Why don't grants from publicly-funded organizations systematically demand code and data to be released?

Because there has not been a strong enough push to require it and some researchers prefer to keep code/data confidential. This is currently a topic of discussion at the national level led by organizations such as EFF. This is hopefully a situation that will soon change for the better.


Is it ok to share/show(for review) the proof that you made for your research paper on stackexchange

You've done some original research, you get very exited, and you want someone to share it with. Often MSE is the easiest place to find an audience. I am often tempted to post parts of my research there, but try not to.  For one thing my discoveries always seem obvious after I've made them, and I worry about being scooped.  That's my biggest fear.  And your posts on this site stay up FOREVER. Most journals will probably not care because most accept papers after they have been posted on Arxiv.  But, if you end up using part of someone's answer in your paper, ethically you should cite them. I would rather torture myself for a few more days and come up with a perfectly clear and logical proof on my own than cite some guy on SE.

That being said, if you really want to use MSE for proof checking here's what I suggest.  Try to find the specific part of your proof you are unsure about, and then craft a question that is as general as possible but such that an answer will let you know if you were correct.


Why data falsification / fabrication is found after degree is awarded?

There are two things to consider, in my mind, when thinking about your question.

The first is the possibility for sampling bias. If someone is caught falsifying data prior to their degree being awarded, they are likely expelled - and it's unlikely for the work to ever see the light of day. These detections are largely "silent", while the flashier ones that involve clawing back degrees, retracting papers, etc. are likely over-represented.

The other issue is to consider how data fabrication is detected. On a crude level, it's a function of both time and the number of people looking at the work. Inherently there's more time post-graduation than pre-graduation. There's also a larger number of people looking at it, especially if the work is being published. So if the detection of any given fraudulent work has a fairly low probability per person interacting with the work, it's entirely reasonable that the majority of these cases would arise after a degree is awarded.


What field? What's typical in your area? Ask your advisor.
When I was a student, in my area, computational fluid dynamics using the finite element method, things tended to go:

talk or poster (with no paper/abstract only minisymposium)
journal paper or invited paper to conference proceedings

unless it had been a while since we'd been to a relevant conference, and then we'd take a recent paper and make a talk or poster out of it to give at an upcoming conference with some added results if we had them or could make them in time. But, that may have just been my advisor's preferred manor of working. Doing that, we wrote a few papers and did a lots of talks and posters in the time I was in my PhD program. Sometimes we'd do a paper for a conference that required a full paper (e.g., the AIAA annual meeting) and have to wait much longer on acceptance than something that was reviewed only on abstracts or extended abstracts.


Releasing one version of a Scientific Paper under an Open License

A Creative Commons License is a good way to achieve this.  It doesn't really matter how you convey this information, as long as it's clear.  (A footnote on the first page is fine, for example.  Whatever you prefer.)  The attribution license (CC BY) sounds like a good choice for what you're looking for.

However, this definitely conflicts with the copyright form.  You can try asking the IEEE for permission, and there's some chance they will agree, but they tend to be picky about copyright.  If you can't come to an agreement with them, then you will have to decide whether publishing in this conference is worth giving up copyright, and they will have to decide whether it is worth losing your paper over this issue.  (If you have already signed the form, then there's nothing you can do except ask them.)


First, deal with your collaborator, then notify the conference asap. If they figure it out and you then are like "oh, yes, sorry, I know, I will change it." you are in a bad place. Not only did you waste the reviewers time with a version you knew was wrong/has to be corrected, your late excuse might also not seem honest.

If, however, you inform them yourself, apologize for the inconvenience and the mistake and give the corrected version, they might well forgive you.


How can I minimize the damage of my PhD advisor's bad recommendation when applying for industry jobs?

You are worried to much.

My PhD advisor also has several connections in HR. This can also be
damaging if a company background-checks through the university HR
department.

First, HR is not allowed to say anything bad about you with no clear evidence (for fear of being sued). They will just give minimal information, and that's it.
Second, background check is often done by a third-party, who is only interested in ticking all the boxes that you declared. They are not interested in hearing some random stories.

I do not know how references work in industry, but I can certainly
exclude my advisor in any list throughout a recruitment process.

For non-research positions, nobody care about references.


Should I leave out research in my NSF fellowship application if I'm not getting an LOR from the professor I worked with?

As someone who has reviewed applications for the NSF Graduate Research Fellowship program, it would definitely be weird to see someone talk extensively about a research project and then not have the advisor write a supporting letter. It would certainly raise questions among the panelists assigned to review the application, especially if no other explanation were provided.

Normally I would not make such a suggestion, but this might be an instance where you should list the experience (if you can), but not talk about it so effusively or in great depth.


Talks and Workshops at professional conferences like PyCon and various un-conferences

List them the same way as you would any other talks.  They may not have the same standing in terms of content, but they show that you have practice grasping new material and presenting it, which is important for Ph.D students and graduates to be able to do.


What is a learning agreement used for and when it is necessary

As the comments have mentioned, this is not a standard thing. It's possible the university doesn't even have a standard learning agreement, although it might.

  It seems that this "learning agreement" is for those people who are going to take courses in a university other than their home university. Am I right?

It's not strictly for exchange students. A local student doing something similar would probably have to do one too. Basically, for "independent study" courses where you aren't taking a class, and are working one-on-one with a professor, it outlines the expectations and grading criteria for you, in lieu of a syllabus.

Especially because you are coming from a different county, they don't want you to a) show up and not have a productive experience because your goals aren't well defined; and b) they don't want any fraud occurring, after all, they are sponsoring you for a visa (presumably).

Unfortunately, I find it unlikely you and your sponsor can prepare this in a day or two.


Is reapplying to the same PhD program looked down upon by admissions?

There are generally three types of candidates for admissions:

Clear-cut admits
Clear-cut rejects
Borderline cases

If you're in the first group, you'll get in and don't need to worry about reapplying. If you're in the second group, not much time will be spent on your application, which means that you're not likely to be "remembered" in future cycles, and your application will be re-evaluated the following year.

The main issue is if you're a borderline case—that's generally where much of the discussion time by an admissions committee is spent. If you're going to reapply, it's likely that someone will remember that you've applied before, and they will want to see what's changed. So it may help you in getting in the following year if they thought you were close but came up "just short."


Can one or two emoticons be used in a PhD Thesis?

I highly value humor and love to entertain whenever I can. In formal writing, I would encourage you to go ahead and write something that you think would be funny. Then reread it. Then reread it again. Read it aloud. Read it silently. Read it again tomorrow while you edit it. And read it again. And again. And again. Imagine reading it out loud to the people with the least sense of humor you know. Imagine reading it to a person with a furrowed brow, in a bad mood, who is trying to find anything they can to rip apart what you have laid down, to find a reason to cast it aside as useless junk.

Then read it 10 more times, as any good writer must inevitably do. Now imagine reading it again in 10 years (if you are lucky and what you've done turns out to be of use).

Personally, I have found that after the 20+ time I've read something, it isn't even funny to me anymore - and I think I'm hilarious! But even the best jokes I've ever told never landed 100% of time, or to 100% of the audience - and in formal writing I don't even know who the audience is - they might speak my language as a 2nd (or 3rd or 4th) language.

Being stubborn, I like to write humor into anything I make. But after the 20th read through I realize it just isn't funny any more, even to me - and if that's how a reader would feel who doesn't get or appreciate the joke, it just isn't worth it any more to me to include it. I'm basically writing a technical instruction manual, and there's a reason those things aren't really funny - you are supposed to read them and refer back to them repeatedly, and jokes get old fast.

If I really like a joke, I'll save it for when I can make it in person, in a talk or in a presentation, when I can personally hear the laughs (or gauge the room and know to skip it entirely). Or I'll be funny on a website like this so I can wallow in a mass of glorious unicorn points.

But in formal writing like a thesis or important research paper? Well, you decide after you've read it for the 30th time if it is still worth inclusion, or if that emoticon makes you smile - or if you want to poke it in its tiny little semi-colon eye.


Undergraduate not doing homework (case method)

I have some experience with lab practice in physics and chemistry, where we routinely ask students to read up on the work planned and do some preliminary calculations before they can come to the lab, in order to maximize their use of actual lab equipment. It's sometimes hard to motivate students for things that should be done in advance, but there are ways you can improve their involvement:

Make sure that the amount of material is compatible with the time they have to study it, and the demands on their time by other courses. If you're going to require something of them, it should be within reasonable limits. Also, make sure you convey that point to them: I have, on a few occasions, had to reschedule things to give them more time, because the material was very heavy and taking more of their time than I had assumed, or because they just had many other things to do (e.g., a full week of exams).
Be crystal clear that reading the material before classroom is actually one of the requirements of the class, and that it is entirely necessary to actually pass the class.
If you want further motivation, introduce some sort of evaluation of their reading at the beginning of the lecture: get two or three students to come up, and argue the case (or whatever it is you do in those lectures) before the others. Then, give them a frank assessment of how they fared, including “you failed miserably because you didn't do your homework”. Even if that evaluation doesn't count for the final passing/failing grade, it will motivate them and might introduce some friendly competition.
If some of them still don't do a thing, fail them. After all, you had told them (and more than once) that reading the material is a requirement for passing.


Is it a lack of passion or competency if I don't want to leave my current position for 6 months?

It would depend, perhaps, on how you characterize your "gap" to a future potential employer. If you treat it as a negative that might be easily picked up. But needing to unwind after an intense five years  is pretty normal. Wanting time to publish is a positive thing. Wanting to continue current productive relationships is also a good thing.

So, characterize it positively and it shouldn't be an issue. The competency is judged by other things (publications, dissertation...) and the passion is something that will be seen if it is there.

But don't apologize. There ins't any need for that.


Mentioning a personal tragedy in an academic style paper. Is it allowed?

Since you are the editor of the volume, it is you who decides whether it is allowed. There isn’t any codified set of rules specifying whether any given content is allowed or not. That’s exactly one of the things editors are supposed to do - to edit.
Consider whether it makes sense to have such a paragraph in the volume given its topic and purpose. If you think it is appropriate, allow it. If not, don’t. If it is a borderline case, you can raise your concerns with the author and suggest that they change or remove the problematic paragraph, without requiring it outright.


Is auditing graduate physics courses (officially or unoffically) a viable way to eventually get into a PhD program?

I cannot speak for Physics, but I can speak generally. Generally, auditing courses is unlikely to get you noticed in any way and is unlikely to generate the sort of information that the admissions committee will value. I cannot assume that you will be able to develop the connections that you desire because I doubt such opportunities will be available via auditing classes.

In my field (though perhaps not Physics I warn) a way forward with a poor undergraduate result but a desire to do a US-based PhD is to do a one-year master's in the UK or Europe, and to do extremely well in that programme. Via this route you show that you are able to complete very high level coursework and, further, are able to produce actual research (in the form of a master's dissertation). These are much better indicators of PhD success than audited classes or GRE scores. Also, if you have, say, a UK distinction in your master's, in your PhD statement of purpose you can address your poor undergraduate performance head on: say you were dealing with personal circumstances but your demonstrable success in the higher degree programme evidences your abilities to succeed at real research.

In other words, you are giving them real evidence of your commitment and abilities, while auditing doesn't do that.


Why some university asks for recomendation letter directly to be sent from the recommender?

By forcing the letter to be sent directly from the institutional email of the Professor, the university makes sure it is a truthful recommendation and not a modified or faked one. Such practice of faking documents in unfortunately happening in any recruitment environment, not only academia.
Even worse and common practice in academia, my own phd adviser asked me to write my own recommendation letters because he lacked time, and he just signed them.
Such practice as described in your message partially prevent this.


Whether to publish one big paper or many smaller papers for a given research project?

The way I see it, there are a number of factors at play:

Your goals: Do you want your paper to be published in a high-impact journal? If so they will most likely be interested in the whole story rather than a small piece of it.
Readability/General appeal: Can you make a coherent story with individual components? Will they all be interesting for wider audience on their own? In other words, if you opt for multiple papers out of one project; can you make sure these will be able to stand on their own? I personally think going for multiple papers is only valid when combining them into a single big paper would push aside some of your interesting results (or methods) to a metaphorical corner
Limitations imposed by the target journal: Can you actually put together all that in a single manuscript? In biomedical research you always get a limit on the number of words in the manuscript, and there is only so much you can put in supplementary.

With regards to quality-vs-quantity, I heard that early on in your career quantity is more important while as you become more and more senior, quality becomes the main concern. I am often told that as a PhD student I can, and should try to get involved in as many papers as I can. Around the time I do post-doc, however, it's time I pay a lot of attention to where I put my name and try to work on a good paper, preferably in a high-impact journal.


Can a university suspend a student even when he has left university?

Yes. The university can revoke the degree. Example, which was about a PhD degree being revoked because the student later went on to commit academic fraud.

If the student hasn't graduated then the university can also withhold graduation, which as far as I know is quite common. For example if the student has outstanding library loans, the university can withhold graduation until the loans are settled.


Should I tell a colleague that he's serving as an editor for a predatory journal?

First, you need to have very solid reasons for considering the journal to be "predatory". I bring this up because the only concrete reason you gave in your question is a rather poor one: rapid peer review cycle is not necessarily evidence of being a predatory journal, even if it might be unusual in your field (as it is in mine). My point is not to dispute your assessment (I have no idea of what journal you are even talking about); my point is that if you would consider discussing it with your colleague, then you should certainly focus on explicitly disreputable behaviour. In particular, the publisher's journals should clearly be listed on at least one website that tracks disreputable journals. That way, it is not just your assessment; you would have others who would support your concerns.
That said, a publisher with some disreputable journals might have some very genuine journals in its portfolio. This is a very important point: you cannot automatically denigrate one journal just because of other journals from the same publisher. And I repeat, a rapid review cycle is rather weak evidence. Stronger evidence would be actual access to review reports that you can examine and judge to be of unusually poor quality.
So, this brings me to your direct question of whether you should share your concern with your colleague. If you are afraid that she might get offended, then it seems that your relationship with her is not sufficiently close that she would trust that your concerns are personal concern for her. In that case, it would be especially important that you have strong evidence of disreputable behaviour before accusing the journal she is involved with of being predatory. If you do not have such strong evidence, then it is best not to mention anything but to politely decline the invitation with a truthful but evasive answer (e.g. "I am unable to commit the time to such a submission"--this would be truthful since you are unable to waste your effort and time on predatory journals). But then, even if you do have sufficiently strong evidence to accuse the journal of being predatory, you would need to determine how comfortable you are with this colleague. Only you know that, so ultimately it would be up to you to decide whether she might be offended by your presentation of evidence.


For PhD, prestigious fellowship at university with poor infrastructure, or prestigious university?

As astronat says, the prestige of the university matters very little when you do a PhD. However, the prestige of the fellowship that funds you matters even less. Divorce yourself from the notion that these are the important metrics to evaluate, and instead look at:

Which advisor will you work with, and what are their students doing now?
If you have a chance to talk to PhD students at both institutions, do so.
Which university/grant will offer you better conditions, such as salary (of course after taxes and costs of living) or teaching load?
Which city would you rather live in for the next 5-ish years?
And, last but not least, which of the options makes you more excited, personally?


Possible to put online a PhD dissertation under a Creative Commons license, as some text is (c) by publishers?

If the copyright in the material is held by someone else, you cannot license the entire work CC-BY. The Springer (etc) permission for a doctoral thesis is a specific exception and does not extend to allowing you to relicense the underlying work.


Research fellowship after undergrad helps with PhD admissions?

I don't see how it could hurt. The degree of added value most likely depends on what your background is prior to the year as a researcher. If you already have a very strong research background as an undergraduate, an extra year of experience will not help as much as if you have very limited research experience.

I suppose it also depends what you get done during that year. It certainly helped a former student of mine, who didn't get into his desired programs straight out of undergraduate. He took a year to work as an RA in my lab, wrote a first-author PNAS paper, and then was admitted into the top program in his field.


Would it be appropriate to send your CV to a researcher who gave you their business card a few years ago?

Why not just a simple email asking if she has any opportunities and reminding her that you met at that conference.

Include the cv as an attachment and she can open it, or not, as she wishes.


Are masters programs generally easier to get into than PhD?

Not every STEM Master's program is going to be easier to get into than every PhD program, but on the whole they are easier. Universities are much more likely to take you if you're paying your own way (aka. a Masters) than if they have to fund you. In the US it's  common for students who didn't do so well in undergrad or are from a lesser known international school to pay their way through a Masters first and then go on to a PhD after proving their worth.

That being said, do not discount how helpful research can be. A published paper or a good letter of recommendation from a known professor can go a long way to erasing some bad grades. What counts in a PhD program is your ability to do research.


Is it acceptable to only use refererences from other universities?

It is certainly acceptable to not have references from your current institution, but it could raise questions, implying that something went wrong in the current position. Having trustworthy, high-quality researchers, as you've indicated, can overcome this problem, though the question still will remain.

Your references do not necessarily need to be familiar with all of your work, just enough of it, and more importantly, how you are as a researcher and person. Having a more recent reference letter would give a better description of how you are performing now, in particular, after you left the safety of a PhD position. That is, how you are performing now that you've gone out into the world on your own.

My inclination would be to include a local reference for these reasons.


Efficient process for writing a STEM journal article

I think the process of writing papers is pretty individual to each researcher. What works for me may not work for you. That being said, the following are a few rules that I usually give me mentees and students when we start writing a paper together:

As "Not Quite An Outsider" states, do start with an outline. Look through related work for papers with a similar scope / methodology / idea and start by imitating their outline. However, do not do so blindly. Instead, focus on understanding why the authors of your related work chose to structure their paper the way they did, and check whether their (assumed) reasoning is also useful for your paper.
Keep in mind that your paper needs a "story" - you know your material and reasoning, your readers do not. Start at the beginning, and end with the conclusions. Avoid statements that are not understandable at the point in the paper where they appear (rule of thumb: when you feel writing something along the lines of "as will be explained later on", you likely have a bug in your structure).
Plan the length of your paper. Fill each section with some Lorem Ipsum filler text of roughly the same length as you plan for this section. This allows you to see how much space you actually have for each part of your paper. During writing, when I start a new section I remove the filler text and replace it with what I actually plan to say at this point. I sometimes even go as far as drafting where in the paper I will have which figures, and put placeholder figures there instead when doing the outline.
Write the paper in order (i.e., in the same order as it will appear in the final paper). This is a bit controversial - I have seen many experienced paper writers suggest various other orders ("Start with Related Work" - "Start with Conclusions" - etc.). To me, the problem with writing in a different sequence is that it is very easy to lose track of what a reader actually knows at this point in the paper (hence destroying the story of your paper). For instance, you would end up using concepts and ideas that you actually only discuss at a later point. This makes papers unnecessary difficult to understand. I feel it is also much easier to produce a convincing line of argumentation when you produce the material in the same order as it will be read.
In any way, later rearrangements will be necessary. After reading the paper, you decide that you need to switch some subsections around, or that you do not need Section 3 at all. Stay flexible and don't be too much in love with your current outline just because it is how you initially wanted to do it. One additional sidenote in this is that you write your paper in LaTeX. This makes later changes in the outline trivial.
Write the text the way you suppose it should appear in the paper. Do not draft too much - there is no point writing throwaway text unless you really do not know how to write this section / part properly at this point. Only go on to the next section when the last one is pretty much done.
As soon as a section is pretty much done, get some feedback on it. Remember that your paper should already be coherent and complete up to this section, so there is no harm in sending it to colleagues or your supervisor and asking them to tell you whether the paper makes sense up to and including Section X.


Etiquette: asking for postdoc position to seminar speaker

Conferences and seminars are not only here to present what you are doing, but also create and expand your network of contact with people from your field.

Any form of contact is good, provided you put the respect it deserves. If the person is too busy, maybe it's best to send an email or try to talk to him in a very short availability period and drop your card.

If you have a meeting, that's even better. You already got his attention, it's the perfect moment to ask him the question directly. If you're interested in his research topic, just ask if he's looking to having a post-doc on the subject. He might not have a position available, but maybe he can ask for one.

There is no official method to contact for a post-doc, unless it's advertised on a website, then the preferred method should already e described.


Would a question that requires an amount of text to explain be good to send?

As a busy person who receives these sorts of emails, my response to email tends to fall into two categories:

I can respond to this right now, and get it out of my queue.
I'm going to need to think about this some, I guess I'll put it off for later... and later turns out to be days, weeks, or months before it surfaces again, if ever.

Unfortunately, your draft email above will most definitely fall into category #2.

"What do you think about..." is an open-ended request for an essay. Is one sentence enough, or a page, or a full scientific paper?
You want the reader to digest 16 lines of technical discussion with an unclear goal of evaluation.
You also want the reader to go read your blog post, which makes me wonder if that's the real point of this.

You've thus got 3 different things you're asking of the reader, none of which actually says what you really want to get out of the interaction.

And that's the real problem: why are you writing to this person?

Do you have an answerable question they can help you with? (i.e., not "what do you think..." but "Does Concept A actually mean that Red Ones Go Faster?")
Do you want to show them your work and see if they think it makes sense?
Do you just want them to be aware that you exist?
Something else?

When you figure out what you most want, focus the email on precisely one thing that can be addressed quickly, and try to keep the whole thing to only 3-4 sentences.  If you can do that, you also will have forced yourself to be clear enough about what you want that a useful answer is much more likely.


PhD application: bad grade in relevant subject at master's

I believe it is very normal to have some drawbacks in every university experience, especially in the situation you described. I believe most people would be understanding if you explained to them what caused that specific grade (the changing masters and countries, etc), and I would explain how you are improving (extra hours of study, asking for advise of older students, learning better organization techniques, things of that kind). It's all a matter of how you expose the situation; if you expose it with a positive output, they will get a positive impression of you!
For my master thesis internship interview, one of the topics I talked about was how I in one semester had very low grades (average of 13/20) and even failed at one subject, and how I decided to turn things back around, got up on my feet and in the next semester, did one extra subject and ended with an average of 18/20, and they loved it, I was actually their first option for the internship! It's all about how you deliver the info :)


How does a committee select received manuscripts for poster presentation?

It might be useful to look at it from the conference organizers' perspective:

Accepted full papers usually require the author to give an oral presentation at the conference. But the number of time slots for those presentations is usually limited by the size of the venue (number of conference rooms), and extending it either costs the organizers additional money or is not possible at all. So there is a strong motivation to limit the number of accepted full papers, and to choose only those that represent the largest impact/progress to the research field.
Accepted posters on the other hand are usually presented at a short (~1-2h) poster session, where many posters are presented at the same time in a rather small area. Each conference room booked for the oral presentations can probably be used to present 50-100 posters in a single session, and scheduling a second poster session can cheaply double that. So there is no real motivation to limit the number of accepted posters, beyond making sure that they make sense and represent at least a minor step forward.

These perspectives also match my experience on acceptance and gained reputation in the field of computer science: You can get pretty much anything accepted as a conference poster, while getting a paper accepted is much harder. For that reason, accepted posters are largely irrelevant scientifically, and - in my experience - are usually not even actually published in the conference proceedings (sometimes the proceedings at least contain the extended abstract that was submitted for poster acceptance, sometimes not even that).


Asking a professor to be my advisor (math)

Just ask. There is nothing to lose. Many of us would be hesitant to ask a student, realizing that there are advantages to moving on and coming in contact with different faculty and their ideas. He might even suggest that you move on, actually, and don't take that as a negative.

If that happens, ask for his advice on your next steps. And try to keep in touch with him over the next years. An email every year might be welcome if you are progressing nicely.

These things are best done in person if that is an option.

But think about whether this prof (the easy option) or moving on is the best option for your future.


Will a 5 year gap between Undergrad and PhD hurt my chances?

I worked for 2-3 years after my undergraduate degree before applying to doctoral programs, and I think my work experience only helped. Like you, my job was relevant to the programs to which I ultimately applied. I was able to explain in my statement of purpose how my job experience strengthened my research skills and actually motivated my decision to apply to graduate school. As long as your application is strong (good letters, good GRE scores, etc), I can't see the gap between undergraduate and graduate school mattering that much.

That being said, one point you may want to address is how you kept your "academic muscles" toned over the last 5 years. Some people find the transition back to academic life difficult after extended periods away from it, and it may be useful to demonstrate somewhere in your application how you have kept in contact with the academic world, even if it was only indirectly.


In U.S., why do many engineering departments care about professional engineer registration?

There are 2 major theories about credentials: human capital theory and signaling theory. Under HCT, a license (such as a PE) shows that you have accumulated a credible amount of knowledge (you must graduate from an accredited engineering school) and experience (you need to have worked for 4 years after your bachelors to sit for the PE exam). Under signalling theory, the PE shows that you have done what it takes to legally call yourself an engineer.  One interesting comparison of the differences of HCT and ST is The Career Consequences of Failing versus Forgetting. You may know just as much as another person, but the one of you that passes some hurdle signals to prospective employers that the hurdle passer is the better candidate. This is because hiring a person is trying to predict future behavior/success with limited information, and many people use signals as heuristics.

You will also find out that universities hire people who have degrees. A cynical view is that they have a vested interest in maintaining the supply of people who get degrees. A signalling theory viewpoint is that universities think degrees are important enough that they only hire teachers who have them.

In many fields of engineering, your working career will be very short if you do not pass your PE. Civil is one such. Other engineering fields, such as Electrical (which is mine), typically have state exemptions for manufacturing, so very few EEs take their PE. When I was younger, I was quite opposed to licensure. Now, I see it as a way to distinguish myself from other candidates. One interesting blog post that inspired me to sit for my PE exam is this one. Another is a dissertation (which is not online) titled "Hiring and Inequality in Elite Professional Service Firms".

My advice is to take your EIT and PE exams as soon as practical. Some US universities require you to take your EIT exam during your senior year (as in they won't issue your diploma without passing it).

Disclaimer: I am registered to take the PE exam this April.


Which is the more competitive path to grad school for mathematics?

Let me start by saying that while I have never been involved in graduate admissions (my college does not offer a graduate program in mathematics), I'm an assistant professor of mathematics at a well regarded liberal arts college whose graduates regularly go on to attend top graduate programs.

As you acknowledge in your question, the reality of the situation isn't nearly as black and white as your dichotomy seems to make it out to be. In my experience, the most important aspects of your graduate school applications will be (in no particular order):

The classes you took and your grades in them. Since you say your goal is to attend a top PhD program, you should be taking challenging courses and doing well in them. But of course you knew this already. There is a certain balancing act that one has to pull off in selecting what courses to take. Essentially, this boils down to breadth versus depth. On the one hand, you can take lots and lots of fun elective courses in all sorts of cool areas of math. On the other hand, you can choose a smaller number of areas and go really in depth with them, taking the introductory graduate sequences in them if possible. When I was an undergraduate I took the former route and took 24 math courses (I just counted) during my four years of college. These courses (some graduate, some undergraduate) were on topics like mathematical logic, algebraic geometry, primality testing, etc. I don't advise my students to do this, but I'm glad that I did and to this day find it useful in my research to know little bits about a wide variety of fields. Assuming you are interested in pure math, I'd advise you to go the second route and focus on algebra, analysis and topology. You'll likely have to pass qualifying exams in these areas in grad school before you can advance to candidacy, start working on research with an advisor, etc., so the stronger your undergraduate background in them the better. Your application is going to have to convince PhD admission committees that you'll be able to succeed in their programs, and having already done well in graduate courses in core areas (i.e., algebra, analysis and topology) is going to make this much easier.
Your letters of recommendation. It goes without saying that to get into a top PhD program you'll need strong letters of recommendation from professors that know you well. Ideally these will be from people that have taught you in multiple courses (ideally advanced courses or independent reading courses), mentored you in an honors project, or mentored you on a research project. Something that is crucial is that the professor know you well enough to be able to write a strong, detailed letter that says more than just "This student got an A in my class." I find it extremely frustrating when a strong student asks me for a letter of recommendation for graduate school when I've only had them in one course and they never really attended my office hours regularly or do anything else that in that course that let me get to know them at all. In cases like this it's hard for me to write anything but a generic letter that might not do all that much good. Something else to keep in mind as you try to game the graduate admissions system is that good letters are going to compare you to other undergraduates that the letter writer has interacted with. As an example, when I write a letter for a student applying to top programs I'll say something like "Of the roughly X students that I have interacted with during my time at Oberlin, this student is most similar to Students A and B, who are now graduate students at Stanford and the University of Michigan," or "This student is one of the 3 or 4 strongest in their (very strong) class." This kind of thing lets the letter writer make it clear whether you are a very strong student, an exceptionally strong student that is at the very top of their class, or the type of student that only comes along once every few years. If you are going to be graduating from a university that regularly sends students to top programs, having letter writers that can make these sort of comparisons could be especially important.
Your score on the GRE (math subject exam). I don't have much to say about this one. The fact that programs receive many more applications than they have spots to fill in their incoming classes means that scores on exams like this are a very convenient way of comparing people and/or developing cut-off scores. That isn't to say that you won't be able to attend grad school if you don't do extremely well on the exam. It is, after all, a single exam, and one that is primarily (exclusively?) taken by people wishing to go to graduate school in math or a related discipline. I've found that students scoring around the 60th percentile with otherwise strong applications haven't had problems being admitted to good graduate programs. If you're coming from a well known university with letters of recommendation from letter writers whom graduate admissions committees will have heard of, then places might be a bit more forgiving than if you have a low GRE score and are coming from a lesser known place with letters from people that admissions committee members will be unlikely to have heard of.

Returning to your two options, I don't think either of them is optimal. If your goal is to attend a top PhD program then I think that you'll want to find some sort of a compromise between these options. Here's one thing to consider about your Option 1 though. Let's say that you get stellar grades in all of the required math courses at your university, and perhaps take an extra class or two, but nothing else. I'm far from convinced that this will lead to the types of letters of recommendations that will get you into a top PhD program. The issue is simply that I find it unlikely that doing this will lead many of your letter writers to write things about your being at the very top of your department's graduating class, doing well in the most challenging courses your department offers, etc. At the end of the day many of the students that will be admitted to top PhD programs will have done very well in a lot of very challenging courses. Taking a spot from a student that has done this when you've decided that you're only going to do one of the two (get really good grades or take really challenging courses) doesn't seem all that likely.


Having Trouble Finding a Faculty Member for Math Undergraduate Research

I'm going to suggest that you take a different approach, for now.

When you visit or email a researcher, start by reading some of his or her writing.  The start the conversation by speaking about the article you read.  Mention something you found interesting or well explained.  Ask a question about something you didn't understand.  If necessary ask for some recommended background papers.  Ask a question about future directions.  Then ask the researcher what s/he is working on currently.  Be a good listener.
Keep a notebook of project ideas.  Put your current project in this notebook.
Ask each professor you visit if s/he has any projects to offer for summer.  Listen carefully to the project description.


Put good GRE scores on resume submitted with grad app?

You typically have ETS send the school your official GRE scores anyway so this information is going to be redundant.

It shouldn't bother most people if it is on there but I don't see it helping you really either. I would only do it if I have some space needing to be filled on my resume and my scores were really high.


Applying to several faculty positions within the same institution

I advise against applying to all open positions at once. Not only are you likely not to match the criteria for many of them, but you are also not interested in accepting the majority. By doing so, you just add to the workload of the hiring committee. Furthermore, you decrease in a way the value of your applications, as you should be striving to emphasize how you are the best fit for that particular position and that gets very hard when trying to apply to many different positions. You'll likely end up with mediocre applications everywhere or worse with the same application everywhere.

Typically, there is one position (as you say) which you would like to get and are probably best suited for (depending on your qualifications). So I suggest you narrow down the open positions to at most 2-3 where you would most enjoy working, if you insist on having a safe option, and try to write strong applications for all of them.

Finally, I don't see how a "preference statement" would help you. If you get your desired position, then it is not due to your preference, but because you had a stronger application than other applicants. If you, however, fail your best option, other options might see it as a negative thing, if you stated that you'd prefer to work at some other position and only failing there, apply to them. So, the idea is to apply everywhere with the same zeal. That's also why you have to narrow down your options, so you can accept any outcome, if needed. If you are not comfortable with that, it means that the options aside your primary are not attractive to you and I would refrain from applying to them (assuming of course you are not in a position that you have to accept any job). In the case you get accepted on more than one position, you are of course free to choose.


Now about "introduction and definitions".

Unless you really cannot do this, the introduction should in the ideal case be more accessible (say, understandable not only to an absolute specialist in your subfield). Even more importantly, the introduction should motivate the problem and present an informal overview.

This is introduction:

  The order of the sepulation of sepulka is a well-known and important problem in Sepulka Sciences. We suggest an ordering of sepulation that increases the performance of almost each sepulka bundle.

This is main paper text:

  Let ∆ be the main sepulation index of the current sepulka bundle, orderded lexicographically [Lem, 1957]. We denote with ∂µ the difference of sepulation gradient for...


Should I use "I" or "We" in Peer-Review Journal Submissions?

Follow the conventions in your field. I suspect that in most fields papers use 'we' since most papers are authored by more than one person. I would personally use 'we'.


Can I perform and publish studies on patented chemical compounds?

Patent law varies around the world, but in general doesn't prohibit study and discussion. Lots of things that are covered by patent are regularly discussed in popular and scientific literature. You don't need Apple's permission to analyze an iPhone, for example.

One of the reasons behind patent law, in fact is to make the essence of the thing known to the world. The patent application has to reveal everything essential on which the patent claim lies.

Patent is intended to prohibit you from reproducing the thing for most purposes, but you aren't doing that.


Graduate coursework for graduate admissions

The answer strongly depends on the programs you apply for. As a very general statement, I would say that getting a good grade on a more advanced/challenging graduate class is better than getting a good grade on an undergraduate class.
Grad classes carry several benefits in terms of the signal they send to prospective admission committees. First of all, they show that you are ready to handle independent studies and the advanced material that is given in these classes. Moreover, graduate classes tend to be smaller and offer more intimate interaction with the lecturer on a topic that they care deeply about (they probably involve their own research papers in the class) - this means you get the opportunity to receive a good reference letter from someone who can personally attest to your capability to handle graduate level material.
All of this is premised on the assumption that you can get a similar grade on both - failing (or barely passing) a graduate class sends a very bad signal to admission committees, as opposed to doing well on an undergraduate class.
So - be sure that you are indeed ready for the class, and the types of materials covered there. Good luck!


What should the purpose of a draft of a research paper be?

The draft itself is only the term for something that is surely not finished. The purpose depends on what you intend to do with it.

Drafts are often shared with collaborators to have a common ground for further discussion, fixing some notations and in general keeping them up-to-date with the progress.
Drafts can be just for personal use to keep track of ideas and what has already been done.
Draft is also the version of the paper that is 5 pages over the limit and you know you will need to make changes to fit in.

Draft writing is normally not the goal itself, instead it makes sense to think about what the draft will be used for and then write a document that is useful for this.


Appropriate to mention using a lab's dataset when seeking grad student position in that lab?

Interest in and knowledge of a potential advisor's work is a big selling point for a prospective student, and this is a great way to do it.  I would definitely recommend playing around with the data, and it becomes a great way to connect with the professor, providing a basis for conversations while demonstrating your skills and interest in the work.  Even if what you can do is quite limited, your willingness to "get your hands dirty" and actually dive into the data is a good thing.

Do this as a learning experience, not to discover something.

You mentioned "I'm afraid of appearing disrespectful or full of hubris", and you are right to be concerned about this.  There is a big danger of doing so if you come to this professor claiming to have made a new discovery.  It could come across quite poorly, almost appearing you think you know more than the professor.  And unless you are an absolutely exceptional student, you probably aren't yet fully equipped to evaluate whether you have really discovered something interesting and valid.

Instead, I would to this as a learning experience, and start a conversation with the potential advisor framed accordingly.  Ask questions if there are things you don't understand.  Or say, "I did some analysis like this, is this valid?" And so on.

Even if you do think you have made an interesting finding, frame it in the same way: you have done some analysis as a learning experience, and want to discuss it with the professor to see if you are doing things the right way.  If there is a real discovery there, let them come to that conclusion.  At this stage in your career, it's much better to take a humble stance of desire to learn.

Also, this is a great chance to learn about this professor as a potential advisor. Are they interested in discussing what you are doing and answering your questions about their work?  Are they supportive of your interest in pursuing further study?  Do they make time to talk to you?  If so, there is a great chance that they would be a supportive advisor.

Conclusions:

Your interest in the professor's work, initiative to explore the data yourself, and any skills you demonstrate in the process all sell you really well as a potential PhD student.
This learning experience will be valuable for you: both in gaining necessary skills, assessing whether you want to do further research in the area, and whether you want to work for this advisor specifically.
Actually making new research findings from the data should not be your focus.  If you don't have the skills yet, acting like you think you can do this looks bad.  If you are the rare undergrad student who can operate at this level, let the prof discover it rather than claiming it.


Grad School ~ Submitted Personal Statement Instead of Statement of Purpose

No one can really judge how others will look at your application, but there are a number of people here who are currently involved in doctoral admissions who say they ignore (or merely scan) the SoP. You missed an opportunity to detail your future plans and a specification of field, unless you stated that elsewhere.

But, I doubt that it is disqualifying. If your admissions materials paint a solid picture of your accomplishments and your letters of recommendation stress your likelihood of success you should be fine.

But if you have a chance to amend your application, you might want to do that. And fix it for future applications you might make.

This might be more of an issue outside the US-Canada region, I think, but probably not a huge deal here.


Yes, it is possible.

If you want to invite the reviewer to be a coauthor, send a request through the editor.  If the editor agrees, they will forward your invitation to the reviewer.  If the reviewer accepts, they will reply to the editor, who will introduce the reviewer to you, and off you go.


"But in the other course this was different!" - How to react on this if the other professor did not follow the rules?

This is a standard problem in places where a mentality of unwritten rules has become standard (you know, the places that have "rules" and actual rules). If this becomes ingrained in the university culture (both in the student body and the faculty), nobody can really tell anymore what is a an actual rule and what isn't (and, really, the answer will be different for each teacher). For this reason I prefer a relatively strict no exceptions policy in my courses. I understand the downsides of this model (see for instance also here: How do I appropriately penalize late projects?), but at least everybody knows where he stands in such a model.

I understand that you are not in a position to change university culture, so you need to play the hand you are dealt. I see two main ways to go forward:

Become more lenient yourself. If a number of senior professors deems it fit to not enforce the official rules or implement weaker rules, then maybe the official rules are in fact perceived too strict. In that case, maybe the answer is just to run with the herd and allow for more exceptions etc. yourself. Of course the preferred solution in that case would be to change to official rules, but it is well conceivable that this is not feasible for one reason or another.
Announce very, very clearly at the beginning of the semester that in your case the rules will be the rules, no matter how things were in previous years or with other teachers. Follow through on your claim, and build up a reputation as being a strict guy. Note that being strict is not the same as being an unpopular / bad teacher. I have continuously followed this strategy in my teaching, and still receive good to excellent teaching evaluations.

Of course, if you follow the second strategy, some complaining, accusing and guilt-tripping  will happen. It is your task as a teacher to be able to distinguish between warranted complains (and react to them) and more manipulative ones (that are to be ignored). These examples you give quite clearly fall into the second category. What you need to do is find a number of polite standard answers to these statements, and then forget them. Examples:

  Hey, professor XX did not have the rules last year. Why do you have them? That is so unfair!

Answer: sorry, but it is impossible to change anything in a course if I am forced to always do things exactly like the were done in previous years. I am trying to be more strict this year because I have seen that unclear rules are also not beneficial for many students, as nobody really knows anymore what the actual rules are.

  Cmon, we will not tell anyone!

Answer: while I appreciate that, I am afraid that I do not want to make an exception here. Making an exception for you is unfair towards the other students that did not get this exception.

Some other minor comments:

  I could go to the head of the faculty or the university who will end all that

I am unsure if that is even true. In all places that I have been to, it would be very unlikely that a head of faculty micro-manages how professors do their teaching.

  Also, I want not to damage students and declare their passed exams as illegal.

This is understandable and correct. If you truely think that students were under the impression that a certain rule or exception would apply to them, I would let them pass as part of a transition period. If you think that they were aware that they should actually fail, but simply try to come up with a reason why this is not the case, then be strict and let them fail. Note that this is the reason why announcing your strict rules enforcement as clearly as possible is key. In your situation, being strict is only fair if you give your students advance warning, as the seem to be trained by your university that, by and large, teachers are lenient.


Will it be a good idea to write professor who has just interviewed me for a PhD position?

If you have questions then ask them. Otherwise a simple Thank You note would be appropriate. But just asking questions in an attempt to pad your application probably won't do any good. But thank him now and ask questions later if they arise.

How long it takes is variable and up to them. But they need all required information before they make any decisions. There is probably a committee that has to get involved in such decisions in the US, also.

Patience. Keep all your other options open.


Is it customary to include a dedication in an honours thesis?

Dedication generally comes in your front matter section in your thesis. It will depend on your university rules and guidelines. Generally "dedication" is not mandatory in most of universities. However it is advisable to check with your academic office.

Quoting from Harvard guidelines for thesis writing,

  Front matter may include: acknowledgments of help or encouragement from individuals or institutions; a dedication; a list of illustrations or  of tables; a glossary of terms; one or more epigraphs—pertinent quotations at the beginning of a dissertation or a chapter

My personal opinion is that dedication gives emotional touch. It is good to have dedication page in your work.


Writing two papers on the same topic with the same data

It is entirely reasonable to produce more than one paper from the same project, focusing on different aspects of the the project.  Legitimately complicated projects often produce many papers worth of results: it only becomes unethical salami slicing if you're trying to "stretch" one paper into many.

The type of situation that you describe, however, is an extremely common circumstance for ending up with two papers, one focused on method (in this case, your algorithm) and the other focused on results (in this case, what has been learned from the biological data).  The two papers will necessarily be quite different: the methods paper must investigate questions of scaling, scope of applicability, etc., far beyond this particular dataset. Complementarily, the applications paper needs to consider underlying theories, alternative explanations, hypotheses, etc. with little bearing on how the data happens to have been analyzed.

From my own personal experience as both an author and a reviewer, I would recommend doing this in one of two ways:

If the two have similar audiences, you can co-submit two papers that reference one another to the same journal.  Explain this in the letters to the editor, and they will likely receive special handling that considers them as a linked unit, e.g., the same handling editor, possibly shared reviewers.
If the two have very different audiences, publish whichever is ready to go first, mentioning the issues of the other only briefly, then follow up with the other citing it.  This can be in either order, though if you're dealing with a high-impact biology journal, it may be wise to go with the biology paper first, since such publishers are sometimes touchy about "novelty" concerns.


How does shifting of jobs affect designation and tenure in academia?

This all depends on what is offered in the new position and on your negotiation skills.

Generally one tries to go up-hill, so to speak, or at least stay on the same level. The new institution hardly will expect you to make the transfer if they offer you a lower position and tenure track when you have tenure already.

If you are forced to move, then you have a weaker bargaining position and might have to take a tenure track position, and go through all the evaluation process again.  But this would probably mean that you have bargained poorly or accepted bad working conditions, or it simply could be because there are so few academic jobs these days.

I have heard of one case where someone traded in a tenured Associate Professor position for an untenured Assistant Professor position at a better institute. (The risk paid off in the end.)


My advice would be to be honest, not argumentative, and explain exactly what happened.

I pulled the phone out with the intention to cheat.
I did not complete the cheat as I was caught in the attempt.
I turned the paper in immediately after being caught.
I have not habitually cheated.
I will accept whatever disciplinary outcome is assigned.

Maybe write this down and hand it in at the beginning of the meeting.

Accept the sanctions--not with a "crucify me" attitude, but phlegmatically.  Then, go and sin no more.


Under what circumstances would a professor be offended at students taping or recording his or her lecture?

I do not believe it had anything to do with the act of being recorded by itself. Most universities are beginning a process of recording lectures for later consumption by the students anyway.

Instead in this case it is likely because the professor was unaware they were being recorded. They may do or say something that they regret or which gets them into trouble. If however they knew beforehand that they were being recorded it would be unlikely that they would do that since they know the repercussions would be more severe. I think it was an instinctive reaction to protect themselves from others using the recording against them.


Should references in the supplementary information be included in the main text?

Citations that do not appear in the main article should not appear in the bibliography section of the main article. Instead, you should create a separate references list in the supporting information, and use a separate numbering scheme. Usually you can use the same numbering scheme as in the main article; it will be clear that references apply to the supporting information, rather than the main article. (You could add a footnote to that effect if you want to make this clear, since supporting information is usually handled "as is" by the publisher.)


GPA calculation in German Grading system

I'd guess your subjects are part of modules?
Then you need to calculate and round every module on itself and afterwards you can calculate your GPA based on the modules.

Have you checked your Prüfungsordnung (examination regulations)?
In it the calculation method of your GPA is stated.

If the GPA is still unclear after checking the document, you should contact your Examination Office.
Maybe they have a system/display bug and/or some "buffer marks" (have you something like 18 credits open, i.e. registered, but not taken yet, then grading it with 4.0 in the system would yield a grade of 2.2) or something that cannot be checked or verified from outside.


How to cite primary source first found in secondary source?

If I'm understanding correctly, you are saying you read a secondary source, which led you to a primary source; then you cited material from the primary source that wasn't discussed in the secondary source; and your question is whether you need to cite the secondary source because it led you to the primary?

If so, I do not think you need to cite the secondary source. It feels polite to do so, sort of like using "via" on Twitter. But in an academic paper I do not think it is required.


First, you'll need to identify what kind of reviews you're planning to write. Just to name a few: critical review, integrative review, literature review, meta-analysis, scoping review, systematic review, etc. The methods differ somewhat regarding the types. For example, if you're writing a systematic review, then you'll need a much heavy focus on how you searched for the articles and how you sorted/selected them.

Second, most reviews are question-driven and according to the types, the specificity of the questions also differ. Scoping reviews may have a looser definition of questions while meta-analysis and systematic review may have a set of tightly defined questions.

In other words, it's likely not something we can introduce on a Q&A website like here. As a "review" varies so much that can be as quick as an afternoon of search or a five-year PhD project.

What I'd recommend:

Identify about 5-8 review articles in your field that you'd like to model after. Most reviews are pretty apparent in terms of what type of reviews it is. But if you're unsure, talk to a librarian.
Read up about that kind of review. There are books (like Booth's Systematic Approaches to a Successful Literature Review) and guidelines (check www.equator-network.org) on how to carry out the search, arrange ideas, and present your interpretation. Again, your library would be a great start.
Consider working with someone who had experience in writing a review. They can help you with revising subtle things like how to tabulate the data to make them digestible and useful, and how to present your findings, etc.
Budget a lot of time.
Develop a system of keeping good notes and bibliography. People have used index cards, highlighters, Evernote, etc. to keep their thoughts and their quotes clearly laid out and discernible from each other. Bibliography management software is also a must, as there will be intensive referencing.
If you have tuition remission/support, consider register for a course in your school on literature review. Most of these courses require students to have an independent project (you may petition for one if there isn't.) That way you can get to work on your topic and obtain guidance and input from the course instructor. I think 13 to 14 weeks of weekly effort should get you a very strong draft. (According to your school policy you may want to give the instructor a heads up and seek approval on using your research topic, though I don't see any conflict here.)

What I'd privately recommend:

Evaluate if you truly need a review. While I understand it sounds logical to "read up and write about the field" before you joint in. It's true that it's easy to read a lot of articles about a field, yet it takes time/experience to be able to tell the intricacy among them. So, most reviews take a much, much longer time to write compared to, say, writing up about an experiment. If you don't have much time before the application, consider at least another shorter paper such as a part of your PI's research that you are involved in as a side project.
I am not at all familiar with agronomy, but I'd guess that the topic may be already too broad for some kind of reviews as it covers all "ornamental plants." Dissect the sample articles you got and examine how the authors specifically model their question statements.
Most common newbie mistake is writing an annotated bibliography. If the review reads like "A says a, B says b, and C et. al. says c," chance is it's not being done quite right.


Is developing a cheaper method ever considered to be originality in academic research?

What are the necessary conditions, if any, that allow X and Y to be published as a journal paper?

That the method or equipment is new and interesting. It is really as simple as that.

It is completely ok if the improvement or motivation of your technique mostly lies in cost savings - that is common in many research communities. If the way how you achieved these cost savings is by applying simple technical optimisations, you will have problems publishing your results. On the other hand, if you reduced costs by fundamentally changing the way how your technique approaches things, or if you manage to reduce costs by orders of magnitude, journals will presumably be interested in how you achieved these results.


Conducting a Podcast with A Star Researcher In Our Field

I have only been on one podcast, but in my experience there was very little ice breaking. They just confirmed a few pieces of information they wanted to make sure they got right during the interview, made sure I was aware of the audience and goal length of time for the interview, and then we jumped right into recording.

Similarly, when I have interviewed people for my class (I do video interviews with people in the field), I don’t do any real socializing beforehand. We may say a few small pleasantries, but we jump right into the work of preparing and creating the video content.

If you do feel like you need a warm-up question, “what inspired this line of work/this paper?” is always nice.


There's no suggestion of dishonesty in the word.

scoop:
Informal:
Publish a news story before (a rival reporter, newspaper,
or radio or television station).
"time and again we have scooped our rivals with the top stories and pictures"

https://languages.oup.com/google-dictionary-en/
But do listen to Tom Lehrer's  Lobachevsky.


What's the easiest way to get a references section into a single citation format if they vary to begin with?

Doing this in a reference management software (I use Zotero, which you mention, but there are others) is absolutely the way to go. Of course, setting up the reference database for one paper may take the same amount of time as manually reformatting, and learning how to use it in the process may take longer. The advantage is in reusability. For any single paper the up front cost may not be worth it, but the time savings on paper number 2 and beyond is incredible.

Unfortunately you won't just be able to paste in the formatted citations and have Zotero recognize them (so far as I know). Zotero does have a way to add items by an identifier, so if your coauthors included DOIs, adding the references should move quickly. Additionally, if your coauthors used any reference management software themselves, you can ask them to export it to a common format (BibTeX is pretty commonly supported) and import those files.

If worse comes to worse, searching for each reference title in Google Scholar and using Zotero's automatic ingestion should also be pretty quick.

Zotero's documentation on these various ways to create items:

https://www.zotero.org/support/getting_stuff_into_your_library


Editor didn't invite for a second review

There are always difficulties second-guessing from what others actions result from. The fact you did not get re-invited, is not strange in my experience (as reviewer and editor). First, I assume you do not know what the other (I assume the journal uses more than one reviewer) reviewer provided in a second review. It may have been minor revisions and the editor could make a decision to provide a major revisions verdict but go directly to accept if he/she thought the corrections were good enough. This is an editors prerogative.

It is always possible that an editor chooses a different reviewer for the reason you mention but given that you have done many reviews before, I sincerely doubt this is the case or reason. Another possibility is that the editor felt someone with different expertise was needed for some aspect of the manuscript, perhaps based on comments by the second reviewer. But, you will never know the details of the story and I would not think twice about the event. The fact that you keep getting requests shows your expertise is in demand.


Who should be proofreading journal articles?

To proofread something, you need somebody who knows about the subject matter. They have to gain something too, doing the work just for "fun" doesn't cut it. So your best bet is a coauthor, a colleague who is willing to swap proofreads with you, someone in the research group (understanding what others are doing should be beneficial), even perhaps your advisor.


Do you need to state that you have written permission from the copyright holder of the image I use as cover

It is common in book length material to give a citation of the photo, perhaps in a footnote. The title page, if present, or a page just following, is possible. So is a footnote on the last page, which is probably a list of references. Another possibility is on an "Acknowledgements" page, if present.Just mark the citation for the photo as "used with permission".
The citation is necessary in any case since the work isn't yours.
It isn't necessary to include the entire permission statement. But keep a copy of the statement.


What is the difference between a Case Report and a Brief Report?

Short answer
In NEJM, case reports are called brief reports.

Background
A case report is in general a report on a single subject/patient. It is a broadly used term in many journals. From the wiki page:

  [A] case report is a detailed report of the symptoms, signs, diagnosis, treatment, and follow-up of an individual patient. Case reports may contain a demographic profile of the patient, but usually describe an unusual or novel occurrence.

The NEJM in specific does not feature an article layout for case reports in particular; instead, they have devised a common outline for those papers that either report on one case (case reports), or on a bunch of related cases, or of one specific family. From the Author's instructions of NEJM:

  CLINICAL CASES
  Brief Reports usually describe one to three patients or a single family.

Hence, in the NEJM, a 'case report' is one of the article outlines under the header 'brief report'.


Why is it so difficult to find a topic for my thesis research?

Your supervisor or potential supervisors should be able to help - and I don't necessarily mean by talking to them.  First of all identify potential supervisors whose (recent) work you like and (mostly) understand. In the first instance look at their recent papers, and particularly concentrate on any points they raise in discussion or future work.  In particular do a SWOT analysis and note what are the best and worst features of the approaches, and whether you can see opportunities for different, even interdisciplinary, work to be brought to bear.

To the extent you don't understand anything, don't keep reading and rereading and struggling with it, go back to the earlier work and the citations.  Try go be back to the originators of the concepts you are lacking or find difficult, and the commentators who clarify the insights behind the formalisms.  Look for conference and workshop papers for these early developmental versions of work, rather than the erudite and impenetrable journal versions.


Should I challenge my professor who thinks he's always right?

Short answer: Probably not.

As you pointed out, you may lose out on grades by challenging this professor. A larger problem, in my opinion, is when you (the student) approach the class with an attitude of discovering the professor's many mistakes. With this attitude, you also lose out on the opportunity to learn from his expertise. While this particular professor may not be as modern as you would like, it does not mean you cannot learn from him!

Keep quiet until the end of the semester, except when you have a valid question. And don't  approach intending to prove him wrong; approach intending to find out how you can learn from what he knows.  Ask questions because you want to learn, not because you want to prove the professor wrong. If you believe you know a better solution, it might be appropriate to ask "Would this solution also work? If not, why not?" Ask, don't tell. Your professor is human too, and most of us have a hard time always responding graciously to a smarty-pants student who thinks they know more than we do!


What is the best way to solicit teaching feedback from students (before the class is over)?

A method which I learned quite recently is the Start-Stop-Continue. I think it is a great method, as it is quick, and it does not require much effort both on your part and your students. You will need to distribute three small pieces of paper (e.g. Post-it) to each student, ask them to label Start, Stop, and Continue, respectively, on the top of each paper, and then ask them to list on each paper, according to the label, what they think you should start doing, stop doing, and continue doing. Ask them to submit their papers before they leave.


How to handle requests for a race-based exam structure?

I would suggest offering something in response that makes the students feel like their concerns are heard, without compromising the academics of the course.
For example:

I understand that this is a difficult time, especially for minority students. Unfortunately, if I cancel the final exam, I won't be able to assign a grade to these students and they won't get credit for their work this semester. But in recognition of the extra challenges some students are facing right now, I am going to schedule an additional review session and office hours before the final exam. This way, students who are struggling can get additional opportunities to master the material before the exam.

A response that communicates empathy and understanding is much less likely to develop into a PR disaster than one that is irritated, defensive, or dismissive.


What are some of the task planning tools people use in academia?

I have tried many kinds of the task planning apps/softwares for organizing reseach projects. At the end of my search, I interstingly find that ('old school') simple online spreadsheets (Google sheets or Microsoft excel etc.) are the best tools  by many standards as outlined below.

Simplicity: Just make a column for date/time and rest can be the variables such as name of the project, members of reaserch group etc. The  entries in each row can be task planned for each member.
Customizability: Every project is likely be different from each other. So rather than sticking to the pre-alloted platform, spreadsheets allow wide canvas to add all and any kinds of variables (eg. holidays etc.) into your plans.
Sharability: Applications such Google sheets and Microsoft Excel are well developed, cross-platform tools which allow user friendly sharability and simultaneous editing by multiple users.
Quick analyses: Since it's a spreadsheet afterall, one can easily plot numerical variables such as time wasted per day, number of pages written per day etc. This allows pretty good real time progress reports of the projects.

I would therefore recommend spreadsheets!


Citing yourself on slides when your lastname consists of multiple words

It's an informal convention, so I think the answer is as much a matter of personal style as anything else.  I would most expect "vdB", but if someone used "B", I wouldn't be confused by that.


How to prepare for the French language exam as part of PhD program?

Yes. I took both German and French. I was already fairly comfortable with French from having studied it in high school and in university, so I'll write about German instead. I prepared for my German language exam by going on to the GDZ server (a program to retroactively digitise documents, including a lot of classical mathematics papers) and downloading some papers in mathematical analysis (my field, sort of) from around the 1950s to 60s (when still a lot of the papers were published in German). I then went to the library and borrowed the copy of Hyman's German-English Mathematics Dictionary (for the nouns) and a copy of a normal German-English dictionary (for the verbs) and sat myself down and started translating word by word. After about a month I translated about 30 pages or so of math papers (and at the same time learned about uniform spaces), and proceeded to take my exam.
Not much. I have absolutely no conversational German, and only very rarely do I have to look something up in German that I cannot find a write-up in another language. (So far twice only, one a slightly obscure result in algebraic lattices that the only reference I could find is to a paper in the 30s.) (French on the other hand has been useful; mostly because the abovementioned "write-up in another language" often turned out to be in French.) Given how much I've found French to be useful for me, I'm sure that if I had actually properly learned the language, German would be just about as useful. Conversely, if you don't really learn the foreign language, you will probably be able to get by through other means in this day and age.
The canonical place to find French papers to read is NUMDAM. Of course, for practice, you can also check out Bourbaki from the library; it may be slightly less intimidating to start working first on the language by reading something whose mathematics at least you are familiar with.


How to justify an application for research funding if the only cost is my own academic or intellectual labour (without any equipments) etc?

Now, the application form asks me to explain how I plan to use the funding. What would be the best way to respond to this question when I only incur the personal costs covering the time for my intellectual work?

Funding will cover x% of monthly salary costs for the PI, over the duration of the project. (The remaining y% will be funded by the PI's university to perform duties beyond the project scope.)

I only need to spend time reading related works, code a bit, and write a paper.

Those activities will require office space, IT equipment, etc. Those expenses can typically be included.


Where to find latest videos of colloquia or other talks in your field?

Mathematics

From my experience not very many schools record talks as a matter of policy. But the special institutes often do.

MSRI has videos available for workshops dating back to at least 2004.
Fields Institute also has a large collection.
Newton Institute records almost all of its seminars and colloquiums.
IHP has a Youtube Channel, and if you follow them on Google+ you get updates (sometimes even hourly) on new videos.
Clay records their research conferences.
Simons Center for Geometry and Physics no longer maintains a central list of videos. But if you visit the individual workshop pages the videos are made available very soon after the talks.
QGM (Centre for Quantum Geometry of Moduli Spaces) records their conferences and master classes.
Banff International Research Station (BIRS) makes conference/workshop videos available.


Is there any academic advantage of being the submitting author of a paper?

No, there is no academic advantage of being the submitting author of a paper.


Job applications reviewed "until the position is filled" (i.e. soft deadline): What does that really mean?

"Review of applications will begin on Day X, and continue until the position is filled" is also translated as:

We want you to get your application in on time, but if you're totes amazeballs and late we'll overlook it.

The motivation is the same as what was mentioned. If you say that there's a hard deadline for submissions, and then Dr. Awesome Sauce applies a day later and gets hired, you're opening yourself up to a lawsuit from all the Dr. Not-So-Awesomes.

Practically, academic hiring works on a calendar, and universities compete with each other. For example, in computer science it's rare to be making a first offer well into May unless you're at the University of I'm-So-Cool and know that you can afford to be last. And even then it doesn't always work. So practically speaking there's a deadline of sometime in March to make decisions on offers and start wooing your preferred candidates.

This means that you can't realistically process a new application any later than early-mid February (because it takes time to collect references and organize a trip)


Difference between "2-year community or junior colleges" and "4 year undergraduate program" in USA

Two-year degrees in the US often award either an "associates degree" or some technical certification/profession-specific degree.
These degrees are not typically part of the "bachelors -> masters -> PhD" pipeline or more generic "bachelors -> professional degree".
Some students may start taking courses at a 2-year school and then transfer to a 4-year school (with or without actually completing a 2-year degree, and hoping to have as many of their 2-year credits count/transfer towards their 4-year degree), because 2-year schools are both less expensive and less selective. 2-year programs rarely have any sort of on-site housing ("dorms") and limited "student life" opportunities (clubs, social facilities, athletics).
Not all 2-year schools are appropriate for this track. Some are specifically designed as technical degrees to get students into a specific career, and do not provide the "general education" credits (basic math, science, social studies courses) that are useful for transferring to a 4-year program.

If you wanted a MSc in the US, starting from high school you would either:
A) Enroll at a 4-year program, and then
B) Apply to Masters programs*
or
A) Enroll in a 2-year program,
B) Transfer to a 4-year program (bringing with you some or all of the credits you already earned), and then
C) Apply to Masters programs*
If you plan for the "ABC" pipeline it is definitely worth exploring the requirements of the 4-year institution(s) you plan to attend so that you know which courses you take will transfer (some 4-year schools have explicit relationships with particular 2-year schools to define classes that will count for transfer credit). Most students who would follow this path instead of the "AB" path would be doing so either for financial reasons or because the student does not feel academically prepared for a 4-year school (the quality of high school education varies quite a bit in the US, and even a very good student at a disadvantaged high school might have trouble with the jump to a 4-year school).
There is no particular advantage to completing a 2-year degree program before starting a fresh 4-year degree - the only reason to start at a 2-year program if your goal is a MSc would be if you can transfer credits from the 2-year to 4-year program.
(* - it's possible, though not particularly common in the US, that you enroll directly for a combined bachelors+masters program)


Is it appropriate to wear an honor stole/cord to my doctoral hooding and convocation?

Formal regalia for convocations are highly stylised - even the side to which a tassel falls can have meaning. It would not normally be appropriate to wear representations of achievement that are unrelated to the degree you are about to receive.

If the honor stole/cord has particular significance to you, you can write to your university to explain your situation and to ask for permission to wear it at your convocation. You should then abide by their reply.


Grants: how to acknowledge collaboration, techniques from postdocs or students?

Regarding "sometimes a postdoc has significant relevant experience that a PI lacks", I have been referred to by name in (successful) NSF proposals I have co-authored to highlight some expertise I bring to the project, e.g.

  ff524, a PhD student whose efforts have contributed to the research component of the project, will also be engaged in X. [insert my impressive background in X here]

or

  This interdisciplinary collaboration is facilitated by ff524, a PhD student in Department A who has previously worked with PI X in Department A as well as with PI Y in Department B.

Presumably one could do the same with postdocs.


Can we modify some part of a standard benchmark? Will the results be accepted by the community?

You can always propose a new benchmark and demonstrate that it measures what you want. Once you've done that, you can show how your new thing compares. The scientific is not guaranteed to care, but if your methodology is good, it may catch on.


Is it my responsibility to point out that a paper has been plagiarized from another researcher's blog?

Ignoring the journal in question is probably an overreaction.

However, the best route to take is the first one—the author of the copyrighted material is the one that has the most responsibility to assert her rights. Your duty is to notify the person whose work has been infringed upon that the violation has taken place. Once you've done that, you've achieved what's ethically required of you. You are not obligated to take the matter up directly with the journal. (However, you may do so if you so choose.)


Personal statement to apply for graduate school with a change in major

People's interests change.  This doesn't require an explanation.  Here's an example:  I started college unsure whether to major in music or math.  I started out doing both.  It worked great the first semester.

Second semester: I got to my first day of Calculus II a few minutes late, and had to sit in the back.  It was a terrible room, long and narrow, and I felt disconnected from the teacher, and completely lost.  I was a pretty immature 17yo, and decided then and there to drop the class without giving it even a second chance.

Fast forward: I did the music degree, worked in an orchestra job for several years, paid off what I owed a relative for my cello, and went back to school for math and computer science.  I spent a year and a half taking math and CS courses, and got a programming job in my college's IT department.  I found out COBOL was boring, and applied to grad school.

In my personal statement I left out ALL of the above, and talked instead about my interest in combining math and computer science.

I didn't say, If I never play Ravel's Bolero again, it will be once too often.  I didn't say, As a COBOL programmer the closest I got to using my math was calculating GPAs.

Math is the language of science.  Statistics help us make sense of experimental results.  There's plenty of positives about statistics you can talk about in your personal statement.

There is no need to cover whatever meandering route got you to statistics.  All the committee will want to know is whether you are academically prepared for graduate study in statistics, and whether you have the imagination and commitment to do original research.


How to write literature review when several systematic reviews already exist

Your systematic review (SR) need to fill a gap in knowledge that was not covered in the existing SRs.

By filling this gap, you will be building on, extending, and/or updating the existing SRs and the related literature.

Normally, the research question in your SR should therefore be novel and not duplicate of those in the existing SRs. This will produce different and novel findings.

In the discussion/synthesis of your SR, demonstrate how your findings fill the gap, and put your SR in the wider context: your narrow (and possibly wider) field, the exiting SRs, and other related studies.

Also see this question: A systematic review already exists in the literature. When is a newer one required?


My answer depends on how far along you are in your research and whether you are in PhD or MD?PhD program.

If you are in a PhD program and you are less than a year in leave the lab. If you are more than a year in at you next Thesis Committee meeting, if it's scientifically reasonable, try to either set a date for graduating or ask for a co-PI.

If you are in the MD/PhD program, you will have to consider your PI's position and whether a lukewarm letter from someone in his position is worth your staying in the lab. If you plan to go into a competitive surgicial or medical subspecialty, it just might be.

I, sadly, think that checked-out PIs- even those without the excuse of having to go see patients- are increasingly the norm. Getting to be a professor is a great way to age rapidly and burn out, especially in the biomedical sciences. Also, professors aren't selected for their mentoring skills so much as scientific productivity. Often scientific productivity means exploitation or disregard because of self-involvement rather than nurturing.


How to reuse a figure from a patent? Is it free to reuse?

It depends on how the figure is being used.  If it is for non-commercial purposes -- e.g., in a scientific journal to support a study -- then it will likely fall under the 'fair use' provision.  If it is for commercial purposes, such as a book that you are seeking to publish, then it is likely considered commercial purposes, and you will need to work out the permissions.

http://patentdocs.typepad.com/files/memo-on-use-of-npl.pdf


Respected journal uses only a single reviewer and has a high acceptance rate (>85%); could this be an acceptable practice?

By saying

  This incidence demonstrates the poor review process of ApJ

you are already asserting an answer to your question.  What you can say based on the facts you have presented is that the peer review process failed in one instance.  The document you have linked indicates that the ApJ publishes roughly 4,000 papers per year, so one failure per year would represent just twenty-five thousandths of a percent.  Extrapolating based on that seems wrong (and in any case, you haven't mentioned any failures of the system in previous years).

The term acceptable refers to agreement of a group of people.  The refereeing process of the ApJ is clearly not only "acceptable", but in fact accepted, as it is a leading journal in its field.

More generally, should a high acceptance rate be a cause for concern?  Independent of other indicators, I think the answer is no.  A high acceptance rate for a leading journal may be surprising to researchers from other fields.  But it seems the ApJ is mainly interested in the correctness of a paper (rather than, as you say, whether it is fashionable).  So the acceptance rate should depend on the ratio of correct and incorrect papers submitted.  Here of course "incorrect" means fundamentally incorrect and unfixable.  I don't know of any fundamental reason that there must be a large fraction of incorrect papers.

Should the use of a single referee be a cause for concern?  For many (including myself) this is very surprising and goes counter to familiar practices.  But the ApJ is being up-front about this, so any group that wants to change the practice could start a new journal or lobby the editors of the ApJ.  I think this question is one the astrophysics community should handle for itself.  So far, their answer seems to be "no".


When should I register for an ORCID identifier?

PhD is not the requirement to get ORCID identifier. You will need it mostly when you are ready to submit your research work in journals. In my area of research (Computer Engineering) most of the journal has made mandatory to have ORCID identifier.


Own Idea vs Professors Project for Masters Thesis?

Pursuing a topic beyond a school's core competencies (e.g., security) might result in worse supervision. For instance,

Due to the inability of staff to provide the required guidance. That said, at your level, competent staff should be capable of supervising you.
Poorly aligned student-supervisor interests. (Ill-alignment shouldn't matter in theory, but does in reality.)

These risks can be mitigated against, e.g., by finding an external supervisor/mentor.

Beyond your short-term goal (getting a degree), you should consider the longer-term: What do you want to do next? If you want to entertain the idea of pursuing a research career in security, then pursuing a thesis on the topic will help you decide whether that's the right path and will help you get on that path.


What tense should we use when referring to a paper or experiments from other researchers?

I present established facts in present tense, indeed. Other people's work that has led to these facts is presented in past or present-perfect. So for example: "Snippert et al. established a confetti mouse-line, and after doxycyclin administration showed that intestinal crypts tend towards clonality."


Should I tell a senior collaborator how disappointed I am?

From your description ("final deadline") it sounds as though there is no way to fix the situation with the paper. Moreover, you say have decided not to work with this person again (which seems reasonable).

So there is most likely no benefit to be had from expressing your disappointment directly. Frustrating as it may be, cutting your losses and moving on is the better option.


How to effectively explain casual research assistance projects on CV

In order to answer your question, you need to first understand who your CV is written for. If your CV is for you, and you are simply trying to document what you did, then you can simply list each research involvement as something like:

January 2014--July 2014 Research volunteer, Dr. Bigwig's lab. Collected samples from subjects and ran computer simulations. Contributed to 5 publications.

Ideally, you will also be able to list the publications to which you contribute.

If you are building the CV because you want to actually use it for something (getting a raise, getting another job, going back to school, etc.), then you should seek to formalize your relationship with the lab:

Do you have a title? If not, ask for one. Since you say you are being paid, you probably have one already. You should know the title and list it.
List the dates of the appointment. Typically they are for a year or a few years, even if you are only being paid for a small fraction of that.
Since you are currently a high school teacher, you may wish to list your research appointments in a different section of your CV than your teaching appointments.

Good luck.


Students' illicit access to answers for online homework systems

I talked to a group of students about this, with the understanding that of course they would have no personal knowledge of it, but ... er... they might know someone who had experience with Chegg.

Before I had even finished explaining the question, some of them were already laughing. They say that 100% of MasteringPhysics questions are on Chegg, including both the conceptual questions and the quantitative ones.