.g. https://academia.stackexchange.com/a/3543/68222.

The situation you describe is different. You weren't one of the official reviewers of the paper. As stated by @Dirk, this situation is uncommon and might not be compliant to the journal policies. Because of that, I suggest to not mention this specific "review" on your CV.


Legal protection for the title "university" in California

Unlike some other countries, there is no strong federal regulation that controls the titles like "University" and "College".  A few states have state level regulations, but federally there isn't any.

By the looking at the number of degree factories in California, I doubt that state of California has strong control over the title as well.

Some people became professors in regular four year colleges outside of the states with PhD's from these colleges without attending the class once or even visiting the campus - well, there isn't any campus to visit anyway.


I'm assuming you have a math background?  If so, I would say go with regular stats and see if you can gear your course of study more towards the medical side of things (by taking a course in epidemiology or other medically related courses, and doing a research project in the biomedical field).  I think you will leave more doors open this way.  I think that Biostats is generally geared more towards biomedical research.  You collaborate with doctors and scientists.  Taking statistics would allow you to go this route if you desire, but also leave doors open to the quantitative social research/data mining that you mentioned in your post.  Then again, take what I say with a grain of salt.  Do more research on each subject to find out what is best for you.


What are the super cool tricks to getting published in high impact journals?

High impact journals, or in other word, top ranked journals (based on IF) are those publishing the state-of-the-art research works with high percentage of novelty and originality. In my own opinion following tips are very important in getting into the high impact journals:

Select a real challenging problem whose solution/amendment significantly impacts on the domain.
Formulate the problem (using mathematical modeling, visualization, or empirical experiment depending on the domain) and let peers/reviewers see the significance of the problem.
Propose a solution with high degree of novelty in a way that has not been undertaken before for the same problem.
Throughout the research try to follow the conventions of research in your domain in the highest possible level, especially when it comes to evaluation and validation of your work.
In data collection phase, try to follow the most appropriate approaches and use accurate tools to measure/quantify. Maybe looking at similar papers can help you in this.
Avoid silly mistakes. Usually reviewers do not expect to see silly mistakes in the work. If you make small obvious mistakes, how can reviewers ensure the rest of your work is error-free.
Show high level of confidence in understanding and expertise over the domain. If you need to review related works in your paper, try to select those closely related to your work; not any work.
Present your work nicely. Avoid English errors (no grammar and no spelling). Use professional drawing tools to draw high quality figures, draw nice tables, use proper sizing for objects in the paper, not too big, not to small.
There is an approach by some young authors that leave some works to be done in revisions stage, which is not correct to me. Don't send incomplete work to any high quality journal. There will hardly be any chance to correct mistakes. The review is more to evaluate the significance of the work, the novelty, relevance to the journal, and research practice presented in the paper. Reviewers are not English proof reader and their job is not to correct you.

There may be lot more tips that I will compile as I noticed. Hope it works.