How should I handle reviewing a paper that is very similar to something I am working on?

I am going to answer based on an implicit assumption I feel much of your question hinges on:

  One of the problems is, they did not mention that part in the abstract, therefore I have accepted.

This sounds like had you known that their work is so similar to yours, you would have rejected the review.

However, I would argue that that cannot possibly be in the interest of the review system.

Yes, you could argue for a conflict of interest, but it is the conflict of interest that exists generally, based on the simple fact that other people beside you do research in the same or similar topics as you. It is not a conflict of interest on a personal level (e.g. you being part of the team whose paper is being reviewed).

Instead, it is a conflict of interest that, in theory, should quite often exist in the review process - for reviews to be meaningful, reviewers need to be familiar with the topic to some extent, and thus, a similarity of the research topics between authors and reviewers is hardly avoidable.

I see your concerns about what the authors of the paper under review might be thinking, though you might have to brush them aside for the time being. However, what you can do is draw the benefit from being the reviewer and thus having early access to a manuscript:

While your method may be very similar, it is most probably not exactly the same. When describing your method, try and insert a few sentences that focus particularly on a few aspects that you do differently from them.
For future publications you might write on similar topics, keep in mind that there may be a similar publication by those authors around that you can cite.

This has advantages for both sides:

You increase the chances to include a relevant citation that you might otherwise miss (and thus the authors' chances of being cited by you are increased).
Even though you cannot yet cite the work of the other authors, your clear description of some different aspects serves as a way to "preemptively" establish the differences between your work and theirs.
If they happen to publish a revised version of their paper after your work has appeared, you have already provided them with quite a straightforward foundation for describing their differences to your work.

In the comments, the concern has been voiced that even without the assumption of plagiarism, the authors of the other paper might still feel by rejecting their work, you intentionally stalled their progress for long enough so you could publish your own very similar work first, and now it's their problem to care about the prior art.

However, there are some aspects of good scientific practice that speak against that line of reasoning:

You do not provide an unjustified judgement, you provide a review. If you choose to reject the paper, you have the opportunity to describe objectively and in detail why you deem the work in its current state not ready for publication.
The other authors have not yet published their work in a properly citeable fashion, but that still just means you have plausible deniability on your side when you are asked whether you knew about the other work. Scientific integrity still demands that you consider the existing prior work, published or not, which is exactly what you are doing by specifically describing some aspects that you do differently than the reviewed paper, as described above.


How are academic relations between mainland China and Taiwan?

The relationship between the Chinese and Taiwanese academic research communities are generally friendly from my personal experience (a family member of mine is a professor at a Taiwanese university, and has collaborations with Chinese universities).

As far as I know, getting involved in the research community does not get you into political obstacles as long as you are not doing research in politics (which the Chinese government might be more sensitive to).


What are the consequences of refusing to grant honorary authorship to a superior?

I'm surprised this is still an issue - though I guess not as surprised as I'd hoped to be. It's rather sad that there are still people out there who demand to be credited for work they haven't done.

Some journals have clear guidance for what merits authorship. For example, pretty much all medical journals sign up to guidance from the International Committee of Medical Journal Editors (http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html#two) which requires

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.

(So in the example above, getting the grant money would probably count as contributions to conception or design, so warrant authorship as long as the putative author then didn't abandon the project but could meet the other three criteria; but providing space for the work e.g. in a lab or recruiting participants, on it's own wouldn't be enough)

Most journals then require a statement of what the authors did to meet these requirements which is published with the article - so in order for someone who doesn't warrant authorship to claim it they, and their 'co-authors' have to lie in print.

So in the unlikely event my head of department, or anyone else, insisted on being added as an author when I thought they didn't warrant it, I'd ask them to justify the request using the ICMJE criteria.

Of course - thats the easy bit.

If you're working in an area which doesn't work like this, you have to think about keeping on board with the community. If someone senior really thinks they deserve authorship on your paper, and you don't, you have to decide whether you're going to keep them happy.

I'd suggest you may need to find someone else to persuade them they should't be named. That may be someone superior to them in your institution, or you may need to discuss with the editor of the journal you're submitting to - who can then ask for justification of contributions should they see fit.

Fundamentally though it seems that attitudes like this may suggest something rotten in the culture of either a department, or possibly a discipline. And culture change like this will take years.


I'm only going to answer the first part of this question:

  How should we deal with this opposing constraints (evaluation is serious matter but time is limited)?

It is true that it is often rather time consuming to do these evaluations. But I think ultimately, you need to apply the categorical imperative. In other words, you need to spend as much time and diligence on evaluations as you would expect your evaluators to spend on yours.

For a two-page application for a sabbatical, this may not be very much. But for someone applying for tenure, surely a thorough reading of at least the most important papers, along with some research about the impact of the candidate's work, is appropriate. This is thankless work, as you don't usually get a lot of credit for it. But it is nevertheless something that can't be taken lightly because of its outsize effect on the candidate and the importance of your evaluation. Consequently, if the case is not completely straightforward, if you find that you need to spend a couple of days on it, then that is what you need to do -- because you would your evaluators to do the same.


How do I inspire my students to work through problems on their own?

By giving students assignments that they truly work on their own, with minimal hand-holding, then assigning the appropriate grade. Some students will be upset enough with their less-than-desirable grades such that they become "inspired." The other students who fail to keep up with the pace of the course will earn the grades which truly reflects their lack of ability/skill/etc.

Sitting down with the under-performing students, and explaining that they may benefit, for example, from retaking the necessary prerequisites may be in order. It's not easy to tell a junior/senior that they should probably go back and retake a sophomore-level class, but that's life, and it's better for everyone in the long run.

Although I've not been in my current faculty position for very long, I've already seen the consequences of dumbing down the assignments, and the effect that it has on the quality of the follow-on courses, both in student capabilities and my ability to teach the things that need to be taught at the appropriate pace.

The way I see it, you can either make your assignments easier, or be tough: I have (somewhat reluctantly, at first) grown to prefer the tough route.


Awaiting recommendation will take how long time?

Check if there are any major holidays in the editor's country. If not, three weeks should be enough to make a decision. However, it can be that the editor invited another reviewer to have a look at the paper (possibly after receiving the 2nd round of reviews), which will cause a few weeks delay.

If you don't want to wait longer send a short, friendly email to the editorial office. They should be able to tell you if the paper is still in the pipeline or whether it got stuck somewhere, and maybe when you can expect an answer.

Maybe the editor is just on holidays...


One possibility to check about—which I took advantage of at the end of my own graduate career—is that of being hired short-term as a teaching assistant. The good news is that you would have extra time to find a new position. The challenge is that you would be making a commitment to teaching for an additional semester. It would have significant ramifications if you were to  skip out on this duty if you obtained a job offer to start immediately at a company, or a postdoc offer at another university.


Should one cite unethical research that may contradict one's current research?

Are you conflating evil people with scientific results that they achieve (by valid means)? They should not be conflated. Condemn the people and the evil acts that they do, but not any valid results obtained by honorable means. Evil monsters don't need to always act in an evil manner.

There is, for example, a lot of both computer engineering and mathematics that was done by total racists. This was in the US and in fairly recent years. This doesn't make it invalid to use computers, nor does it invalidate the mathematics itself.

It isn't even necessary to state that X was an evil monster otherwise when citing X. However, if you are writing about racism or other evils, then it is perfectly appropriate to point out the flaws.

Of course, the spline research would be discredited if to do it evil acts needed to be carried out, but you don't seem to be saying that here.

What is true is true, even if uttered by monsters. What is false is false, even if uttered by angels.

Since the question was changed, I'll add this. If "research" has been discredited for any reason then there is no need to cite it other than as something not to be done. There is no need to cite failures to prove a theorem when you provide a proof, and there is no need to cite research that was done unethically. The results themselves are in question.

There are a lot of ways to fail at research. Lack of ethical behavior is only one. Don't cite the failures, except as failures.

In the case at hand, the research resulting from unethical behavior doesn't "contradict" the current work. It wasn't valid in the first place.


Ownership of environmental samples (or other material) analyzed during a PhD

Since you ask for legality, you need to consult a lawyer for an answer. Everything expressed here is my personal opinion based on my experience as a researcher. It is not legal advise.

You say, you received the sample based on a collaboration of your university with the sample supplier. This probably means, you acted as a representative of the university when receiving them, because you wouldn't have received the samples if you were not affiliated to the university. From this it follows that the university owns the samples. This is also reinforced by the samples being processed with university resources.

I wouldn't do anything with these samples against the university's or my supervisor's wishes.

However, if you have disagreements about this with your supervisor, you should try to solve this conflict or even find someone who can mediate the dispute. A compromise that makes both of you happy might be achievable.


What can first author do if co-author who submitted paper put himself down as corresponding author without first author's permission?

Legality doesn't really come into this, but academic ethics most certainly does.

The real problem here is that the paper was submitted without a clear agreement amongst the authors that it was ready for submission and about who would submit.

From your story and comments, I assume that you are "N", but you don't say which of co-authors B, C, or D submitted. I am guessing that one of those co-authors is your advisor, and I believe that's who you need to have a conversation with.

If your advisor was the one who submitted (or told the other co-author to submit), they may have had good reason for doing so, or may have thought that you had already consented to submission.
If your advisor didn't think the paper was ready to submit, they need to know that it has happened so that they can help defend both of your interests.

Depending on what happens in your conversation with your advisor, there are three basic paths from here:

It was a misunderstanding of some sort or a basically harmless error, and nothing needs to be done,
The journal editor can be contacted to change paper meta-data, or
The article needs to be withdrawn and resubmitted at a later date.

From what you have written so far, however, it is impossible to tell which is the appropriate course.


Re-using text from a grant proposal in a paper (or vice versa)

Copying proposals to papers: I am sure many have not thought about this but many have copied material to and from proposals. Copying from a proposal to a paper should not be a problem since a proposal is normally not a publication and I have never come across a funding agency that claims copyright on proposal texts sent to them. If anyone knows of exceptions, it would be very interesting to know how they handle proposals. Taking the idea to the (silly) extreme one could argue that copying what you write in a notebook to a computer-written manuscript is self-plagiarism. The key lies in what sources are considered published and which are not.

Copying papers to proposals: Copying from a journal paper to a proposal should normally not be a problem either since the proposal is not a publication and not something that should be distributed. But, the journal text may be subject to copyright so it makes sense to see to what extent one might infringe on those rights by copying text to  a proposal. I doubt any journal would care much (or indeed find out) as long as the proposals are not made public. Since most application processes are very strict and reviewers are not allowed to disclose materials (some actually ask you to physically destroy any printouts) I doubt there is a problem but strictly speaking this may indeed be a grey zone.

EDIT: I will add a definition for self-plagiarism: Copying material you have previously produced and passing it off as a new production from the site plagiarism.org. From this perspective the question becomes, is one trying to pass of the copied material as a new product?


It depends if these procedures common in your field.

If they are you can briefly describe them as established (or widely adopted) practices in the field or naming the well known techniques. e.g., We used sample prep technique X, measured Y with Z equipment, and used A, B, then C tools to analyse it. Another option is to cite the published method or protocol in a journal and describe how (and why) your lab modified the procedure.

This citation does not have to be reputable journal (although it is preferred), it could be a thesis from a previous lab member or a lab's website, blog, or GitHub repo as long as the source is acknowledged and the full procedure can be accessed (reproduced, critiqued, or verified). Perhaps considering putting your procedure on GitHub? We do this for both our workshop lesson resources and procedures shared within the lab.

Failing that, your other options (in order of preference) are to cite articles "in press", "unpublished work" or "personal communication". Generally this refers to early access to data that your audience should be able to access once it's been published too. These are accepted practices in many fields but generally used as a last resort when a paper can't be given. Note that a "personal communication" is generally citing a person rather than a group, in this case probably your professor. Personal communications are cited in text but not listed in the bibliography. How accepted this is depends on the person the reputation in the field of you're citing and whether you can describe how they communicated it (e.g., in lecture notes, a seminar, or course laboratory manual). For example it is clear here why the personal communication is from a reliable source:

  This analysis used the method of Parker et al. (2009) designed for microarray data with the following modifications for RNASeq data (J. S. Parker, personal communication 2016).


It is a bit easier on the reader if you say, instead:

  to enable personalized Web searches was first proposed by Smith in [32], however in [9] Jones, et al., showed this to be computationally inefficient. And Lindqvist in [33] iterated upon the method and made it suitable for real-time use....

It is easier, I suggest, for the reader to have something like a "picture" associated with a name, rather than just a reference number. And if the same author wrote more than one of the papers it brings them together in the reader's mind.


Importance of QUANT score on GRE for math grad school

In the US, at least, no single thing is likely to knock you out of contention. Aim high, but don't put all of your eggs into too few baskets. The competition is fierce, of course, in top level schools, but if you put together a good application that clearly predicts success you should come out well. But, make sure that you have very strong letters of recommendation from people who can speak both of your past success and your likelihood of future "wins". How hard you work, how serious you are, etc.

I suppose there are a few places that might have a cut-off score, but not everywhere you might want to go would do that. It is rather foolish in any case.


Was forced out of PhD for academic/health reasons, need advice on what to do next

If you want to continue at the same school I'd start by going to talk to the administrators in your department, hopefully as a PhD student they will be familiar with you and your situation. Ask about your options to continue your studies, and possibly seek out a new supervisor.

I'd also make a list of other schools you'd be interested in attending, and find faculty there with similar research interests, ideally you could try setting up a meeting to discuss your shared interests and ask them if they might be willing to supervise you or if they have any projects that might be a good fit for you as a PhD student.


Explaining contribution of book and journal

X, Y and Z present ABC [1].

is appropriate regardless of whether [1] is a technical report, published manuscript, thesis, chapter, book, ...


How much should poster/talk prizes be spread at a symposium?

I am a volunteer with the IEEE in Connecticut, USA.  Each year, we give prizes to EE-related projects at the Connecticut Science & Engineering Fair at Quinnipiac University. This is a fair for High School students (mostly) to present their projects.

What we do is award a first place for each of the Senior and Junior sections of the fair. This prize is worth $200.  Then we award $100 prizes to 6 other students as "Honorable Mentions".  These other six tend to be 3 for the Seniors and 3 for the Juniors, but it depends on the relative quality of each pool.

To answer your question is a little hard. Here is the full list of science project abstracts at this year's fair. Not all of those (or even half) are EE-related. My guess is that we'd start with a list of about 100 projects (50 each in Senior vs Junior) and then make a determination from there.


My work was published before me. What should I do?

Option 2 is the right one.  Do more research that builds on the ideas, advance the field more, and publish that, citing the first paper appropriately.  Maybe they're also doing further work and advancing the field and will publish that too.  If so, great!  That's how science works.  People publish papers and then they and/or others continue building on it.

While the authors of the first paper could have included you in the acknowledgements, the fact that you had talked about ideas with them isn't necessarily enough to warrant authorship and you certainly can't make the statement that "I am the original author." Unless you're accusing them of plagarism, one of the main points of free exchange of ideas within academia is so that somebody can build on those ideas and develop them out into a publication.

Imagine going to a conference and discussing ideas with people (incl. those from other institutions) and then somebody takes one of those ideas back and does all the work that's needed to develop it into a formal research contribution.  They publish it, great.  Then you read the paper in a venue for your field and build on the work, citing it and extending it further.  That's basically how it's supposed to work.

  nobody will believe similar papers are a coincidence or a an independent inventions. (And they would be right. It's not.) I think that in the worst case it can destroy my reputation and career. Or maybe it's a non-issue and I'm worrying too much.

Yes, I think you're worrying too much.  It's fine that you had some conversations with colleagues exchanging ideas, and then cited a paper they published, in your own new extensions of the work.  It is even possible for you to have extensions that are similar to extensions they may be now independently developing.  If your colleagues did a good job of making the path forward from the last paper clear (to an expert in your field), it wouldn't even be that surprising if one or more others were doing a similar extension elsewhere.  Credit your colleagues' publication and move the work on.

If you're concerned about duplicating efforts in expanding the work, you could consider whether or not you want to formally collaborate with your former colleagues on doing that expansion.  Maybe they just figured you weren't interested or didn't have time when you left, but would appreciate having you on the team for further work (if they're still working on it); it seems they like the ideas you have to offer.
It's also possible they don't even know that you feel offended, especially if they're under the impression that these ideas were generally percolating in the department for a while before they actually did the work for that paper.  They may have discussed the ideas with other people in advance, who are in a similar position to yours, some of whom may still be in the department, and some of whom may just feel happy that somebody actually did that work.  It'll be your decision about whether you perceive enough of a breach of trust to prevent future collaboration or not.


Must bibliography entries match the original title's German orthography?

I would always prefer the original title of the paper (only ignoring all-caps or similar), even if it contains spelling mistakes, as this is the most likely search term, somebody is going to use (and not all search tools do autocorrections). This in particular applies to titles in spelling conventions that readers might not be familiar with. A German paper from that time might use the spelling Oscillator instead of the modern Oszillator or Maasssystem instead of Maßsystem¹ – would you also change these?

As a sidenote:
Uppercase umlauts (such as Ü) only came up in German in the nineteenth century and were only fully established as a consequence of the spelling reform/establishment of 1901. Thus, it’s very unlikely that Ueber was used due to typographical restrictions and one could argue that it is the more correct spelling here. Also note that nowadays, substituting Ü with Ue is only allowed as a makeshift solution and the two are not regarded as equivalent.

¹ Taken straight from Max Planck – Ueber irreversible Strahlungsvorgänge.


Professors are busy and are always juggling multiple commitments.

This does not mean that you are unimportant to them but maybe some judicious memory jogging is required for them to remember what X has promised you.

Another excellent strategy which I have adopted is to show up to my committee members' open office hours with issues when I need them solved instead of bothering them over email. Usually I need 5-10 minutes of their time to explain my issue and solicit future directions. That works really well. I am not a big fan of long meetings.

In response to your specific question, if you want to not work with X just tell X that you do not feel that you can work with them in the future. It might be helpful to have someone else lined up before you do so though.


How long should it take to read a paper?

As you have alluded to, there are many ways to "read" a paper and the first question to straighten out is for what type of information are you reading a specific paper. A beginner's mistake is to believe you need to read from the first to the last letter of everything you find. This way you never get anywhere and it is the beginning of the learning curve for undergraduates.

If you are surveying a field, you skim through by reading the titles first of all just to spot the ones of interest. This reading takes much less time than to actually find the title. Once you are past this you may take on the abstracts to weed out the ones that sounded right but were off topic. This will take a few minutes per paper. The next step is to read the parts that are of interest to you. Are your summarizing a field then conclusions and the discussion may be what you focus on. Maybe your summarizing methodology then those chapters are of interest. In any case, you will read parts of the paper that are mostly relevant to what you are trying to find out. This may take a on the order of hours, sometimes less per paper.

Sometimes you need to spend time on papers to understand the nitty gritty details. I spent 4 days reading three papers to understand the details. I needed to write down equations and try to see the missing steps between the paper equations to understand the derivations etc. This type of reading is not what you normally do but it certainly happens.

So in the end, what you will learn through your PhD is to hone your skills to be able to focus on the details you really need from any paper. It is rare that one reads one paper at a time, usually it is a collection of papers and one often has to return to check on details that you either have forgotten, or may have missed, or, in fact, the author has missed. The need to go into the smallest detail of a paper depends on what you need to get out of the paper and with time (continuing through your professional life) you will improve on these skills through additional reading.


Is it okay to change the research area of interest that I specified in my statement of intent after submitting an application for a PhD program?

Under the conditions you state it is perfectly ok for you to change areas. I doubt that it is even necessary to state it prior to a decision being made on your application, since they don't assign supervisors early on. It might be different if you needed to pick a supervisor prior to acceptance.

In fact, you would be wise to look carefully at potential supervisors now and after you arrive to be sure you have someone compatible who does work you are interested in.

However, just as an option, you might want to correspond with the professor mentioning your "broadened" interests and asking for advice. I wouldn't claim you have made a firm decision, but are just exploring your opportunities and would like advice. However, I don't guarantee this is the right approach since I don't know either of you or your past correspondence. You have to judge it.


Who do I email about a question on a paper?

Papers usually have one (or more) designated corresponding author, or “contact author”, or “author to whom correspondance should be addressed”. That's whom you should contact.

Sometimes it's indicated by a footnote, an asterisk, or at the end of the paper. Sometimes, it's indicated by the fact that only corresponding authors have their email address listed.

If there is no corresponding author, then email either the first author or senior author, depending on the nature of your question and how confident you feel in communicating with them. I would refrain from copying the email to all authors (except maybe if there are only two): if he wants to, the author you will write to can forward your query to others.


How to describe a previous uncompleted PhD on postdoc applications?

I think this is a non-issue. When I review resumes from new PhDs (note: for non-university research positions, not post-docs), I rarely care about anything that happened prior to grad school. Any of these are likely to be fine. Still, my thoughts....

I think the most elegant way is to omit it completely.

Under education, you can list your completed degrees. As you say, anything impressive that you want to highlight from earlier years can be bullets here.
Then under work experience, you start with the first position after leaving the unsuccessful PhD.

That will take your work history back 8 years and give a reasonable explanation for what you did between undergrad and grad school. No need to account for every single year during that time.

Your option #3 also seems reasonable, though I don't see the upside.

It is perfectly honest -- that was your title, and the technical staff will immediately see what happened (they shouldn't care)
Non-technical "resume screeners", who are more likely to be off-put by this, are less likely to pick up on it
But, this reduces your signal-to-noise ratio (you want your resume to pack a punch, not list irrelevant details), and you won't get many points for transparency.

I see even less upside for option #1, though my analysis is basically the same as for #3.

I would avoid option #2 -- it has the same upsides above, but could be seen as deliberately obfuscating (which is basically true) or trying to oversell.


What is the difference between falsifying data and just being wrong?

The clear difference is intent.

Human error occurs when people make mistakes accidentally. For instance, in my first paper, I submitted a graph that was physically implausible because of an error in a code I had written, without realizing it at the time.

However, if I knew the work was wrong or, worse still, if I intentionally made up results, we would cross the boundary from human error to fraud.

Unfortunately, it can be very difficult to detect intentional fraud without some assistance from the perpetrators themselves. A major example of this was the Jan-Hendrik Schön scandal of the early 2000's. Schön's fraud was discovered because he was reusing the same figures to different ends in papers in various journals.


Strategy for using a Virtual Learning Environment (aka Blackboad/WebCT/Moodle)

Moodle
I recommend you to try a demo site of Moodle. It would be specially helpful to try one that has content. Here you can find one. You can choose which role to use, so you will be able to see what students see and to see some settings for each activity.
Moodle's documentation is the bible for using Moodle. You just have to make sure to review the documentation of the current version of your site. For instance, the capabilities of versions 1.9 or lower are much more limited than those of versions 2.0 or higher. However, if you are beginner I suggest you to visit first the demo site. Moodle's documentation could be more difficult to grasp if you do not know how a site works.
Contents
I am not sure if you are going to use Moodle as a support for classes ("blended learning") or if you are going to teach an e-learning class. However, regardless of the kind of use, here you can find interesting ideas and concepts about distance education using Moodle. These ideas will be useful even if you are teaching a blended learning class. This document explains some principles for distance education (e.g., the course interface should be simple and intuitive).
Tips

The module called "Lesson" is very flexible to show and assess content. Some creative users have used it to simulate a situation where students have to make choices. Depending on those choices the module shows them different contents or questions.
The "Workshop" module allows you to implement a peer review system in a class.
The "Assignment" module can be used as an "electronic mail box". Students can submit their project reports online.
In the newer versions of Moodle there is an option to create a "Rubric". So you can quickly evaluate projects clicking on the rubric.
You can set up a "Wiki" in the course's page. For instance, you can ask students to use the Wiki to document their progress on a project, so you can directly comment in there.
You can create groups of students in the course's page. One of the advantages of this is that you can implement forums for each group, so students can exchange messages within their groups.
If you are teaching a class that uses a lot of math, you can write in Moodle using Latex syntaxis.


Presented a paper in a conference, but my paper did not get published in proceeding

If I were you - and if I could publish that research in a peer review magazine, in your situation - I would do so. If your research didn't make it to proceedings (for whatever reason), it is open for subsequent submissions. It is practically same situation when your paper is rejected in a journal - you can re-submit it elsewhere.

Now - is it justified to submit that same talk for some other conference where it has not been published (in a journal)? - thats dubious and might be frowned upon depending on the size and praxis of your field, but I believe submitting it to a journal is pretty much ok.


What if I can make a profit for an assignment/project I did similar to "Google"?

This cannot be answered in general.

It depends on the contract you have with the institution and the applicable law in your jurisdiction. It may depend on how you were funded as well.

I know of examples from both extremes: your university owns 100% and your university owns nothing, as well as everything in between. Some intermediate setting is probably more common, but, as I said, it depends.


I believe my department is failing to enforce standards in doctoral examinations. How to proceed?

Yes, I have seen some similar things in my life and this is indeed a very tricky question. There is a strong tension between our ideals regarding the quality of PhD's (and other degrees) we feel our institutions should be awarding and the practical realities on the ground, which involve messy and awkward decisions that have a direct influence on people's lives. This reality is such that sometimes we feel we have no choice but to compromise our lofty ideals to some extent. As long as the compromises are small, this is probably as it should be, but when the compromising reaches alarming levels, it is reasonable to start becoming seriously concerned.

What I would suggest is this. First of all, it may be worth remembering that the behavior you are describing is not your doing nor your responsibility. The chair and the members of the doctoral examination committee are the ones who are making those decisions and putting their own reputation and credibility behind them. So, although you find the behavior concerning and perhaps for a good reason, you cannot reasonably be expected to fight all instances of poor decision-making at your university. Thus, one option is to simply do nothing except to resolve privately that if you ever preside over a doctoral examination yourself, you will follow your conscience and let the chips fall where they may, and thus play at least a small role in making your department and university better.

If you want to be more proactive, an honorable course of action would be to actively pursue the role of chair or member of the doctoral examination committee so you can put the goal of raising standards directly on the agenda. Or you could strive to be appointed to the departmental committee that decides the makeup of the doctoral examination committee, and thereby help get people with high standards be placed on that committee and help prevent the kind of conflicts of interest you are describing. Through such behavior you will be setting a personal example and showing that you are not just criticizing others but willing to take action yourself for the goal you believe in. Since you mention that you believe others in your department feel the same as you, you may find that you have a good number of allies who will support you in your mission, and even your opponents will respect that you are acting on your convictions. Of course, it will take time and effort to bring about change, so be prepared for a long struggle ahead.

Finally, if your position within the department does not make it realistic for you to seek the kind of active, visible role I suggested above, or you are unwilling to make such a large effort to see change happening, I don't have much to suggest. I don't think there are easy fixes; someone will have to do the work to change the culture of your department. If it's not you, maybe you can work behind the scenes to identify more senior allies willing to take on that role. You might get lucky and find someone passionate enough about the subject, but probably you won't.


Publishing a book based on long journal article

I am not a lawyer, but John Wiley owns the copyright of your current article, and if you just copy larger parts of it into the book chapter, the german publisher will need to obtain permission from John Wiley (that would already be the case for individual figures) and this can well involve transfer of money. That they allow you to publish a pre-print or put it on your personal website is a concession made to you as a person, but not to other (commercial) publishers.

To avoid any of that you would need to re-write (and ideally expand) the article significantly.


Who usually submits workshop proposals to conferences, and who usually pays for the workshop?

Generally faculty or industry researchers propose workshops.
Workshops generally have an additional registration cost. From what I have seen, the conference pays for the workshop and coordinates a budget with the workshop but the money comes from that extra registration cost. I suspect that some larger workshops may not fit this model and may be entirely separate, but co-located.


First, note that there is a difference between refereed in a peer-review journal and refereed in a conference proceedings. It sounds like your case is the latter.

In both cases you are correct in saying it received peer review (if it did), but the moniker of 'refereed', in my mind, suggests the work could be rejected.

You note that you received 'reviews' but it isn't clear whether these are non-binding 'comments' or part of a dialog ending with accept/reject. If they were indeed just comments, and there was no possibility for rejection, I would not say it was 'refereed'.  Like in sports, referees make calls, not suggestions.


What kind of papers is it acceptable to read during working hours?

A perspective from (theoretical) computer science:

One of the things that distinguishes academia from some other lines of work is that there is no well delineated line between "working hours" and non-working hours. Since you can probably be better paid elsewhere, academics tend to enjoy research. You seem to as well, since you read papers during your free time.

But that is the great thing about academia. Reading papers that you enjoy is work, since as you observe, reading in a field different from your own can nevertheless give you tools useful for your own work. So, I would say that you can read any paper you like during "working hours" and not feel bad about it.

Incidentally, one can always switch areas. If you feel that you are "forced" to read the papers that come out in your area, but there are other areas that you read for pleasure, perhaps you should work in those areas!

(Disclaimer: needless to say, to have a successful academic career, you can't spend all your time reading -- you have to spend some of your time writing! But there is no need to arbitrarily partition the reading into a work and pleasure pile.)


The answer of JeffE is the morally correct one. The answer of ZeroTheHero is the political one.

I'll give the self defense answer. If your advisor has power over your future, then I advise you to go along. But move away from her orbit at your first opportunity. What she is demanding is unethical and seems to be trying to boost herself at your expense, rather than supporting a former student as she could.

But if that power is there, and she has a grudge, then she can use that power to affect your future. You probably don't have any countering power to contest it, though some do.

The order of authorship, I'll add, varies greatly by field. In some fields there are tremendous fights over it (lots of evidence in posts here). In other fields we just list contributors alphabetically, but they need to contribute. Some with very minor contributions show up in acknowledgements, but not as authors. My advisor (mathematics) helped me a lot and did, in fact, contribute to my dissertation, but no one would have thought he should be co-author. But he was acknowledged and cited.

In other labs, the PI is always listed (often last) and people make different assumptions about that. Some have said they always assume the last author did all the work. Others assume the last author provided funding and encouragement, nothing else.

But, in your case, think long term about your career and protect it. This paper may wind up with, to you, an unhappy listing of authors, but it won't be your last work, nor, one hopes, your best. If you need to submit to protect yourself, then do so, but, as I said, move away quickly. Don't look back. Find a better circle of collaborators.


Completed writing a first author paper, not submitted

In my field (Mol Biol/Genomics) I'd say most papers are submitted after the first author has left, as grants/studentships don't generally last long enough to complete a project and get the manuscript submitted.
In theory there is nothing to stop you submitting the paper without an affiliation. In practice it will be much more convenient if the paper is submitted by your PI, who would presumably agree to pay any charges associated.


Is one spelling mistake in the academic CV a big deal?

I'll give the same answer as Allure, but for a very different reason. Not only is it common, but most people won't notice it. And of the few that do, fewer yet would think it an important enough issue to bother with.

"Egad, this person misspelled a word. Horrors."

Nope, it ain't gonna happen.

But, you also need to be assured that no single thing, whatever it is, would likely derail an application (yes, a few obvious exceptions). Your acceptance is based on a judgement and the judges try to look at a complete picture of an applicant; both their past accomplishments and the likelihood of success in the future. The CV (as a whole), your statement of purpose, your grades and test scores, your letters of recommendation. Each of those contribute to a (fairly) complete picture. Flaws or issues in one part can be balanced and overcome by the positive and supporting parts elsewhere.

Relax. The judges are no more perfect than you are.


How to make a presentation that includes math symbols?

I've found that the secret is (1) good tools to create equations, plus (2) liberal use of arrows and text, plus (3) animations linking the two.

I've found the following two programs to be indispensable for writing talks:

LateXiT for the Mac
KLaTeXFormula for a number of OSs, similar to latexit but less functional

The goal is to make the math (1) visually distinctive, so that the reader can easily tell when you're discussing an equation, and (2) easy to interpret. Remember, in a paper, you have text such as  "...where n is the number of..." after the equation is shown. This typically isn't done in research talks, and even worse, once you're off the slide, the reader has to simply remember what the equation was; they can't flip back a page.

My technique (you can see it in action in this presentation) is to put equations in a unique font (I use Times New Roman, with bolding and italics), and using the above tools to typeset equations in latex and insert them as images as necessary. As you introduce each equation, explain all the variables using text and arrows. Every variable should be explained... yes, this is slow, but learning is slow. If you're going to re-use the same equation multiple times, put it in the top-right corner of the slide - with arrows and text sometimes included - so that (1) they remember what you're talking about, and (2) so you can refer back to those equations.


I have always used the following words:

Program - as in "our undergraduate finance program"
Course - As in an "international finance master course": WARNING: This can be confused with an individual class/module

I would avoid the use of the word degree because it can be confused with the piece of paper one gets at the end. I would also avoid the use of coursework as it implies the subjects one will study. However, to be fair, I have heard both of those words used quite frequently and one fun thing about English is that it gets modified by common usage, even when that usage seems wrong to some of us - we must go with the flow.

Another reason to be cautious about using the word degree is the common separation, by some, between a certificate (short duration), a diploma (medium duration), and a degree (longer than the other two). Using the word degree could cause confusion to some who might be looking at a certificate or diploma program.


Does a ResearchGate profile count as a "personal website" for green OA purposes?

The 2009 blog post you linked to makes the claim that

  each profile page within ResearchGATE is legally considered the personal website of the user

Similar claims had been made by Academia.edu and Mendeley, according to Michael Clarke at the blog Scholarly Kitchen. He elaborates on these claims following an incident in 2013 in which Elsevier sent large numbers of DMCA takedown requests to Academia.edu:

  William Gunn [of Mendeley] puts forth an argument that Mendeley has long used for hosting content they do not have explicit permission from rights holders to host: that an individual’s profile page on Mendeley (or by extension, Academia.edu) is that individual’s “personal website” and therefore covered under the exemption that many publishers provide to authors in both copyright and exclusive licensing agreements, allowing authors to post PDFs of their work to their own personal or institutional (e.g. their laboratory or departmental) website. Since papers are loaded to both Mendeley and Academia.edu by authors, the argument is that the paper is “self-archived” to the author’s personal website.

  Leaving aside the fact that many publishers permit only the author’s accepted manuscript (and not the final PDF) to be self-archived, were one to accept this argument, by logical extension this would mean any commercial site (Academia.edu, ResearchGate, Facebook, LinkedIn, Scribd, Google, etc.) that sets up a profile page would have the right to host any research loaded to the site by an author. The distinction between a profile page on an academic or professional network and a personal or institutional website does not strike me as difficult to make and if it were ever an open question, as Mr. Gunn asserts, the question seems to have just been answered by the legal department of his own employer.

More recently, some publishers have begun to explicitly specify authors' rights regarding posting on sites like ResearchGate, and that these are different from authors' rights regarding posting on personal web pages. For example AIP defines

  Within a commercial scholarly collaboration network (SCN) site:

  An SCN is a professional networking site that facilitates collaboration among researchers as well as the sharing of data, results, and publications. SCNs include, for example, sites such as Academia.edu, ResearchGate, and Mendeley, among others.

as a separate category from "authors’ personal web page and employers’ web page".


Which of the items below are worth mentioning in my admission documents?

This list does reflect your technical abilities and not your research-based activities.

Therefore, all things listed here should be packaged and be presented under a section
(e.g., such as 'Related Technical Activities'); to represent your technical abilities to program and contribute (e.g., Github).


Etiquette to recontact the editor when he says the he will give the news as soon as he has some

Although it's arguably dependent on field, 10 months is well past the time it should take to be able to provide a status update.

I remember reading this story about a woman who was bedridden for years. A doctor eventually examined her and found nothing wrong at all. Asked what the problem was, the woman said a previous doctor had left instructions for her to stay in bed "until he returned". The previous doctor evidently forgot about it, and the woman just followed instructions. This situation is similar.


I mistakenly chose the CC BY 4.0 license on arxiv. Can anyone take my paper and publish it in a journal or conference?

Can anyone publish my paper in a journal or conference?

They'd need to attribute the paper to you.  Most journals will only accept papers written by the person who is submitting the paper.

Can a journal publish my paper on its own?

Yes.  You already gave permission to do so.  A legitimate journal probably won't do so.
Possibly a predatory journal might do so if they wanted to pad their journal.

Is there any way for changing the license?

Effectively, the answer is no.  The CC BY 4.0 license is irrevocable.  If you release the paper under a different license, people can just take the copy they received under CC BY 4.0 and distribute that.

What are the consequences?

Anyone can take your paper and publish it wherever they want, even if you don't provide individual permission.  However, they will have to cite you.  https://creativecommons.org/licenses/by/4.0/ provides an overview of these permissions.

How bad is the situation for me?

It's not that bad for you.  CC BY 4.0 still requires attribution.  Unless you're trying to make money selling your paper, there's usually no reason to care if people freely distribute your paper.  Of course, many journals will refuse to publish a CC BY 4.0 paper (e.g., because they sell access to the paper or because they want an exclusive license).
Edit to add more details in reply to comments

Is it legal for someone to publish my paper without asking for explicit permission?

Yes.  Anyone is free to "redistribute the material in any medium or format." Mind you, they still have to attribute the work to you.

Can they do so without contacting me?

Yes.

Someone I dislike published my work.  Do I have any recourse?

Not usually.  Many licenses, including CC-BY 4.0 are specifically designed to prevent authors from having recourse, except if the license terms were violated.

Why would someone design a license that blocks authors from exercising control over how their work is used?

By disclaiming control over your work, licensees are protected from rogue licensors who later retract permission.  Similarly, licensees can spread the work without working with the licensee.  Licensors wishing to spread their work as widely as possible may wish to avoid placing any barriers on distribution of their work.


Online venues that promote networking among scholars -- alternatives to Academia.edu and ResearchGate

Have you tried linkedIn? They have tons of mathematics groups on there you just have to use the search bar. Or have you tried joining a meetup group? You can go to www.meetup.com and find groups of you interest that are near you area. It is not solely online but it is a great way to meet different people who have the same interests as you.


This entire answer is US-centric, since I have no clue how other countries work. This is not to say that I know the US system that well - but rather that it's the only system I know at all.

Public universities work differently from private universities. Public universities usually have pay scales and these are often public since professors are considered state employees (yes, my salary is public knowledge). So you can start digging around there. Usually there's a range within which you can hope to negotiate: moving out of that range is beyond even the power of the university to authorize.

Private universities usually have more flexibility and it might be harder to get the range of salaries. But if you get an offer you can ask around to get a sense of the ballpark.

As for what a reasonable range is, getting data is very discipline-specific. For CS, the CRA puts out stats fairly regularly and there's the Taulbee survey. For other disciplines, there might be something similar.

Salaries in academia at least at tenure-track level are less flexible in general. Probably the best way to get to the top of the permissible range is to have another offer. Other than that it's hard. Often, the things that are most easily negotiated are other parts of the startup package. Which is not to say that you shouldn't negotiate salary - but unlike in industry, it's less likely to be as beneficial.


Suffering boredom in proofreading own paper

Just a few conceptual points:

  For two years I've been working on drafts of a paper. I'm happy to
  keep incorporating new sources and improving the paper, because the
  topic is fascinating

This is a debatable action because it can delays your publication rhythm. For every paper, lay out the hypotheses, research questions, or objectives clearly and then work on the piece. Once the conclusion answers the questions, either seek feedback or submit it. New findings are going to emerge constantly and if one "keeps incorporating" new sources the paper will never leave.

In very rare occasions, one may want to add some new thing. For instance, by chance a very relevant paper was published during the composition of the final draft. To improve the relevance of the paper it'd be good to include that new work in the right section. Otherwise, there needs to be an end date in sight.

  However, when I print the current draft out to look over after making
  edits, I can barely read a paragraph before my eyes glaze over and I
  lose interest

This is not abnormal because you have read this multiple times and no new stimulation is coming out. Here are some ways to work through it:

Circulate it among peers for a round of proof reading. Pay them with something: pizza, chocolate, a favor, etc. Consider forming a writing club, in which everyone can circulate works in different stages of development.
Hire an editor, preferably knowledgeable in your area, to proof read it.
Put this project down and work on some others, return to it again when you're ready.
Read it out loud. It's actually very helpful because reading out loud lets you hear the rhythm of the words and this helps isolating clunky parts in the paper.
Read it from the back. Start from the paragraph, and can also consider start from the last sentence and working its way up. This technique breaks the contextual flow and allows you pay more attention to missing words or typos, etc.

  I wouldn't expect anyone else to read something that I can't, which
  makes me reluctant to seek feedback

Why not? This is one of the mind blocks that scares a lot of writers. You don't need to share only perfect works. When you circulate the piece, just be sure to:

State what this article is for and what stage it is in: is this a draft, a revised and resubmit version, a grant proposal, etc.
Be very specific on what kind of advice you seek: for more drafty work you can ask for comments on overall big picture and structure. For more developed work you can ask for comments on prose clarity and wording. For final draft you can ask for proof reading level comments.

Overall, as a comment has pointed out there are some conflicting thoughts within your question and I'd just humbly advise you to let the security issue go and be open to criticism and comments. Your writing is not the entire you; no need to shy away from people's criticism. After all, writing is about communicating ideas and it's better to get early and frank inputs from peers and friends now than from the reviewers with the rejection letter.


Getting a Postdoc, Dropping out of PhD for Greener Pastures (I hope), or else Staying Competitive in Current Position

How do I let go of the "once in a lifetime" PhD position I could have had?

This is far beyond the scope of mere academics. Life is full of choices, some of them will be bad. Some of it is in our control (in retrospect, hindsight is 20/20 always) and some if it is not.

I think that apart from going back in time - there is nothing that you can do. What you can do about your situation now though, is talk to someone.

You are not alone in this.

I had suffered (and perhaps still am suffering) from impostor syndrome at times, and I know that I could've done much better if I had made better choices.

It's good to have someone to talk to about these things. This could be a trusted friend, a loved one, or a trained professional. There is no shame in seeking help! Universities often have excellent mental health services, and graduate students are a vulnerable population in terms of mental health (not alone, remember?).

  What do I do to become a marketable mathematician? How do I get a postdoc?

The academic world has very clear rules on what could make you a marketable academic: publish good papers or preprints, impress some well-known people in your field, present your work at respectable venues, get amazing teaching evaluations that'll land you a lectureship, be an active member of your research community and so on.

If you feel like your current (unmarketable) field is not sufficiently exciting, and you aren't making progress, switch. I have done so twice in my career (and I would like to think that I'm not incredibly old!), and many others I know have as well. What were papers that you read that made you really curious and excited? What skills have you acquired that may help you along the way?

In the professional realm, again: seek advice and help. What does your advisor say? I'm assuming that your relationship with them is not at 100% (else you wouldn't be asking this question here), can you try to make it better? Are there mentors in your department that you look up to?

If you are dead set on staying in academia, the reality is that you'll have to extend your time to accumulate a better portfolio (especially if you want to switch fields). Either extend your PhD if possible, or get a temporary research position. I don't know the postdoc culture in mathematics, but perhaps a lower-tier research assistantship would be within reach?

Good luck!


tl;dr Agree with your advisors on how you communicate

You've certainly not made a "mistake". But what you're realizing is that your assumptions about:

Which language to use?
What information should be shared?
How verbose should you be?
Whose responsibility is it, and who has permission, to update the 3rd person of the triangle about communication between the other two?

and so on. In your place I would talk to both my advisors, separately or together if you ever meet, about your "email routine" - what they expect and what, and what you expect and want. Then none of you will surprise/annoy the others with undersirable email practices.

And this is basically true about most kinds of collaborations in groups of people which don't all communicate together in a common forum.


Why do some admissions processes request an exhaustive list of jobs held?

My suspicion would be that the school with such a requirement has a very narrow age window it desires in its graduate students, or at minimum desires that the ink still be wet on their baccalaureate diplomas -- the "train them up young" approach. Listing all post-high-school jobs is not usually terribly onerous for the typical 23-year-old.

I can't speak to how appropriate this is across disciplines. I can only say that where I am we only ask for a résumé and do not specify how far into the past it need go, because we value learners of all ages.


As it seems unlikely at this point that this question will receive an appropriate answer soon, I'll answer my own question and give the best answer I came across.

Someone who is in Education research has told me that he and his colleagues use Academia.edu and ResearchGate. So, while there are certainly repositories out there, it would appear that they are not widely used. In the end, I recommended to the author of the thesis that they use these two sites.


Is there any obligation for authors of a paper to provide the dataset used in their research, upon request?

Inherently? No. While it might be good for science generally, they're under no obligation to do so.

That being said, some funding agencies require data be made available as a condition of their support, and some journals require it as a condition of publication. Absent that though, there's no obligation to do so.


What is the maximum time-span of a referee?

Maybe there are cultural differences, but when I am writing a letter of reference for a student, it will hold lifelong. The rationale is simple:

It has a date on it, so the other side can see when it was issued and decide by themselfes how valid my interpretation of the student's performance is at the current date
I'm writing my true opinion on the student, there is no reason to change my mind.
If someone want's an updated version, they can call / contact me via e-mail.

I know of no official or inofficial rules (in Germany).

The situation might be different if you need a new reference letter. Then I would only write it if I can tell something new about you.

So if you need an updated letter of reference, the referee should recieve some content from your side to put into this letter, together with a brief explanation of your goals, how you improved, etc.


Is there a better measure of undergraduate academic performance than GPA?

I believe that there cannot be any single numerical statistic or small set of such statistics that summarizes the nature of a student well.

The first reason for my assessment is that there are too many different ways one may wish to use information about a student, and too many ways that a student can have an unusual background that will not fit into those boxes well.  The second reason is that any metric, once established, can (and will) be optimized against, thereby undermining its value.

Summarizing a student on one or a few metrics is no better than the much-bemoaned practices of judging faculty for tenure by a few metrics.


Is some foreign experience necessary to attain a professorship in India?

In general, the best way to answer the question "What qualifications do I need for job X?" is to look up people who currently have job X and see what their qualifications are. So I suggest you go to the websites of several professors in India (ideally junior professors who were hired recently) and see what they did beforehand.


No, Students don't need a book. They DO need good resources.

Maybe its an eBook or a PDF compiled from your teaching notes or outline/slides (Hopefully cited well) and things like short stories needed for a language class can often be found online in their entirity, for free legally, when copyright has expired.

For a language class, using a Sherlock Holmes story could prevent students from needing to buy a book as they're out of copyright. You can also look for material that is licensed as Creative Commons which allows for free use, such as material from MIT open courseware, Khan Academy, and P2P Univerity. You can learn more about Creative Commons for Education here.

Long story short, make good content, and use it legally, either by using stuff people have given to the public, or under doctrines such as Fair Use.


Is it appropriate to mention personal lessons learned in the defense presentation?

A bachelor's or master's degree is about the knowledge that you have gained. A Ph.D., on the other hand, is about the knowledge that you have contributed to humanity.  As such, the defense is not really about you: it's about your work, and you need to treat it as such.  Think about the other high-level scientific talks that you have seen (or given), and treat your defense in exactly the same way.

That's not to say that you can't weave in personal experiences or anecdotes if they make sense as part of the presentation of the technical content.  Some of the best talks that I have ever seen have a component of the personal in them.  The important distinction is that any use of the personal should serve to illuminate and illustrate the scientific point, rather than standing apart and distracting from it.


What should I do if I end up without an adviser?

I think that your best option is the first, but that is based on my personal preference and may not be yours. So let me explain.

Many students choose an advisor late and are then guided by ideas of the advisor. There is nothing wrong with that.

Finding an advisor at another school will cause lots of complications both in the short term and in getting everything finished up.

Moving to another school may not find you an advisor for "your topic" in any case. It will require a new advisor.

As a student, your short term goal is to get a degree and then move on. There is nothing to prevent you from then going back to your original ideas and developing them. There is nothing but time and hard work to keeping your hand in on those ideas so that you don't get too far out of the current loop if the topic is popular.

To expand on the first choice, I would choose a highly regarded advisor who has a lot of ideas. Work with him/her on something that is as close as you can get to what you really want to do, but, primarily, work to finish and move on. Your career will last beyond your student days, but you have to get there first.

I didn't have an advisor (in math) until about your stage.

I'll note that there is another option that may be open to you. I mention it for completeness, but it is a difficult path to follow. Some students work without much of any advice from an advisor, being very self directed. They need a formal signature and some letters at the end, but the behavior during the course of studies is more like that of a colleague, rather than as a student. You need to arrange this sort of relationship in advance, of course, but it works for some.


Anthropology vs. Religious Studies graduate programs

Think of anthropology as more scientific and religious studies as more historical. Or Hard science v humanities, if you find that distinction meaningful. The processes of each are a bit different.

I'll just guess that there are more opportunities in anthropology and if you are on the cusp of the two fields there are probably more things open to you with a credential in anthropology than if it were more religious studies based.

Being associated with a broader field is an advantage in that it gives you flexibility to choose, even if you choose a narrow part of it. Being associated with a narrow field is probably a disadvantage.

Graduating from a "top" institution is a benefit for your first job, most likely. Graduating with great recommendations from recognized experts in whatever field is a bigger initial advantage.

I suspect that you know that some "religious" studies folk are more interested in preconceived notions of how things work and more interested in proselytizing than in learning. Avoid those sorts of things and you should be fine.

Obviously this is not a real answer. That can only come from you. But discussions with people you know is a good way to explore it.


Should I cite Papers to acknowledge usage of tools?

I would be pragmatic here. Citations are a currency in science. If the authors of a tool help your research by providing the tool to the general public, it is only fair to reference their work in the way they requested it to happen - and, certainly, citing a given reference in a paper that uses their work is not an unreasonable request. I cannot image why it would be unethical to say something like

  We have used Theano [1] to evaluate XY (...)

in your paper, where

  [1] J. Bergstra, O. Breuleux, F. Bastien, P. Lamblin, R. Pascanu, G. Desjardins, J. Turian, D. Warde-Farley and Y. Bengio. “Theano: A CPU and GPU Math Expression Compiler”. Proceedings of the Python for Scientific Computing Conference (SciPy) 2010. June 30 - July 3, Austin, TX

As to whether this is common, I would say yes. Most authors of well-known tools in my area specify a preference for how their work should be acknowledged.

If you are bothered by not having read the paper you are citing, there is a simple fix for that - read the paper, and decide for yourself whether it is worth citing in that context (but, generally, the answer will be yes).


How to approach a professor giving a presentation to work with him?

I would send an email a week or so before the visit, saying about what you have said here and asking if the two of you could have a conversation during the visit. That would be better, I think, that surprising him at the talk. It will give him a chance to review any opportunities that there might be. He might also think of others who might be able to help you.

If you just surprise him with a request he won't have that opportunity to think about it, and the circumstances of the visit might make it impossible to make contact in an ad hoc manner.

But if there is nothing he can do for you directly, perhaps the contact can develop into something longer term.


Chicago manual of style block quote reference placement

According to the style manual itself, the preferred placement is generally after the quotation. However, it allows for placing it before the citation as well.
From CMOS 16th ed., section 15.25:

Text citations in relation to direct quotations. Although citation of a source normally follows a direct quotation, it may precede the quotation - especially if such a placement allows the date to appear with the author's name.
...
When the source of a block quotation is given in parentheses at the end of the quotation, the opening parenthesis appears after the final punctuation mark of the quoted material. No period either precedes or follows the closing parenthesis.

This doesn't directly address the case when the author's name is already present in the preceding sentence. However, if we instead look at Kate L. Turabian's Manual for Writers, 8th ed., we're given an example in line with your second example. A similar example is shown in these notes.
All in all, I think your second way is generally preferred. Nevertheless, there is some freedom you can use if it makes things clearer. For example, if the parenthetical citation does not include the year (which seems not be required for block citations) putting the citation (including year) before the quotation may be a good idea.


Advice for a PhD... who is aiming for industry

In general, the optimal thing for a PhD student aiming for the private sector is to quit the PhD as soon as he or she can get a relevant job.  There are exceptions if the private sector job involves actual research, and some private sector jobs require the specialized knowledge of an MS or MA degree.

Beyond the basics and the necessary theoretical knowledge, the soft skills and the relevant technical skills are much more easily picked up while working in industry, since you get daily practice in the specifically relevant skills.  In addition, one generally gets paid much better in the private sector than as a PhD student.


How does a 1 yr. Visiting Assistant Professor (in physics) position look to a small liberals arts college

I'm in applied mathematics, at a school that you would probably describe as "R2" (the old Carnegie classification system has been replaced by a newer system that no longer uses terms like "R1".)  In my department, that year of experience as a VAP would make you a more attractive candidate, since you don't currently have enough teaching experience to be a very strong candidate.

It would also be helpful just in terms of your having a broader range of experience in higher education- many candidates that we talk to simply have no idea what it would be like to be a faculty member at our institution and have unreasonable expectations.


How to politely ask for recommendation letters to professors

I don't think you're doing anything incorrectly.  Sometimes people get busy, sometimes people are thoughtless and inconsiderate.  I'm afraid you're going to have to use a combination of persistence and politeness.  The tricky thing with the politeness is that you don't want to lay it on too thick -- as that in itself can get annoying.

Please consider using a combination of email and phone.

If things are still going badly after about two weeks, then I think it's time to contact a department secretary, dean, assistant chair or assistant chair.

I can see that in some departments it might be easier to pester someone by knocking on their door, but that really shouldn't be necessary; and you can use the department administration to accomplish the same thing.

(As mentioned in a comment -- please, no gifts.  It's not the custom in the U.S. and therefore would be too weird.)


When did it become inappropriate for a professor to smoke during lectures?

Some older universities have lecture theatres of mainly timber construction.  At those places, I'd suggest it was always inappropriate.  Otherwise, I'd say it became inappropriate as soon as there was clear evidence in the peer-reviewed literature that passive smoking has serious deleterious health effects on otherwise healthy adults.  A quick Google Scholar date-range search suggests that this happened between about 1979 and 1981.
The "universally accepted" half of the question, of course, may be a very different matter.


Will a journal reject a paper for citing an Encyclopedia?

No
If other secondary sources like review articles are acceptable, then an encyclopedia is acceptable.
If the information is a well-documented, undisputed territorial boundary, then secondary sources should be adequate.
Personally, I have never heard of a paper being rejected for citing the wrong type of source in my field of research.  If the source is wrong or irrelevant, that could be a problem, but type of source does not matter.  In physics, non-peer reviewed sources like ArXiv can be cited, and these are less reliable than encyclopedias.


What would my Higher National Diploma be considered in the United States?

From the website:

  BTEC Higher Nationals are internationally-recognised Higher Education qualifications at level 4 and 5 that are equivalent to the first and second years of a university degree, providing progression to both university and employment.

This means it will probably be considered as something like an associates degree. Some 4-year US universities might give you credit towards undergraduate classes. I doubt any well-respected university would give you credits towards a graduate degree. It is probably insufficient to get admitted directly to a graduate program.


Discussing an unpublished approach of a former team member

I need to justify...why I decided to use MY approach and NOT X's approach.

I don't think you need any such justification: "[X's approach] does not work....nothing has been published by him." Thus, the literature contains nothing about X's work and you need not compare your results to his unpublished work. Nonetheless, if you feel that some reference to his work is necessary, then you could mention that X is working on the topic or that some of your ideas followed from discussions with X or ...

  It's...interesting...to know...why X's approach...does not work.

Many approaches don't work. You cannot possibly mention them all. It is perfectly reasonable to omit discussion of X's approach. That said, in some cases -- e.g., when the obvious solution seems feasible -- you might like to very briefly mention why the obvious solution doesn't work. For instance, you could mention: This problem can be intuitively solved by ABC, however, ... (You could also mention that X pursued some of these ideas, or that you pursued some of these ideas with X.)


Comp Sci PhD Admissions: How often are Skype interviews requested?

Time is one of the most valuable resources for professors – I know no one who just offers interviews for fun.


Easy going advisor versus expert advisor and research experience

How you approach the professor for acceptance would be very similar to how you speak to your current advisor (should you choose to*) about your decision:

Be objective, there is no need to mention anything about either academic in a personal way, this decision is purely one for an academic reason - you want to be 'closer' to where current active research is happening and amongst those actively involved in research in your field.
Related, be polite and direct to the point.

The fact that the professor has expressed interest in writing a paper with you is a strong indication - perhaps accept this offer and at that stage mention that you wish to pursue your research under his guidance and to work within his labs.

Once it is definite that you'd get in and although you are not obligated to explain to your current advisor, it is advisable to explain clearly and positively about the opportunity to work directly with one of the top researchers in the field - I am sure your advisor would understand.


How long does it take to get a reply to your PhD application email in Germany?

Usually, in Germany you get an answer even if it says that you don't get the position. I wouldn't worry if it takes a few weeks which (depending on the institute) can be absolutely normal. You also have to consider that there maybe is a deadline (in German often: Bewerbungsschluss). Normally you get notice a few weeks after that.

It is also absolutely acceptable to write a mail asking for the status of the application (after a few weeks). You also have to consider that currently there are semester breaks in Germany so the professor can be on vacation not reading any mails.


Are Scantron Sheets under Copyright? Or are there non-proprietary alternatives?

The scantron forms and similar forms are not subect to copyright. US Copyright Office Title 37: Patents, Trademarks, and Copyrights §202.1 Material not subject to copyright. (c) Blank forms, such as time cards, graph paper, account books, diaries, bank checks, scorecards, address books, report forms, order forms and the like, which are designed for recording information and do not in themselves convey information.

So to answer your question, no. As long as the school or university doesn't photocopy the actual scantron sheets from Scantron. inc. But it's not illegal for them to create their own version of the scantron sheets that can be readable by the official Scantron machine itself.

Plus, there are numerous companies, not even associated with Scantron. inc. in any sort, That sell scantron compatible sheets for cheaper prices than the 'official' scantron sheet. Amazon and eBay are full of them. So, yeah...


Are there ethics concerns when students conduct human subjects research?

You can find a list of IRB Exemptions online. If the research falls under one of the exceptions then IRB consent won't be needed.

But otherwise, who does the research would be immaterial.

However, I think that special care should be taken here since undergraduate students might not be deeply aware of the ethical principles behind assuring the safety and privacy of human subjects. A naive approach could result in great harm.

So, at a minimum, even if the research falls into one of the exceptions, I would advice that a knowledgeable faculty member oversee any such research, both to educate the student researcher and to assure safety and privacy of subjects.

The other concerns you express are also valid, of course.

But, for the topline question, yes, there are always ethical concerns when humans are the subject of research. The concerns always need to be addressed, even in simple cases where it is clear no harm will result. How formally they need to be addressed is a function of the potential for harm as long as the formal rules are followed.


Would it be better to drop a class or receive a D?

Take the D and move on.  It is just one course.


What can be listed as "invited talks" on your CV?

Your first question is addressed in the answers to this question mentioned in the comments: Difference between contributed and invited talk

Namely, it is standard to list seminar talks under the heading of "Invited talks", so you should do this.  Some people separate conference talks vs colloquium talks vs seminar talks under appropriate subheadings.  I don't know whether it's standard in your field for junior people to do this, but you could try asking colleagues.  I am in pure math, and I don't, though at some point I started margin symbols to highlight conference talks.

For your second question, it depends upon the reviewer, but in my mind there is some value in seeing a bunch of seminar talks.  It means if we fund you, you'll be active in telling people about the research we've funded, so that's a positive.  It's of course not a primary deciding factor, but grants are competitive so even small positives can make a difference, so it is certainly worth listing your seminar talks on your CV  (assuming you're talking about applications where you send a standard CV, rather than a mini-CV with page/content limits).


Should I Quote Scholars (Dead or Alive) in Past or Present Tense?

There is no universal answer to this question.  Different writers take different approaches, and either one may be acceptable under the circumstances.

What you should try for is consistency, both internally in your own work, and within your field of study.  The first one is easy; whether you are going to refer to what another scholar said using the past tense or the "historic" present, you need to be consistent throughout.  All references should be handled the same way.

The second point, external consistency, is a little trickier.  You should look at how other people in your area of research deal with the question.  If there is a consistently preferred usage (whether it's past or present), you should probably adopt it yourself.  On the other hand, if different writers use different tenses, then you should feel free to choose whichever one you feel sounds better in your work.


Average time alloted for manuscript review across disciplines

For mathematics, here's the latest survey done by American Mathematical Society:

http://www.ams.org/notices/201410/rnoti-p1268.pdf

You can find median times from submission/acceptance to acceptance/print/electronic print for various math journals as well as other statistics like the current estimate of waiting time for each journal. Not surprisingly, the median time from submission to acceptance in 2013 varies greatly; some take only a few months and others nearly a year and a half.

They do this survey every year. For instance, here's the one published 2 years ago:

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

The worst offender that took the longest between submission and acceptance that year was Annals of Mathematics (which happens to be among the most prestigious math journals), and the median was 24 months.

I don't know if there is data for other fields. But American Physical Society occasionally makes statistics for their journals available, e.g., pages 14-17 of this PDF slides:

http://www.phys.nthu.edu.tw/~colloquium/2009F/T2.pdf

From my own experience as an author and reviewer as well as from what I hear, it appears that math journals typically take longer than physics journals. But probably things are drastically different across subfields even within one discipline (e.g., theoretical vs. experimental).

In any case, as the fact that they publish statistics indicates, both disciplines seem to take turnaround time very seriously. But for some reason, it appears that review tends to take more time if a journal publishes more mathematical papers. This seems to hold true for electrical engineering, too; the journal I have published in most frequently belongs to electrical engineering but is known for being heavily mathematical, and, lo and be hold, it's notorious for its slow, slow, slooow review...


Trouble with getting PhD recommendations - almost 60% turnover in faculty

The most common and most valuable letters come from the professor(s) that were your academic advisor(s), or that otherwise directed or participated in your thesis work.

Not to be acerbic, but you made the mistake of treating your master's program as a place where you went to sit and look at powerpoint slides, and made use of your professors as if they were just there to read from powerpoint slides.  A typical response to a recommendation query from such a professor is likely to be "I don't think I'm a good person to write you a recommendation, because I will not be able to speak to your strengths and abilities."

They say this to you because there is a well-established unwritten and unspoken protocol in PhD admissions, that of the "damning with faint praise" letter.  The committee reads that letter as "this professor either had nothing to say about the candidate, or chose not to say bad things about the candidate.  In either case, the professor had nothing GOOD to say about the candidate."

Beyond that...It is quite acceptable to ask an inactive professor (retired, on leave, etc.) to pen a recommendation.  It's entirely their prerogative whether to accommodate you though. Only your direct thesis advisor feels a burden of responsibility to write anything at all.


How do citations get counted for a book and for an electronic book?

The answer varies with the service you use. I only know something about two services:

Google scholar: It crawls the web to get a database of publications and citations (and it often counts something as publication which is not one, e.g. slides, lists of presentations…). I guess (but I am not sure) it also gets formatted data from publishers. It tries to identify similar publications (I have no idea how this is done precisely) and it also relies on user input (you can identify two things as the same by yourself if you have a verfied account and Google thinks that you are an author). In my experience, the database Google scholar is quite messy. Wrongly identified authors, lots of non-publications, double or missing citations.
MathSciNet is a service for publications in mathematics run by the American Mathematical Society. It gets data from the publishers and imports it automatically into their database. It has people to check the database, to identify duplicates (very rare, basically only reprints), to keep different authors with same names different and to identify authors who appear under different names or spellings. This is done by hand and also uses user input. As GEdgar points out: MathSciNet is very accurate and pretty fast to fix things.


How do I appropriately decline an invitation to an appointment lecture ("Probevorlesung") without burning bridges?

You should communicate clearly (and swiftly) that you are declining the invitation because you are accepting the offer of a professorship at another university. In fact you should not just 'decline the invitation', but completely withdraw your application to your hometown university.
I would not be worrying too much about burning bridges, most likely the view of the hiring committee at your hometown university will be more like 'Shoot! We have lost an excellent candidate to university X. We have to be more attractive/move more quickly/offer better working conditions next time'.
Finally, let me say that this seems like a true luxury problem! Being offered a professorship 'a little further from where you live' and being invited for a Probevorlesung at your hometown university is something that most aspiring researchers would only dream of.


How to approach professors for funding after acceptance into PhD program?

First note that what has happened to you is a failure on the part of the academic community to ensure appropriate employment conditions for junior researchers. A PhD candidate is a junior researcher - someone who will do research work, albeit of a limited scope, and with initial meandering, and with some supervision - who should be paid.

This perception will also guide you regarding what to do about funding. If you ask Professors for a handout - because you're a nice guy with high grades - you'll probably not get it. You will essentially be asking to be "posted" in their group as an employee, in which case they will (hopefully) be inclined to pay you a salary already.

For every lab you're considering:

Check, if you can do so easily and outright, whether the lab has paid/funded open positions. If you know that it doesn't - it's not relevant. (That is, since you didn't say you know what you want to do research-wise; otherwise most of my advice is irrelevant.)
Make sure the research work there actually interests you. Otherwise you'll sort of be scamming them for your salary - which is quite legitimate considering the situation the university has put you in, but is psychologically difficult for all concerned. This means, in particular,
Go visit the lab, physically. Try to arrange meetings with grad students and/or postdocs in the lab, to hear about what they're working on. This is common practice for new grad students and usually encouraged. During that visit (and not just then),
Try to figure out how your experience can be relevant to what they're doing - or to something they're not doing, but would contribute to their research objectives. It can be either in advancing their research proper, or in building things, or using some software you're proficient in, or writing code, or using materials or processes you've had experience in etc.
Now write your email, asking to meet with the PI to apply for the open position. Or, if you can schedule such a meeting directly when visiting the lab, based on some 'hook' of a suggestion from somebody there - that's even better. Base your pitch on your experience and conclusions from the previous phases.

Note these phases may not happen in this order, or in any order (i.e. these may overlap). Also, you probably want to parallelize this for different labs rather than go one-by-one.


How to translate French "colleur"/"khôlleur" position into english?

I would suggest using the official title and then adding a brief sentence describing the job duties. This way you provide ask the information in an accurate and accessible way. Having to look up a job title is not a big deal when evaluating foreigners.


My own work is on the STEM / hard science side of Academia, so I don't have first-hand knowledge about this qualification, but I would read it as a Licenciate degree in Management.

A cursory search turns up a few institutions that offer such a degree:

University of
Tampere
Lund University
Universidad de Navarra
Pontifical University of Comillas
Universidade Lusófona


Should I include 'future work' in a paper, when I don't intend to do that future work?

It depends how you phrase it.  Do not write This will be shown in a subsequent paper.  Do write This and this still needs to be done.

I think it is very informative to inform the audience of the next steps that need to be taken in this research.  For example, shows you are aware of shortcomings of work done so far, and it can be useful to refer to in funding applications.  However, there can be many reasons why next steps are not actually carried out.  It might be your personal interest, but more often than not, project-specific funding runs out, PhD students or postdocs finish and move to new institutes, etcetera.

This is particularly true for PhD theses.  The final chapter may be full of future work, which, in many cases, is never carried out.


How can a researcher from a third-world country publish or otherwise disseminate an interesting result?

I guess that no one is going to invite you from overseas for a seminar unless they know you already. One of the best ways to disseminate your research is conference participation, but coming from a third-world country puts you at a disadvantage in terms of funding and travel possibilities. Sometimes conferences have travel grants for students and early career researchers (I don't know if you fit inside this category), which you can apply for. This can offset some of the costs (but not all, unfortunately). Watch out for this kind of opportunities.

Another thing that you should do is writing down your results in a preprint and trying to get it published. Once you have a preprint, you can send it to a (small) number of researchers working on the same area to try and get them interested. This could be a subset of the people you cite, for instance. Watch out for signs of feedback (positive and negative) from their part and don't overdo it -- you don't want to be considered a spammer.


Working with a supervisor who is not expert in my research field

Can I still be a successful PhD student if I pursue deep natural language processing on my own without getting much help from my supervisor?
The core task of a PhD supervisor is not necessarily to be an expert on the content of your research. Sure, it will help if there is some overlap, but even if you pursue a research direction that is well aligned with your PhD supervisor, it is very likely that you will surpass their knowledge within the first year of your PhD. Key is, that your supervisor can provide you with a tremendous amount of help on how to do research productively. If you get stuck, which strategies are available for overcoming the obstacle? How does one balance reading, programming, writing (everyone prefers some of these tasks over others, but you'll need to overcome your instincts to spend the bulk of your time on your preferred tasks because the other tasks also require time investment) such that publications result? Once the experimental results are in, how does one convert the programming and experimental results into a publishable manuscript? How many citations are enough?
Your questions is best answered when taking two distinct approaches to two halves of the question. "Can I still be a successful PhD student if I pursue deep natural language processing on my own?" Yes. "[...] without getting much help from my supervisor?" It is probably most productive to reframe your thinking about this: you will get much help from your supervisor, just not in the way you imagined.

Should I try finding external collaborator?
This depends a bit on your personal style, and the preferred working style of your supervisor. I am always more than happy to have my PhD students interact with more experts in the field; it's good for the network. In fact, your supervisor may have people in their own professional network that may be helpful in this matter. Consider discussing this with your supervisor: the first paper that the two of you have worked on has been rejected, and you think that the work might benefit from bringing in outside experience. Would your supervisor be open to opening up the collaboration to more NLP researchers?

What should I do?
This is impossible to answer, since it involves you caring for your personal wellbeing in the specific circumstances in which you find yourself. You write that you feel doomed and depressed; you should definitely talk to people, whether those people are mental health professionals, or 'just' friends and family. Asking the question here is a healthy thing to do, but you may also consider finding out whether your university has support groups for PhD students; social events, mailinglists, other ways to interact informally with your peers. Sharing experiences can be very illuminating.


How frequently do pre-tenured assistant professors switch institutions?

It does happen. But it's not that common. I've been on faculty search committees for a number of years now, and out of the hundreds of applications I've seen, it's very rare to see pre-tenure faculty from other institutions apply. If and when they do, it's because

they're worried about their tenure case
there's a two-body problem (this is in fact the most "reasonable" reason to move)
they have other reasons for wanting to move (location, opportunity)

But it's not a frequent thing. Because it's hard to do: clocks have to be negotiated, research programs have to be uprooted, students have to be moved (and let me not even start on the logistics of moving a family that might just be getting settled in the first place)


How should PhD Students/Researchers take notes?

In this article, "The Pen is Mightier than the Keyboard," the researchers tested this very issue.  They found that taking notes with pen and paper is more effective... but, that was because students who typed their notes were copying lectures verbatim whereas students who took notes by hand were taking in the information and then writing it in their own words (thus processing the info at a deeper level).

So, the key is the way you process the information, not necessarily the method you use to take notes. But, at the same time, it is noteworthy (no pun intended) that longhand notes tends to lead to that deeper level of processing more so than does taking notes digitally.

Personally, I'm all about taking notes longhand, and I print out articles that are important to me/my work.