Possible to leave a contract academic position shortly after signing new contract?

The only real recourse that they would have is to sue you for breaking the contract.  Although that's possible, chances are that they wouldn't be able to prove substantial damages and that even if they prevailed you wouldn't have enough assets to make the suit worth while.  This is why academics who break their contracts are seldom sued for breach of contract.

However, depending on how you do this you might end up losing any chance at a positive reference from your former employer.  This is probably the biggest risk that you face.


First impressions: CV or research statement?

The first impression is, ideally, when you first talked with a prospective adviser and/or researchers in the department or lab before applying. Some people have small interviews (such as by phone or Skype) before application time, and it varies by person whether or not anyone will have even seen a statement or CV before/during this process. This naturally varies by region and field, but this is not uncommon in the US.

Naturally this is not always possible, in which case you'll just have submitted an entire application packet and have no control of the first impression - so literally anything you submit with the package could be  the first thing a member of the admissions committee sees.

The typical routine is that an administrative department (generally "admissions" or a "graduate studies" coordinator) collects all the materials and puts all the information into files. Admissions committees then generally split up the applicants into sets and distribute them to individuals on the committee, with usually 2-3 people reviewing each applicant. It seems this particular handling of the process is very common (I've heard it from dozens of people in different fields throughout the US).

The first read varies by committee member, and it seems that absolutely everyone has their own weightings and order in which they review packets. Some professors say they think the  personal/research statement is silly and the first thing they look at is the reference letters. Meanwhile some say they look at the reference letters last, as they want to see what the candidates own words are and then only see if the reference letters agree with that image. Some people think the CV tells the true story, while others think the CV is little more than a laundry list and nutshell reminder of what's listed in the other materials. Some professors have been reported as saying "I only accept people I've already worked with in the past" so the application materials are really just there to make the bureaucrats complain less, and pre-selected candidates need to just not screw up too badly on anything.

So in the end, in writing your materials you cannot assume any proper ordering whatsoever - everything has to be suitable if encountered first, last, only, or not at all!


In mathematics in the US, as far as I know, I have never known any professor to ever not return midterms. I always do, and everyone else I know does as well.

Seeing their graded midterm gives useful information. It lets students know what they have gotten wrong and what they have gotten right; it also lets them know what answers they thought were "right" but in fact are incomplete or inadequately explained.

I personally believe the downsides are miniscule in comparison to the benefits for the students.


Presenting the idea of a PhD research project before publishing it

I think this is a good idea. There are many conferences in which they invite exclusively the Ph.D. students in different domains to a co-located workshop. There the students present their work (so far) and get comments and feedback. Further, there is a chance of getting collaboration by senior researchers.

Have a look at this: https://www.eurosla2019.se/programme/doctoral-student-workshop/


It strongly depends on the country and/or institution. To give an example: In the Netherlands, an Assistant Professor usually has a 60% teaching load and 40% research time (i.e., they are spending 3 days on teaching and 2 days on research - of course, this is somewhat blurred in daily life). If you bring in a major grant, you might use some of the money to buy off teaching time, so that you basically pay yourself 30% of your salary in order to arrive at 30% teaching, 40% 'old' research time, 30% additional reasearch time.

The department then basically has to hire someone else to take over the teaching duties you bought off.


What is the time and topic etiquette for a first meeting with a professor to discuss research?

Typically from personal experience these types of meetings are informal so no need to get overly dressed or prepare a large portfolio. Casual but nice clothing is definitely appropriate. It won't be a job interview but rather just a friendly discussion. If this is your first meeting about research, it will most likely just be a brief overview of what he does and potentially what a student would be doing. If you decide to do research with him then he most likely have future meetings in which he will discuss things more in depth, give papers to read to begin learning area of research and explain what is expected.

A professor is usually more than happy to discuss their research and take on someone whose interested and determined to conduct research if they have room. That being said, often times the professor would like that you have at least a general idea about what he or she does in their research and areas that interest you. You can expect a question such as, "What about the work I do stuck out for you and made you want to pursue this?" as I can recall being asked this more than once. It is also a good idea to have a few questions for them about their research, labs, etc. Again questions don't need to be an in depth inquiry on their research but just some light questions to get to know them and their work.

It's ok to be unknowledgable on the area of research as that's the point of research; to learn about the field and discover new concepts. The important thing is showing the desire to learn. Also you are an undergraduate so it's more expected that you don't have much experience in a research field.

All in all, from my personal experience it's a quick informal discussion with the professor to provide insight to you so you can decide if you want to conduct research with them. I've had nothing but pleasant experiences with this since professors love others interested in their research and I'm sure you will have the same experience! Good luck!


Can you submit the same session proposal to two different conferences?

Normally, two different conferences with the same session topics will result in two groups of work that are different, but compliment each other.

For example, assume I run a session called "Computer Forensics" at two different conferences. We will either invite different speakers, or use peer review for submissions to the session. In either case the result will likely be two sessions with the same general topic, but very different specific topics.

If the governing associations do not want the same topics, then make the topic title more general, but still related.


How do professors spend their NSF grants?

Ficticious but reasonably realistic example; YMMV, sometimes significantly:

Fall/Spring:

Stipend: $9,000/semester
Tuition: $7,000/semester @ 50% off
Health insurance: $1,000/semester
F&A overhead: $5,400/semester @ 60%

Summer:

Stipend: $9,000
Tuition: $0
Health insurance: $1,000
F&A overhead: $5,400 @ 60%

Total: $60,200 per student*year. In the example above F&A overhead is 60% of stipend only, with no overhead on tuition or health insurance. Tuition is 50% off because it's an overhead-bearing grant.

So your $200,000 would be 1 student over 3 years plus some leftover for PI Summer salary, travel, misc. expenses, etc.


Is it possible to do a state of the art paper with less accuracy than previous paper with 100 accuracy?|

Since you are aware of the other work you should report it. But you should probably also try to verify its claims.

Whether your own work is worth publishing or not depends on some things. To be valuable, it needs to advance the state of the art on some dimension and accuracy is only one. If you can achieve "really good" results in half the effort/time/cost, you probably have something worthwhile. It might make the difference between something that is feasible or something that is not.

But it would be a serious breach to ignore the other work.


Should I use lighter or heavier paper for my printed dissertation?

I don't think the weight of the paper is as important as the material from which it is made. So long as the paper is "archival quality," meaning no acids or other components which will allow it to degrade more easily over time, the choice is somewhat arbitrary. Willie Wong raises some valid points in his answer, though—the slightly thicker paper will help future readers more than the thinner paper, and the relative change in weight is probably not so large as to make the thesis cumbersome as a printed volume.


How is the transition from computational to experimental scientific research?

I, a Chemical engineer by paper and I recently made a big leap from desktop work - purely predictive modelling of process plants and systems, to experimental lab based work in the field of Biotechnology. Back to the world of pipettes, organic chemistry and filtration!

The experience I feel depends on whether you are going from computational modelling to quantitative experimental work in the natural science field ( like what I have experienced), or to qualitative (or even quantitative) in the social field. I have experienced both!

From laptop work to the biotech lab!

Challenges (I have faced):

It is difficult to get from an experimental planning to execution stage in the labs (often due to over researching online)
There is little evidence of your work ( it is all sitting in a lab).
It is harder to see mistakes and to correct them. It often requires you to restart an entire experiment from scratch ( can not use the find error tool!)
I struggled with work hours and location. When I was doing desktop work, I preferred to change my settings and venues. Also I could work whenever I wanted to. You will now be confined to the same building in the same space, everyday. Your progress will also be limited by this.
not knowing how much time is 'enough' time spent in doing experiments
practical experience is very different from theory - I struggled with dimensions, spatial awareness and quantities. When stuck behind a laptop all day, you lose touch of how much space (and mass) 1 litre of water would take up compared to 1 litre of ice.
when reporting back, colleagues are less interested in your journey to the result or your assumptions. They want results and graphs with error bars.
you have to be more considerate of your work colleagues space and time as you will sharing equipment. I was so used to be only worried about my computer and laptop
your progress seems to be measured on how many times people see you walking up and down to your Lab space ..

Advantages of having done desktop research before:

you can use predictive models to predetermine expected behaviour. I do less experiments on average than most of my colleagues
we have a slightly stronger grasp of factorial design of experiments (looking at all relevant angles and factors)
It seems to come naturally to desktop researchers to immediately interpret results with statistical tools (I am sure you have used a lot)
I seem to have some of my final report already typed out - doesn't seem common practice for my colleagues who spend day in and out in the labs.
our report writing skills seem to be better - maybe due to sitting in front of the computer all day
you are already familiar with the scientific method and hypothesis driven research so this part of the transition is easy.

From laptop work to the social science field ( interviews)

Challenges

you will have to develop real empathy and defer judgement
listening is a skill, evenmore so listening and taking notes
being objective
interpreting results without inferring your own judgement. How does one deal with words and quotes, rather than hard facts and numbers!
Must use words like maybe, could be, I think that, whilst being conscious of context all the time! Which differs heavily from the scientific method that must use x is bigger than y by z% because of factor h.
Being okay with not having an answer but a description of a scenario.

Advantages of having done desktop work here

being analytical
being well researched
easily find the critical function or important points to investigate


How to know if a topic is completely explored?

Welcome! The answer is usually that the topic is not completely explored. When you're new to an area, it can be hard to see what the open questions are. Hold off on asking the authors anything until you've asked your advisor and really dug into the topic (reading related papers, working through the problems).

There's a nice answer to this question about approaching a new field:
Exploring something completely new, even silly.

Beyond that, I encourage you to look at the Illustrated Guide to the Ph.D.
http://matt.might.net/articles/phd-school-in-pictures/


What to do on immediate rejection from journal citing "Similarity Score" that is too high, but specific instances are just boilerplate text?

I cannot find anything about the use of the ithenticate in the ACM CSUR instructions for authors. The ACM magazine Inroads says:

  Please note that ACM Inroads as well as all ACM publications expect new, unpublished material, unless specifically reprinting an item from another publication with attribution. In support of this goal, ACM Inroads uses iThenticate to develop a similarity index for all submissions. As a first step after an initial submission, iThenticate compares the text to published material (at least 43 billion web pages and over 130 million content items). It provides editors with a set of similarity indices and helps them identify original material, including prior publications of authors.

This suggests that there is not a hard cut off, but rather a set of metrics and comparisons that the editors use in making a decision. While it is possible that the ACM system is poorly tuned, this seems unlikely. In my experience, a 13% similarity is quite high and is often indicative of issues.

While it is not cheap, you can purchase a single paper use of iThenticate. It appears that iThenticate is owned by TurnItIn which many universities have access to. It is not clear what the different systems do, but it may help you identify what is being flagged up.


When was the Bachelor degree of Occupational Therapy introduced in Australia?

The government board wasn't really helpful, but I found the answer:

  For a few years there had been a combined Physiotherapy/ Occupational
  Therapy Degree course at The University of Queensland. In 1955 the
  Occupational Therapy three year Diploma course was introduced.

Source: http://www.occupationaltherapyboard.gov.au/documents/default.aspx?record=WD12%2f8399&dbid=AP&chksum=SfMd1xjsN%2f1k47blbbm7MA%3d%3d


When a professor commits scientific fraud, are the journal reviewers and editors of the paper also discredited?

A note about the nature of academic fraud: Merely being wrong is not fraud.

In the case where something is indeed fraud, it will depend very much on the paper in question - it would only discredit the reviewers and authors if there is the reasonable expectation that they could catch it.

Consider some examples:

Fraud by Omission: You run a study twenty times, and report the one version that gave you a significant outcome. That study is well-conducted and correctly analyzed - it just also happens to be cherry picked. How could a reviewer know that?

Fraud by Modification: You alter your data in some way to give you a desired answer, and then re-analyze it. This analysis is done correctly, you provide the reviewers with this "raw" data and they reach the same conclusions, etc. There are some mistakes you might make that could alarm a very alert reviewer, but it's also possible, being aware of these mistakes, that you wouldn't make them.

Similarly, if you edit some figures, reviewers might catch egregious versions, but some people are caught out by things like particular artifacts in the image files, which is not something to necessarily expect the reviewers to catch, or even necessarily to have seen (as sometimes we don't get the raw figures, but versions processed by the editorial software).

Fraud by Just Outright Lying, Absurdly Unethical Studies, etc. Most of the vaccine denial literature falls in this category. Deliberately misleading statistics, results not supported by the data, etc. These I do expect reviewers to catch, and do think less of the journals that let them go into print.


My main research advisor refuses to give me a letter (to help for apply US physics program). What should I do?

Yes, it might look a bit weird, but you don't have control over that. And he is giving you good advice that he shouldn't write you a letter. Not every advisor is willing to be so honest.
But, I don't think it is an absolute block to your plans. Find others to write you strong letters and (US perspective) you should be ok.
What you need are letters from people who can confidently and honestly predict your future success based on their experiences with you. This advisor is not that person.
And FWIW, it is his problem, not a problem with your work mode. And no admissions committee should make any decisions based on guesses or suppositions. They should take your materials as they stand.


Is there such a thing as fraud in mathematics?

Wikipedia defines fraud as "deliberate deception". A couple of mathematical frauds I could think of:

Passing off someone else's result as one's own; plagiarism.
Using a result in a proof although one knows full well that its preconditions are not met.
Making other claims one knows are false, e.g., "it is easy to see that" or "by a tedious computation we see that".

Fraud is certainly possible in mathematics. It's probably harder to distinguish fraud from bona fide errors in math than in other sciences. Who is going to prove that you knew your "simple but tedious enumeration" would not work? Conversely, reusing graphics ostensibly stemming from very different experiments is very hard to explain as a simple error.


Does this imply that I am ineligible to apply for this grant?

It’s hard to say for sure, but at larger granting agencies, different review panels may focus on different areas and have quite stringent guidelines for what is considered on-topic. It may be that you need to have a statistical test as part of the guidelines for the area under which you asked your proposal to be judged. The reviewer’s response may be suggesting your submission falls out of their purview.


What category does a collection of mathematics tricks come under?

A number of people have correctly told you (I can see the article) that this is a collection of mathematical puzzles, rather than a research paper.  So let me tell you a little more about this type of article.  Martin Gardner is considered by many to be the biggest popularizer of recreational mathematics in the 20th century (perhaps ever).  For 25 years (1956-1981), he wrote a column for Scientific American called Mathematical Games.  Many of his columns have been collected into books (such as Martin Gardner's Mathematical Games).  Some other well-known examples of similar writing include that of Douglas Hofstadter, Ian Stewart, and Keith Devlin.


Is it normal to spend a whole day reading and writing about a single paper for a literature review?

Just to expand on Peter's answer, there is a saying on the University of Canberra's Academic Skills Centre: Reading and Remembering regarding academic papers:

Academic material is not meant to be read.
It is meant to be ransacked and pillaged for essential content.

Particularly, some of their advice for reading academic texts may be of help in helping you with the time taken to read and summarise the texts that you have, specifically before you start reading, have a question already that you want answered and very importantly, to optimise your time in reading academic papers:

If there is a summary, a conclusion, a set of sub-headings, or an abstract, read that first, because it will give you a map of what the text contains. You can then deal with the text structurally, looking for particular points, not just reading ‘blind’ and so easily getting lost.

I always have a subject-based dictionary on hand as well.


I asked my supervisor the exact same question while writing my master thesis. He said that it is a matter of style, he preferred putting an introductory text under each heading. I looked over some articles in my field as well, and they were pretty divided on it.

If you have a style guide from your university/publisher, or if you have examples available, I would say, follow those. Otherwise it's up to you.

I found it good practice, because those are the places where you write a short summary/introduction for that chapter, which could help you organize your thoughts.


Do grad school admissions care about course load?

"In your experiences how do grad schools weigh overall GPA vs overall
class loads?"

GPA is much more important.
Course load is often not even seen, unless people dig into your transcript to more details such as which courses you took and which ones brought up/down your GPA: In this case if you took only 3 courses/term throughout your undergrad, it might raise eyebrows but you are saying it's only your senior year so it won't likely be a problem.
More important than GPA and Course Load combined, is reference letters and publication/research-experience if you have any. GPA means very little to me because I know that a 70% at Oxford (where I did my PhD) is considered a "1st" which is the highest-level of honour and is only awarded to the best of the best students, yet in Canada (where I did my undergrad degrees) it was common to get 90s or even 100% occasionally. Furthermore even within Canada a 90% at University of Waterloo might mean something different from a 90% at Laurier Unviersity (in the same city), and a 90% in Psychology might mean something different from a 90% in Literature (even at the same university), and a 90% in PSYCH 101 with a leniently grading TA might mean something different from a 90% with a harshly grading TA (even for the same course in the same university in the same country!). Your volunteering and experience-gaining, which you say is the reason why you're taking 3 courses instead of 5, might actually be benefiting you more than you imagine, because if you do well you might get a strong reference letter, which is usually more powerful than a good GPA alone.


PhD. in the US directly after European BSc., or is it better to go for a MSc. at first?

In my opinion,

there will be many challenges in deciding to move to US.

First of all you will have to adapt to a society that despite having a western culture, is still very different from Europe. If you are not able to adjust culturally, it is highly possible that this will affect the progress of your studies. Cultural shock is something most international students experience and usually takes a semester or a year for its effects to wear off... However some people have more difficulty adapting to specific cultures from what I've observed.

Secondly there are many structural differences in US and European PhDs. For example, you will have to earn a Master's degree by attending classes while you do your PhD in US. At the same time though most professors will pressure you to make progress with research, which makes things really tough. Keep in mind that in order to maintain your visa status in most universities you will have to maintain a relatively high GPA. On the other hand you will also have to please your advisor with your research progress or he/she may convert you to Master's status, and you will loose the opportunity to earn a PhD.

The rationale behind taking classes, is that Americans want to guarantee that their graduate students have a certain amount of exposure on advanced scientific topics. Whether this is a better practice or not compared to the European programs that give much more emphasis on research, I believe is a matter of personal taste and preferences.

What is more if you earn a Masters from Europe and then move to US for a PhD, it is highly likely that not all the classes you had, will be transfered to the new program. You will also be older while you enter a commitment that may last many years. Some may argue that you will be more experienced to face the challanges that come. However I think that the younger you finish your PhD, the better...

Also keep in mind the following general things (some of which also apply for European PhD programs):

PhDs in US take longer to complete (Europe = 3-5 years, USA = 4-6 or
more years)
Before joining a lab make sure you can collaborate with the professor
that leads it. If you feel that you can not collaborate leave and
search for other opportunities that interest you. Although many departments allow grad students to change labs after joining the program, it may not be an easy process due to starting over with a new topic as well as politics between different labs.
Additionally, ask in a polite way the professor running the lab or other lab members what are the requirements to graduate from the lab (e.g number and types of published papers). If you don't get specific answers be careful before joining.
If you pay a visit to a lab for an interview make sure the testing
period lasts for at least two weeks and try to find out how other members of the lab feel about what they do. If the majority does not
seem satisfied leave and search for something else (pay attention to
people who exaggerate though...)
Depending on your field there might be more job and money related
opportunities in the US, but I believe the whole experience will be
more tough and you will have to decide whether this thing contributes
to your career or not, from early in order to not regret spending
5 years on something you did not like.
There is a high dropout rate in American PhDs. However, I think
that the fact that you will have international experience might make you
seem more valuable in the eyes of potential employers in the future, if you manage to complete the program.


Are there no footnotes in Vancouver referencing?

This is correct. See the last page of this pdf for an example of a Vancouver references section:

http://guides.lib.monash.edu/ld.php?content_id=14570618

In response to a comment below about the in-text citations coming after the punctuation, here is another example where they use brackets but don't mention if it is in-text citations (but the references section/end of essay references match the guide above). When I use Vancouver style in my own writing, Mendeley defaults in-text citations within the period.

http://editor.citationstyles.org/styleInfo/?styleId=http%3A%2F%2Fwww.zotero.org%2Fstyles%2Fvancouver


Student leaving before completing PhD - how to write about his motivations for switching in recommendation letter?

I think you probably are overthinking this somewhat.  I have written a number of letters for students in similar situations--wanting to leave my department's doctoral program (sometimes after earning a masters, sometimes not) for a better one (sometimes in a different area)--and they have generally been successful in getting into excellent programs.  (These students, naturally, tend to be among the best who are enrolled in our program.  On the one hand, I hate to lose them, but for the students themselves, moving is probably the best choice for their careers.)  In my letters, I try to give a modest amount of context for why the students are leaving, but mostly I just try to write them a conventional very strong letter.

I don't have any firsthand knowledge of what the admissions committee at a top institution would think of a student who has switched areas multiple times, but if you explain that the student wants to switch fields and that the new field has always been his real passion (and explain why he has been unable to pursue that area previously), I imagine that would go a long way.  The people reading the application might still look a bit askance of somebody who has changed subject areas repeatedly, but I don't think there's much more you can do to address that point specifically.  Just make the overall letter strong.

I seriously doubt that the admissions committee is going to refuse admission to somebody who already has a funded position elsewhere.  They want to get the best people for their program, and if the student has a valid reason to want to move, I think that ought to be enough.  Even my own (middle-ranked) department gets some applications from people who are already funded in graduate programs at other institutions, and this has never been an issue in our decision making process.

In the long term, I don't think anybody is going to look back over a student's record and be concerned that he jumped around a few times before completing a strong Ph.D. at a good institution.  People transfer between programs fairly frequently.  (Most people don't move, obviously, but movers are not rare either.)  And again, moving should not hurt his admission chances right now, provided he (and you) give a good explanation of why he wants to move.

So I think the most important thing you can do is to write a strong letter.  Emphasize that the student already had demonstrated skill in research working with you and that you believe he has excellent potential in the new area he wants to work in.  Explain why the student wants to move and that you support the decision, but don't let that be the main focus of your letter.  That's just there to assure the admissions committee that the student doesn't have some problem.  The core should be your strong evaluation of the student, just like in any strong recommendation letter.


Can two PhD students publish without involving their supervisors?

There is nothing unethical about publishing something like what you suggest. Personally I would be happy and encourage a student of mine if that happened. So from a formal side you need not to worry. I can add that authorship, or contributorship, does not include adding names to a paper if they have not contributed anything (or enough; see posts on authorship on this, Academia.sx, site). I would, however, be open about it with your advisor. I assume you have a good working relationship with him/her? The only thing that could complicate things would be if you are in a bad working relationship with your advisor or if your system is very hierarchical and not open to initiatives. Clearly only you can assess this. But, I do not want you to over-emphasize these "risks". If you get stuff published on your own and in a field that is not directly within your topic, it will only be viewed as  a positive in your resume when applying for, for example, post-doctoral positions.

As for risking rejection, I suggest you have someone whose views you trust to read and comment on the paper. Having someone independent look at the work is always good to work out details that can otherwise distract reviewers. This is always a good idea so it is not unique to your case.


Taking my Ph.D. advisor out for dinner after graduation

What is the professional/moral way of doing this?

I think that if you have never invited/been invited to a casual gathering involving the advisor's family, it will be awkward to do so now. If you feel like a one-on-one dinner invitation is too much, how about a lunch appointment?

I will say this - many universities have strict rules on receiving expensive gifts from students/subordinates. If your meaning of precious is simply "of significant emotional value" (say, you made a piece of art yourself, or found a book that they really like) that's fine; if you mean expensive (say, an expensive watch) - your advisor may not be able to accept the gift at all (or, as is the case in my university, will have to report the gift and then give it to the school).


How to "cultivate" a postdoc position during PhD program?

You want to establish substantial professional contact with the head of your target group long before your doctoral period is about to end.  They need to know who you are already when your postdoc application crosses their desk.  It is never too early to start.  Here are a few suggestions.

Ask your advisor to invite the head of the group to give a talk in your department.  Meet with them one-on-one.  Ask about the possibility of a short visit to their lab to give a reciprocal talk.  (Prerequisite: Have something compelling to talk about; be a good speaker.)
Ask about the possibility of summer internships.  (Prerequisite: Be a good candidate for a summer internship.)
Ask your advisor to suggest a one-semester student swap.  (Prerequisite: Be someone that the other person would want to hire as an RA.)  More generally: Convince your advisor to collaborate with the other group.
Ask the head of the group to be an external member of your dissertation committee.  Ask at least two years before your defense. (Prerequisite: Have a thesis topic that they will care about.)
Talk to the head of the group and/or his students at conferences.  Join them for lunch, or dinner, or coffee, or beer, or whatever.  (Prerequisite: Be an interesting human being.  Know a few good places to get lunch/dinner/coffee/beer/whatever.)
Don't put all your eggs in one basket.  Cultivate multiple colleagues.  Some may develop into future employers, others into future research collaborators, still others into letter-writers, still others into mentors,  perhaps a few into friends, and most into nothing.  (Prerequisite: Know more than one person.)
Most importantly, don't think of this process primarily as "cultivating a postdoc position".  Think of it as cultivating a research community.  People will notice if your motivations are mercenary, if only subconsciously.


How to give a credit to the sources on the Internet in an acceptable way?

How should you cite?
There is a format for citing web references for nearly any citation style.
In the MLA format

Last, First M. “Article Title.”Website Title. Website Publisher, Date Month Year Published. Web. Date Month Year Accessed.

In APA style

Author, A. (date). Title of document [Format description]. Retrieved from Website

You may leave out the author field when it is not possible to retrace the original author (as described here)
When should you cite?
If you were to refer a material that has sufficient information to be given credit for your work, then by all means you ought to cite it. But first, try to find the roots of the idea, if such idea has been published elsewhere before this web-page was published. On-line content is highly susceptible to contain plagiarized content. See if you could locate the original source. If found, cite the original source instead.


How to make lessons more concrete for undergraduate students when my institution lacks lab facilities?

Why not make a more graphical simulated environment inside of a web browser? All sorts of dynamical systems problems are prettified up and turned into browser games these days, whether in flash or JavaScript on HTML5.

If you make a simplified system, like an inverted pendulum, in a browser, then it can be nicely visual. If you give a set of manual controls in the program, then students can get a feel for it. With appropriate piping, you should then be able to hook it up to Matlab for them to control as a real-time system from there. You can also inject noise and control errors to bring more realism and prevent unstable solutions from working.

In short: our computers are powerful enough these days that a satisfying virtual lab is quite within reach.


What classes to take in undergraduate for graduate school instead of graduating early

It really depends on where you go for graduate school. Some schools may accept graduate courses from other places, some will allow you to use them to test out of prerequisites, some won't accept them at all.

That being said, taking gradate courses as a undergrad will look good on your gradate school applications. Depending upon your subject, if you can also manage to swing some undergrad research experience, your gradate school applications will be in really good shape.


Completing a PhD sooner: what does it take?

The first thing you need to ask yourself is: do you really want a PhD? At its core a PhD is nothing more and nothing less than "vocational education for researchers". In a PhD program you will learn about and get some experience in doing real research. If you don't want to become a researcher, then what is the value to you? There is the status that some feel comes attached with the title, but is that really worth a couple of years of your life?

Assuming you really want to go through with this, then you need to realize that it will take at least 3 years and probably more. That is a long time, so you need to approach that more like a marathon than as a sprint. So don't go in and start burning the midnight oil, because you will only burn out yourself before you are done with your PhD. This is a very common mistake among PhD students.

The only PhD student I know who made it in about 3 years had a completely different approach. She had a plan that was realistic, and she stuck to it. Making a realistic plan for your thesis is very hard. She managged because she already had experience doing research and was already well versed in her topic. She was also extremely disciplined in how she managed her time, and this ment that while at work she worked very hard, but she would not work in the evenings and not work in the weekends. She was able to work that hard and that focussed for 3 years on end because she did not work in the evenings and in the weekends.

I am not that person. I whish I was that disciplined, but I am not, and it took me 7 years to finish my PhD...


If supervisor has no expertise in your research work, is it possible to do a PhD under that supervisor?

In summary: is it possible? Yes. Should one do it? No.

You need an advisor to tell you which problem is important to solve, which direction may not be feasible to investigate, which conference to submit your work etc etc. If you have to do all these alone, you may waste years going nowhere.

That being said, I happen to know a couple of people who successfully did their PhD without working with their advisors. All are very talented, and extremely confident with their research. One of them is a very young PhD student in my former school, who has published 3 solo papers (and co-authored some others), and invented a new sub-field of cryptography.


How important is the write-up of a PhD thesis for an academic career?

Your thesis and what is written about it your letters of recommendation will have a big effect on your career initially.  To get a good postdoctoral position, you'd better have a good thesis.  Later in your career, your thesis won't matter much any more, because people will be more interested in your recent achievements.


Topic C is seemingly a prerequisite to topics A & B, therefore topic C must be introduced in papers that deal with topic A, B or both, to ensure that such papers are self-contained. That said, if topic C is standard, then there's no need for an in-depth introduction and a citation to an introduction will suffice.

It is unclear whether the introduction to topic C in the context of topic A will be the same as such an introduction in the context of topic B, because different aspects of topic C will be relevant. So, some differences between introductions are possibly when topic C is introduced in the context of topic A and when topic C is introduced in the context of topic B.


If you have a good relationship with your advisor, consider informing him or her early in a very respectful way. He or she will appreciate you took the time. Why give them a reason to (potentially) write a less than stellar letter?

If you do NOT get a letter from your current advisor and go for another post doc, yes it will absolutely raise a flag. You could expect the topic to come up, or the interviewer make even contact your advisor directly.  However, if it really only has been a few months, simply stating the environment/locale/work/etc wasn't matched may be sufficient.


How to reference and cite the osgeo package from Python

I want to cite and reference all my used Python libraries which i used for my masterthesis.

It is usually enough to cite just the package (not individual libraries), unless there are special circumstances.

Libraries / datasets with a science background (rule of thumb: papers were published introducing the library and/or it is part of an academic project) usually have somewhere on their websites some information about how it should be cited. In those cases, you should obviously use that. Example for MatPower - a Matlab package for power systems analysis (emphasis mine):

  Terms of Use
  Please see the LICENSE file for the details. But here is the summary
  ...

  Beginning with version 5.1, the code in MATPOWER is distributed under
  the 3-clause BSD license. MATPOWER is distributed in the hope that it
  will be useful, but WITHOUT ANY WARRANTY. While not required by the
  terms of the license, we do request that publications derived from the
  use of MATPOWER explicitly acknowledge that fact by citing [2].
  Additionally, we request that publications derived from the use of the
  MATPOWER Optimal Scheduling Tool (MOST), explicitly acknowledge that
  fact by citing [4] as well as [2].

  [2]    R. D. Zimmerman, C. E. Murillo-Sánchez, and R. J. Thomas, "MATPOWER: Steady-State Operations, Planning and Analysis Tools for Power Systems Research and Education," Power Systems, IEEE Transactions on, vol. 26, no. 1, pp. 12-19, Feb. 2011.
  [4]  C. E. Murillo-Sánchez, R. D. Zimmerman, C. L. Anderson, and R. J. Thomas, "Secure Planning and Operations of Systems with
  Stochastic Sources, Energy Storage and Active Demand," Smart Grid,
  IEEE Transactions on, vol. 4, no. 4, pp. 2220-2229, Dec. 2013.

For libraries with no such information, it is usually enough to put the link, or permalink if at all possible, to the website as a reference.

You should also check the institution's (or publishing venues's) reference guidelines, there should be something about citing online resources.


How do I follow up with a potential PhD supervisor?

PhD supervisors are generally quite busy, particularly, if they have multiple PhD students, and courses to coordinate. So if he said 3 weeks and has failed to get back to you then it is likely that he has been busy.
Wait for a few days, and then politely send him an email requesting an update on the status of your application. Let him know that you are looking forward to the next meeting and are keen on working with him.
Also continue to look at his group's website, if any. Many times, after having been ignored by the potential supervisor, I have found new students on their website, indicating that my application has been rejected.
It is an impolite world, it is not necessary that the supervisor or for that matter anyone in academia shall get back to you, particularly from top universities who receive bucketloads of emails every day. For example, one of my supervisors used to ask his research assistant to man his email account with instructions to ignore emails with 'certain' characteristics.
In your case, the potential supervisor seems to be interested in your application and it is highly probable that he will respond.
Best of luck!


How should a supervisor deal with a PhD student who behaves badly

There's obviously no universally accepted policy here (e.g., there are labs where brashness unfortunately starts with the principal investigators). You also need to be careful about what is meant and perceived as rude, as it is, partly, an artifact of culture (e.g. I've witnessed Japanese managers fake sleeping during business meetings, which I would be inclined to perceive as negligent or rude, but apparently expresses ritualized trust in their underlings acting for them). That said, and assuming there is confirmed rudeness, here is how I would handle this.

There should be a zero tolerance policy for rudeness towards staff as it is likely abuse of power, or perceived status. If you experience such rudeness towards other students during meetings, etc., I'd call the offender out as it happens ("There's no need for (X). We are all working together/(Y) didn't mean to imply this."); if during inter-student conversations you happen to witness, I'd first confirm with the person on the receiving end if they share your perception ("Is everything all right? You feel comfortable in our lab? (...)"), if the case is not blatantly obvious. In all cases that warrant action, I'd call the offending student for a personal meeting, in which you could outline that you prefer a more mellow lab, with suggestions how to better handle what happened. If this is a meeting with a repeat offender, be more forceful and tell them that they continue to be out of line, and that this has to stop.

If you are personally disturbed by the noise level, you should say so - it's your lab. However, if you'd rather provide a quieter lab for your students, this is a common workplace problem with few known satisfying solutions. Here is an old question discussing the issue. The main problem is that some people prefer to talk while at work, others prefer to focus; if you take one side, you are likely to annoy the other. I find loud talkers rude and inconsiderate, but have never managed to change my surroundings in a lasting way.


Just realized I may have accidentally plagiarized some of my bachelor's thesis

This is an appropriate thing to be concerned about and want to rectify; you don't need to fear dire consequences, especially if you take steps to address it. There are different kinds of plagiarism, and also different levels of awareness of what one is doing. Turnitin has an interesting diagram with catchy titles to distinguish them; yours sounds like a mix of "hybrid," "recycle," "aggregator," and "retweet." Probably the hardest overall concept to understand--and one that may not be fully comprehended by many undergraduates--is that when a key source shows you the way to other sources, you need to be careful that your paper isn't entirely dependent on that key source for its content and/or structure. You should also make sure to acknowledge if a quotation in your paper from a third source is there by way of that key source.
I tend to agree with Anonymous Mathematician's answer to a similar-ish question about plagiarism in a doctoral thesis. In particular, identifying the problem and issuing some sort of errata or revision, prior to anyone else coming across it, is likely your best path. Making a mistake as an undergraduate, and recognizing it and working to rectify it, is unlikely to pose problems for you if it later comes to light. (This is largely the tenor of the answers to a question by an undergrad about publishing in a journal, realizing later that the work contained cited but unquoted direct quotations.)
That said, it would be wise to seek counsel from an ombudsperson at your undergraduate school and your graduate school, as well as your undergrad advisor and your new advisor. You don't want anyone to be surprised by anything and jump to the wrong conclusions. Exactly how to handle the process of corrections might be delicate, but it is certainly the right path to take. The worst case scenario would be if you confessed this to your undergraduate institution to address it, and they were required to report this to your graduate school, which only read the words "academic integrity issue" and rescinded your admission. With proper communication and feeling things out with ombudspeople at both institutions (confidential advisors who can help you navigate the system), you should be able to avoid such a misunderstanding.
Minimally, you should probably clearly and concisely acknowledge your reliance on the other thesis, perhaps as an erratum sheet you could send to your undergrad advisor to stick into a copy of your thesis. It might say something like:

Much of the literature review and methods sections rely on the work of Prior Student's thesis, and I would like to properly acknowledge that debt.
I found sources A, B, C... (discussed on literature review pages X-X, Y-Y, and Z-Z, respectively) through Prior Student's work.
Prior student did similar experiments on __, and I relied on their phrasing for much of the content on pages X-X.

In another approach, you could produce a revised version that somehow does not rely on the previous student's work, and mention in a note that you produced the revision because you realized that you had inappropriately relied too closely on the other student's work. (For instance, find several more papers, read them and reread the sources you had before, and write a new literature review.) However, if you expend this effort without any guidance, you might not distinguish your new work enough, and/or you might be moving toward a different resolution than your advisor and undergraduate institution would find acceptable.
Good luck!


NSF GRFP Application for a Rising Undergraduate Senior

In the US in neuroscience, most people apply for grad school without their own funding.

Funding for your research is provided by your research advisor; in your area of interest this will likely come from the NIH and possibly other private organizations specific for AD. You may also be funded for between a semester and a year to rotate with different potential advisors, such as via a T32 training grant from NIH (training programs apply to these grants, not students; students are funded by applying to graduate programs that possess such a grant).

NSF grants for students in neuroscience are very rare (looks like about 60 GRFPs were awarded this year in neuroscience; only 4 don't have an institution listed so I presume applied before being admitted); it's a good goal to shoot for, but not something to rely on. The requirements for the specific fellowship you are looking at specifically exclude disease research because such research is already substantially funded via other means; NSF is trying to fill the other underfunded gaps in very basic work. I would not suggest trying to bypass this by tweaking the language of your application.

NRSA grants (the NIH equivalent) are also somewhat rare, but more achievable. You apply after you are already part of a PhD program, sometime before the end of your second year most often.


Abbreviating the middle-name in the future publications

Let me suggest to you to aim for consistency.

Secondly, in databases like the above mentioned (and Thomson Reuter's Web of Science, to mention another, aiming less on engineering than Scopus), you may search for researchers by family name and initial of the given name; however I personally find it more straightforward to narrow the research by knowing the complete given name, than guessing if "Doe, B" refers only to "Doe, Bill" or / and "Doe, Benjamin", "Doe, Barry" I would prefer the same for the middle name (if existing).

For the databases like Thomson Reuters' Web of Science, or Elsevier's Scopus, or Scifinder Scholar (by the American Chemical Society), these databases do not mind terribly much how much of the middle name of the authors is provided.  Either one finds you and your publications taking into account field of research, or affiliation to a group as additional criteria while doing the literature search the classical way.  Or, while launching a query based on the alpha-numerical badges (ResearcherID, ScopusID, Orcid), because these publications are associated with you, because you taught the database that the publication in question actually is one you ("Doe, Benjamin") contributed to, and not "Doe, Bill".

As a side note to the second paragraph, if you manage your publication record with ResearcherID, you may sychronise these entries with Orcid (and the other way around, too).  Web of Science even lists both the own ResearcherID and Orcid in its abstracts, where available.  Likely, such a link may be established to Scopus, too; hence this work needn't be done each time from scratch for every database in question.


How much do editors care about author affiliations and previous publications in the field?

In principle your background and affiliation should play no role, and the manuscript will be handled and reviewed on its merits only. Now, in practice, editors are only human, and may subconciously show some bias against unknown authors, and may deal with the paper with more skepticism than usual. However I do believe that most editors are professional enough to give the manuscript a fair evaluation.

Of course the very top journals are very selective, so that even for well-known authors in the field it is difficult to get published there. Especially if you are new to a field, it might be a good idea to first get feedback on your manuscript from someone who is more familiar with the field, to avoid disappointment.


What should I do if my advisor and committee members want me to do two different things?

The way you present it, it sounds like the two are mutually exclusive, but they are not really: a "stapler thesis" generally contains an introduction and a conclusion that are there to tie the papers together into a whole. This implies a unifying theme and a narrative. It's only a few pages, but it makes a big difference.

You should probably at least make some effort to introduce a narrative, despite your advisor's opinion. Of course you know them best, but in general it's less likely that someone would refuse to sign off on something because you put in more effort than they thought warranted, and more likely they would refuse because you didn't put in enough. Better to err on the side of doing more.


I do not think that you'd be limited in publishing your research results or finding collaborations if you do not have a PhD. You pretty much need a PhD for the academic career path, basically if you want to become a professor some day.
The major issue is if you are able to support yourself doing what you do. And if you can allow yourself to do research, and to do the research you want to do, while working in the industry.
To give an example, Peter Montgomery published his multiplication long before he obtained his PhD, while he was working in the industry, as far as I understand his circumstances.


Writing a single authored research paper in a math journal: Is this a significant achievement?

Writing single-authored papers in math is extremely common, much more so than in other disciplines. It's not considered a significant achievement on its own in the context of applying for jobs.

Writing a paper before the beginning of a PhD is however certainly a big plus for you. But how much this will help depends on the journal: if you had the misfortune of publishing in a bad journal, I am sorry to say that this will actually hurt your application. It also depends on your field: I'm in pure math, but maybe in some areas in applied math it's expected of applicants to PhD positions to already have papers. Your question is a bit too general.


Does starting a question with 'what is the impact of' make a good qualitative research question?

For any decent research question, I try to test it with all these criteria. Some of these sound very simple, but as I try to answer them, there isn't one of them that I find consistently simple. That might just be an indicator of my own limitations, though.

Does it look like the sort of question that gets answered in the journals (/ conferences / predominant outlet in my specialism) I want to publish in? In your case: are there impact studies in the literature that use qualitative ethnography?
Does it tell me who, what, when, where, why, and how? e.g. What sort of impacts? How will the impact be studied? Over what time period? Impact by whom, on whom? and so on.
How will I know when it has been answered well?
Is this a definite gap the literature?
Will answering it make the world a better place (in however small a way, but at least in a net positive way)?
Is this answerable with the resources (time, human, material) that I have available?

It's worth putting a lot of effort into getting the research question right. John Dewey is credited with saying something to the effect of "A question well put is half solved". Richard Feynman described research as being along the lines of: "write down the question;  think hard about it; write down the answer"; and it's too easy to assume that the middle part deserves all the effort, but the first part and the last part repay effort too.


Effect of PhD advisor name/department on my future

For most people, any such effect is very short lived. It can help you obtain your first job, of course. But after that your reputation is your own and after a while, no one will remember or care who you worked with prior to earning your doctorate.

There are exceptions, however. Some, usually prominent, people maintain long term relationships with their former students and write co-authored papers. They might also have an active visitation program in which people visit one another's institutions to work on things or just give seminars. In a situation like this, it is the group founded by the professor that helps you build your reputation and keeps you connected to the larger work of the group. In such a situation your relationship with the professor moves from student to colleague and can be mutually reinforcing. Working initially with such a person can have long term effects, of course.


Reproducible science: do entities exist requiring Level 3 of TOP standards?

There is at least one peer-reviewed journal, reScience, that explicitly publishes replication of existing work.

  ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research is reproducible.

So as such it does require high TOP levels.

Overlay journals such as those in EpiSciences play well with reproducible science, since their model is that you put everything online first, and the "journal label" is applied by a review committee that agrees that the results are correct and worthy of inclusion in the journal


Should I cite the article that I am writing an opinion piece on?

I agree with the comment saying that you should see other opinion papers in the same venue. I personally think you should - it seems logical. If someone wants to read the original paper, they need some way to be able to know where to find it.


Is it considered cheating if you post assignment questions on a site but no one answered it

At my university, the answer is definitely yes. The rules here clearly state that even the attempt to cheat is misconduct (e.g. bringing a device that is capable of cheating to an exam is considered cheating even if it not used/touched).

(However, if asking a question about your assignment in some forum is cheating, depends on the rules for your course/institution. In my courses, this would not be forbidden for homework assignments, for example.)


The ‘defense’ is part and parcel of the work itself. Typically you must first produce some novel work, and at the very end, you must ‘defend’ this work in an act of oral discourse. The defense is mostly a rite of passage in most disciplines. Your advisor and committee usually won’t let you get that far if the work is sub par and you’re likely to ‘fail’. Officially, you must be able to speak intelligently about the work and address criticisms on the fly, proving your scholarship and deep knowledge.


Value of scientific community statement on brain training

In addition to finding what the truth is, an (often underserved) responsibility of the scientific community is to get that truth out to where people can use it.  I wouldn't be surprised if systematic reviews and meta-analyses like you mention have already been conducted.  Those, however, will probably be effectively inaccessible to the general public, from some combination of where they are published and how they must be written.  Public statements in plain language like the one linked are important for getting the scientific consensus out where the public can use it to avoid wasting their time and money on products that don't work.


Should I resend CV if I just have an accepted paper after submitting the application?

Most searches move slowly, so if you contact everyone with an updated CV, you may have to update them again later (and later again and again), which will really annoy some search chairs (I can attest to this, having served as chair on search committees).

Best approach? Wait until there is another reason to interact with the search committee. For instance, if you are going to talk with them on the phone, see them at a conference, or even if they call you to clarify something, then you tell them that your CV has been updated and you want to send them a new CV. If your initial CV was fairly strong.

Did you indicate that these works were under review when you first submitted your CV? A good rule of thumb - when on the job search, put the titles of papers on your CV as under review and leave off the name of the journal you submitted to in order to.

Good luck!!!!


What is a better point in an academic career to move to the U.S.: as an assistant professor or after tenure?

As someone who is just now making such a transition, my sense that it's hard to make the transition in either direction at any stage of your career.

My sense is that as a less senior faculty member, you'll have an easier time getting things going, because the expectations on junior faculty are lower in the sense of ramping up the group in the first few years. But whether or not you should wait is really a function of what you're looking for in your career.


Re-applying PhD after already starting one

Part of the reason I would like to re-apply is that I do not want to feel like a failure down the road, which is admittedly not the greatest reason.

"Feeling like a failure" when you got admitted into a good PhD program is absurd. Look at it from a broad perspective: only around 2% of the population in the US have a PhD, it's clearly not rational to consider yourself a failure when you're in the top 2%. This feeling indicates that you are a perfectionist person, which is common and a great quality in academia... unless it's excessive and leads you to being constantly unsatisfied with yourself, undermining your motivation and eventually the quality of your work. It's good that you're aware that this feeling is not a good reason to re-apply, before any decision make sure that you completely get rid of this feeling: it's irrational and has nothing to do with where you do your PhD, because what matters in a PhD is the quality of your research. Don't let this kind of feeling grow, because a PhD is already challenging enough for one's sanity.

  However, I think that it does not have the same name recognition of US universities or professors that are exactly specialized in my area of interest.

There are lots of unknowns when one starts a PhD, and it's human to try to find certainty in objective facts such as the recognition of the institution. Unfortunately it doesn't work this way: the recognition you will get after the PhD has very little to do with your institution, it will depend almost only on the quality of your own work. A major factor for this is the compatibility between you, your topic and your supervisor. It's true that top institutions tend to have good academics, but this compatibility is not automatic: many PhD students in a top institution underperform, and many PhD students in non-top institutions succeed. At the end of the day, the recognition of the institution plays very little role in your own success. However your area of interest is important: if there are no potential supervisors in your institution who are specialized in it, then it's reasonable to consider moving to a "more compatible" institution.

So my humble advice is:

  (1) it is worth it to re-apply or should I just stick with where I am, and if so,

Not worth for the reputation of the institution; you should consider it only if you think you're not going to be able to work on your topic of interest with a good supervisor in your current institution.

  (2) how do I ask for recommendation letters again without my professors feeling that I am wasting their time.

If you decide to do it, you can ask them if you can re-use their recent letters of recommendation.

  (3)Is there a cost to re-applying again?

No idea but it should be easy to find out.

  (4) What should I change this time?

If you decide to do it, you should probably explain that you now have a precise idea of the topic you plan to do and demonstrate why it makes sense for you to work on this topic at this institution, i.e. make it interesting for a supervisor to accept you.


Idea stolen from proposal. What are my options?

What country are you in? You may well have legal recourse.

Disputing the validity of their patent as suggested by others may or may not be possible, depending on documentation, publication and technical similarities. It's highly technical and will certainly need legal help.

But it might not just be intellectual property rights either -

For example, you may well be deemed to have an implicit or explicit contract with them - if you sent in a paper, it is implied that they will do or not do certain things with it. It certainly wasn't a gift to them without any restrictions as a reasonable recipient would have understood. Do not underestimate the power of claiming implicit terms (conditions that would reasonably have been understood, such as that they would return and not use your ideas if they didn't like them). Contract is based on balance of probabilities, so that helps.

There's also what lawyers call "tort", roughly meaning wrongful behaviour ("someone isn't legally allowed to wrong someone else that way"). Taking ideas without credit, harm to your ability to develop the ideas yourself or gain prestige from them, and so on, may be covered.

Finally consider what they may say - go softly. Don't threaten anything you can't do. Speak to a lawyer to find what they say is your best approach h, and consider what you feel a third party will say, if their reply is that its nothing to do with your work.


I absolutely hate my PhD and I don’t understand the purpose of it

Now I am depressed, lost, and hardly do anything. I wake up go to the lab and pass time. I absolutely hate my “thesis”

This is the problem; you are stuck in a vicious cycle. You need to meet with your advisor and come up with a solid plan - including a timeline - for what will happen in the next year or two.

Given that it has already been 5 years, I suspect this plan should involve you finishing your current work, writing a dissertation, and graduating. But, you and your supervisor could also choose a different direction (i.e., starting a new topic or choosing a new advisor).

  I don’t have anything meaningful or useful for my future career. I don’t even know the purpose of my thesis topic.

At this point it's probably time to decide what your career goals are and make sure your plans are aligned with reaching those goals.

This could mean spending 1/3 to 1/2 of your time learning skills that will be useful for an industry career, and spending the rest of your time preparing for graduation. Given your level of burn-out, I suspect this is the wiser course, but I'm just guessing.
Or, it could mean switching topics / advisors / institutions so that you will be competitive for academic positions in topics that interest you more.


Are extra classes and extra research worth it?

A better GRE score is worth more than a 2nd online independent study project especially if you expect good letters of recommendation.

Think of it this way:  online 4.0GPA + bad GRE score = looks fishy  =  you might not be as good as claimed and maybe you cheated your way through the online education system ("outsourcing" online classes is not uncommon these days).  then it won't matter how many independent study projects you did.


Do UK's 1-year taught MSc programmes provide any scope for research roles either in the industry (R&D positions) or in academia (through PhD)?

You will need to enquire specifically about the particular MSc. Because MScs are short, they tend to serve very particular purposes.
They might provide the opportunity for someone who did one subject, to gain enough knowledge in another subject to work or do research in that subject (e.g. someone with a Mathematics undergrad to do a computer science job).
They might provide specialist training in a very narrow part of a subject. E.g. we do a degree called Human Molecular Genetics, which is basically training to work in an NHS genetic diagnostic lab, or my friend runs an MSc in Mammalian Zooarchology, which will train people who did a general archology degree, and now want to either get a job as a animal bone specialist on a commercial archology unit, or do a PhD in Mammalian Zooarch.
Or they might be for people who's undergrad degree wasn't good enough. Say you only got a 2:2, or you went to a university that isn't very well regarded, but want to do a PhD... they give you a second chance. We offer one of these. The students combine taking a selection of our final year undergrad courses with special lab skills course, an extended literature review and a lab research project.
I should add that all our MScs provide an extended research project (3 months, full time in the lab), but I don't think that's the case for all MScs.
I always advise student thinking of doing an MSc in the UK to know exactly what it is they want out of it, and to know that the particular MSc they are thinking about will provide that.


My coauthor's university address has a typo in our published paper. What should I do?

You should not do anything about this.  Nobody will use this information for anything.
Do not assume your coauthor was responsible.  It could be the journal.


You'll want to check the details of the scholarship, probably searching for terms like "deferral", "cancellation", "forfeit", etc. Most large scholarships will have handbooks, FAQs, and maybe even someone you can email directly to ask a question.

Some scholarships/fellowships can be combined, so you can accept more than one, and some can't. This is generally an unusual enough case that you'll need to ask the program administrators for the answer. In the programs I've seen, you are free to cancel or withdraw at any time with the only limitation perhaps being that you may not be able to reapply for that specific program again.

Given that you won't know for a few months, the only thing that might not be a good idea is to reject the scholarship which is offered now, on the hope that you get the other one. Admissions, and especially scholarship money, are never guaranteed until you have been formally offered them.

Based on the limited information here, if I were in your shoes I think I'd take the guaranteed offer now, and then don't worry about it. If you get offered the other scholarship, then inquire at that time with your program and the previously accepted scholarship what your options are. Then, with the new information in hand, choose what is best then, now that you have the offers.


Can I slack and get a PhD?

Yes, definitely. I have known PhD students that graduated, which I can only describe as lazy.

Now the more important question is Why the heck do you want to? If your goal is to stay in research, slacking off during your PhD time is career suicide. If you do not want to stay in research, and you are not particularly interested in the research contents, then a PhD degree will not be much more than a piece of paper to put on your office wall. A piece of paper for which you have accepted 3+ years of lousy pay.

Edit:

  I want to become a college professor so a PhD is a requirement I need to fulfill.

I correct my point from above: "If your goal is to stay in academia, slacking off during your PhD time is career suicide". Let me put it this way - faculty positions, including those at liberal arts colleges, are typically competitive to get into. Having a PhD that shows that you are less than enthusiastic about your field will likely not land you such a job. If this is your career goal, you need to ask yourself not "What is the minimum amount of work I need to put in to get a PhD?" but rather "What is the minimum amount of work I need to put in to have a real shot at scoring a position afterwards?" (where the second effort is substantially larger than the first effort).


What are the expectations for a Ph.D. candidate in Scandinavia in particular?

In Finland, you usually start your PhD studies after your MSc studies. If you don't have an MSc yet, get it first.

Other than that, there are no unusual requirements or expectations. You just have to convince your potential supervisor that you personally are the best person in the world for this position. Hiring a PhD student is a huge investment — in the ballpark of hundreds of thousands of euros of grant money, plus numerous hours of their time to supervise the student — and you really have to convince the professor that you are worth all that.

A fairly common approach is to do your MSc studies in the same place, get to know the professors, work as a summer intern in their research groups, write a MSc thesis under their supervision, etc., and this way gradually convince them that you really are not just an excellent student but you also could become an excellent researcher.


What is the process for getting a non-EU PhD "validated" in Germany so I can continue working as university associated faculty?

PhD is often less problematic than MSc. It helps if your country is in the EU, but expect some bureaucracy. Contact the Bavarian ministry of education.


How do academic position job search committees evaluate potential for intellectual leadership?

As a postdoc applicant, you should be starting to develop a distinctive, compelling research agenda and vision.  As a grad student, it's usually enough to work on problems someone gives you, and you can go to your advisor for help as needed.  If you never move beyond this, it's not a great outcome, but you'll eventually get your Ph.D.; you just won't be on track for further research success.  To be a successful postdoc, you need to develop the ability to work more independently.  However, intellectual leadership is more than just independence.  It's not enough just to write papers.  Instead, these papers should fit together and be aimed towards larger goals, in a way you can articulate coherently.  If someone asks you what sort of research you do, you should be able to explain what you are aiming for, how your work differs from other people's, and why your approach is worthwhile and even important.

This takes time and comes only with experience - more will be expected of tenure-track job applicants, or people being considered for tenure or a full professorship.  But a postdoc applicant needs to demonstrate a start, by writing a research statement that sounds exciting, and ideally by publishing several papers that build on each other to accomplish something larger than any one of them.  It's even better if other researchers have already started to take up your ideas and apply or extend them, although that's more common in fast-moving fields with short publication cycles.

What you don't want is to come across just like your advisor, but with less experience and perhaps less talent.  You can succeed that way if you do fantastic work, but it's not a wise approach for most students: it's just not good advertising to say "I'm basically a less good version of my advisor."  Even while you are still in graduate school, you should be aiming to differentiate yourself a little from your advisor (with your advisor's help - after all, they shouldn't be trying to produce a clone).  Find some important aspect of the subject that interests you more than your advisor, learn some useful background they don't know well, or find a collaborator who doesn't work with them.

As for how committees judge this, you've got to make a convincing case in your application.  Your research statement should sound like a future leader, not a student (don't be arrogant, but you shouldn't sound like you are implementing someone else's vision - you need to demonstrate clearly that you understand how everything fits together and are adding your own ideas).  You need to back your research statement up with publications worthy of it, as well as some concrete ideas for future work.  Your letters of recommendation should convey the impact you are already having on the field.

Of course this is the best case scenario, and not every application will achieve this, but if you want to get a prestigious postdoc position and go on to a tenure-track job at a research university, then this is what you should be aiming for.  You may feel like a fraud even trying to do this, since you know perfectly well that you still have much more to learn, but you should ignore these feelings.  Everyone recognizes that postdoc applicants are still developing their research abilities, but it's important to be ambitious and show what you are capable of.  (In fact, no matter how far you progress in your career, you'll never reach the point of being able to say "OK, I've reached my full potential and know everything I need to," but you can't let that stop you.)


Conference presentation of a weak paper to an expert audience.

Answer inspired by @Roland's comment.

First of all, have a little faith in yourself, your supervisor seems to believe your work is good enough and so should you.

Otherwise, if you really do have some doubts about the relevance of the paper you can stress the fact that these results seem to be unknown in the community.

Raise awareness on the fact that your project is interesting and that some work and results have already been made, yet seem to have passed under the radar of many.


How do I start publishing when my job is not research related?

To be honest, I think it would be extremely difficult to publish independently, in a forum that would matter.  That is, there are predatory publications that will take just about anything, including a publication consisting solely of the repeated sentence Get me off Your F--king Mailing List ... but if you want to publish real work, there are a lot of hurdles.

I'm not going to google for you to point at how-to's that must say things like how you need to state a thesis, provide background, do some evaluation, compare to prior art, and so on.  I don't think the issue is the mechanics of writing a paper, though the English in your original post indicate that will be a problem if you publish in English.  (I sympathize with those for whom it is not their first language, but it doesn't make it easier to publish.)

The issue is really, as a junior software engineer, is it really true that you can could squeeze some of [your] knowledge into some kind of publication?

It's surely the case that some people have published with minimal background and sometimes even made monumental contributions.  But the bar goes up with time.  There's a lot of cumulative work.  If you really think you can add to that, you probably should start with the "prior art" part I mentioned before.  Read a bunch of papers, for instance in a conference pertaining to your area of interest, and see if there is something there where you think you can add on to it.

But I think a better approach is to do accomplished work as a software engineer, then apply to a PhD program, and have the professors teach you what is involved in publishing.


I have no experience of Phd forums, so I am wondering if it is worthwhile to participate at one of them.

As usual, this depends on many factors:

Are you attending this conference anyway (e.g., because you have a paper in the main research track)? If yes, the opportunity cost of participating seems very low, so why not?
Where are you in your PhD? In my experience, the "best" time for such events is around Y2. By then you already have some initial experience doing research, but there is still time to do a major pivot if you get good feedback that you want to incorporate.
Not all PhD symposia / forums are the same. Is this the best conference to participate in such a forum for you? Most importantly, is it likely that other PhD students that attend will work on somewhat similar theses? Will the senior people there come from a similar field?
If your primary goal is to meet postdoc advisors, the PhD forum does not seem like the best way to go about this. By definition, there are more young people there than senior PIs. However, I am not familiar with the "speed dating with senior researchers" agenda item - maybe that's useful for career planning?

In my lab, most students participate in exactly one of these events during their PhD. Most (but not all) say that they profited from the event, but attending more than once is typically not seen as a good use of travel budget.


How do I, or should I, bring up research that I did under someone who was fired for another reason?

From the tags, it seems you are an undergraduate. Therefore, I am assuming you don’t have a lot of other research experience to list. You also specify that the misconduct was not research-related.

Based on these factors, I would suggest keeping this work on your resume/CV. I would stress the topic and content of the work rather than the person/group. Perhaps where you would normally list the faculty you worked under, you could list the university and department. Or you could perhaps list a post-doc who was a more direct supervisor, if applicable.

You are concerned about negative consequences of being affiliated with the professor in question. People don’t generally hold undergraduates responsible for professors’ conduct, so I think anyone who really considers the issue will not blame you. Personally, I would be more inclined to pity an undergrad in such a situation.


Why do breakthroughs in science and research that have enormous (and obvious) potential often not (or barely) go beyond the lab?

They are just flashy press releases.  They're really not as cheap (including both capex and opex), easy, high yield, resistant to catalyst impurities, or scale-up able as written.

I've been seeing these flashy press releases on thin film fuel cells and the like (methanol production, energy production, F-T synthesis, biodiesel, switchgrass etc.) since at least the 90s.  The current press releases look amazingly similar to the same press releases from back then, with little evident improvement in the field.  Or realization of (or shame for) the past press releases that went nowhere.  Just a new assistant professor and another press hungry R1 school putting out more sizzle, sans steak.

And don't get me started on "nano".  That was already max hype in the 90s and has basically gone nowhere commercially (i.e. outside the realm of ivory tower careers).  And it still seems like a hot area for NSF funding and the like.  And it's a field that really attracts the ego scientists and self-promoters.


Restricting details in privacy-related research to prevent abuse

From a practical perspective, even if you omit the implementation and mathematical details from your paper, large companies like Google and Facebook, or state agencies have significant amounts of manpower and talent. And if they really wanted to they could probably get very close to the results that you are obtaining in a short period of time.

So it is unlikely that any obscuring on your part would halt these entities from following through with whatever agenda they have. On the contrary, omitting too many details will only make it harder for you to publish.

On a more philosophical note, any machine learning model can be used for good or for evil. Linear regression models I'm sure have helped people to win wars as well as eradicate diseases. As a result, one can easily argue that any attempt to prevent abuse is equally preventing progress in other domains.


On some cases where exam results are manipulated

There is no counterneasure which is bulletproof and administratively feasible. If I want to cheat as a teacher, I will always find ways around such a system.

The only way would be to have the exam taken by independent administrative staff, they scan all answers as proof, and then hand it to the teacher.
Online results could be watermarked (e.g. by an MD5 / SHA hash), but I don't know if such systems exist.

If I really want to upgrade or downgrade a student, I would not take the risk of manipulating the exam, but to adjust my measures for deciding what is true and what is false and to which account I'm willing to accept "a good idea which did not lead to the correct result".

As a teacher, I like to have electronic submissions since they are a proof and students usually have nearly no means of changing them afterwards. But I prefer  doing the grading with paper and pencil.


A professor may have stolen an idea I discussed with him: how to proceed?

I think it's very clear that you should talk with (B). You had previously discussed this idea with (B) so s/he knows that it was something that you had been considering. Furthermore, (B) also presumably knows the situation within the department better than you. Maybe (A) is known for doing things like this. Maybe the overlap isn't as serious as you think and (B) can reassure you that you can still do your thesis as you wanted to. No one here can decide whether either one of these is the case.

One word of advice: in talking with (B), present this situation as something that you are concerned about, but stay unemotional and stick to the facts: (B) knows that you were interested in this similar project, you discussed it with (A), and now another student is doing this project with (A). You do not need to connect the dots and accuse (A) directly of plagiarism or dishonest conduct in an initial conversation with (B). If this is a misunderstanding or miscommunication then doing so makes you seem aggressive and prone to jumping to conclusions. If (A) did something that is as blatantly dishonest as you have suggested, then that will be obvious to (B) as well.


This question might very well be closed as not being about academic careers, or as an opinion question, but I'll give an answer anyway...

I studied math and computer science as an undergraduate in the early 1980's and ultimately ended up with a BS in Computer Science because it was a better degree for getting a job.  After a few years as a software engineer at Motorola, I went back to graduate school in mathematics and then entered into an academic career as a math professor.

Although some of the more theoretical aspects of computer science that I studied in the 1980's are still relevant, the programming languages, operating systems, and computer hardware that I worked with are long out of date.  To paraphrase a quote from Charles Stross, having a degree in Computer Science from 1984 is somewhat like having an Aeronautical Engineering degree from the 1920's.

On the other hand, most of the mathematics that I studied in the 1980's is still relevant and hasn't changed very much.  For example, I've recently taught an Intro to Ordinary Differential Equations course using a later edition of the same textbook that I used as an undergraduate in the early 1980's.

The two points that I'm trying to make with this story are that

Computer Science and Software Engineering are very rapidly changing fields.  You'll have to keep updating your education as the technology changes if you want to stay in it.
You might very well change careers one or more times over the next 30 to 40 years. It's unwise to plan for a career as if you'll be doing the same thing for the rest of your working life.


How to request that collaborators add my supervisor's name to a manuscript

While conventions vary greatly from field to field, if your supervisor has made literally no contribution, he or she should not be listed as an author. There is been plenty of discussion here of this issue; see e.g.

Co-authorship for not very involved supervisor
When should a supervisor be an author?
What are the minimum contributions required for co-authorship


Has a journal ever switched between being a predatory journal and a reputable one?

This question isn't really answerable because what's predatory and what isn't predatory isn't well-defined.
If you define "predatory" as being on Beall's list, then the answer is yes: MDPI was on Beall's list in 2014, and then removed in 2015 (there are a few other publishers that bounced back and forth on the list too, e.g. Hindawi). However if you believe that MDPI was not predatory to start with, or if you believe that MDPI is still predatory, then saying this publisher has switched from being predatory to reputable makes no sense.
The same goes for the other bullet point you mentioned (of a reputable journal becoming disreputable). In 2016, OMICS - a publisher generally held to be disreputable - acquired two Canadian publishers Andrew John Publishing and Pulsus Group, as well as their journals. You can see from the Wikipedia page that this "led to a decline in publishing standards". However if you read the quoted source, the objection is:

Rose Simpson, the former managing editor of the Canadian Journal of General Internal Medicine, said that after the OMICS deal was announced in January, she went on the company’s website and immediately noticed red flags as she started browsing through the journals.
“There were all kinds of typos, the grammar was wrong,” she said in an interview from Ottawa. “In medical journals, everything has to be accurate -- every comma, every word -- so that was my first suspicion.”

In other words, the decline in publishing standards is based on poor copyediting. Does poor copyediting make these OMICS-acquired journals predatory, given that poor copyediting can happen even in reputable journals? You'll have to come to your own conclusion. Rose Simpson clearly thinks so, but not every reasonable person will agree with her.
Edit: to further illustrate how much of a grey area there is in what's predatory and what isn't, consider a journal that doesn't perform peer review. Say this in a vacuum and most people will immediately assume the journal is predatory. If this is your definition, then there has indeed been a predatory journal that "reformed" and started implementing peer review: Medical Hypotheses.
The problem is, as you can see from the "Peer review debate" section of the Wikipedia article, this journal was started by a reputable academic (David Horrobin) and published by a reputable publisher (Elsevier). David Horrobin's stated reason for starting the journal is that peer reviewers tend to dislike ideas outside the scientific mainstream, which makes it hard to publish new ideas. His solution was to not perform peer review, and to worry less about whether the paper is true but whether the paper is interesting. Ironically, when put this way, there are people who agree with this sentiment too.
The upshot of this policy is that in 2009, Medical Hypotheses published two papers arguing that there's no proof that HIV causes AIDS. There was a backlash, the media got involved, Elsevier investigated and subsequently demanded the journal implement some level of peer review. The then editor-in-chief Bruce Charlton refused and was subsequently sacked. A couple of years later, 198 academics published an article in another journal defending Bruce Charlton and Medical Hypotheses' original peer review model.
Is Medical Hypotheses predatory? It didn't perform peer review and published pseudoscientific papers! Is Elsevier predatory? It fired an editor that didn't do what it wanted! Again, you'll have to come to your own conclusions. There's no clear answer.


How to gracefully leave a research lab (due to major change)?

Nobody expects undergraduates to have their life plans all sorted out: if you tell the professor you are changing majors and planning to leave the lab, it shouldn't be all that shocking to them.

What you should do, however, is make sure that you leave things in good order.  Plan to complete your work for the current semester, and set up a plan with the professor and whoever else for how to leave things in a state where it will cause as little disruption in the work as possible.  This might be cleaning up your lab notebooks, or about finishing a certain set of experiments, or training another person who will take over your tasks.  The key is to have the discussion as early as possible, and make it clear that you take your responsibilities to the lab seriously, and want to act professionally in using your remaining time to wrap up and/or transition the work.


From whom do prospective grad students get recommendation letters?

In general, I don't think all that many students have three unique reference letters, all of whom can vouch for research ability. Two is quite common, as most undergraduates who pursue graduate degrees (at least in the sciences) do have some research experience at their home universities. Many of them also pursue a summer research project separate from their main undergraduate research project (or projects), providing another reference.

But I do agree that the third letter usually comes from a non-research source. I wouldn't even necessarily expect a third research letter.


Plagiarism is passing someone else's work as your own. If the source is referenced, then there is no plagiarism.

Quoting the whole algorithm verbatim may be considered as bad writing style, may be against a particular journal's rules, or may simply demonstrate a certain lack of creativity. However, this is not a plagiarism, as long as the source is cited.


What should one do with his/her manuscript after some sort of academic misconduct

I think that the action was a serious breach of trust, but I think there are better ways for the PI to deal with it. If the student didn’t mean malice but published because of inexperience, there should be a way to correct the action and move on.
Concerning a student, I think the best choice is for the student to contact another member of the faculty committee and obtain guidance in how to deal with the PI. I’m suggesting this because the question, while superficially only addressing a paper, cuts much deeper: If your PI advisor is so angry with you as to not coauthor a paper, the relationship may be fractured to the point that efficient mentor ship and guidance has become impossible and the student might be best advised to consider changing advisors.
The answer to the question about the continued membership in the lab will then determine the best path forward for the manuscript as well.


Type of non-university, research jobs suitable for a mathematician turned computational neuroscientist, with coding experience

Your questions are rather broad, so let me just point you to some resources.  For the first two questions (and possibly some info about the third) check out some info from the AMS:

http://www.ams.org/profession/career-info/math-work/math-work

http://www.ams.org/profession/career-info/new-phds/new-phds

For 3, some online academic resources to find jobs both in and out of academia are: mathjobs, the AMS's EIMS, the LMS site, the EMS site.  Some universities also have Career Fairs and Career Service Departments which may be able to give you more help in your job search.


How should I prepare my write-up for an internship program?

You could Include the following (in order) -

A very brief introduction about yourself and the motivation behind working in the field of the internship you are applying for.
Where you have interned/Projects done
The skills developed from point 2.
What you hope to acquire from the internship and how it will benefit you (very short sentences)
An ending touch.


The most common issue I observed is looking at other students' exams. A student who has a particularly good eyesight sits behind a second 1-alpha student and copies from the sheets of the latter student.

You forgot several variations on the topics you've mentioned, such as hacking to

obtain the exam in advance
modifying the exam in advance
modifying the student's answers a posteriori.

We see attempts of such actions, and we have no idea of how many such attempts have been successful. It can be anything between 0% and 99%.
Another common thing we see are attempts to bribe the teaching assistants. It does happen, although rarely.


How do I ask my professor to recommend me to a few specific industry positions?

It is appropriate for you to ask for a recommendation. However, the professor may not feel it is appropriate for him to ask them directly. But it is part of their responsibility to at least write you a letter of recommendation. And they may be willing to do more.
But the "way" to ask, is just to ask. Ask for a recommendation, preferably a letter and something more personal. It is up to them how to proceed after that.
I'd guess that even a letter would be pretty effective given the relationships.