What incentives do academics have to write text books?

Another reason to write an advanced text is that you have developed a body of research around a topic, and it's stabilized enough that you can present the material in a structured form. The incentive here is that the distilled understanding helps you understand your field, and it helps others work in the area as well. In addition, a well-written book can get you lots of citations, impact, and recognition (the same kinds of things you get with papers, but possibly even more).


How to deal with cheating when university policy is ineffective?

Since you speak of "a small group who cheat," it sounds like most of the students do understand the policies and importance of honesty.  That remaining small group who cheats?  Nothing that you do or say is going to convince them not to cheat.

Likewise, university policies often make it hard to actually punish cheaters, because they begin with the presumption of innocence, which is generally a good idea.

A better way to approach the problem is to adopt a "layered defense" strategy of a number of small actions that reduce the cost/benefit ratio available from cheating.  Some of the sorts of strategies that I have seen include:

Increasing the separation between desks
Randomized assigned seating, which is likely to break up cheating conspiracies
Printing less questions per page, with lots of white-space for working the problems, so that an answer will not be visible for as long a period of time
Problems that are based on "showing your work" rather than obtaining the right answer.
Problems with many possible solutions, that convert copying into plagiarism.
Putting more credit into projects and labs, rather than exams.

None of these alone will solve the problem, but the more of them you can enact, the harder it is for cheaters to prosper.  Some of them may even help the non-cheating students, by forcing them to engage more deeply with the material.  The balance, of course, is that it all takes time and effort from the instructors and TAs, so you need to make your own cost/benefit analysis as well.


How does making notes of what you read help you in research/teaching?

It's an old adage that "You don't truly understand something unless you can explain it completely to someone else". Writing notes effectively forces you to explain the topic to yourself. Oftentimes, when writing over notes from a class or from what you've read, the simple process of re-explaining it to yourself will clarify points that may have been confusing earlier.

For this purpose, I try not to write notes as I'm reading, but rather I'll read a section and them summarize that in my notes. Having read the full picture, I can then ensure that my understanding of the topic is more complete, and my notes should reflect that.

On a different note entirely, repetition enhances retention, and writing notes is at the very least doubles the number of times you'll see it (once in the book, and once as you write it), which should help your remember it that much better.


How would you, as a teacher, decide if a particular topic/ concept should be tested as multiple-choice questions or as free-response questions?

In the absence of other factors, in my opinion, at least in mathematics, a free response is always the more valuable type of question. The educational value of getting shown, where precisely your argument went wrong is much higher than just being told if the final result was right or not. It also allows for a much finer grading, as I can both give partial points for an almost correct reasoning leading to a wrong answer as well as deduct points for incorrect reasoning leading to the correct answer.
That being said, a test question never happens in a vacuum and the problem usually is lack of time. This can occur in two forms, lack of working time to correct the test and lack of time during the test.
Personally, I believe the former is a bad excuse. Unless you have a 200+ people class without any TAs (in which case, clearly something else is wrong), it is always possible to correct a full-text exam in a reasonable amount of time.
This leaves the latter point. Any exam has a limited duration and it might not be possible to cover all topics in this time. My personal response would be to leave out some of the less important ones at random. As long as the topic selection is not announced to the students beforehand, they still have to study all of them and the results will be similar. But this is a point where a good argument can be made for turning part of the test into multiple-choice. In this case, the most important topics should still all be free-responses, but you could add a small multiple-choice section covering the rest. However as these are not the important part of the test and they are there to save time, I would keep them simple. (E.g. picking the right definition or "does A imply B?") After all, if marking the right answer is not substantially quicker than writing it out, then you are not saving time.
In any case I would always invert the original question. Don't take a concept and decide of it should be multiple choice, but instead decide how many multiple choice questions you have to make and then pick the questions that work best.


Email Asking for Appointment Letter of Reccomendation

You could do sort of a hybrid between an ominous email and a surprise appointment by asking for a letter over email and also asking to meet with them. It could be written something along the lines of:

Dear Dr. Professor

First sentence is a simple introduction stating your first and last name, the class you had with the professor, and the semester/year you had it with them (if the class was a big lecture it could be helpful to also include your grade, but it may not be necessary). This sentence lays out your academic career path (applying to graduate school program in field). This next sentence explains how this professor/class has influenced your academic career path choice. The following sentence asks if the professor would be willing/be comfortable writing you a letter of recommendation. Next, if they are willing/able/comfortable writing you a letter, you would like to arrange a meeting at their convenience to discuss/answer questions. This last sentence thanks them regardless of their reply.

It doesn’t need to be lengthy, but this basic structure allows you to jog the professor’s memory without being too overbearing. It also allows them to have an easy out to decline writing a letter for you (which is beneficial if they do not feel comfortable writing you a strong letter). Remember, it is possible that the professor may not remember you even if you meet in person, or they might completely remember you just by hearing your name again.

If asking over email is really not your thing, you could make an appointment to discuss graduate school so that the email hasn’t asked for the letter yet, but it’s much less ominous.


How soon can I poke a potential PhD advisor for a response if contacting them about an advertised position?

I do not think it will be disrespectful to send a follow-up email. I would craft it in a way that shows you value his/her time, but also demonstrating that you have an immense interest in the project, which is why you are reaching out. I would have a backup plan just in case.


I'm thinking about leaving after 6 months as a PhD student

I just read your question and I decided to sign up here so that I can answer your question.
As you say PhD is a long "journey", you are going to spend several years working on that project, and I really think that you should "believe in" your project to keep motivated. If it helps, I'm in my 3rd year of PhD, I am studing microbial ecology, which is not exactly my field (I studied Biotechnology and little ecology), but I was interested in the field I could see why it was important. Although I don't see future applications in industry (at least right now), I am aware of the importance of doing "basic research" and builging a general knowledge that help to better understand the world...
During my 2 and a half years I have had good and bad moments, and sometimes, talking with my supervisors helped (I must day that I'm very lucky because they are great persons), but most of the time, motivation depended on me, on seeing through the "bad days" and working on mental health, which includes not working on the week-ends, spending time out of the office, doing sport, talking about my work-related problems with other people in and outside academia, taking holidays...
This is my experience, if you have just started and you already have this feeling, I think you should look for other project or other type of job. Sometimes, deep inside, you know what you want but you are a bit scared/worried/embarrased to confront it (I don't want to make any assumptions). Problems with invoices, books, money etc are usual in all labs (in my experience), so you might encounter similar problems if you move to other lab. But mental health is so important!! If talking to your supervisor doesn't help, try other people around in the lab, with the experience of doing a PhD. You should be the most motivated person about your project, if you cannot see its usefulness, or you don't like it, it will get worse... In the next years, you will need to defend your project in papers and dissertations, you will have to read a lot of literature related to that to build a good knowledge, so at least you should enjoy reading and learning about that topic, if not, everyday will be a torture...
In any case, don't feel bad about your supervisor if you finally decide to leave, I know it can be embarrasing after the month he/she has spent teaching you etc, but if you think it is the right decision, you will be grateful in the future ;)
Hope this helps!


Is it acceptable to write a reference letter for yourself?

I don't think this is a grey zone at all. Senior professionals in all domains, not just acadaemia, routinely sign letters that they did not pen:

Directors signing press releases written by communications managers
Vice-chancellors signing letters to government officials written by deputy vice chancellors
Academics submitting journal articles that were written by a co-author, although the research is shared.

It's completely irrelevant who actually put the words together, unless there is a question over the copyright of the text - which there clearly isn't here. All that matters is that the person signing the letter stands by its content and takes responsibility for it.

If you write a reference letter for yourself that is over the top, they won't sign it. No ethical issues here whatsoever.

(I can't answer whether other institutions would frown on the practice for other reasons though.)

EDIT

Ok, some research.

  Tip: Don’t ask the candidate to write a draft of
  the letter for you. Most heads of labs say this rarely
  saves time and sometimes leads to a weaker letter.
  It is better for the candidate to provide you with
  all the necessary information, from which you can
  then pick and choose as you write your letter.

... (and for the applicant)

  You may be asked to write a draft of the
  letter. As mentioned on page 1, many
  heads of laboratories say this is not a good
  idea. However, if you are asked to do it,
  do it!

http://www.hhmi.org/sites/default/files/Educational%20Materials/Lab%20Management/letter.pdf

  When requesting a letter of recommendation, don't be surprised if your instructor or supervisor hands the forms back to you and says, "Sure, why don't you go ahead and write the first draft yourself, and I'll revise it and sign at the bottom."

http://www.petersons.com/college-search/letter-recommendation-writing-yourself.aspx

  The “draft” that you provide to the recommender to sign shouldn’t be a draft at all – it should be a perfectly polished letter ready to be signed, sealed and delivered.
  Don’t be insulted when your supervisor decides to edit.  They’ll want to apply their own language and voice to your content.
  ...
  I’ve been asked to write lots of letters of recommendations for students, but I’ve never felt strongly enough to throw the responsibility back at someone.  That’s not to say I haven’t managed some phenomenal students; I just haven’t had someone come along who I think is up to the task.  So, when he or she does come along, that person will really be top notch.

http://studentbranding.com/writing-your-own-letter-of-recommendation/

  While the standard practice is for references to write their own recommendation letters, it’s becoming increasingly common for time-strapped individuals to ask you to pen the first draft of a letter yourself.

http://www.vault.com/blog/job-search/how-to-write-your-own-recommendation-letter/

  Question: Is it OK to Write My Own Letter of Recommendation?
  Answer: The only time it is acceptable to write your own letter of recommendation is when the person you requested the letter from asks you to do it. Even then, it is important to be honest in the letter. Don't write anything the other person wouldn't have written. When you have finished, ask the person to look over the letter, verify the information, and sign. You should never forge someone else's signature.

http://businessmajors.about.com/od/recommendationletterfaq/f/WritOwnRecLet.htm

I don't see much (any) evidence of any ethical quandaries in a professor requesting and submitting a letter of recommendation directly from the student. These examples aren't cherry-picked - they're the first few hits that came up when searching for phrases like "own letter of recommendation" or "letter of recommendation myself".

In summary:

Is it acceptable to write most of the reference letter and have the prof make minor edits?

Clearly, yes - if requested to do so.

Do academic institutions frown upon this practice?

No.

Would it be considered an academic offense if a student wrote a reference letter for themselves and had a prof sign it?

Hell no.


How to validate and submit for publication a paper as a graduate student?

Your situation is just like that of any other researcher. Work out your ideas. Write them up with proper citations of past and related work and submit to a journal that might be interested. The journal may be one of those you have found in your work and have cited.

Your advisor will give you initial feedback on your idea I hope and the editor and referees of the journal will also provide some validation. Your advisors likely have more experience and perspective than either of you, so take their advice about originality and possible importance. But, basically, in order to publish, you just do it and wait for feedback from the journal. Expect, as a minimum to have to rewrite based on reviewer comments.


"Awaiting Reviewer Invitation" after "Acceptance with Minor Revision"

I don't know what "awaiting reviewer invitation" means.
But usually, the paper with minor revision will be sent directly back to the same reviewers for the final decision. They need to check whether you revise according to their reviews.


Proper citation of equations in scientific papers - terminology

From Higham, Handbook of writing for the mathematical sciences (emphasis mine):

Referencing Equations
When you reference an earlier equation it helps
the reader if you add a word or phrase describing the nature of that
equation. The aim is to save the reader the trouble of turning back to
look at the earlier equation. For example, "From the definition (6.2)
of dual norm" is more helpful than "From (6.2)"; and "Combining the
recurrence (3.14) with inequality (2.9)" is more helpful than
"Combining (3.14) and (2.9)". Mermin [200] calls this advice the "Good
Samaritan Rule". As in these examples, the word added should be something more informative than just "equation" (or the ugly abbreviation "Eq."), and inequalities, implications and lone
expressions should not be referred to as equations.

Pro-tip: arguing with a referee on such trivialities is rarely worth your time. Just do what they suggest.


Negotiating 1-year delay to my Assistant Professor Offer

Well, as a department head, I would be slightly annoyed that (i) you applied for a position you knew you couldn't take, and (ii) you didn't mention this earlier.

But it is what it is: You have no other option than coming clean, and so being honest should be your first priority. The people you're going to talk to are going to be your future colleagues and you will rely on their good will for the next many years. So playing games is not a useful strategy and all you can do is be forthcoming in explaining your situation, and ask whether there is a way to delay your starting date by one year. There is really no negotiating in this case: You need the department to agree to your demands, because if they don't you have a contract you can't keep (because you can't show up in person) and will likely lose your job. In other words, you're completely at the mercy of the department, and that's how you should treat it: With honesty and humility.


What is Cumulative Impact Index of a journal?

The term "Cumulative Impact Factor" (or cumulative impact index) has been used with different meanings by different authors.

One definition is that the cumulative impact factor for an individual author is simply the sum over all papers that the author has published of the impact factors of the journals that the papers were published in.  e.g.

You've published 3 papers in Journal A that has impact factor 1.2.
You've published 1 paper in journal B that has impact factor 1.9.
You've published 2 papers in journal C that has impact factor 1.7.

Your CIF would then be

CIF=3*1.2+1*1.9+2*1.7=8.9

Like all bibliometrics, it's a very crude measure.   You can get a high score on this measure by publishing a lot of research in journals that aren't very prestigious, or by publishing a very small amount in highly prestigious journals.

Furthermore, the metric says nothing about the impact of your research compared with other papers in the journals in which you've published (e.g. you might have published a very widely cited paper in a journal with a low impact factor but you won't get any extra credit for that.)

The term "cumulative impact factor" has also been used for measures of the impact factor of a journal over extended periods beyond the usual definition of impact factor.  See for example:

http://www.garfield.library.upenn.edu/papers/impactofcumimpfacs.pdf

I don't believe that ISI has ever defined this term in their formal reports on the impact factors of journals, so I'm afraid that any use of the term will depend on the particular group or person that is computing the cumulative impact factor.


Is it fine to use a startup as an affiliation?

I was asked to provide an affiliation [for a paper]. Not providing one is not an option, in the sense it's a mandatory field on the form.

You could write N/A or unaffiliated, since this seems like the most relevant answer.

  Does it make sense to use [my startup] as my affiliation (which is 100% true though not necessarily relevant)?

Just like your employer decided that they didn't want their company name on your paper, you should consider whether you want your startup name on your paper.

On an aside, I wonder whether an employer (generally) has the right to deny an employee of listing the employer as their affiliation. (Some employers -- especially those in R&D -- will explicitly define contractual conditions, but generally they will not.)


Does significant editing of a paper with the possibility of minor contributions to its scientific content warrant co-authorship?

The short answer is: it should not. But the reality is some think it should. Since there is no law that dictates authorship the closest to an answer is to look at the Vancouver Protocol and derivatives here exemplified by the ICMJE (Internationa l Committee of Medical Journal Editors) which defines an author as follows:

Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND
Drafting the work or revising it critically for important intellectual content; AND
Final approval of the version to be published; AND
Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

With these guidelines in mind many co-authorships would disappear but it becomes quite clear that help with language simply is not enough for co-authorship.


Why do so many publication venues have their own citation styles?

It is a matter of history, technology, and personal preferences. Different citation styles have arisen in different times to serve different needs.

A citation answers many questions, often including:

Who did it? Sometimes the citing author wants to give credit to earlier work, and sometimes the reader is just curious.
Is it new to me? The reader often wants to know whether they are already familiar with the cited work. I use a combination of authors, title, publication venue and/or year, depending on the article. Other people may prefer using other information.
Where can I find it? Traditionally we needed information like publication venue, publisher, volume, issue, and page numbers. DOIs and URLs are often better in electronic publications. Many people just do a web search with the title and use the rest to confirm that the returned result is correct.
Where was it published? Some people are interested in the prestige of the publication venue. Many want to keep track of interesting venues.
When was it published? Publication years help to establish a rough timeline of events.

The in-text style also depends on the typical amount of citations in the venue/field. The less work you cite, the more of the above questions you can answer in the text, and the reader does not have to jump between the text and the bibliography. On the other hand, verbose citations can get confusing, if you have too many of them. In such cases, it is better to refer to the bibliography.


Paper on project without any result - how to conclude

I think the conclusion of a paper and the conclusion of a project are two different things.

In my view, the conclusion of a paper is the summary of the paper while the conclusion of a project is the end results of the project. Your paper has the current state and the future plan of the project. These can be the conclusion of the paper. They are not necessarily the conclusion of the project.

If you don't feel comfortable with having "Conclusion" section in your paper without stating the true conclusion of the project, my suggestion is to write a ""Summary" or "Future Outlook" section at the end of the paper. This is a personal taste, in my opinion.

There are many papers without "Conclusion" section either by authors' choice or the final conclusive results for the problem/conjecture were not obtained yet at the time the paper was written.


How to add a citation to a sentence that has parentheses at the end?

This depends on the writing and citation style you are using. In APA you should use a semicolon to separate the citation from the acronym:

However, methane has a higher Global Warming Potential (GWP; IPCC, 2013).
Most environmental impacts were due to methane emissions (which has higher GWP factors; IPCC, 2013).

Source: http://blog.apastyle.org/apastyle/2013/05/punctuation-junction-parentheses-and-brackets.html


Release application of research before publish its paper

Your threat model just doesn't work out in reality. By knowing your code well (because you wrote it), you have a huge advantage over everyone else in the world. It is very unlikely that someone, even an expert in Domain Specific Languages, will pick up your application, fully understand it, and be able to write an article about it before you can finish your article and get it submitted. I really wouldn't worry about it.

Besides, my experience is that people are out there talking about their open source codes well before they get their marker papers published. It's good to be able to discuss your work with colleagues and to drum up users before you finish the paper. Perhaps you will find several collaborators in the process.


How to ignite your research career when your advisor is so disappointing?

As mentioned in the comments, if you are not happy with your advisor, find a new one.

I think there are some misconceptions underlying this question.  Typically graduate students write papers, not faculty members.  Publishing is up to you, not your advisor.  Faculty are typically not trained as managers.  Therefore it is up to you to give yourself direction.  I think you should consider these features important in an advisor:

Can obtain funding you need to complete your research.
Can add to your reputation and connection to other researchers.
Knowledge of the discipline (less important because it's easier to get this elsewhere)

From a faculty member's perspective, the best way to achieve all of these things is to be involved in as many projects as possible.


Can I use the term 'abuse' if someone submits five papers to a conference?

Why would you think of it as abuse? If the conference has rules that prohibit it then the author is breaking the rules, otherwise not. The more important question is whether the papers have merit. If they do, all is good. If not, they will be rejected in due course. In the latter case, the committee can admonish the author about a flood of junk.

The conference program committee doesn't need to accept a lot of papers from an individual and I think in most cases they would like a variety of authors to be represented, but that is their concern. It also seems a valid "policy."

The committee also needs to be prepared to review, according to their normal methods, all papers submitted. The selection, however, probably involves actually accepting fewer papers than the reviewers approve, just for time and space.

The "problem" if there is one, will resolve itself.

If the committee doesn't want this to happen in future, they can write rules into future submission criteria.


Appendices usually come before the bibliography (as you may need to cite things in the appendices). It's worth checking if your university has its own style guide, just in case.


Taking a break from industry and becoming an unpaid research assistant (or atleast getting involved in reserach at a school)

In my field (though different from yours), 3-6 months is not nearly enough time for a novice to approach a research project.

Student volunteers (undergraduates, who may also get credit for the work so not entirely "volunteer") may take on projects of this duration, but there is little expectation that they accomplish anything concrete - they take more time to train than their research output is worth.

That said, a university has a mission to educate students, and that trade-off is okay for students - it's a service to the next generation of researchers, to make sure students get exposure to what research is like. If you aren't a student, it's harder to make a case that the time should be spent with you rather than those interested, enrolled students. Yes, you may be interested in maybe switching to a research career, but you're not nearly as invested in that exploration as someone who is enrolled in a degree program.

Additionally, there are the legal issues with what defines an employee as in the answer you already linked.

There are more issues as well involving privacy, data security, intellectual property, etc: universities have policies and agreements in place to address these concerns for both students and staff; you can't really sneak a volunteer in without going through those same processes, so it isn't quite as simple as just "showing up".

Lastly, just a bit of a caution:

  an enthusiastic individual who has a decent academics and willing to give up 6 figures

does not seem to me nearly as impressive as you make it sound, especially when you've made it clear you are secure enough financially to go unpaid for a bit. Any university is full of currently enrolled students who have financial and life difficulties and yet are working towards a degree already without the security that you've built for yourself. They are enrolled and earning meager salary despite having those responsibilities like children, sick parents, and family members in dangerous situations elsewhere in the world. It's fine to be proud of what you've done for yourself so far, but I'd be very cautious in thinking that it positions you above others in any way.


Two potential ways of presenting results, is there a preference?

I'm inclined for the second, but having a clear explanation of your goal in the abstract, so the reader knows what you are getting at.

Your want your readers to know you are taking the path to Oz, but not necessarily how the sightseeing are until you get there.


Is a break-of-study a hindrance to getting a PhD?

A "break-of-study" is not a hindrance per se. It has side effects (you get older, acquire a family, and so on), and some of these can make it a little trickier to get a Ph.D. In particular, you might find the answers to this question: Can one excel in graduate school with a demanding family life? very relevant in terms of the challenges of doing a Ph.D with a family.

But again, a break-of-study in and of itself is not a bad thing. Now if the job you are looking for takes you far away from your intended field of research, then you might have to explain your background on your application and somehow establish that you have a continuing interest and basic knowledge in the field (which may have changed since you graduated). You can do this by taking courses online, or by doing research projects on the side, and so on.


My wife's contributions are not acknowledged in our group's paper that has me as coauthor. Should I speak up for her?

I think you should talk to the group leader about the appropriateness of an acknowledgment  for the drawing (not coauthorship).
This is the right course of action for any contributor. The fact that she's your wife is not relevant, and should not be a part of this professional conversation.
How to approach the group leader depends on how you usually interact. I think a short conversation is probably appropriate. You could follow up with an email for the record if that seems appropriate.
Of course the group leader probably knows about your relationship, but that should not affect the decision.


How to deal with incommunicable co-author

When dealing with extremely busy people, you want to formulate your emails in a way that makes it as easy as possible for them to give you what you need.
Providing one's opinion on a paper is a complex, open-ended process. Even more so if you are a coauthor - you need to not only read and think about what is written, but also consider what else could have been written to make the paper busy. In a situation as you describe, I'd consider it perfectly normal for the professor to take a few months to get back you even they seriously intend to do so. Thus, your request is not a good choice.
Instead provide them with a straight-forward way out that works for you. Thus, complete the draft and makes sure it is completely polished. Make a plan regarding what you want to do with it. Then send it to the professor, pointing out that you and B agree that the paper is finished, and that you want to submit it to the arXiv/Journal X, and that you just ask for their consent to proceed. If the contribution of the professor is very limited, you can consider also stating merely acknowleding them as an option. If C or anyone else respected by A has read the draft and also considers it ready, include this information. Overall, you want to make it very easy for A to just respond "its fine, go ahead".
If this doesn't work, there is one way to escalate further, but I'd consider this borderline from an ethical perspective. That is to let A know that if they don't object within eg 2 weeks, you will consider this as permission to go ahead with the plan. Only ever think about this if your draft is really, really done.


How to evaluate a book, rather than a paper, on a scientific subject?

Obviously, this question asks about reliable predictors for the quality of a book. Otherwise the answer can only be: You evaluate a book by reading it. With this out of the way:

Ask around. In particular when you are interested in using a textbook for a course, ask people who have directed similar courses.
Publishers. There is an informal hierarchy of publishers that can be used to predict a book's quality, just like conference venues and journal ranks for papers. This differs between disciplines, but the edge-cases are vanity presses (low-end) and Famous University Presses™ (high-end).
Citations. Just like for journal articles you can count the citations of a book to estimate its impact (with all the known caveats).
Reviews in journals. Many journals publish a review section. You can search these for discussions of the book that you are interested in.
Peer review. Some publishers also send full book manuscripts or at least the book proposal with sample chapters out for peer-review.
Professionals. Ask your trusted librarian for advice.


Mailing list for internships and full time jobs for computer science PhD students

For computer science, the CRA computing jobs site is a good central clearinghouse for a large fraction of faculty postings and some non-faculty research positions.  For industrial jobs in computer science, however, there is no such central location.


How can I let google scholar find conference name of an arXiv paper?

Google scholar crawls the web automatically and indexes all the papers that it finds. Your paper will not be listed with the conference name before it is actually published. And since the conference has not taken place in your case, it will not be listed as such (and how should google know that the ArXiV paper and the official versions are exactly the same - which they probably aren't?).

So you have to wait until the official version of the paper appeared (e.g., on the publisher's web page). You can then tell Google Scholar to merge the two papers into one in your account.


Fail to reproduce results in a published paper. Is this an academic misconduct?

Academic misconduct is the last thing you have to consider, not the first.

First, you have to consider that there might be something you are overlooking (e.g. an updated version of the code, or the data set is not really the same, or something related to the machine or etc.). Then, you have to consider that mistakes happen, and as I wrote in this answer, yes, there are plenty of errors out there, that do not come from academic misconduct: a mistake can have leaked somewhere in the paper, code or graphs.

Therefore, if you have reasons to consider that difference significant, you can contact politely the authors trying to set up a scientific discussion -- not an accusation -- to understand where the difference comes from.


Without making it known to the journal that he is not actually writing the review it is (usually, as far as I know) not supposed to be like this.

Here is one example, a quote from the PLOS One reviewer's guidelines:

  Confidentiality

  Reviewers are required to treat all submitted manuscripts in strict
  confidence and should not share information about submissions with any
  other parties unless previously agreed with the editor. The
  involvement of a third party in the review must be declared at the
  time of the submission of the review.

If you ask the editor before you are sharing the publication with someone else, it can be okay. I have been "co-reviewing" with someone else (not my supervisor at that time), which was known to the editor and our names were both attached to the review.


Caregiver of disabled teenager returning to study, but can't find funding. (UK) Any thoughts?

But now I am doing a PhD at a top UK university and am winning awards for my projects and am devising and teaching courses.

In my experience, once you start a PhD in the UK, it is extremely difficult to get a studentship. It is not clear if you are looking for a full time studentship or a part time studentship. UK studentships tend to come from four sources of funding: university/school level funding, doctoral training center (DTC) grants, individual grants from charities and research councils given to a supervisor, and individual studentships awarded to the student.

As UK PhDs generally last 3 years of full time work, asking for less than 3 years of funding will result in odd gaps on any type of grant. While funding directly from the university or school is more flexible, unfortunately, if they did not offer you funding when they accepted you, they likely are not going to offer you funding now.

That leaves you with "special interest" funding, but again, having already started, will put you at a disadvantage.


Tactful way to discuss an error in a published paper

Use neutral and respectful language, but don't beat about the bush. If the model is wrong, say so. And remember to attack the idea, not the person.

Perhaps say something like:

"This work determined that the while the assumption that [quantity] is conserved is correct in the simpler case of model 1, this does not appear to be correct for the more complex case presented in model 2. This was established by [details of work that lead you to this conclusion]. It was instead found that the quantity is determined by [formula]. Model 2 therefore needs to be amended to [something]."

(I'm not sure if I've quite met all the requirements I've listed, but hopefully it'll give you something to go on.)


How to ask for lettler of recommendation from supervisor when he would be interacting very little with me?

The solution seems fairly simple. At your next meeting with this professor, or one you can arrange sooner rather than later, let him know of your future plans and that you will eventually want to ask him for a letter. Make a special request that he "follow your work" enough that he can write such a letter. But also ask hime for advice about how to be a success in the project and to prepare yourself for later academic work.

The goal is just to get him to notice you even if you aren't interacting much. But, of course, this assumes that your work will be very good overall so that there are only good things to say about you when the time comes.

It is helpful for a professor to know that students have certain aspirations beyond the current project/course/degree. Make him aware early on, rather than later.


What is a good way of getting peer feedback on my draft cover letter?

The most German universities have career service departments for questions like this. If this is uncommon in Sweden, I agree with Kimballs comment: show it to people you trust.

In addition: the Internet is full of resources like guides and tips. Just be aware of possible cultural differences that may appear between countries. A guide targeting to US audience could suggest or advice elements that could count as "no gos" in other cultures. If you want to check your cover letter against some online guide I suggest you to search one in Swedish that considers the national or cultural specialties.


Applying same graduation school with my girlfriend, is it ethical?

At best, that information would be (should be) irrelevant to them. You want to be accepted on your own merits in any case and a fair evaluation will, hopefully, assure that.

But you also need to be flexible in planning your own future. For example, if there are other universities nearby, it would be good to also make application there. Then, if you don't get accepted into the same place, your relationship can still survive.

But a relationship can, if strong, still survive a couple of years of separation.

But give it your best shot. Riding someone else's coattails isn't a strong point in your favor and people are unlikely to change relative rankings of candidates for such reasons.

And yes, it is ethical to apply to the same programs, if that is your real concern.

Let me give you a worst case scenario, though it would be unethical and I doubt that any university would follow it. But suppose you tell them and they decide not to accept you and think that she, then, won't come either. They then rescind her offer and offer it to someone else. Some programs, notably in medicine, need to fill every slot since it is expensive to run a program partially populated.

I seriously doubt this could happen, but I recommend against inserting wild cards into the decision process.


So when is it appropriate to use \part? Any specific document length in pages or number of chapters?

It is appropriate when you feel it appropriate! Seriously though, assuming that there isn't any guideline from your university (otherwise, you probably wouldn't be asking the question), it's really a personal choice, the same than about the splitting chapter/section/subsection/subsubsection/paragraph. The structure of a document is there to help the reader, in particular for long documents. A part could be something that can be read separately (i.e., with no references to the other parts), or could be something containing some huge chapters; tt could reflect a chronological order (before, during, after), or a conceptual separation (theoretical, applied), etc.

In case of doubt, talk with your advisor!

  When you use \part then a page is cleared after the text. Is this a style that is used in American PhD thesis documents? Why is this done?

As @Daniel pointed out, this is a rather technical question, that is more likely to be answered on tex.SE.


Is the distinction between qualitative and quantitative methodology still significant today?

In nearly every scientific field you will find that some investigations are more heavily quantitative while others are quite qualitative in nature.  I find that the difference tends to be that qualitative investigations are more exploratory, observing a phenomenon in its natural conditions to establish that it really exists or to gather case-study sorts of information, while quantitative investigations are more aiming at firmly establishing an explanatory model.  The boundaries, however, are quite incremental and blurry, and I'm not quite sure what the value is of trying to draw a distinction, rather than simply saying: "this is the mixture of methods that can best study these phenomena at present."

Thus, while I don't know what the current vogue in theory of science is, I would be startled if it did not include a spectrum.


Is it possible to pursue PhD in different area than master's thesis?

Yes, definitely

Of course you can! The specific subfield is mostly limited by (a) your interests; (b) availability of a suitable supervisor who knows that field, and possibly (c) availability of funding/equipment/etc for that research direction.  It may be that a particular university/department doesn't accept your chosen direction (e.g. they don't have the researchers or funding for in-depth high energy physics research) and you need to look for other universities to do the PhD, but your master thesis topic is not restricting in any way.

It can be slightly useful to do a PhD that aligns with your master thesis, as it gives you some head start and possibly some publishable research already, but it's not a race and you definitely can do it in a different direction, many people do.

Researchers work in multiple areas

To expand on this - there are few general restrictions. It may be that a particular organization (or funding source) or person at some particular time nudges you do do something specific; but in general, there are no universal restrictions and people can:

Pursue PhD in a different subfield than Master's thesis (your example)
Get PhD in a different subfield and topic than what you submitted at the start of your PhD
Pursue PhD in a different field than Masters (e.g. physics PhD after mathematics masters, computer science PhD after economics masters, etc)
Do research in a completely different area than your PhD (e.g. linguistics PhD publishing CompSci papers)
Do publishable research without being connected to a PhD process in any way.


Accused of cheating on a class that I passed a year ago. Can my "pass" be revoked? Could this missing prerequisite affect other classes I have passed?

Universities have revoked degrees and titles on the basis of fraud, years or even decades after granting them. This is certainly allowed. The bar for revoking a class should be expected to be lower so this seems perfectly fine. Of course only your university can tell you the finer details of their policies.


Is it mandatory to include the registered trademark symbol ® next to the name of a computer program?

APA, MLA and Chicago style manuals all recommend not to use trademark symbols.
Chicago

In publications that are not advertising or sales materials, all that is necessary is to use the proper spelling and capitalization of the name of the product. A trademark attorney can tell you when the use of the symbol is required.

from The Chicago Manual of Style Online
MLA

Although owners of trademarked names may suggest otherwise, publishers are not obligated to denote the trademark status of a name when that name is mentioned in text. Authors representing trademark owners frequently feel obligated to use the trademark or registered-trademark symbol (™ or ®) after the first mention of their product names but often do not use these symbols consistently to indicate the trademark status of other names not owned by their particular sponsor or employer.
Because the fair and consistent use of these symbols (or of footnotes denoting the trademark owners) requires exhaustive verification and vigilance on the part of the editor and because the use of these symbols (or footnotes) is not required by law, do not add trademark symbols, registered-trademark symbols, or trademark-denoting footnotes to trade names in MLA publications. In the interest of consistency, editors should also delete such references when inserted by authors.
At the same time, MLA recognizes that authors are often supported and encouraged by their institutions or other funders and that this support may be what enables an author to produce any written work at all. MLA editors are therefore advised to consider carefully an author’s express request that trademark status of particular names be denoted (merely including symbols or footnotes in the submitted manuscript does not constitute an “express request”).
If trademark status is denoted in a particular case, these guidelines should be used:

Use the trademark or registered-trademark symbol, not a footnote.
-The author must specify which words should be denoted and with which symbol (™ and ® are not interchangeable). Trade names not specified by the author should not be cited with these symbols.
Use the symbol no more than four times in one article for each trade name: the first mention in the article’s title, the first mention in the running head, the first mention in the abstract, and the first mention in the article’s text.
If the article is part of a JMLA symposium, add symbols to the trade names in question in all other articles in the symposium for consistency.

In all cases, whether trademarks are denoted or not, the proper spelling and capitalization of trade names should always be verified and consistent. See Appendix C for a list of trade names common to MLA publications and their proper spelling.

from the MLA Style Manual
APA

No, it's not necessary to include the trademark symbol for a trademarked term in academic writing. The trademark symbol is generally necessary to include only in commercial writing, meaning writing that pertains to commerce or the buying and selling of goods (e.g., advertisements). The word Twitter (and other names of companies) can be written in regular, nonitalic font as well.

from the APA Style blog (answer by the author to a comment)

In certain jurisdictions the trademark owner may be required to use a trademark symbol or may benefit from the use of such symbols in a law suit (see the International Trademark Association fact sheet on Marking Requirements).


I put a paper on arXiv and now I want to send it to a double-blind journal. What can I do?

This may seem like a digression at first, but wait for it:
The main purpose of double-blind peer review should not be to prevent the reviewers learning the authors’ identity by all means.
This can be a welcome side effect, but often this is impractical not only due to preprints but also due to previous work, conferences, idiosyncrasies, etc.
If a malignant reviewer wants to break the double blindness, they often can.
Fortunately, many peer reviewers don’t want to do this:
They are completely fine with performing an unbiased review of a paper that is only based on its own merits – as they ideally should.
However, no matter how good our intentions, we are still prone to subconscious or at least implicit biases.
The main goal of double-blind peer review should be to help reviewers to eliminate (or at least reduce) those involuntary biases¹.
By contrast, with single-blind peer review, it is impossible for reviewers to be unbiased, as the names of the authors (and their affiliation) are inescapable.
In light of this, I suggest to submit your (anonymised) paper. In the submission note that you published a preprint already, but that this does not relevantly compromise the double-blindness of the peer review (as it is about allowing the reviewers too be unbiased, not about forcing them). Bonus points if you can point out other ways in which a malignant reviewer could have found your identity despite the preprint. Should the journal not be convinced and actually reject your paper because of this, they should arrive at this conclusion quickly and you waste not too much time.
On the other hand, even if you should somehow manage to unpublish your preprint from the Arxiv, search engines and similar would still connect your paper to your name for a while and thus a malignant reviewer could find out your identity anyway. Therefore, it does not matter for the double blindness at all, no matter what your stance on its purposes is.

¹ … or analogously to prevent authors from flashing in their or their affiliation’s reputation at the reviewers without them having a chance to ignore them.


Is this level of publication politics normal in academia?

When it comes to a workplace, politics is inevitable. There are always bias in opinions, bureaucratic criteria that are bendable to some, possible hierarchical influence. These are all common in almost any workplace (at least AFAIK). Academia is no different in this case. There are people who prefer quantity over quality and some others the other way around.

At times, the level at which you could be a part of this depends. You may be able to avoid in being a part of this to some extent, but you may have to witness this nonetheless.


Is "inadequate referencing" a euphemism for plagiarism?

I think that's a rather unkind interpretation of what happened here. Books aren't the same as research articles - especially for text books, it is par for the course that large swaths (most?) of the book are not actually about the author's own ideas.

Further, extremely detailed referencing can easily reduce the readability of the book, so oftentimes book authors are given a bit more leeway than what would be acceptable in a research article.

What I assumed happened here is that either some references are simply missing (as Solar Mike said), or that it has been later on determined that some parts of the book should really reference more explicitly where the respective content came from (either because the original author complained or because the book author decided that some more references would help a reader find additional information). I would not assume this to mean that the book author blatantly copied material from somewhere (this, presumably, would not lead to a correction but to withdrawing the entire book, because it also sounds like a copyright nightmare for the publisher).


Does presenting results in conference and publishing in unreviewed proceedings prevent better publications?

While I do not know accelerator physics in particular, for most fields and most journals, a non-reviewed publication does not count as prior publication.  If this is the case for accelerator physics as well, then putting an extended abstract in a non-reviewed conference will not block you from publishing an improved full paper in a journal later.  The prior version should be explicitly acknowledged in the journal submission.

The other reason that you might end up with less publications is internal rather than external: once you've put it out and gotten your feedback, you might not feel as strong an urge to do a formal peer-reviewed publication.  If this is the case, then you need to ask yourself whether this is actually a problem for you or not.  I, for example, have a number of publications that have never gone beyond technical reports or white-papers, but am comfortable with that because I think most of them did not need to have a full publication, and I've got enough others.  If you are a person who has difficulty motivating yourself to writing up results for peer review, however, you may want to consider the spur to publication as valuable and therefore avoid the non-peer-reviewed pre-publications.


Do you need first authorship to use a publication for your PhD thesis?

Authorship issues within a group should be resolved by supervisors. This is easily found out by a simple web search or by simply asking lab members. It’s probably on your university’s website.
Authorship order can include two lead authors. This can be explicit (ie written in the submission notes) or implicit (by authorship order conventions in your community).
However, from what you describe your coauthor is abusing their position, or just given a lot of authority by the PI. If any of my students threatened a labmate they’d be in trouble. Ultimately the supervisor should decide material access, and more. Indeed, as you say - since two funding agencies are involved the two supervisors (yours and theirs) should be involved if only to agree whose grant the paper goes on.
Finally, this has nothing to do with thesis work. You can definitely include coauthored work in a thesis, with the express permission of your coauthors. I ‘donated’ a nice figure to a coauthor’s thesis and was happy to do it!


How can I run a keyword search that targets only papers resulted from industry or industry-sponsored research?

A proxy would be to search by affiliation (link to Scopus doc, probably feasible with other tools). List companies working in the topic and search papers with at least one author affiliated to them, or possibly with the company name in text (acknowledgements).
This will miss companies you did not think about and those with weird affiliations (for instance if "Foobar Inc." has a research division "FB new stuff", the affiliation does not include the string "foobar").


Recommendation letters when changing between two unrelated fields

If someone in your undergrad math department has actually evaluated your work, then the year and a half is not an obstacle for a recommendation. Best if they know you as more than a body who occupied a seat, of course.

But in general, if no one has seen your work, nor had a chance to evaluate it, then they can't really attest to it, ethically or practically.

Since your situation is described as a bit unique, let me suggest, at least, a unique solution. You could ask a mathematics professor, either at your original institution or elsewhere, to evaluate your skills. There are at least two ways that could be accomplished. They could just give you a final exam from some recent course and decide whether you have the skills. But a fifteen minute or so oral exam should be enough to get an idea. They could then, simply certify about what they did and how you did. It wouldn't be a real letter of recommendation, perhaps, but might fulfill your needs.

An alternative is just to suggest to an admissions committee that you would be willing to take such an exam if there is any doubt about your qualifications. That alone might be enough.

Thirdly, nothing at all might be needed. The program seems pretty flexible. Perhaps flexible enough to accommodate your self study as valid.


Is a preprint considered as dual publication?

Nature encourages the use of preprints, as noted on their journal's policy page:

  Nature Research journals encourage posting of preprints of primary research manuscripts on preprint servers, authors’ or institutional websites, and open communications between researchers whether on community preprint servers or preprint commenting platforms. Preprints are defined as an author’s version of a research manuscript prior to formal peer review at a journal, which is deposited on a public server (as described in Preprints for the life sciences. Science 352, 899–901; 2016); preprints may be posted at any time during the peer review process. Posting of preprints is not considered prior publication and will not jeopardize consideration at Nature Research journals. Manuscripts posted on preprint servers will not be taken into account when determining the advance provided by a study under consideration at a Nature Research journal.

The webpage then proceeds  to provide the details for their policy.


What can happen if someone acknowledges a grant on papers not related to that grant?

The big underlying question here is what it means for a paper to be "related to a grant". Different funding agencies have different rules on this, either a more "staff-oriented view" or a more "topic-oriented view".

Many pure science funds, for instance the Swiss National Science Foundation, take a liberal stance on what kind of science can be enabled through each individual project. Essentially, while a project is given to support a specific idea, they are fully aware and quite happy that in addition to, and sometimes instead of, this project, other more or less related studies will also happen by the staff paid partly or in full through the project. At the end of the day, the SNF and other similar agencies care not so much about the specific piece of science that is described in the project, but that some valuable science is happening and that PhD students are graduating. Based on this view, researchers funded through SNF are expected to acknowledge them on every paper they do, no matter if it has to do with any of the science described in the project description. The collection of all papers acknowledging this project is then  not understood as "all papers on topic X", but rather "all topics enabled by funding project Y, on topic X and any side projects that the funded students did in addition or instead".
Other, especially more applied funds such as most of the European Commission's Horizon 2020 programme, are much more interested in specific topics than in funding just about any research. For them, acknowledgements have much more the meaning that you seem to imply, that is, that citing this project in the acknowledgements of the paper implies that this contributes to the mission of the project. How strongly this is enforced or checked depends on the project officer. Most people also seem to take a rather liberal approach in practice, but there are certainly project officers that have formally complained about projects using the allocated funds to sponsor other research.

  Might he go into troubles if it is discovered by the funding agency that the papers are actually not related to the grant proposal?

So at the end of the day, it really depends on whether the agency actually considers this "topically unrelated but financially enabled by the grant" paper as "unrelated". I would say, in absence of any other information, you can safely assume that your co-author did nothing wrong, and that the agency may be fine with this acknowledgement.


Tips for useful note-making when learning by oneself

Here's the method I found works best for me:

Read a section
Put the paper down, summarize verbally (mentally or out loud)
If you can't summarize, re-read the section. If you can summarize, write down the summary.

This method has the benefit that your notes don't reflect the stream of consciousness that I found went through my brain as I read the paper, but rather only a concise summary of what I actually understood from the paper.

Note that there were definitely papers where I read a particular section numerous times and had no idea what it was talking about, and I wrote that in my notes (e.g., "The authors then performed a mathematical transform involving  technique, and I was not able to figure out how it works from reading the paper.").


How to boost academic profile for Master's application

If the master's degree you are pursuing is a technical degree (to enhance your technical skills to land a job in robotics), then a professional experience in a related area should greatly help your application. Is there a faculty member you could work with on a project or perhaps a firm where you could intern before the start of the academic program? Even if you can't complete the professional experience before submitting your application, it will likely be helpful to note the upcoming professional exposure on your resume and in your application. Securing a recommendation from an internship supervisor would be good as well. My vote would be to focus on professional exposure in the field.


How best to format and position legend in line chart when legend text is long?

When it's not too big, I recommend shrinking the legend font size and whitespace and reducing the complexity of the labels.  If it's very big, however, I recommend instead moving to a systematic coloring scheme and explaining the coloring scheme in the caption rather than a legend.


Without teaching experience, but industry experience, how can I begin teaching at college level?

I've seen community colleges hire people with less than a master degree to teach IT. These people did have quite a few industry certifications, held respectable positions in the local community, etc.  I heard people at the school saying "If anyone questions that person's qualifications, we have enough to support our decision." The CC in question was in a very small town, which I think had  a lot to do with that decision.

In the end, your qualifications might be just fine. The issue is whether a school needs someone. The only way to know the answer to that question is to ask. Meet with the appropriate people at some local schools and explain your situation. It is quite common for schools to use adjuncts: partly because they are cheaper, and partly because they have current industry experience.

I have never seen a school which is angry when presented with an additional labor choice. So, you do no harm by scheduling a meeting to see if they would be interested.

As far as the teaching experience, that is more easily gained than you might think. You can see my answer here to a related question.


The standard rule in my community is that once I finish reviewing a paper, I'm supposed to pretend that I don't know the paper exists.  In particular, I am not supposed to use any insights I gained by reading that paper in my own research.  I am not supposed to reveal the results to my colleagues.  Some venues ask that I destroy any copies of the paper I'm reviewing, along with any programs or data I used to verify the paper's results.  This embargo lifts only when the paper is finally published, but I am never supposed to reveal my identity to the authors, even indirectly.

Under those rules, publishing reviews is completely unethical.  Maybe it would be okay if I had the explicit permission of both the authors and the editor, but I would expect most authors and reviewers to vehemently object.  I would feel weird even asking.

But even under less stringent reviewing rules, I think posting reviews is a very bad idea.  Criticism is best given privately.  One of the purposes of anonymous reviewing is to give authors brutally honest feedback on their work.  Referees can offer direct criticism without worrying that it will harm the authors, and authors are more willing to hear that criticism because they know it will never be public.

Yes, that means authors sometimes get credit for ideas that I suggest in referee reports.  (Most authors are nice and thank the anonymous referee.)  On the other hand, several referees have offered suggestions that have significantly improved my papers, so it all comes out in the wash.

Update: I should add that these ethical constraints attach only to reviews of unpublished papers being considered for publication.  Once a paper is actually published, everyone is free, if not encouraged, to publish their own reviews of the published version.


Is dishonesty sufficient to terminate a grad student?

Termination of the advising/mentoring relationship

You should check with your department or university policies, but at most places you can unilaterally terminate your advisory / mentoring role by emailing the department chair or graduate coordinator. This is, after all, a voluntary role for you. And given that you no longer trust the student, I don't think you can operate as their advisor in good faith yourself (you couldn't write the letters of recc that they'd need for funding or jobs, for example).

If you don't feel the relationship can be repaired, then you should drop them.

If the student has no other advisor, they may be at risk to be an orphan. Since most stages of graduate school (orals, candidacy, continuing enrollment, funding, research) require an advisor, a student who has no advisor is at risk of not being able to continue in the program. There is often a short period of time that is given to the student to find a new advisor. At some places students are formally terminated if they can't advance; at others not being allowed to advance puts them in a limbo state where they cannot enroll but are not terminated.

Departments tend to not like the creation of orphans and there may be informal sanctions for an advisor who orphans students for no good reason. However, you do seem to have a good reason and if true, your colleagues should back you.

The real result is however that the student may have to leave the program.

University Expulsion

Not being able to continue for lack of an advisor is much more common than actual expulsion, given that expulsion procedures usually require a hearing and the presentation of proof of malfeasance.


Why do academics work only nine months of the year?

The following applies to a previous version of the question: "Why do academics get paid to work only nine months of the year?".  The question of whether academics do work work in the summer, compared to whether they are paid to work over the summer, is more difficult.  Most faculty in the U.S. have 9-month contracts, but in my experience most faculty nevertheless work on their research and teaching during the summer.

In the United States, it is very common - nearly universal, in fact - for a standard academic contract to span 9 or 10 months. There are several reasons for this:

It allows the university to pay less. The standard rule of thumb is that a 9 month contract pays 9/12 of what the corresponding annual contract would pay. Many (most?) faculty have their 9 months of pay split up into 12 months of paychecks -- but this is an accounting fiction, not a sign that they are paid for 12 months of work. If few students are around over the summer, there is less reason for universities to pay salary to their faculty for that time - having a break in the contract balances the university income and expenses.
It allows faculty to be paid more. This is the flip side of paying 9/12 of an annual salary: the faculty member can, in principle, take another job during the summer.

Many grants, for example, are able to pay "summer salary", which is really just extra income. But these grants do not allow the faculty member to take salary from the university at the same time they take salary from the grant. The "9 month contract" resolves this: the faculty member can state they are actually only paid for 9 months of university work, so the grant can pay 2 or 3 months of extra salary during the summer.
Similarly, some universities pay extra to faculty who teach during the summer - that would not be possible if the summer was treated as part of the basic contract.
A smaller number of faculty use the summer for consulting work, or other jobs genuinely different from their university position.

Faculty like to travel over the summer. During the academic year, it is hard to leave for personal reasons, because of class. By claiming that the summer is "off contract", academics can travel however they like during that period of time, without having to justify their time.  So having the contract pause during the summer makes the job more attractive to job candidates, allowing the university to attract some people who might otherwise take higher-paying jobs elsewhere.

The reason I just cited are all purely economic - they can be justified solely in terms of saving money for the school, increasing pay for the faculty member, or attracting better candidates. There is also "tradition" as a reason for the summer break, as is also the case at lower levels of education.

However, the "9 month contract" is fictitious in a few ways:

Most faculty still have access to their office, library, email, and other university resources even when they are technically not "on contract" over the summer.
Research faculty usually continue to work on research during the summer, and travel to conferences (which may even be reimbursed by the university, even though the faculty member is technically not on contract!). This often happens even when the faculty don't have grants or other summer funding.
Many faculty use some of their summer time to prepare for their classes, even though they are not being paid to teach over the summer.
There are other activities during the summer: committee meetings, advising, etc. Some faculty participate in these, for various reasons, even when they are off contract.


Does an industrial internship instead of a research internship hurt my chances at scholarships for masters?

For specific schools you need to ask them. However, in general, at the MS level in the US, I don't think that any sort of experience will harm your chances. Some may contribute more and some less, of course.

I would guess that even top universities in the US accept a lot of candidates with no experience at all beyond the BS/BA degree. Of course, the competition at such places is fierce with few seats available and many well qualified candidates.

But, if the purpose of your question is to pick which of two internships to accept, the research one might be marginally better. But who knows? Real world experience in engineering is pretty valuable.

If you have already done one of these then there is no question at all. Your record is what it is and it is up to you to present it in the best light.

The answer might be different at the doctoral level, of course, and may be different in other countries with different educational systems.


"Withdrawn" grade from an undergraduate class vital to my Master's application

A withdrawal on a course that appears key to your masters' studies is probably a big deal.  It would be one thing if your W was in something more tangential to your onward studies.  But if you have withdrawn from a class in the exact same topic that you now want to study for your masters' degree, you really do need an explanation for it.  And it may hurt your chances.

Unfortunately, you don't have a great story to tell.  It may well be true that the professor was a poor teacher, unfair, and even biased against you.  But you don't really have any way to provide evidence of that.  The admissions committee will just be going on your word.  And unfortunately for you, those are the exact sort of things that poor students tend to say as excuses.  Saying such things is likely to reflect poorly on you rather than justify your W (especially if the professor is respected in the field).  I would avoid saying these things. If you get asked about it, focus on the fact that you were taking too many credits at the time and needed to cut back.

So, what are your options?

You could always just go for it.  This might be a negative on your record, but still you may get accepted into programs anyway--especially if the rest of your track record is excellent.  It would be less worrisome if you have other classes or projects that demonstrate your ability/interest in AI.
Try to fill the gap somehow.  Either by retaking the course, or doing some other research/work in the area to prepare for grad school.


Does being a member of IEEE make it easier to publish in the transactions?

Simple answer: no. I'm not an IEEE member and none of my coauthors are, but we regularly publish in the IEEE transactions.


My understanding is that you generally cannot. F-1 visas holders are allowed to hold part-time (up to 20 hours/week) on-campus jobs during all semesters enrolled (though I'm told that some positions don't count as on-campus, despite physically taking place on-campus). Authorization for off-campus work can only be granted after the first academic year.

As scaaahu suggests, you should ask the international office at your university about your specific situation. They should be able to advise you also about potential exceptions to what I wrote above, e.g. unpaid internships.


How relevant can be the major corrections in PhD dissertation?

From this and your other questions, I think you want a fight you can never win. If I remember correctly, you have actually already moved to a different institution and it is just a question of finishing your degree so that you can move on with your career.

When a king has life and death power over you and makes a demand, the only response is "Yes, your majesty". And you say it with a smile. Even that may not be sufficient, but any other response has a guaranteed outcome.

I suggest that you write the thesis in such a way that the advisor will accept it. Even, dare I suggest, accept it gladly. Fair it is not. But, you will get to live for another day.

I don't know exactly how your viva will work or whether you get a chance to respond to any objections made. I hope so. And make the required changes to please the "court". But if not, and the deck is stacked, don't present them with an excuse to condemn you.

If the situation were otherwise with your advisor being on your side and major revisions suggestions made at the viva (in the public session, not written comments later), I would respond to the reviewers that we (my advisor and myself) considered those and rejected them already for the reasons...

But that doesn't seem like the situation here. Bowing before a tyrant isn't pleasant. But, perhaps the "madness of the king" will be obvious to others.

I suspect that, having seen the worst of academic advising, you have some incentive to do a better job of it yourself, provided that you get the chance. Get past this hurdle, however you must. Good luck with it.


Urgent Help: Company asked me for my research proposal

This is a sufficiently common request that I'm actually surprised that you didn't get it ahead of time. Breaking down your question:

  My question is, should I send the actual proposal (about 100 pages) or a summary?

The actual proposal, with a summary in the front for the TL;DR crowd.

  Is it ethical?

Unless there is identifiable information about your subjects, proprietary information about the other company, etc. in there, is there any reason why it would be unethical to send a research proposal? Just asking "Is this ethical" isn't terribly useful - you should have a specific concern. In that case, you could leave out that information with a note as to why it has been omitted. But a research proposal usually doesn't contain information like that.

  Am I allowed to do that?

No one can answer that but your advisor, but I'd be surprised if the answer was "No".

  I cannot contact anyone from my school to ask these questions but until Monday. I really would like to reply to the company right away because I need the participants.

If it would make you more comfortable, you could prep everything and then check early Monday morning - it's doubtful a delay over the weekend is going to change the company's response in a meaningful way.


How do I answer a question on the ethical implications of my work at PhD viva?

I'm not an ocean physicist, or anywhere qualified in oceanography, nor do I have a slight idea of what your topic is on.

That being said, research involving water, and any political ramifications that may impact it, typically will impact commerce related to the oceans.

In this case, theoretical commercial impacts:

Fishing. Your research may potentially result in a ban on fishing, or make it harder to obtain fishing licenses.
Trade commerce. Ships are still used to transport goods around the world, including oil. As above, any sort of research that indicates that the oceans may be unsafe or bars certain trade routes will result in economical impacts down the line.
National borders. Traditionally, countries own a specific amount of shoreline before international waters. A shifting shoreline may result in a changing border and or possible border disputes.
Tourism. Obviously, effects of the water, even perceived, may impact tourism.
Insurance. Rising tides = rising premiums.

Whether or not these apply to your topic, I can't really tell, but it's better to start with a list of things and then check them off as irrelevant gives the no ethical impact argument more weight.


In order, yes, and no.

A thesis is a public document and thus helps establish "prior art" in terms of research. Of course sometimes researchers come up with the same ideas simultaneously, or certain work is just not known as widely as it should be, so sometimes work gets innocently repeated (as compared to plagiarised, which can also happen, but reasonably rarely).

As for publication, a thesis is an entirely different kind of publication to a paper, in every discipline I am familiar with, publishing papers drawn from work in a thesis is expected, sometimes even required. The only (?) way you could interfere with further publication would be if you published your thesis as a monograph.


How to get the PDF of a hard-to-find paper?

I see that quite a few people have cited the work. The authors of those papers can be contacted for help. I'm hopeful that they will respond kindly.

I've experienced this before. Don't hesitate to ask them by email. But also, be ready to explain why it is needed and what you've tried to find it yourself. All the best!

Edit: The link by user 101010111100 looks like it!


What should you do if you cannot reproduce published results?

Just publish. Publish your attempts to replicate the findings, documenting the discrepancies, together with the nice results you've obtained by extending their work. Consider sending a draft to the original authors for their comments.


On the verge of being "fired" from post-doc position, how to act towards supervisor?

There are two problems here. An academic dilemma and a legal issue. The latter is specific to country's immigration, workplace rules, your residency status, etc., therefore I will politely keep the focus to the first one. There are also good comments to your post, so keep them in mind as well. Needless to say, the legal problem could be more intimate to your situation but you will find actual support from a legal authority as you yourself have stated. Now, to the academic dilemma at hand: first of all, I suggest talking with your supervisor and make your position clear in an honest sober way. Your problem is a practical one and need not to be emotional. Here, I would suggest and stress on keeping the best of relations with your supervisor (even if you decide to leave or they decide to let you go), especially if this is your first ever post-doc position. This is important for two reasons: first, you want to leave on good terms even if it didn't work out for you and so you don't need to give an impression of personal grudge. Second, there might be opportunities in future where you will have to work/collaborate with the said supervisor or the university. You also don't want to ruin the possibility of good references for your own future work from this university - hope things will work out for you, and my two cents help. Good luck.


This depends on the university and the field. In some fields/places the professor has little say in who is a TA or RA. In others, the professor actually hires the RA directly, especially for grant-funded positions.

Likewise, in some places/fields the professor has little say in the admissions process. In others, he/she has a large influence on who is accepted.

So, depending on your case:

If the professor is directly involved in admissions, contact him/her early.

If the professor isn't involved in admissions, but does hire TAs and Has directly, contact should come after you get admission. You can write earlier to express interest, of course, but not to request (or expect) and action.

If the professor isn't involved in either admissions or funding, you can probably wait until you actually arrive, though expressions of interest can come earlier.

If you send too much to a prof too early in the process it will probably be ignored since they may have no influence and so evaluating it is just wasted time. After you are admitted, it becomes more meaningful to them as well as to yourself.

How and when you get confirmation depends on all of the above as well as the rules of the university. And different fields have different traditions.


Does scientific experience matter for a funded PhD application?

From personal experience, and this is not always the case, publications matter and they matter because they show prior research which helps in situations of lower grades.

However, do be prepared to receive questions in either the interview phase or via email when discussing with the university you will be applying to on why you are leaving in your last year. If your current advisor is in knowledge of your current situation and is willing to recommend you then this may not be a problem at the end.

Hope this helps...


General considerations about sharing referee reports

It is not common in my field as well to publish the referee reports. I don't think it is a breach of confidence of the anonymous referee; (s)he remains anonymous anyhow. My guess is that scientists are human too, and when they receive criticism of their work they want to get it over with as quick as possible and then forget about it...

There are arguments for publishing all referee reports: An article does not become "scientific" because it is written by someone with a PhD or someone employed by a university, but because we give enough information that anyone can reconstruct how we reached our conclusions. Referee reports are part of the process, so being open about them would fit.

However, I would consider it unprofessional to selectively share referee reports. That decreases the openness of the process, as now the reader starts to wonder why this report is shared and the others are kept secret.

I have refereed once for a journal (BMC Medical Research Methodology) that had a policy of publishing the non-anonymous review reports with the article. I actually liked that process: there was interaction with the authors to make the article better. What is important for this question, is that that interaction is public so the reader can see the development of the article.


Continuing to list as second affiliation an institute where you've never had a paid position

It’s dishonest (and therefore unethical in almost all normal circumstances) to represent yourself as something you’re not. That’s what your grant employee wants to do by listing his affiliation as a place where he doesn’t hold an official title (and it’s irrelevant whether “someone said it’s okay” unless perhaps that someone is a dean or a similar high-ranking person who has the authority to give people official titles; it’s also not strictly speaking relevant whether he had a “paid position” or not - some official titles are unpaid).
As for what to do, I agree with your reasoning that this is your responsibility since he is paid with your grant funds. It’s perfectly appropriate for you to say that he cannot write this dishonest affiliation in any paper that is funded by your grant. If he does not accept this, you should check with your institution what enforcement or disciplinary measures can be taken in connection with this type of employee insubordination. It may also be worth trying to talk to him informally (perhaps in the presence of a “neutral” senior colleague) and see if you can understand the motive for this behavior; possibly it’s based on some misconception on the part of the employee, and you may be able to convince him that there’s nothing to be gained, and much to be lost, from this type of dishonest behavior.


Is publishing in a special issue of a Q3 Journal as relevant as publishing in a Q1 Journal?

How would you, as a hiring committee when applying for a postdoctoral position, see this? Since I've been on "hiring committees for postdocs" quite a few times, I'll just share personal experience.

1) As to me, I wouldn't care at all where you published but would look directly at what you published. As one of my colleagues in Wisconsin put it "I just want to know what his (applicant's) signature theorem is". So as soon as your paper is on arXiv, I'll have an opinion about you. Not all people are like that, of course, but given that the postdoctoral positions are often given to people somebody in the department seriously considers working with, you may be pretty sure that if your result is good, then the interested in you person will spare no effort explaining to others why it is so and that "this guy solved a 40 year old problem on which Terence Tao had only a partial result" is stronger than "this guy published in Acta".

2) It may be beneficial to have a publication in a higher ranking journal on your record later in your career (some university promotion guidelines explicitly count Acta papers as 5 points and "University of Urjupinsk Seminar Proceedings" as 0 points).

3) The formal "publication score" is not everything. You also make professional acquaintances and get friends and enemies over time. Sometimes I choose the journal based on personal relationships (existing or the ones I would like to establish) rather than according to any ranking system and I don't think it is such a terrible idea.

Just my 2 cents :-)


Does the name of the signing officer on the official transcript must match with the one on the envelope seal?

Generally, the transcript itself will be signed by someone with a title like Registrar, at least in the United States.  The signature on the envelope will be that of the university employee who mailed the transcript.  Sometimes, maybe even often, the signatures will not match, and that is likely OK.

If you are concerned about a particular case, contact the university that sent the transcript.  They can tell you who is allowed to sign the envelope, and may even provide a facsimile signature via email.


How can I stop a "citation cartel" still active?

Are there uninvolved editors you can report it to? Do you have enough evidence to contact Retraction Watch, which might take an interest? If the journal(s) in question belong to a scholarly society, perhaps a report to the board would suffice?

The ten-ton anvil would be contacting Thomson Reuters to ask for an investigation -- they'll boot journals they catch manipulating Journal Impact Factor out of the Impact Factor rankings altogether -- but I am not entirely sure how to accomplish this feat.


Reapplying to a previously accepted Ph.D. program, will this be considered rude?

It is possible you don't need to reapply to B and C. Here was my experience:

Applied to uni A and B, got offers from both
Accepted offer from B. Rejected offer from A.
Attended B for one year, decided to transfer/start over at A
Contacted uni A. They were happy to accept me based on the previous application. I didn't even have to reapply, they simply considered it deferred matriculation.

I don't know how typical this is, but it may be something to discreetly look into. Maybe you know an administrator or faculty member at B or C that could give you the inside scoop.


If by "supercomputer" you mean a "computer cluster," there are lots of people with such experience in the US and Europe, and many universities even have their own. (My university, for instance, operates its own 25,000-core cluster.) If you mean "supercomputer" a machine like one on the Top 500, that may be worth mentioning. However, indicating that you have experience running calculations in high-performance computing environments is certainly worthwhile to mention if it's relevant for your graduate program.


Consequences of taking 5 years to graduate with a double major?

Your circumstances are very different than when someone does a single-major program in five years. Two majors—in this case, both in engineering!—and effectively two minors (if you do years of Japanese and Russian) are non-trivial, and as you mentioned, trying to do it in four years would require extensive "credit overloading." If you can afford to do so, it would be better to do things well in five years rather than rush in four years and do a mediocre job, if your goal is to go to graduate school in the long term.


does a database containing list of all journals and related meta-data exist?

Since "the impact factor" is a product of Clarivate (formerly Thomson Reuters) the only databases that include the impact factors of all included journals are the ones of Clarivate, i.e. Web of Science (WoS). To get access to the databases a licence is required. Maybe your library has licenced the databases. But be aware of the fact that WoS only includes selected journals. If a journal is not in WoS, it officially does not have an impact factor.


Generally speaking, if a particular set of tools was permitted - in your case a scientific calculator but not a graphing calculator, I would assume those would be the only tools permitted.

This is especially true for tools, like Wolfram Alpha, that duplicate functionality of things that have been disallowed, like graphing calculators and calculators that can deal with symbolic notation.


(Un)realistic expectations of PhD supervision?

From my own experience with different PhD supervisors (I quit working with one, picked up two more) and postdoc supervisors, I think it really comes down to personality differences and communication style.  It's not that your expectations were unrealistic or not.  It's that you ended up with someone who just works differently and expects different things than you do.  For some people, this "independence-oriented" regime is perfect, because they have a specific goal in mind or narrowed down a PhD topic prior to starting the program.  Others need a bit more guidance.  That's not bad or unrealistic; it's just where you are in your academic journey.  If possible, try to find a supervisor whose expectations and personality match yours.  Or try to figure out exactly what you want from your relationship with your current supervisor, be as respectful and open as possible about it with him/her/them, and try to work out a plan to make that happen.  If your supervisor isn't keen on this approach, then you have two options. 1) Stay in the relationship, accept it will suck until it's over, and focus on getting what you want out of the experience (presumably a Ph.D., papers, etc.).  You can seek out other mentors in the meantime. 2) Find a new supervisor.

Edit: now that I understand your supervisor is a first-timer, I think this is further an issue of lack of experience on their part and perhaps a reflection of how they were supervised throughout their career.  If presented in calm, reasonable fashion, your supervisor might benefit from hearing what a student's expectations are, at least for when they supervise future students.  It's unlikely their overall modus operandi will change, though; these things take lots of time and mistakes.  And I would reiterate again that calm, straightforward communication is important.  Passive aggression or hoping that your supervisor picks up on subtle cues is counter-productive.


Host Institution - Marie-Curie individual fellowship

For Marie Curie fellowships you shouldn't already be employed by the host institution. These fellowships are meant to encourage mobility so you must apply to go to some other place.

  could I assign a host Institution and in case that I receive the fellowship, I can then start working on it?

Yes that's exactly the principle. However be careful: you don't just pick a host institution, the key factor in these fellowships is to have a strong research plan prepared in collaboration with the host institution.


Permissions and copyright for a figure from an unavailable source

We have a serious problem, worldwide, with copyright now. To protect yourself and your reputation, I think you are better to assume that you cannot use the figure or a recreation of it unless and until you can determine positively that you can. Copyright differs greatly by country now. Unfortunately many works have been abandoned by their authors but copyright law generally makes no provision for that. Fair use and "use for research" differ greatly by place.

My suggestion is to give a reference to the original, even if it cannot be found and to create your own figure separately from this one, using, if possible, different data. Don't try to make it similar. Don't try to disguise the original. Make a new figure that illustrates the point you are trying to make in your own work.

I would do something like presenting my own figure illustrating the point I'm trying to make and the note that author X made a similar point at Reference Y, including illustrative figures (without reproducing them). Your readers are informed. The previous rights holder is respected. You have done the best you can do given (possibly unreasonable) restrictions on sharing.

Whether or not you would be "caught" or "challenged" in reproducing something without permission, your own reputation can suffer. It is better to be conservative here.

But it is also better to use whatever position you have to work toward more sensible copyright rules that deal with abandoned works and with scholarly research without having the original rights-holder suffer.


How to deal with students who refuse to do anything except take exams?

Welcome to higher education! Students will use formal assesement to guide their learning, and no amount of cajoling, or appealing to their sense professional or intellectual propriety will change that. Some students will always work above and beyond what the assessment requires of them, but most won't.
Assessment is how students comprehend what is the stated aim of a course. Instead of fighting against it, you might embrace it. For each learning outcome there should be an assessment that is aligned with that outcome - that is, it is impossible to successfully complete the assessment without have met the learning outcome. The learning activities are then designed to meet the outcomes. This might seem like "teaching to the test", but in fact it is the opposite: in "teaching to the test", the assessment defines learning outcomes, here the learning outcomes define the assessment. Biggs and Tang [1] refer to this as "constructive alignment". [1] is a good read for the evidence that students have more or less always measured what they are supposed to learn by what they are assessed on.
Thus you would ask "what learning outcome am I hoping my students achieve by this homework, and where is that assessed?". If the learning outcome isn't assessed anywhere, then it should be. If it doesn't meet a learning outcome then perhaps it shouldn't be set.
In practice we either make homework credit bearing (even if only a tiny percent of the overall credit), or, more frequently, ask an exam question that tests the learning outcome that a homework is aimed towards, and a student won't be able to answer without having done the homework. The final possibility is that the homework is practice for what will be tested in the exam. In this case you need to make this abundantly clear to the students. Even then, you will probably only get a fraction of the class doing it. The consolation is that this is the part of the class that deserves to do better in the exam and undoubtedly will.
[1] Biggs, J and Tang, C. (2011): Teaching for Quality Learning at University, (McGraw-Hill and Open University Press, Maidenhead)


When a conference has an abstracts and a later papers submission date, is okay to skip the abstract submission and just submit the paper?

No.

It's a deadline.  Follow it.

Program committees ask for abstracts early to streamline the reviewing process.  Asking them to make a special exception for you because you're not ready yet is unfair to the program committee, who would have to do extra work (however small) to accommodate your late submission, and to the hundreds of authors who got their abstracts in on time.

  The issue is that I am still working in tabulating the results from my experiments

The tabulated results of your experiments are not going to appear in your abstract anyway; only the conclusions from your experiments will.  If you don't know yet what those conclusions will be, you're not ready to submit.  So don't.  There's always another conference.

But! Remember that you are allowed to revise your abstract in the week before the paper submission deadline.  It is perfectly acceptable to submit a tentative abstract, which describes your results in enough detail to assign reviewers, and then include a more detailed/updated abstract in your paper submission.  If your conference is using EasyChair or HotCRP, you can change your abstract in the electronic submission form, and the committee will no longer see the old abstract.

If you make significant changes to your abstract in the paper submission, you risk angering the program committee members who were assigned your paper, who could (legitimately) reject your paper without review.  So don't do that.