Is it common that my work is wasted since a collaborator who is the first author does not submit the manuscript that I have worked on?

If your contribution is just to the writing and not to the underlying research then you don't have much invested. However, if it helped you improve your writing skill in any way then it isn't wasted.

But the best way to capitalize on it directly is to stay with the project if it continues but get more deeply into the research behind it.

But don't minimize the impact of the experience. Think of it as an investment that will only pay off longer term. I assume the first author also put a lot into the work and is a bit disappointed also.

But you should verify everything with your supervisor/advisor. Perhaps the other student is being overly pessimistic.

OTOH, discarding work partly done is common enough. Not the norm, perhaps, but sometimes you need to get fairly deep into it to learn that there is less there than first anticipated.


Postdoc salaries/taxes in California (Caltech) for foreigner

The National Postdoc Association has an Overview of Tax Issues for Postdocs that may be a good starting point.

Here it seems that some of Caltech are exempt from federal tax, but I am not sure if this applies to postdoc researchers.

This just means that Caltech itself is exempt from paying income tax. By default (that is, unless there's a tax treaty), a postdoc receiving money to cover living expenses will pay tax on their income. In California there would be both federal and state income tax.

Also, how does one being a foreigner (with a work VISA) affect taxation?

This can depend on whether there is a relevant tax treaty or not, and how long they've been present inside US borders. See e.g. International Postdoc Survival Guide - Beginner's Guide to Income Taxes for International Postdocs for resources.


How can I get the key to my professor's lab?

Couldn't your problems be solved -- or at least, manifestly made your lab director's responsibility -- just with some planning in advance?

You wrote:

  An issue that came up today that made me vent off some steam on the Academia StackExchange. Instead of going home, I stayed after my morning class so that I could go to the lab and get some research done. However, no one was in the lab. I called my lab mates, but they either had work, had their key taken from them, wasn't answering, had gone on a trip... You get the idea. I ended up investigating the lab equipment of an adjacent lab.

(By the way, you had a morning class and then couldn't get into the lab on a Saturday?  That makes me wonder where in the world this question takes place.)

You make it sound like your decision to "get some research done" was made more or less on the spur of the moment.

  This isn't the first time either. One time I had arranged with two people to come the next day: neither came nor informed me. This is especially inconvenient when the lab is on a remote section of the campus.

This time you planned it one day in advance.

  Once, he said that he would give me the key, but only if I came to the lab more often. I explained that as a human I do get tired and need rest: as much as I love research, I don't want burnout either.

All of these things add up to the following conclusion: you and your advisor don't have a clear understanding of when and how often you'll be working.  So you drop by sometimes, find out that no one's there, and maybe that's your fault because somehow you've implicitly agreed to show up as much as you can but at random times.  That's not professional behavior!

I see a rather easy fix: first, agree with your advisor how much time per week you'll be spending in his lab.  If you hear a "As much as possible if you don't want me to think you're lazy" response, you'll have to move the conversation past that.  You can promise in advance to devote XX hours per week -- i.e., you have to figure out in advance how many hours -- to the lab.  (If you and your advisor can't agree on how much time you'll be spending the lab: sorry, but you don't have a wonderful working relationship, you have an entirely dysfunctional one.  But since you have mostly positive feelings about your advisor, I am optimistic that he will listen to reason here.)  Then you need to make a schedule with your advisor about exactly when you'll be in the lab.  If he doesn't want to give you a key -- okay, but then it's his problem when you get locked out of the lab, not yours.  Every time that happens, you don't call up every other member of the lab, you leave, and then the next day you approach him and say that unfortunately you couldn't get into the lab at the time you had agreed upon, so is there some aspect of the agreement he'd like to adjust?

Bottom line: if you model the behavior of a professional rather than someone who drops by when he's interested, you'll implicitly challenge your advisor to be professional to you in return.  It seems unlikely that someone who cannot rise to the standards of professionalism set by a conscientious undergraduate could be a successful lab director, so I am rather optimistic that this strategy will work for you.


Is my supervisor making things clearer or confusing?

When and why would I, as a supervisor, ask students "What's this?" rather than just telling them (assuming that "this" is something I already know about)? The most likely situation is that I can't tell whether the student understands the relevant definition. If I already knew that the student didn't understand the definition, then I'd explain it, but if I'm unsure about the student's understanding, then I might ask questions intended to show me what the student knows or doesn't know. The student might view such questions the way you did, as "making things doubtful", but that wouldn't be my primary intent. (It might be a good side effect; if the student has a wrong idea, causing doubt about that idea might be a good preface to explaining the correct idea or to sending the student to study it.)

I'm worried by the last part of the material you edited in at the end of the question, the part about multiple definitions of the same term, assuming the wrong definition, things not defined in a good way, and a confusion of concepts. This sounds like a recipe for a disaster. I would recommend that, as soon as you see two genuinely different definitions of the same term, you try to determine whether they are equivalent. If they aren't, or if you can't decide whether they are, then ask your adviser to explain. Are there really two different concepts with the same name? If so, which interpretation of the name should you use? Getting the definition clear is necessary before any other work involving that concept; anything built on unclear definitions will be unclear (if not outright nonsense).


What reason would someone who offered you a PhD position give a recommendation letter for another position?

Yes. There is a good chance that they will support you by writing a letter. This happens frequently.

More generally, they will probably support you when it doesn't seem to immediately and directly benefit them, because everyone benefits from a supportive and connected community. People moving between institutions is almost always considered to be a good thing. Even if they lose a good student now, the community is what brings most good students; you and your future advisors will likely recommend your current advisors to students at your new institution(s), for example.


Is there any reference management software that supports hierarchical tagging?

JabRef is a reference manager using the BibTeX format. It uses the concept of groups, i.e. papers can be put into groups, and it allows to create a hierarchical group structure. Since one paper can be put into any number of groups, it is essentially hierarchical tagging.

With JabRef, one can even configure for individual groups whether a group will automatically include the content of any subgroups (analog to tagging), or will include the content of any supergroup (refining), or just include the papers assigned exactly to this group (as in a classical folder structure).


In the United States, how customary is it for professors to not check their emails around Christmas?

Yes, it's common. Many take a break from work entirely during this season. Some reduce their working hours to spend time with family, and only answer urgent email. Some may be traveling and have limited or no access to email. Some (like me) may be swamped with grading and other end-of-semester duties and are focusing on those at the moment.

If you haven't heard back by mid-January, try a polite follow-up then.


Can I upload a pre-print during peer review that includes changes suggested by reviewers?

The link to the Wiley policy states that you cannot update the pre-print (submitted version) with the accepted version: "Authors may also post the submitted version of a manuscript to non-commercial servers at any time. Authors are requested to update any pre-publication versions with a link to the final published article." The update is only a link to the published version. The accepted version can only be posted open access after 12 month as stated in Sherpa/RoMEO.

A version including changes that came in during peer review is no longer the submitted version.


Why does or did Elsevier make PDFs grey and therefore unfit for printing?

This often happens when a document uses the CMYK color space and the black is set as (0,0,0,100).

When you go print in a monochrome environment, the document's color information is converted to grayscale first. Because black ink on white paper can't actually create gray, a halftoning process is applied, where the shades of gray are hinted at by using a circular-like pattern.

Because CMYK (0,0,0,100) black isn't seen as being as black as it gets, in the conversion process, it gets turned into something more like 90% dark gray, and the halftone pattern appears.

Probably somewhere along the production process, someone got their blacks mixed up, and if it's consistent with all their PDFs it could be in the scripted part of the process, there's an issue either between color spaces (CMYK vs RGB) or a conflict between the source documents and the imported parts.


How do admissions to UK PhD programs work?

How does the usual process look like?

Differently.

Are you applying for a 3+1 degree? Or a studentship? Or a normal PhD?
(Note: 3+1 (or 1+3) degrees are a combination of a 1-year Master's and a 3-year PhD. Their first year is equivalent to a Master's, and upon satisfactory performance at the end of your first year, you are allowed into the PhD programme. Sometimes the first year is done at one university, and the remaining three years at another university. Example 1 Example2)

Does the application require a research proposal? And/or a writing/work sample? And/or a personal statement?

Do you have your own funding? If not, what type of funding are you applying for? If the funding applications are separate, do they require their own documents?

Etc.

Would I first contact a professor I would like to work with and then apply to the program?

Unless it is a 3+1 course, then normally yes. You would have to find a supervisor willing to supervise you, and to help you properly form your research proposal.
If you are applying for a studentship, then it is likely that most, if not all, the information needed to write the research proposal is already available.

In 3+1 courses, the applications tend to be much more general. They often do not require research proposal, but rather personal and/or research statements. Also, you typically are not required to get in touch with any of the supervising staff, because the topic of your PhD is decided toward the end of your first year.

And how specific should my research idea be?

Research proposals are very specific. It is rare for students to deviate too much from the core of their research proposals during their PhDs.

To get a broad idea of how specific your research proposal should be, I can tell you that your research proposal would need to have introduction, background, aims, methodology, possibly a strategy/schedule, possibly a section about the importance of the research, etc.

But, many people (and most, if not all, successful candidates) get help from their potential supervisors with forming and writing their research proposals.

How do people do this?

I cannot say how other people did it, but the way I wrote my research proposal was I started with a more general idea, then I read a lot about it, which helped me to reduce it to a somewhat specific idea and to find a couple of possibly suitable approaches to achieve this idea. Then I got in touch with a potential supervisor who pointed me to a few recent papers, which further narrowed down my idea to something that looked like a proper PhD project. He then helped me write my research proposal by providing me with tips and very useful feedback.


Reading (& understanding) a lot of papers is hard. How to deal with it?

The good news is that you have a good 4-6 years of time to learn how to process that sort of material, and you aren't expected to be able to do it immediately.  A professor once told me (about physics papers, but it translates into mathematical and CS papers fairly well) that eventually you start to read the math-heavy parts a bit like music -- you see familiar patterns, and you get the general idea without having to dig deep into the details.

Additionally, you'll find that the more classes you take, and the more reading you do really does prepare you for that next paper and that next step.  You'll find that as you start specializing on a particular topic, most of the papers in your topic will become easier to read, simply because you have the experience and have gained the knowledge about the particulars over time.  Furthermore, you'll start coming up with your own ideas in the subject, and this just happens to be the goal of graduate school!

  There are lots of things (like bloom filters, k-means algorithms, and a lot lot much more terminologies) which we, normally, don't encounter...but are really crucial to understand papers.

The beauty is that you will start encountering them more, and you'll start understanding them more and more as you continue your education.

To answer your particular question,

  Are there people like me who have done/are doing a Ph.D and had the same problem?

I still have difficulty getting through math-heavy papers (in CS), but I either re-read sections closely until I figure it out, or I ask someone to help, or I simply move on and hope that the rest of the paper fills in the details.  I don't expect to understand everything technical that I read, but it becomes easier over time to get what you need out of a particular paper even if you don't get each and every detail.


Where to find successful proposals of previous ERC calls?

Currently, most people don't share their research proposals, whether successful or unsuccessful in their bid for funding.

However, this may soon change in the near future as it has been noted that more transparency would be extremely beneficial for a variety of reasons [1,2].

That said, there's a nice list of publicly available grant proposals in the biological sciences here. None are specifically for the ERC ADVANCED GRANT 2015 though. Figshare is also a good place to check for public research proposals.

UPDATE - There is now also a dedicated website for openly available grant proposals: ogrants.org it is a Moore Foundation funded initiative. One of the grants listed at that site is a European Research Commission Starting Grant (Strategic Predictions for Quantum Field Theories by John Joseph M. Carrasco).

Further Reading

Mietchen D (2014) The Transformative Nature of Transparency in Research Funding. PLoS Biol 12(12): e1002027. doi: 10.1371/journal.pbio.1002027
Gurwitz D, Milanesi E, Koenig T (2014) Grant Application Review: The Case of Transparency. PLoS Biol 12(12): e1002010. doi: 10.1371/journal.pbio.1002010


What are the flaws of working in a research center department led by young principal investigators?

Some of the disadvantages of young professors vs. more senior staff may be:

Less established in their field. One advantage of a very senior professor for a PhD student is that the senior professor often knows all or at least most of the important players in the area. Hence, he can put the student in contact with interesting collaborators, and open up doors for internships or postdocs. A younger professor may not yet have a network that broad.
Less experienced. This one is obvious, but more senior professors are typically more experienced. They have advised many students before, and make less "beginner's mistakes" (e.g., expecting too much from a student, and then getting angry because the student did not live up to those expectations).
Less laid-back. Non-tenured professors need their students to perform, as their own career is very tightly coupled with their students (mis-)fortunes. Many a high-potential assistant professor will not take an unsuccessful research project lightly. This can be an advantage or a disadvantage - an ambitious student and a non-tenured professor may push each other to achieve great results, but the same
professor and a more average student may lead to some friction and bad feelings.
Less money. Younger professors tend to have less research grants (yet). This has implications for you even if you personally have a stipend from another source, as it means there is less money for travel, less money to fund research students, etc.
Less pull in the faculty. This may be more relevant in some places than in others, but I have certainly seen faculties where working with an assistant professor had the disadvantage that your group was at a disadvantage whenever any sort of global resources were distributed. The senior professors were often able to acquire resources (they did not actually need) basically by appealing to their seniority.
Higher chance that your advisor moves. Non-tenured professors are much more likely to change university (voluntarily or due to not getting tenure) than ones that are already tenured. Especially take this into account if the tenure review of your professor is planned for the next years.

These things just came from the top of my head, I will edit the answer if I can think of anything else.

Sidenote: yes, these are all stark simplifications. No, none of those points has to be true for any given young professor.


Is it bad to apply to multiple master/PhD programs in different universities?

Actually it is good to do that. You want to maximize the chances that you get in to a program that will work for you. Applying one at a time means that it could literally take years to get accepted if your top choices don't accept you.

Don't waste people's time with superfluous applications, but definitely apply to places that you find attractive and that you think might find you a good candidate.

Whether you need to pick a supervisor as part of your application depends on both place and field. Do that if you must or if there are attractive opportunities, but keeping your options open might be a better choice if it is possible to do that.


Mentioning a Professor and his comment in a mail without his permission

You should ask permission from Prof. X.

Quoting a statement like "the analytical results are correct" implies endorsement to some degree.

You should be very careful not to say anything that could imply endorsement without permission of the "endorser."

Note that if he does give permission, you still have to be careful not to quote his statement out of context. For example, you should not say

  Prof. X said my analytical results are correct.

instead, you should explain what he really said, more like

  I showed this work to Prof. X. He said that the analytical results seem correct, but not practical, and he suggested that I look into approximation algorithms.


Why would master student spend more than the normal duration to complete master degree?

Here is one more possible reason: the students may be working so much "on the side" that they need more semesters to complete all of the necessary courses.

Not at all universities are students supervised thoroughly or progress is checked regularly, so that working part time and studying part time is possible even when not explicitly studying for a part-time degree.

It is not difficult to imagine that when working 50% of your time and studying 50% of the time, it takes twice as long to complete the course of study.

Obviously, it depends on the rules and regulations of the university and/or course of study whether this is a possible explanation. As an example, my undergrad course allowed this, and the average duration of study was 85% above the normal duration of study, mainly because so many students studied while working. It was a STEM course. I know of on case where the student actually spent 2/3 of the time working and 1/3 of the time studying.


Why is the variability in faculty salaries between STEM fields so high?

Every job position is it's own little economy, and to understand it fully we basically need a wide-ranging understanding of economics. But we can at least hit the most obvious and easily understandable points, so long as we are clear that each position is distinct and unique in it's own right.

Let's say you need to hire a Professor of Basket-Weave Engineering. How much do you pay them? Well, I say we offer to pay them a $1. Ah, but that would be below minimum wage requirements generally, so that'd be illegal...ok, let's pay them $20,000 a year then.

Why pay them any more? Well, in short, we have a number of problems:

1) Quality of candidates - the best in the field just aren't willing to work for so little, they likely won't even apply even if they were rich because such a low salary indicates a lack of respect and seriousness of the position. So you likely won't get your desired quality of candidate.

2) Quantity of candidates - with such little pay you probably just won't get enough qualified candidates to seriously interview.

3) Actual acceptance - even if you get enough good candidates and make an offer, there is a good chance they won't accept at all because they have better offers.

4) Perception - national rankings and general public perception can be involved. Do you want to become known as the institution with McProfessors who are paid in beans?

5) Turn over - even if you get good people to join, they will likely leave when they get a drastically better offer. Even the most die-hard of loyalists will have trouble turning down an offer that's 4-10 times the salary they get now.

But why are similar positions paid so differently?

Each of the simple 5 conditions I outlined above vary by individual position. A Computer Engineering professor is just not the same as a Chemical Engineer - they are both engineers, but they have very different market factors involved.

Let's say they start off the same though, and you are able to hire and retain both at the same rate of $50,000 a year.

Now let's say IBM wants to put someone in charge of a next-generation computing research lab - will they want a Computer Engineer or a Chemical Engineer? I think it's pretty clear that they may very well have a preference for one particular type of engineer. The research produced could earn them billions, so they'd be happy to pay easily $500,000 a year for the right candidate. Not to be outdone, Intel, Microsoft, Google, Oracle, and a dozen other big-name computer companies also want the same kind of candidate, and all are willing to pay the same.

Now you have a problem. If you want to hire a Chemical Engineer, nothing has changed - $50k seems to get people just fine. But if you want to hire a Computer Engineer, you are now effectively competing with dozens of companies willing to pay 10 times what you pay.

One method of dealing with this is to ignore it. Sure, you'll lose the most money-motivated or even the best candidates to companies, but you'll still be able to get what you want. But what if more and more companies want computer engineers? What if it gets to be that there's a shortage of above-average candidates, and so industry will throw stupid amounts of money at any computer engineer who seems even vaguely above-average? You'll be left with only below-average engineers or ones who are outright hostile towards industry. If you expect to get grant money and support from industry partners, you are going to be in trouble either way.

So it might turn out that it easily makes sense to pay $200,000 a year to get a Computer Engineer (because, frankly, you have no real other choice anymore), but why would you pay any more for a Chemical Engineer? Their market hasn't changed any, so why waste money?

Complements and Substitutes

But now we also realize something interesting. While the tech companies prefer computer engineers, they realize that IT engineers have similar knowledge and work almost just as well. They might still prefer computer engineers, but with less demand or less pay they will make use of them too (even if they were still working slightly outside their field!).

Now you will find, thanks to the concept of substitutes, that other fields are being effected by the tech bidding wars. Pretty soon you'll be paying $150,000 for IT engineers. But what if tech companies realize that, sure they prefer the specialized knowledge of computing and IT people, but research is research - why not identity suitably brilliant Chemical Engineering PhDs and hire them? Sure it might take them a little longer to get up to speed in the field, but whatever - they may still prefer other fields, but they'll take what they can get.

Next thing you know within a few years you went from paying everyone $50k to having to pay no less than $200k for a Computer Engineer, $150k for an IT Engineer, and $100k for a Chemical Engineer - minimum! Any less and all the really desirable candidates pass your institution over with ease as the other offers they get are just too high. Meanwhile professors whose primary role is teaching CS101 still command little more than that $50k, because industry just isn't super excited about people who can teach entry-level courses.

And what if other institutions start competing for top candidates, just like the industry has been doing? As Artelius points out, Baumol's Cost Disease is a hypothesis that seeks to explain increases in salaries when productivity of the job itself hasn't changed, if you are interested in further reading.

This little fictional story isn't far off exactly what has happened not only in Engineering fields, but all fields. My own adviser once pointed out to me that even people who do the same job, in the same field, get paid differently based upon what program they earned their final degree in - Psychology faculty just get paid less than Business or Engineering folks, even if they both work in the same exact applied research field.

People Are Different, Want Different Things, and Value Things Differently

Ultimately this is the bottom-line - people with similar titles are not paid the same because our system is based upon relative values of individuals, groups, and the economy as a whole. People are different, want different things, and don't assign the same universal value to all things. One agent might not be willing to buy something for more than $10, while another agent considers it a steal to get that thing for less than ten times the price!

Even more importantly, no one really wants to pay more than they have to to get something they want. It is almost universally true that if someone pays X for something, it's because they didn't think they could get an equivalent thing for much less.

And we got to this wide variance in salaries even while ignoring concepts like price-based value perceptions (national rankings that weight faculty pay as part of their rankings, for instance), vanity/political capital (deans or department heads who believe larger pay and budgets means more esteem and rank), paying a premium up-front to reduce turn over due to cost considerations (don't want someone in charge of a big funded research lab to leave every few years, so you make sure they are considered extra-well-paid so they don't jump ship), or even differential income value of a position! Not all positions bring in the same amount of community support or grant money, nor do all departments get the same support from higher-level administration (MIT just might not care that much about their history department but considers their robotics department mission-critical, for instance).

But even if we ignore all these factors, the simple 5 factors at the beginning of this answer are more than sufficient to explain a difference in faculty pay, to say nothing of differential industry valuations/competition. The true reason faculty salaries differ so much is due to a combination of all these factors and more.


How to call colleagues who was once your professor or advisor?

[ My updated answer after the OP updated his location and more info. ]

First, congratulations on your Ph.D. That is wonderful. :-)

In Asia, in generally, you probably should always call people, who once were your professors, with the title "Professor/Teacher/Doctor" at colleges, at commercial companies, or even in general social settings.
Note: Even if they are no longer your professors now, and they are working either at the same colleges or in the business environment with you as co-workers, perhaps, it is still a good idea to call them "Professor".
Generally speaking, that shows the respect and gratitude toward your former teachers/professors in Asian culture.
In my country in Asia, I have seen one University professor calls his former college instructor "Professor/Doctor" all the time. They are both teaching at the same college now, and getting along very well as both co-workers and former teacher/student.


Asking about a colleagues post-grad work?

It's perfectly fine for people to be willing to share more "closely-held" details, just as it is perfectly fine for people to be unwilling to share.

Let's take the position of the person you are asking:

they might not want to tell you the salary, because it feels freakishly large to them after living on a grad stipend (or even compared to common academic salaries), and they don't want to make you feel bad or envious
the salary is low compared to what they hoped or thought would be common, and they don't want you to think less of their success or options
the person isn't sure they are supposed to share the non-public hiring data, and most places don't tell you in the hiring process "hey, feel free to tell everyone details of your work and pay!" - so they are concerned they aren't supposed to answer (while many Universities publish salary data as part of open records laws, private industry routinely hides this info)
point-blank asking someone something that they might not feel comfortable asking is often considered rude or excessively direct, especially if you do not show in some way you understand you are asking for something potentially sensitive, and especially if you don't give them a way to save face in declining to answer

To have better luck, I suggest a script something like this:

Setup why you are interested in more details. "I'm going to have to be evaluating offers soon, which is so tricky when you don't know for sure what to expect."
Ask in a softer, less direct way, that makes it clear you understand if they don't want to answer fully. "If you wouldn't mind, could you tell me about your offer?" This sets them up to be vague if they don't want to give details, like saying, "oh yes, XYC Corp is very generous" or "it certainly will be nice not to be on a stipend anymore!" Not helpful, but it puts people at ease.
Some people will just tell you out right, while some will be circumspect. If it's really information you want, you can push a little, with something like a little conspiratorial lean in, and a more direct "just between you and me...can I ask you what the pay is?"
If they tell you, thank them for helping you with valuable information, as this part of the process is hard and often vague. If they don't tell you, it's generally safe to reinforce you understand and 'let them off the hook' with a "totally understand, I don't want to pry". If they let you in on inside information, don't go blabbing about it to everyone, and keep your sources to yourself.
If someone asks you later for second-hand knowledge, be respectful of the fact that not all information is meant to be publicly available. If you aren't sure that you should yourself pass on the information, you can generally safely give a referral. "Oh I'm not sure, but so and so started working there, so you might ask them." Networking.

In closing, I will note that you are in fact correct that this is a cultural thing, and the norms vary. In the US business world it is common to treat salary info like something akin to a state secret, even though some are fine with talking about it openly and directly. I'm told that in east-Asian countries it's often the opposite, where it is commonly to openly discuss matters of pay as it's not considered so private.

As you go you just have to be aware of how people react to things and how people seem to act, and practice finding ways to navigate such varying cultures, as even workplace-to-workplace things can be very different. General rules of diplomacy and tact still hold, they just take practice and awareness to develop and apply as needed.


Overly long review process (>2 years) without feedback

Perhaps the time for being polite is past.
Ask them for a realistic projection about a decision. Perhaps even mention the impact of the delay on the careers of junior members.
There might be reasons for a long delay, but not for a long time between communications. Don't ask for an immediate decision unless you want to risk the inevitable rejection.
But it is their responsibility to choose reliable reviewers.
But if your paper is especially esoteric, making it hard to find suitable reviewers, then starting over will also lead to long delays. If that happens, keep a tighter rein on the process.


Many books are published with something like "translated from the original Spanish (French, German, Italian) by A. N. Author" so go ahead.


How do I know if my research skills is valuable in industry if majority funding is from government?

While I am no expert in material science, I know that a lot of people leave academia and very few of them do exactly what they have done before.
So I would not worry too much, especially as you are already on the applied side.


Reporting a student who may be psychologically disturbed

The "administration" is probably the wrong place to look. Instead, see if you your institution has some mental health staff, whether just associated contacts, or counselors, or even a dedicated behavior concerns advice function, to get proper advice. If the university is well-organized enough to have one of the latter, chances are they've also established policies requiring you to pursue this. And such an advice line would be well suited to tell you how to go about it. If your university doesn't, figure out where to report it.

Note that, unless your institution is highly dysfunctional, reporting concerning behavior and having a professional talk to the student in question shouldn't be considered a punishment, but a safety net.

As Buffy points out in a comment, the law may further require you to do some things, and avoid doing other things. While one would hope that the mental health support staff are well-informed, contacting the legal staff (University Counsel) may be useful. That said, as a non-lawyer person, I imagine most legal pitfalls concern naming the student when you shouldn't. Your initial inquiries need not include the name of the student, until you're convinced that you should.


How to be efficient as a graduate student juggling classes, TA and research?

When your work is way too difficult to achieve your goal of the day in your allotted time

... get used to it. If you are an interesting person doing interesting things, there is never going to be enough time for all the things you want to do. And as soon as the work you're doing now starts to get easier for you, you'll get new, more challenging responsibilities :)

You won't be able to manage your time more effectively until you get a little better at estimating how long things will take, so start there. It's pretty common to underestimate how long things will take - try quadrupling your initial estimate, and see where that gets you.

When you can judge more accurately how long things will take, you will be in a better position to manage your commitments. Once you realize that your homework takes you 8 hours, not 2, you will be able to plan your week accordingly, without feeling guilty when you invariably have to drop something else in order to do your homework properly.

In the meantime,

  Keep forgiving yourself and keep working

That's from this answer by Piotr Migdal, which I highly recommend you read.

  I miss dinner, I sleep late, and the efficiency just plummets through the week.

You don't need me to tell you the answer to this one. Take care of yourself. For more details, see How to prevent physical/psychological health side effects of workaholism in academia and research?.

  do you switch work, or do you keep going?

It helps to have tasks you can work on when you are low on intellectual energy, but that are still more productive than staring at reddit. Here's a list of ways to procrastinate productively.

Ultimately, though, if you need to take a break to recharge, just do it - then you'll get back to work and be much more effective.


Why some papers are retracted and others not?

In general, an editor will choose to issue a retraction when misbehavior or errors undermine the "core" of a paper (authors may request a retraction, but ultimately it is generally the editor who decides).  An erratum or correction, on the other hand, is for when there is a problem that doesn't change the "core" of the paper.

Different editors will draw the boundary differently, and some things are in a grey area.  In this case, it looks like reuse of background material (a grey area on self-plagiarism) shaded over into plagiarism from another closely related piece.

In most cases plagiarism, even of a background section, would be enough for a paper to be retracted due to the issue of dishonesty, which cases doubt on everything else in the paper.  In this case, however, it appears that given the close relationships between the authors and the papers, the editor judged it less a matter of theft than of sloppiness, and opted for the lesser correction.


The meaning of "paper" in the context of undergraduate students

In this New Zealand context, a paper is a course and the terms are used interchangeably, usually with one or other being the formal label at any given institution and the other in common use as well. In either case, it is a single class that can be enrolled in individually, with its own final grade, that can be credited towards a degree, diploma, or certificate.

For reference, we can see this guide from Victoria University of Wellington:

  Courses are blocks of work that are taught over one or sometimes two trimesters—they’re often referred to as ‘papers’ by other universities.

or this glossary from the University of Canterbury:

  Courses are 'classes' or 'papers' that involve blocks of lectures usually taught over one semester.

as well as the University of Waikato's Catalogue of Papers, which lists all the courses they offer, or the similar "Search for a paper" page from the University of Otago, and similar items for the other universities.

It does not refer to an exam or to a term paper. "Exam paper" does refer to the physical document given in an exam and the set of questions on it, but never "paper" alone. All of these terms are often used differently elsewhere.


Using fragments of online images in a paper

As @jakebeal stated in his comment, the copyright for old maps from before 1900 should be expired. I can only comment on base of German Copyright Law:

70 years after the death of the creator, the copyright has expired.
A picture of a 2D object (for example a photograph of the Mona Lisa, a facsimile print of an original Luther's bible, a photocopy of an old map) is not protected by copyright since the threshold of originality is not reached. The aim is to reproduce the original as exactly as possible, hence there is no novelty and no input of ones own creativity. It seems, US law is similar here.

Conclusion: if your map is older than 100 years and copyright has expired, you would not have to ask the company for permission.
In case the map is not as old and copyright still applies, you would not be allowed to modify (also not to crop parts of it) the original without the consent of  the copyright owner.

Any way, you have to cite the source (the original creator of the map, not the company providing the copy).


Is it appropriate if my former advisor is editor of a journal I submit to?

I don't see any conflict of interest on your side preventing you from submitting to this journal. You can only assume that your former advisor has good ethics and will abstain from handling this manuscript.

Consider the consequences if someone you had a close working relationship with being on the editorial board would prevent you from submitting to a journal: many senior scientists could not submit to any journal in their field.


Is it necessary to wear a white shirt inside the graduation gown for Masters degree graduation ceremony?

Faculty do not ask and students do not tell what they wearing under the robes.

Actually, I find that since graduations are in May, the robes are often swelteringly hot (especially PhD robes) in many parts of North America, so the lighter the clothes and the more sweat-resistant and breathable the better. Women can get away with wearing summer dresses. From what I can ascertain (remembering the Don't Ask/Don't Tell rule above), male students tend to wear khakis and comfortable dress shirts underneath. No need to wear long-sleeves if it's going to be hot.

Many students often change into other clothes for the receptions after graduation -- men into longer pants and a sport jacket, women don a light jacket or change into more formal attire. They often keep a change of clothes in their parent's car or in their advisor's office if the dorms are shut.

tl;dr: It's your graduation. No need to be uncomfortable.


What does it mean when a STEM researcher has a lot of "solo" publications?

The normal number of co-authors, if any, is very specific to the different (sub-(sub-))disciplines. In my specific sub-discipline it is normal to have a number of solo publications and a number of publications with one, maybe two, co-authors. But in the same department we have people who do primarily qualitative research and they tell me that it is very unusual to have co-authors and they cannot imagine how that would work. From the outside we would both be sociologist, but even within disciplines there are big differences. In other disciplines it is normal to have 5 or more co-authors. So the number of co-authors per se does not say much without also considering the sub-sub-sub-sub-discipline that that person works in.


Of course, you can use existing theses just like you would a journal article where you extract information to guide your research. However, I'd like to focus discussion here on the role of theses as a tool for teaching you how to write your own thesis.

Choosing theses to deconstruct:
Assuming you are writing a PhD thesis yourself, it can be really helpful to find a selection of other PhD theses in order to give you a sense of what the overall product can look like. Three is a good start, but I would be aiming to find about six or seven. The best theses are probably those that are

on a similar topic or at least in the  same discipline as your thesis and with a broadly similar methodological orientation
follow a similar structural framework to your own (e.g., similar length, same in terms of whether it is a large thesis or PhD by publication)
well written

Things to learn from deconstruction: Carefully deconstructing such manuscripts can teach you a lot about both what a thesis involves and also what are some of the alternative modes of presentation. For instance you can look at things like:

How was it formatted
How many chapters were there and how was content distributed
How were aims presented and how was the importance of the thesis justified
How was literature, method,results, and discussion distributed (e.g., some in each chapter or over separate chapters)
How extensive or focussed was the literature review
What was the overall scale of the thesis (e.g., amount of data collection, sophistication of analyses, etc.)
What is the standard expected of a thesis (e.g., seeing the imperfections of  theses that have passed can be helpful should you fall victim to perfectionism)

When in candidature to spend time deconstructing:
In fact, examining and deconstructing theses can be a useful exercise at multiple stages of your PhD candidature.

At the very start of your PhD it can give you a broad feel for what it is that you are aiming to produce.
When you are moving towards setting out the overall structure of your thesis in terms of chapters and sections it can give you a feel of whether you are on track
When you are making formatting and stylistic decisions, existing theses can provide a useful frame of reference.


How much is submission acceptance to high-profile conferences influenced by internal politics?

It is an often-heard prejudice in CS that many of the top conferences are relatively closed "boys clubs". Indeed, if one just looks over accepted papers for multiple years, one typically ends up seeing the same affiliations over and over again, strengthening this impression.

However, this could be due to a number of (good or bad) reasons:

Papers from professors / labs that are well-known in the field may simply be of much higher technical quality, making it quite natural that they also get accepted much more often.
Professors / labs that are well-known in the field generally know how to write papers for this specific conference. They know what the TPC values, and how to present their results in a way that is appreciated in the field. As these professors are typically in the TPC themselves, they know what kind of papers usually get accepted and which are rejected.
Professors / labs that are well-known in the field often have a better grasp on the existing state of the art in the field, making it easier for them to identify what is good and novel. In my experience, "outsiders" have a tendency to overestimate the novelty of their contributions significantly. Further, well-known labs know what problems are currently en vogue in the community.
It is of course also perceivable that papers from well-known professors / labs are just not judged as critically. For instance, a reader may very well think that a paper is not applying a given technique correctly, but as the paper comes from the group that invented this technique, he gives them the benefit of doubt and assumes that they will know the technique better than him. He would probably not extend the same favorable thinking to an outsider.
Finally, for some topics, it is just easier for some labs to do good research than others. A common example are the web search tracks at the WWW conference. These tracks typically require the validation of new algorithms on real data, to which mostly only industry labs from Yahoo! etc. and their close collaborators have access.

Note that none of these reasons is really politics. Indeed, I would argue that all of the reasons above are significantly more likely than a paper getting rejected for the reasons you cited.

  I assume in good faith that most of the editors may not reject papers without reading them

I would say, at a top conference such as CHI, you can rely on your paper at least getting reviewed thoroughly, yes.

  but does anybody concur with opinion of professors at my department?

Well, given all the reasons above, it is indeed quite likely that your paper will be rejected. By definition, if a conference has a <20% acceptance rate, rejection is always a real possibility (clearly, it happens to most submissions). However, I am wondering why it would be better to not even try if you think your work is good enough for CHI. If the paper gets rejected there, you can still re-submit to a lower-tier venue, and you receive a number of hopefully helpful reviews. The only disadvantage I see is that it prolongs the publication process by half a year, but if you see any chance of the paper begin accepted at the top-tier venue, I think this should be worth it.


How to learn technique from papers (technical fields)?

When you were an undergraduate, studying (I assume) math, the advice you got was good. Read a lot of papers, somewhat superficially, to get an idea of what it is possible to do and how to go about it generally.

But now that you are in a graduate research program you need to do more. The basis you get from textbooks isn't enough to get you to the research frontier in mathematics. It won't get you very close, actually. So, to approach the research boundary of what is known, you need to read (a few) papers fairly deeply. For advanced work, elementary, textbook, techniques may not work. So, you need to delve into the proofs of things to see if there are new and interesting techniques that you need in your own toolkit.

But, as you read a paper there are some things you need to ask yourself, beyond the question whether everything is correct. The big question is whether the paper is complete and is the last word on a topic, or can it, perhaps, be generalized in some interesting direction.

Another big question is whether the techniques used in the paper (not the results themselves) can be used and modified (extended) to solve other similar problems. In this sense the proofs in a math paper may be more important than the theorems.  And it is why some new proofs of old theorems are extremely important. The proofs open up new areas of exploration.

Another area of research can be opened up by comparing two papers and examining whether there is a possibility to combine what the two say to come up with something new and interesting. This may or may not require a deep reading of the papers, of course.

To do math research requires insight. Basically, it means being able to find things that might be true but haven't been proven true. Various limitations of logic make this harder than it might seem. So, when reading a paper, another question to ask is "What led the author(s) to think this might be true?" Why did they think it something worth time studying? That can lead to insights.

But, math research, of its nature is narrow and deep. So, you often need to do deep dives into ideas to discover whether there is something hidden but worth exploring. What works for a textbook learner doesn't get the job done for a researcher.

Caveat: This applies to mathematics and some theoretical aspects of other technical fields. I'll make no claim about "technical fields" in general.


Recommendation Request and Academic Misconduct

If you are willing to strongly recommend the student for graduate study, despite his past cheating offense, then tell the student you are willing  to write the letter, and then write the letter.

Otherwise, tell the student you are unwilling to write the letter, and then don't.

Your edit clarifies that you are unwilling to write a strong recommendation letter, because of the student's past academic misconduct.  I suggest telling the student, "I am unwilling to write you a strong recommendation letter, because of your past academic misconduct."


What should a good theoretical Physics project for an MSc. Physics student look like?

A good way to pick a specific project within a broader area of interest is to find some potential supervisors whose groups are within your desired field, look through their recent publications in the area and their group homepages and see what takes your fancy.

For example, say I am interested in doing an MSc in inorganic catalysis, but don't really know what specifically there is that I could study in that area.

First I go onto my alma mater's homepage (or another desired destination) and see if there are any groups in the Chemistry Department who are interested in inorganic catalysts.

Next I see specifically what particular aspect of the catalysts they are involved in, be it synthesis, computational design, toxicity, etc. I look at their recent publications, if one title catches my eye, or particular paper is really cool, I add that group to my 'possible projects' list. Do this until you have 2-4 possible supervisors/projects. You might even get an idea for a project on reading one of these papers, which you can say you wish to discuss when you contact them.

Then I contact the heads of the groups directly, detailing briefly who I am, something along the lines of:

'I am writing to you to ask if you are currently accepting graduate students because I wish to pursue my interest in inorganic catalysis by applying to the University of blah to undertake a MSc in your group.

I am a recent graduate of blah with a 1st/2.1/2.2/rubber duck/etc. I attach my CV but briefly --short list of most notable and relevant achievements if any--

I recently read your group's paper on blahblah --something that indicates you actually read the paper and thought about it-- and have some ideas for a project I would be interested in discussing with you.

Grateful for the opportunity to explore further possibility of working in your group --propose contact options, indicate if possible that you would be willing to visit, this being the best way to sell yourself and find out a bit more about the group to see if you think it would be a good fit: interviews are a two-way process

Yours Sincerely

yaddayadda'

With respect to what your project will look like, that doesn't need to be much more than a rough proposal until you actually have a place, after which you will need to write (possibly with your supervisor's help) what essentially amounts to a mission statement for what you are setting out to do, why you want to do it/what you think could be gained. More specific guidelines will probably be available on the Department or University homepages.


Collaboration on a suggested project - problem with a colleague

I will come at from the other direction. I will assume that your summary is correct, and that this person truly did nothing other than point you to a question that had already been posed in published work. In this case, you are under no obligation to work with him. You must be careful to cite his work appropriately, and probably acknowledge him in the acknowledgment section as having suggested this line of research, but I don't think he has a legitimate case for co-authorship.
That said, he could still create a messy, public confrontation. So, I would send a note like this:

John,
Some time ago, we discussed collaborating on an effort to prove [blah] as an extension of your work in [blah]. So far I don't think either of us has made much progress, so I wanted to reach out with you about resurrecting this work.
At this point, I think it would be best if I tackled this on my own. If successful, I will write up a paper that cites your paper, and will acknowledge you in the acknowledgments. What do you think?*
-Name

Depending on whether you are willing to consider working with this guy, you could also replace the last sentence with:

If you would prefer to collaborate on this paper as a co-author, we can discuss, but I am hoping to publish in the next ~6 months, so we should meet ASAP to discuss what you will contribute and when it will be ready.

Then there are a few possible outcomes:

If he ignores you, or says "good", then all is okay.
If he claims to be interested in collaborating with you, you will have to discuss this with him.

You may need to be fairly aggressive in telling him that you don't think collaborating will be feasible, but better to have this argument now and in private, rather than after publishing without him.
If you are willing to give him a chance, you can try to define his contributions and the deadlines now, and let him know that if doesn't have satisfactory material by the deadline, you will publish your results without him. If he is serious about working with you, then this is reasonable; if he is lazy as you say, he may withdraw his objections.

If you cannot come to terms, or if he reacts very poorly, then you can decide whether you want to risk a nasty, public fight over authorship, or whether you want to drop the line of research.


Is it good to take a project even if the topic is not what I'm interested?

Sounds like a LOT of negatives in addition to the one in the title even.

Just responding to the one in the title, I would say to do a project that interests you.  Of course be smart about not picking something that involves a jerk advisor, unlikely to work, or 10 years of apparatus building or waiting for next Space Shuttle (even if you like the topic).  But in general, pick something you like.

That one looks like a dud.  Go talk to several more professors.  Have fun scheduling some meetings and talking to them.  Many of them like talking about their stuff and will pitch you on something or even mention a few possibilities.  You need to get a few options in front of you and choose the best one.  For one thing running this process will show you what is available and help you compare by contrast.  Don't marry the first girl you date.  Well, except I should have, but she was special!  ;-)


Refusing a research project and/or assignment because of personal convictions

Standard IANAL disclaimer (I’m speaking from anecdotal experience and could be very wrong).

I had a student who recently refused to work on a political dataset because of her political views. I could’ve told her that this was a material part of our work and she has to do it or I can’t advise her. I don’t think there would’ve been any repercussions to me if I did. Generally speaking, if an advisor doesn’t want a student the reasons why aren’t very relevant, it’s best to part ways.

Eventually I chose not to and assigned her to another project. Did her academic progress suffer as a result? Sure. She made a choice and is paying some price for it.

For funding/collaboration, I can hardly see what legal protections could exist. If you choose not to apply for a DARPA grant or work with anyone there, you can’t reasonably argue any grievance as a result. Say, if you’re up for tenure, saying that you didn’t secure any funding but that’s only because you refuse to work with DARPA sounds preposterous.

A similar case goes for boycott movements (e.g. BDS). My field (computer science) has a very strong Israeli presence; if you’re a BDS supporter it may limit your future academic  prospects. No one can force you to collaborate with Israelis, but in some cases, it may become very difficult.

In the end, nothing in life is free, and you need to decide how important are your personal convictions vs the price of following them.


What do people usually wear to conferences?

It depends a lot on the event (some gatherings are more formal than others) and on your status (win a Nobel prize, and you can wear anything you damn well want), but in general, you're not really expected to wear anything fancier to an academic conference than you would for a normal day at work or in class.

In practice, most people do tend to dress up a little bit, just to look their best, but still, even if you just wear your normal clean everyday clothes, you're not going to embarrass yourself (any more than you usually do, at least). As the other answers note, "smart casual" is the usual style here.

Nothing says you can't wear a suit if you want to; I see people do that all the time in conferences. Then again, some of those people also wear a suit to work every day, so...

Still, if you're in doubt, why not ask your advisor (or someone else in your group who's been to similar events before)? That's part of their job: to teach you the basics of academic work, which certainly includes presenting your work at a conference.


As a student, should I offer alternative ways of understanding a point in lectures?

If you are in a small lecture that encourages participation, then it is definitely appropriate to participate, and understanding things in more than one way is often a great thing.  I would recommend phrasing your thoughts as a question rather than a statement, however, e.g.:

  Would I be right in understanding this like [comparison]?

After all, you're only just learning the material and don't yet know if your comparison is actually right!  If you can concerned that you might be talking too much then a) a very good lecturer may be able to let you know gently in the midst of class and b) you can ask the lecturer their opinion after class.


What kind of content should one avoid when publishing (math) notes online?

Copyright protects published texts and images, not the underlying ideas. A concept such as a "Fourier transform" cannot be copyrighted, no matter how it's written or described. However, what you cannot do is republish the material that's been put under copyright without obtaining permission, or demonstrating a clear fair-use case. For instance, one or two short, relevant quotations that are properly cited in a 50-page manuscript will not get you into trouble. Reprinting larger amounts or more complicated material (tables, graphics, etc.), however, should be done via a copyright request to the publisher.

You cannot reprint the text of problems that have been published elsewhere (unless, of course, it's sufficiently generic that it could be found in multiple books. For instance, the following text would not likely be copyrightable:

  Prove that a connected open subset of R^n is pathwise connected.

for the reason that there is no "unique" or "original" content here; literally any book in the field could pose the same problem in exactly the same way. However, a longer, more detailed statement of the problem, guiding you through specific steps, would probably not be publishable.

On the other hand, the solution of such problems, so long as they represent independent scholarly work, need not be "suppressed." Again, copyright applies to the authors' wording of the solutions of the problems; the method for solving them cannot be copyrighted! If you solve them yourself, and publish your own solutions, that's not violating copyright. (There is the issue of making the lives of future students easier, because you're publishing solutions online that they could plagiarize from, but that's a separate issue from if you're allowed to publish such material.)


How to educate bachelor and master exchange students from Asia?

I teach at a university in Asia and I could say the exact same thing about our European/American exchange students.

Quite simply, exchange students have very different incentives from regular students. They often convert their grades to a simple pass/fail on their transcripts so they just need to pass the class (we get students from very reputable institutions in the US Canada and Europe, I was surprised to hear about that practice at first). In addition for many of them it’s their first time in a new and exotic location. They want to party and travel. With all due respect, lectures are the last thing on their mind.

Some of the exchange students are hard working, but I would say that they are a minority.

To conclude I think your question has a bit of a cultural bias to it. European students can be equally annoying in an exchange program.

Edit: the question is biased because it seems to attribute this behavior to the students’ “Asian-ness” rather to them being in an exciting foreign country, away from their parents, dealing with a new language and academic practices, and all that within a few weeks. All of the bad practices the question describes can be easily observed in European/American students who come on exchange to my Asian university. Also, lumping together all students from Asia (or even just India/China) is completely inaccurate, and an over generalization of a group of people constituting the majority of humankind. I would suggest that the OP revisit their own beliefs and consider the circumstances under which they observe this group.

By the way, we also get exchange students from China and India. Surprise! they do fine in general, because to them our university/location is not particularly exciting or different! It’s like if an American student had a semester in the UK. Sure it’s different, but a lot of things are the same. Have you considered that option?

Edit 2: (reflecting OP's edit and discussion below)

There are, of course, cultural differences between Students from different cultural backgrounds. By and large, students from China tend to be quieter and ask less questions (this is especially true for female Chinese students in my experience). There are several great suggestions in the comments and in other answers: listen to them, do not be confrontational, try to schedule office hours where these students might feel more free to interact with you.

With all this out of the way: I think that the solutions offered above are not quintessentially unique to handling Asian students. They are excellent approaches to handling any reserved student, regardless of their background.

Moreover, exchange students (American, European, Asian or African) tend to be  more difficult than regular students (as I describe above). This is a far more important factor in this equation than the cultural parameter from my own limited experience.

I think it's great that the OP is looking to improve their teaching, I just don't think that the difficulties have so much to do with cultural differences as they do with the universal difficulties that arise with foreign exchange students.

As an aside, there are some comments in the threads that are very close to sounding like "I'm not racist, but...". In my opinion, that is unfortunate.


Using previous student essays as examples

Good question!

I ask students individually by e-mail if I can use their essays as examples for future classes. Almost always they are thrilled and happy. Then again, I only ask people who serve as positive examples. But I think if you explained to an ESL student that they have the bones of a good essay and that you would like to use it as a sample essay for future students to work on to help improve, I think they would be similarly pleased.

This would be more problematic if I wanted to use the examples in a textbook, used negative examples, or if I posted  essays publicly on the internet. Then I might want a stronger version of a copyright waiver, such as what your previous school uses.


According to the New Oxford American Dictionary (that I have by default on my Mac :)):

  The spellings adviser and advisor are both correct. Adviser is more common, but advisor is also widely used, especially in North America. Adviser may be seen as less formal, while advisor often suggests an official position.

Since it's an official position, I'd rather go for Ph.D. advisor


Correct abbrevation of academic titles, e.g., “B.Sc.” vs “BS”

It depends on the degree and the context.  Different institutions sometimes have different conventions for abbreviating their degree names.  For example, Harvard writes A.B. while Yale writes B.A.  It's conventional to use the abbreviation suggested by the university that awarded the degree.

Issues such as the use of periods are a matter of style.  If you are writing for publication, you should follow the publisher's house style.  Otherwise, you can decide whether you prefer to use periods.  However, you should keep in mind what other people are doing (for example, including periods is more common in the U.S. than other English-speaking countries).


When you plan to reuse a figure taken from a journal paper, you should first ask permission to the copyright owner which, in most cases, is the journal publisher. Every publisher has its own procedure to make such a request, but usually you will be at least asked to specify where you want to republish the figure (in this case, specify PhD thesis).

The publisher will typically grant permission to reuse for free and it will also specify how it wants its copyright to be stated. Here are a couple of real examples:

  Reproduced with permission from [1] ©IOP Publishing. All rights
  reserved.

  © 2018 IEEE. Reprinted, with permission, from [1].

If your citation style is non-numeric, substitute the appropriate citation style.

In my experience, many people frequently overthink this procedure, as though obtaining the permission to republish could involve going through an obstacle course race, and sometimes they plan to spend hours to redo a figure which is just a few clicks away.


Submitting a paper without your supervisor knowing, ask for help

Let's go through it one by one:

  How can I include his name?

I think he has already made his viewpoint quite clear, when you quote "I suggest you not to submit because you will burn your name and this is horrible works, etc. He then said if you insist on sending it don't put my name"

So, please don't do it. Any academician would be horribly pissed off if he saw his name appear on a scientific article which he himself deems "horrible", or in more polite language, unworthy of having his name on the author list. You are assuming some malicious intentions on his part, but please try to understand that he may have some very valid reasons for saying what he said.

You are only starting out, and are yet to make a name for yourself, but presumably he already has made one. It is a well known fact in academia that respected researchers would prefer not publishing to publishing a mediocre work. That's because, ultimately in academia, a person is only as good as his work. An average work would be taken to mean that the person doing it also has average abilities.

The last thing he would want is to have his reputation being smothered by an overzealous student, who went ahead and presented something prematurely, and puts it across as done by me under Professor ABC. Because then, it won't be about you and you work, it would be about Prof. ABC deeming a premature work as publication-worthy, which he never agreed to!

Thus, in all seriousness, since you are actually going ahead with the publication, you should do that without your supervisor's name.

  Now I am scared to tell him about the conditional acceptance. Should I tell him?

While you are not obligated to inform him, it is generally very bad etiquette to hold your supervisor in the dark about these things. Of course, revealing this will enrage him, of course you will draw flak. But that's still a better option than him discovering about this independently, or through other sources (he eventually will find out, one way or the other). And in that case, bridges will be burned completely. So, my advise would be, if you were courageous enough to actually go ahead and submit despite your supervisor telling you not to do so, you would burn lesser bridges by owning up the repercussions, rather than running away from it.

Having said that, be prepared to hear a response to the tune of I'm not going to participate in amending the manuscript now, please do it on your own. Which is completely reasonable. If it is helpful to think of it this way, you will also benefit from the confidence you will gain from making the changes yourself, and getting it published. So, better do it yourself.

Finally,

  (Should I) just refuse from doing the revisions and acceptance?

That would be extremely unprofessional behavior and will decimate your reputation. While manuscripts can be withdrawn, what exactly will you say is your withdrawl reason?

"The results are erroneous", then they shouldn't have been submitted in the first place.
"We realized the flaws later", that will present you as a person who saw an opportunity to publish and jumped the gun, particularly true if you do it as a single author.
"I have some other commitments", that's again silly for a PhD student with the little commitments they have besides their work; you should have foreseen whether or not you would be able to attend the conference, and only then gone ahead with the submission.
"Emergency situation excuse", well I have no words how to respond to that, and most likely the conference people would also not have any.
"No excuse", that's extremely unprofessional.

So, my advice would be, own up the publication, and please do not even contemplate this option.


Incentives for independent researchers to work on reproducible research

I hope I understand the intent here well enough to offer guidance. I don't think there is any inherent incentive for most researchers to publish more than they do. The current system works well enough for them, so the added effort makes little sense.

The reason that many US government agencies publish more than the minimum is that much (most?) government funded research here has, traditionally, been considered as owned by the American public. Public Domain, if you like. On an orthogonal dimension, the fact that a lot of science has become politicized, implies that many want to be as transparent as possible so that the inevitable conflicts and charges can be openly refuted. But an additional reason is that "public servant" researchers are also generally interested in others being able to leverage and extend the work they do - for the greater good. They don't work for a profit motive and so have little incentive to hold things close.

If individuals want to publish code and data, it is, for the most part, permitted, as long as journals don't impose restrictions for reasons of copyright, etc.

However, a beginning researcher should carefully consider what openness implies. In particular, while you retain copyright (which you can license), you complicate the possibility of obtaining patent on your ideas. It may even be that others, with whose policies you disagree, can use and monetize your ideas against your wishes. Openness in general is good, and being willing to "reveal all" is commendable, but be aware of the implications when you do.


Logic behind masters programs admissions

You should not pay tuition to attend grad school, excepting possibly certain "professional" schools like medicine, business, law.

That is, grad programs admit a number of students for which they have funding, and have faculty/mentoring support.

Programs do not get tuition money back directly (as counter-intuitive as this might seem), but have to calibrate grad admissions to match the faculty they have ... the numbers of which are determined by essentially unrelated issues. But, approximately, programs will not admit you if they are not confident that you can succeed in their program. So you should not begrugde that judgement. And, srsly, such judgements are made with much experience.

Yes, there is the issue of prediction of success, which is an element that did not enter in undergrad studies. That is, programs do not "admit everyone" and then allow people to fail. Nor is it just a matter of "trying hard". Beyond a certain point, there is an issue of natural ability. It is true that this is highly non-trivial to understand/detect/encourage.

Yes, there is a considerable amount of disingenuousness in how we describe graduate programs...

Perhaps reaction-comments from the OP could help refine useful answers.


How to get SCI impact factor from other than Journal site

To see if the journal is indexed in SCI or SSCI, you can search from Clarivate's master journal list. Checking the Impact Factor probably require subscription to Web of Science. Alternatively you can directly search for the journal titles in BioXBio or find any article for the journal to see Impact Factor in Scinapse.

(edit: I work with Pluto Network developing and servicing Scinapse.)


How to be efficient with large blocks of time?

ff254's comment has a great list of links and I think reading papers is the best academic use of that time time. But I also recommend using the time to relax so your don't get burnt out from work/class. Two hours is perfect amount of time to grab a meal, read a book, take a nap, or hit up the gym. Remember to invest in your mental and emotional wellbeing as well as your academic education.

(This was originally a comment, but it got a little long so now it's an answer. I'm sorry it's not directly answering the question.)


We had some luck in using a Wiki to do this, provided someone has the technical chops to set one up. The benefit is multiple people can comment and provide feedback and everyone can see who's said what. The only drawback we had to this system was that everyone commented at the last minute.

The most important and perhaps hardest part is making sure everyone knows what a wiki is and how to use it.  The specific problems we had were things like people printing things out and marking them up, people writing their own pages instead of working collaboratively, and the inevitable whole nuking of pages of work to make a minor change.  Just required being very clear and explicit, with examples.


Can I hide my master degree permanently?

Hide it from whom? The only scenario I can see is that you want to omit it from your CV. But if you do that, how are you going to explain the one year gap?

It's also worth noting that you didn't get "a first class honour in the BA". You may have got first class honours in one or more years of the Tripos, but your degree certificate will say merely that on a certain date, in a congregation holden (sic) in the Senate House, you were admitted to the degree of Bachelor of Arts. Not that my employers have asked to see the certificate.

Finally, "permanently"? Don't make rash decisions which you might regret. In two years you'll be able to graduate MA and that (in Cambridge terms, at least) is a higher degree than the MMath/MEng/etc. You can put MA (Cantab) as your postnominal letters on your CV and hide the Mxxx that way, although it will still make sense to mention it as an explanation for what you were doing this past year.


Published manuscript to handbook or manual

would it be against the journal policy if I do this?

It is not against journal policy for

  a handbook/manual [to be] based on...published methods in a...journal.

Indeed, anyone is free to write a handbook/manual based upon published materials. (Such a handbook/manual should not plagiarise, of course, and the OP has noted that the handbook/manual differs in content, format, structure, and style. Furthermore, the OP notes that the original sources have been cited.) Regarding,

  we borrowed and cited some of the figures

You need to check this is permissible, it has been answered elsewhere on this site.

There may be other concerns, but the question doesn't raise them.

TL;DR: Write your handbook/manual as-if you didn't write the original sources.


How do I prepare to Skype discussion for PhD admission?

There is really no way to predict who will attend unless you ask. But I would suggest that you think of it the same way you should think of a Statement of Purpose document. Focus more on what you expect to accomplish in future rather than what you have already done. Use the past only to support a trajectory into the future.
What questions are you looking at? Are you close to resolution? What do you see farther out? How will this place help you achieve the goals?
Ten minutes is no time at all. Don't spend time clearing your throat.
But be yourself.


What to do if a colleague plans to submit the paper you worked on together without your name on it?

I have been working with another postdoc on a paper, here is what happened: I presented a work of mine before it was published (but it is in my thesis and on arxiv) and he decided he will use the same exact model with a slight change

There is a misunderstanding about "publishing": you probably mean that it was not published in a journal/conference, but apparently you did publish your model, which means two things:

Your authorship on this is established
Anybody can reuse it, provided they cite your work appropriately

  The methodology belongs to me

Not really: yes you are the established author of the methodology, but it is now available for anyone to reuse it, as per the usual academic process (the only exception would be if you patented the work prior to publication).

  I have talked it out with him and finally with my lab adviser as he was not collaborating, and we decided to send the paper as coauthors after our adviser mediated the issue (though it was bumpy), even sorted out whose name goes first etc.

This is what gives you a (moral) right to be a co-author for this particular work.

  My advisor has asked their collaborating institute whether I could join (the irony that my methodology is stolen but I need a pass to join the project) and they did approve it (I have all exchanges and emails)

Avoid using the word "steal" if you published it: if all that the other author did was reading your thesis/paper, the only requirement is for him to cite the origin of the work.

  I also suspect that my adviser got the patent of the code on his name as I have noticed he took my name out of contacts on github recently.

Are you talking about an actual patent? If yes, for what? If this is about your methodology which is already published or about a code publicly available on github (under a particular license maybe?), it's unlikely that a patent would be granted, but IANAL.

  Today I get no reply from him on multiple attempts and I learnt that he has removed his computer's hard drive and my adviser is off for vacation for an unknown time

Multiple attempts over how long? If it's only a few days there's no reason to panic, he might be busy. Did you agree on a method to write the paper together, a venue to submit it or a deadline?

  I suspect that my colleague will try to send off the paper we were supposed to write together without my name on it, I have email exchanges as proof but most relied on my adviser, whom I don't know if I should trust after the copyright issue. What do I do if he sends the paper without my name? Do I write to the editors? His partner institution? Is there a board for this?

You should rely primarily on your advisor, and if they don't cooperate you should seek support in your institution, e.g. head of department or ombudsman.


How to publish a simple machine-learning approach that cannot compete with the state of the art?

If you try to avoid the benchmark metrics comparison, it is going to be the 900 pound gorilla in the back of the mind of everyone reading your paper.

The alternative is to deal with it from the start. You obviously think there are reasons why your technique is interesting despite its benchmark metrics. You need to communicate those reasons. They should be first mentioned in the abstract. That way, readers are more likely to suspend thinking about the benchmark metrics issue in favor of thinking about what makes the technique interesting.

At some point in the paper you will need to present some metrics, in order to support a claim that the simplicity of your technique outweighs the metrics for some situations.


Can I share an unpublished paper without this counting as prior publication?

As per your comment, your main concern is that your sharing the draft may count as prior publication and will prevent you from eventually publishing the final paper.

Sharing a draft does not count as publication.

Moreover, your draft is most likely going to change a lot before you submit the final manuscript to a journal for review. In general, it is a good idea to share drafts early and often, so you can collect as much feedback as possible.

Some precautions:

make the draft status explicit
ensure the paper can't be found online before acceptance, so as not to compromise blind review (may depend on the field)
ask that the draft paper not be cited or circulated without permission


Many short papers or one big paper for a math postdoc?

This really depends on the situation, and I suggest you consult with some colleagues/mentors/your advisor for your specific case.  Here are a few points to keep in mind.

If these results are completely separate, then it makes absolute sense to break things up into separate parts, then assemble the various needed results for the endgame of your project.
If you're just continually improving results, it may not be worth while to publish every little improvement, particularly if they will not go into good journals, but you might want to look for natural breaks.
One great paper is better than many mediocre papers, but at this stage you should equate a few good papers with one great paper.
There's no general rule for how much you should publish, but a good rule of thumb is to aim to have at least decent 1 paper/year since you graduate.  Keep in mind, that papers always take longer than expected, and the refereeing time is generally long in math (particularly more so for longer papers), so the sooner you can submit, the better.

So you should take into account the rest of your publication record, a conservative estimate of how long the project will take, and what quality of journals you can publish in if you break things up in to parts versus keeping it as a whole.  If you can break things up and still publish in good journals, then I would say this is the safer way to make you a good candidate for tenure-track/second postdoc positions.

Edit: I just realized I didn't directly address the OP's second paragraph.  It's not bad to have many papers at this stage if those are good papers (though it can initially look suspicuous if you have many more papers than your peers, and most don't appear in good journals).  In some fields, it is normal to  mostly write many short papers (and for certain subjects, all papers under 15 pages would be strange).  What's most important is that people think you are doing good research, which will come primarily from letters of recommendations and secondarily your list of publications.  So while you should think carefully and seek advice from colleagues on how to publish your papers, but one long paper versus a few short-medium papers will probably not affect your application too much if they're accepted by the time you apply.


PhD students publish without supervisors – how does it work?

I published two single-author journal articles during my PhD in a field where a PhD student publishing without their supervisor is uncommon. So uncommon, in fact, that I can't think of any other examples in my subfield.
My case is probably unusual in that by a few years into my project, I was far more of an expert in the subject than my supervisor. My former supervisor is a bit of a generalist, so this is not unusual for them. At a certain point during my PhD I started disagreeing strongly with my supervisor about what to do, which is when I started working more independently.
I actually would have been offended if I were required to put my supervisor's name on either paper, as they had negligible intellectual contributions to the papers and were even harmful to them in my opinion. My supervisor made it quite clear that the work was my own, and even stated so during my defense. (They already had tenure so I don't think they needed their name on the papers, though this could be a factor in other cases.)
From my own experience I can say there are advantages and disadvantages to publishing without one's supervisor as a PhD student.
Some researchers will have greater respect for a student who has published independently. I've been pleasantly surprised to be treated as an authority on certain subjects during my PhD. I admit that those people might just be nice all around, but I didn't see most students getting that sort of treatment.
Unfortunately there are people who are suspicious of more independent students. One reviewer brought up the fact that I was a PhD student publishing without my supervisor in their review, as if such a thing were something to be suspicious of. They did not elaborate about what they found suspicious, but in my response I wrote that they are welcome to ask the editor to contact my supervisor if they believe I had not credited others sufficiently. I've also been warned to emphasize successful collaborative work on my CV and cover letters when applying to jobs, as some people will assume that I'm hard to get along with if I work independently too much.
I personally prefer to work more independently. I think the current research environment incentivizes collaboration far too much. I see a lot of groupthink/lowest commmon denominator type thinking in much of heavily collaborative work. Good ideas are avoided too often simply because they are unfamiliar to most people whose approval is needed. Good research often comes from unfamiliarity.
That's not to say that collaboration is often bad, just that it's too often bad. I fully agree that certain projects are impossible without collaboration. But given the choice, I'd bias my own work towards what an individual can handle, which I think is more than most believe.


Should I be applying for positions if my applications were rejected last year and not much have changed since then? Please advise

You should probably be applying but with a broadened scope. Times are tough, both generally in academia and due to the pandemic. What was true this year may not be true next.
The ease of getting a position in a given academic field varies fairly wildly over time. There are downturns and also good times. But, unless you want to give up and become an Uber driver, you need to keep looking.
But you would be wise to expand your search to other sorts of institutions that rejected you last time. Cast a wide net. In fact, you may need to keep trying for more than a year, given current conditions. And bring other resources to bear to help you. Make sure that you have a strong application, matched to requirements with good letters of support. Get, and take, advice from advisors and others who might be able to help.
Times will change, but it will take time for it to happen. Stay connected to your field as best you can and keep producing as is possible.


Colleges have to keep everything that influences grades of students for a certain time in order to resolve disputes over grades. In our case it is 3 years.


part of an algorithm on my paper is based on work described on one of those private documents. I need to acknowledge that somehow.

The algorithm has not previously been published, so you can claim that it is an original contribution of your paper. You can acknowledge the project in your acknowledgements section.

Problems might arise if your paper and the private document have different authors. In this case, you should seek permission from those authors to publish your paper and you should acknowledge the contribution of those authors.


Applying to Teaching Position in the Same Department as My Advisor... Should I Mention Her?

I would mention her, certainly. You don't need to make a big deal of it, but just mention somewhere that you worked on your dissertation under the guidance of Prof M. It is probably a matter of public record in any case.

You should also probably give her a note that you are applying to her department. Under the circumstances you state there should be no issue about it, and she may be able to help you along if your relationship was good. Being at the same place gives you a way to carry on research trajectories already set in motion.

She probably won't do for a formal letter of recommendation, however.

And you can, of course, ask her before you apply about the advisability of it and also this very question.


I agree with Yves that they are selling the books back to students.  Then I think the economics works out as follows:

The faculty selling the books and the book buyers benefit a lot.  The publishers stand to lose some money, since reselling the books hurts the market for new ones.  They presumably pass some or all of this cost on to students through price increases, so the students also lose money in aggregate.  Now the question becomes what price the books are being resold at.  If they are resold cheaply (used book prices), then the students who buy the resold books benefit (they get near-new copies at cheap prices), at the expense of the other students.  If the books are resold at new prices, then no students benefit.


Writing an Original State of the Art Section When There Are Recent (Meta-)Surveys for the Topic

Let me reframe your question somewhat, in a way that hopefully leads to a helpful answer.
It is widespread to think that the purpose of the "literature review" section of an article is to describe "the state of the art of the field, to give a background and show familiarity with related works", as you say. But I would argue that that even though that is very often what such sections do in practice, that should not be their primary goal and that certainly is not the most valuable thing they should do.
Rather than broadly reviewing the literature, a "literature review" section should focus squarely on framing the current article in the context of the literature. It should not do anything more (or less) than that. That is, it should show how the current article fits in the existing scholarly conversation. To do this, it should show what literature is similar, but in a way that clearly shows how the present article is different. In particular, it should clearly show how the present article aims to contribute to knowledge that is currently missing in the literature.
So, coming directly to your question, from this perspective, if there is a recent state-of-the-art review published, there is no problem at all. Such a review should only help you to better frame your own article to show what is close to your work, yet different. Above all, do not try to cite all the existing literature. Only cite the literature that makes your point: your article is different from similar literature and contributes important knowledge that is still missing from the literature.
From this perspective, concerning which work to cite, it is more likely that you would cite the specific original papers that refer to topics that are similar but a little bit different from your own article. You might cite the survey paper as a general source, but citing it does not tell readers much about how similar or different the literature is from your own work. It is your custom summary and citation of each individual paper that is close that would do this. And note that your custom summaries are not summaries of each entire article--that is not very useful, since the survey paper probably already does this--rather, it is a to-the-point summary of exactly in which way each article is similar yet different from your own work. That would be original (since the survey paper does not do that) and would help readers better appreciate the contribution of your own work.


I don't have the theoretical background in my PhD topic. I can't justify getting the degree

First, learn something about Imposter Syndrome. This sounds like a classic case of it. You have been a success already. Your advisor, I assume, had no doubts about your ability. So try to just ignore the "feelings" and keep on doing what you do.

Success comes from hard work, not from feeling like you are capable of it. Your feelings might well change as you produce more in your field. But even if they don't, you can still be a success.

But I suggest, also, that you build up a circle of collaborators that you can interact with. You will learn from them, but you may also learn from them that you have all the necessary qualifications.

Moreover, your education needn't end when you finish your degree. Books and papers can help you fill in the formal bits you think you lack. Your advisor has, I hope, given you feedback. The same will be true of reviewers of papers you submit. If they don't notice and lack, then you probably aren't lacking in fact. At least not by a lot. Everyone can learn at every stage of life.