Can I recover after a really bad first year?

If you do really well from now onwards, then a couple of poor years can be overlooked, for instance if you are going to apply for PhD studies.

Also, it seems that the problem is not necessarily ADHD or Aspergers; it seems to be taking on too many different activities. So prioritising your time and commitments during your degree studies seems to be the solution to the problem and then working very hard, not getting the record wiped.


A postdoc joining my group is interested in my experiment. How to proceed with respect to leadership on the project?

The OP is right to be careful. Much depends on the level of trust the OP has to his advisor. The word collaboration is pleasant to the ears, and fun to act out when it works, but there also needs to be a mechanism that protects the OP's investment, in case things do not work out. Yes, students have been sidelined by higher-level forces after investment, so, not knowing the postdoc, it is wise to be careful. However, on the other hand, the OP should not let it appear as if immediately prepared for the worst case. It's a balance act. That being said, it is worth contemplating if there something the postdoc could bring into the game.

If there is a good level of trust between the OP and the adviser, it may be a possibility of bringing up issues of leadership, credit, etc. in a discreet conversation how the OP's investment is going to be protected, if that's the fear. Unfortunately, it will not cost the advisor as much if things go wrong, so clearly the OP needs to make sure his interests are taken care of, if the adviser is not privy of the possible pitfalls.

If the OP merely wants to keep the experiment and its benefits for himself, there is not much he can argue with, I am afraid, but in this case it won't cost him too much to collaborate, as long as first-author credits and potential leadership issues are taken care of.


Mendeley attempts to extract metadata (title, authors etc) from article PDFs by searching through the PDF content. Since different publishers format their PDFs in different ways, sometimes Mendeley gets more information (e.g. a DOI) and sometimes it gets less. This is not a problem unique to Mendeley – Zotero has struggled with it, too.

There is an article on the Mendeley Support website called 'How does the automatic document details extraction work?' that explains the process in slightly more detail.

Automated metadata extraction is likely to remain imperfect until publishers consistently produce PDFs with standardised data. Several organisations have made progress on this, but it is not yet a solved problem. Until then, if you want good-quality references then it may be best either to generate them manually or to edit Mendeley's automated references by adding missing information.


If asked to submit both a shorter and longer abstract, is it possible just to send a shorter one that meets both word limits?

It is possible, but you would not want to do that.

Apparently, these are the guidelines for some sort of conference. Usually, you send in a preliminary abstract, then you get a message back that they will accept your permission within a certain deadline. Now you can write and hand in your article.

If you haven't finished your article in time for the abstract submission deadline, you basically have to write an abstract first. But after you have written your article there are most likely changes that need to be addressed in the abstract, which is why you get more words for the final abstract to amend your early release abstract that will probably be available on the website of the conference.


Acknowledge startup funding in manucript

Unless you were given other specific instructions from your university, all you need to do by way of acknowledgement is to put “[name of author], [name of university]” on the title page of your paper. This is enough to ensure that people understand that the university is paying your salary, giving you an office, and providing you with any other resources that you need to do your job, including startup funding if applicable.


Letters of recommendation from undergrad professors after you have a masters

There are two general categories to consider for deciding who should write letters of recommendation: the recommenders familiarity with you, and their standing in the field. In this case, those two criteria may be in conflict.

As you have described it, the standing of your masters faculty leaves something to be desired, conceivably being people who do not have tenure, and may not even be in tenure-track positions (as it is unclear what you mean when you say someone is a lecturer, which I realize in United Kingdom may sometimes be the same as a Assistant Professor). While these letters of recommendation are not worthless, they certainly won't go as far as a letter of recommendation from somebody who can more reasonably evaluate you in comparison to other people in the field, and whom people in the field have reason to believe will make that evaluation correctly.

On the other hand, the professors who have advised you as an undergraduate may be less familiar with your work, and therefore less able to write a good letter of recommendation. Importantly, your graduate work may have been at a much higher level of proficiency then your undergraduate work, meaning that the letters of recommendation that your undergraduate professors could write for you would not reflect your more advanced standing in the field.

In this situation, the most important consideration is how good of a letter of recommendation can your thesis advisor right for you? If your thesis advisor can reasonably cover the work that you have done in your masters program, that inclines towards letting your other two letters be tenured professors from your undergraduate institution.

A secondary consideration, however, is how long ago you attended your undergraduate institution, and how long your masters program has been. If you went straight through after undergraduate, and you are essentially only one or two years removed then other than your education, little has changed and your undergraduate faculty is likely to be able to write accurate and helpful letters of recommendation. On the other hand, if you have taken several years off and returned to school, then a lot about you has changed and should be reflected in your letters, and your undergraduate faculty does not know you nearly as well. As a rule of thumb, more than five years without significant contact is too long for a letter of recommendation, but your mileage may vary.


Extent of reuse and reanalysis of data published by others

If you use the figure directly, you'd best get the permissions in line.  If you modify the figure, you most likely don't need to, but properly attribute (i.e., "Modified from...."

My own preference for stuff like this is to use a tool like datathief to grab the data from the figure, and remake my own figure, formatted optimally to make my point.  Attribute the original.


What incentive does an institution have to hire expensive research staff instead of having PhD students fill all those roles?

A PhD is where you learn to do research to a doctoral standard.

A research job is where you apply what you've learnt.

These things are different things. They are not the same thing.

It's like why you see a qualified doctor instead of an undergraduate studying medicine.


Reviewing: potential conflict from knowledge of other researcher's activities

Your job is to do the reviewer, which means 1) evaluating the quality and 2) helping the authors improving the paper. Half of the things below are unrelated to this. You even got a specific task from the editor. Limit yourself to that.

  If I make the comment about interesting question in its own right, am
  I suggesting the separate paper?

This is exactly the only thing you should do IMO: "make a comment recommending that any mention of Field A should be removed from the paper and noting that the overlap is an interesting question in its own right that should not be dealt with from the perspective of just one of the fields within an empirical paper about a specific topic."

  If so, is that a problem given that I know someone is working on
  something similar? Can I suggest to the person working on it that
  perhaps he should involve authors from the other field? Can I suggest
  a workshop to both the person working on it and the authors of the
  paper I am reviewing?

This to me seems not OK because potential conflict of interest and because you are using confidential information for purposes that are beyond the review. I get the impression that you also risk of revealing yourself which you should never do, if it's a blind review. Wait for the paper to be accepted and available online and then you can contact all the relevant people pretending you had this idea reading the paper and without saying you are the reviewer. If the paper is rejected then drop the idea of the workshop or contact the editor and agree with him/her on a proper way to contact the authors.


What should I be asking when publishing my materials with for-profit websites?

Money.

Or clear evidence that "Credit for your work and your name after your articles" will manifest itself as a benefit to you in some clear way.

While the currency of academia is published articles, these won't really count for that (which you clearly know already). You're being asked to supply a commercial entity with product (content) for free. There needs to be some benefit to you.

What you have essentially just been approached with is the classic "It will look good in your portfolio" line that companies use to try to get free writing or art out of creative professionals. They shouldn't do it, and neither should you.

That being said, it's possible just being there is a benefit to you if you want your name out in the public sphere (for example, if you want to work mainly in public health communication, enjoy outreach, etc.) But it doesn't sound like that's true at the moment.


Where should a question mark be placed in a short citation?

As Peter indicates, the question mark should remain with the original quotation, since it's in the original source material. Therefore, your second example is clearly incorrect. In addition, you still need the period following the citation, to indicate that you are ending the sentence in question. Therefore, you should use the last example.

However, I would also note that, as written, it looks like your example would also require the name of the author along with the parenthetical reference, so it would be more like:

  “[t]o what extent do translation theorists engage ith the experience of translators and how are their theories shaped by what happens in practice?” (Smith 16).


Graduate school applications: Should your answers be exhaustive or selective?

Should you see graduate schol application questions as opportunities
  to provide relevant positive information about yourself, or as fiats
  to list absolutely everything in a category of your experience?

From reading some other posts of yours, I am aware you are finding it quite tedious to fill out your applications.  Therefore, for you at least, it is easy to choose the right option:

opportunities to provide relevant positive information about yourself

Your motto should be

" Get 'er done."


How to make the most of a currently unfulfilling post-doc experience

Do I have a future or am I looking at a premature "pink slip"?

This is unlikely, especially in France. The financial savings from firing a one year post doc is pretty small compared to the hassle and bad blood that will result from doing it.

  Although I am in a teaching track from 2015, I feel that this research experience will only enhance my teaching capabilities.

Is this really your goal of the post doc? It is not clear to me how a year spent disentangling spaghetti code is going to enhance your teaching capabilities. Most engineers do not take up a non-teaching post docs to enhance their teaching. I am not sure that most post docs would spend a year disentangling spaghetti code with supervisors hovering over their shoulders. Are you sure that an E2 is really the equivalent of a post doc? It is probably worth talking to your supervisor, hopefully again, to make sure you are both on the same page.

Realizing that you are unhappy with the current state of affairs does not really help you to change things. I think grad students and post docs sometimes have unfulfilling experiences because they do not know what they want. You need to figure out what it is you want to get out of the post doc and then figure out a way to work towards that goal. Often once you know what you want the road to obtaining that goal becomes clear.


Could lecturing from a textbook constitute copyright infringement?

I can't imagine an existing legal regime in which teaching from a textbook and "publishing" the lectures would be considered wrong unless the instructor explicitly made images or snippets copied from the book open to view. Likewise reading from the text verbatim would possibly be wrong depending on how much was read (fair use principles are discussed below). For a sentence or two, there are likely no issues. For a section, beware.
Referring the students to certain page/section numbers in a text is completely innocuous. Putting up page images is problematic.
Paging through a book with the camera pointed at the pages would probably be infringement everywhere, unless the snippets were very small (fair use). But, such paging seems to be blatant misuse in any case. Note, also, that the fair use rules for educational purposes are (normally) a bit relaxed from the general rules, though this has been changing.
But the lecture "belongs" to the lecturer, not the author/publisher of the book.
In some fields the standard for claiming a violation is much higher. If I copy the definition of the derivative (Calculus) onto a whiteboard, I'm not violating copyright even if my lecture is widely available. But that is because of a (typical) exception that things that can be said only one (or a very few) ways can't be copyrighted in the first place. So the author of Rudin (i.e. Rudin) used this exception in writing the book in the first place. But if I copy an equivalent amount from, say, a philosophy or history book, then there might be a problem.
You are much more likely to get a takedown notice at YouTube if you have some music playing in the background as you lecture. But that is because of draconian laws put in place by media publishers, not just copyright.

One of the (typical) standards for fair use is whether the use reduces the market for the item copied. If it does, then there are issues, otherwise there are not likely to be. If you "teach from" the book in such a way that students don't need access to it, then you should reexamine what you are doing. But even that implies that the "teaching from" is extensive. For supplementary materials, it might not be necessary for students to have other access. But there would be a "quantity" assessment made by anyone wanting to claim infringement and any court judging it. Does your use reduce the market?
And note that the laws are different everywhere, hence my use of "typical" etc. in a few places here. Perhaps a king could copyright the alphabet and make all written text subject to rules. See the book Fahrenheit 451 by Ray Bradbury for an extreme example.

I'll also note that, done right, such a course could actually increase the market for a textbook.


Why is the phrase "including but not limited to" used in conference announcements?

This phrase is just standard boiler-plate verbiage.

The title of a conference is generally too vague to define a community precisely, because different people might interpret such a short phrase in different ways.  Thus, when you are designing a call for papers, you generally try to give a bunch of examples as a way of giving a more concrete outline of the sort of community that you are trying to reach.

But it's a highly inexact procedure, and the boundaries of communities are generally fuzzy in any case.  Thus, the "not limited to" phrase is included as a less informal way of saying, "If what we described kinda smells like your research, don't worry too much about whether it fits a bullet point, and just submit."


Can students finish much of their PhD thesis before applying to a PhD program?

I can't speak to whether this is possible, but I can advise as to why I think it's a bad idea.

Firstly, PhD Comics is a largely satirical and humourous representation of life in academia. Some of those comics can be scarily true, but you can probably find a comic that parodies any job you care to imagine. It doesn't mean they all suck.

Even if you could do this, for most people and disciplines it's not a good way to get a PhD. You really should find an advisor to help you guide your research. Colleagues are great to bounce ideas off of. Having an office to work in and access to a good library is a huge advantage. You will have access to high-performance computing and lab facilities, if needed. If you're lucky, you'll find someone to pay you to do your research.

At the end, you will graduate being well-absorbed into academic life. You'll have networking skills, have been to and presented at conferences, your research will be of a higher quality, and you will overall be a much more well-rounded and knowledgeable researcher than had you stuck at it alone. The skills you learn as a PhD student are essential if you wish to have a career in academia. If you wish to go on into an industry job, they're still pretty darn useful.


How will the topic of my Master's thesis affect my PhD?

In the US it should matter very little. Having a closely related area in mind might be an advantage, but changing might not be much of any disadvantage, within limits. In fact, having too narrow an interest might make it difficult to find an advisor in the US. Some flexibility is suggested.

Note that most beginning doctoral students in the US don't come with an MS or with much research experience. The first task is to pass qualifying examinations and some coursework is provided for that. Along the way you choose an advisor and a topic. But the topic has to be mutually agreed on.

It isn't quite correct to say that all they care about is your ability to do research. But it is fairly correct provided that the fields you previously studied and the new one is fairly close. But expect to have to do some background work at least.

And, even having a wildly different MS topic might not hurt your chances for admission. It would just add to the time to completion as it would for someone entering with a BS instead of an MS. But a lot of things will be looked at in any application: courses taken, grades, test results, letters of recommendation...


Do reviewers review the code submitted with papers?

Personally, I always check the code (and I always make the code available as well).

Usually it is just a glance over, unless I want to double check how something was done (and it wasn't clear on the paper). People usually don't do that because "scientific" code isn't always readable. Often is written hastily, as a one-off that can't really be reused only the author can make it work. Even that may fail a couple of years later.

And considering the amount of views I get in my repositories, even a glance over is not common. For my last paper, I had code, live examples, and supplementary material online, and only one of the 3 reviewers checked it (I got only one visit on the url).

TLDR: People usually don't check it, but it is still very important that you make them available.


Exam exceptions for student with disabilities

Exceptions can always be made under certain circumstances. Interestingly in your long and detailed question, there is no trace of a reason for requesting a delay other than your general condition, which I cannot see as a reason by itself. The university/department probably has some rules or policies for such cases. There are usually ways for people with different disabilities to take an exam in parallel with the scheduled exam in a a separate room, sometimes with specific tools and help. I can for example see that hospitalization and family funeral can be clear cases for such exceptions.

So if an exception is made, what would you have to expect? To provide exactly the same exam twice seems extremely unlikely for the reasons you provide. So from the teacher perspective, making a new exam is not something to take lightly, it requires a lot of work (if done seriously). In other words, you would get a different exam designed to be of equal difficulty. From a student perspective a new exam can always appear either easier or more difficult based on what and how well you have studied but in general, the exam would not intentionally be made more difficult.


One idea that could work is to try and do another masters in math somewhere that has a thesis requirement.  You can use this thesis to study a research problem that is currently being worked on by faculty at the schools that you want to get into.

If you can't do a second masters, how about an independent study somewhere with a prof. that could agree to supervise you for a semester or two?


How to deal with advisor who wants me to submit dissertation on time even though there's a major problem?

The following is based on my experience in neuroscience. Not sure if this generalizes to other fields.

I think you have two ways to work here, and each is equally "right".

First, you can do exactly as your advisor suggests, working towards completing the thesis even though there's a major flaw. This happens probably more often than you think; I learned halfway through my own thesis that the work I was doing was not generalizable at all due to bad design, and overall was pretty bad science. Oops. The thing is, it's a dissertation, not a peer-reviewed publication. The goal of your dissertation is for you to demonstrate to your committee that you know how to perform research, not for you to contribute overall to science. Your advisor's pushing you to complete your thesis may be him espousing this very idea; namely, your fixing everything up should be saved for your peer-reviewed publications, not for your thesis. Given that (in neuroscience) it is a pretty rare event for someone to refer back to a dissertation thesis when performing a literature search, the fact that your thesis document may be rendered moot isn't such a big deal; mention it in the introduction, results, and conclusion sections and just publish as is. Fix the problem in the journal articles.

The second approach is that, if it has your name on it, it should be publication-worth, and dang if you're going to let something with this obvious an error be in the public record.

Honestly, I don't think either one is wrong. The first one can save you valuable time and advance your career by months/years, and if you're in a field where your thesis doesn't mean much then it's probably the right choice. The second one may make you look better overall, and may be a requirement if your field places more weight on the thesis document itself.

Not sure if that helps, but it may give you some perspective.


Preprint services other than arXiv (for other fields)

The OSF provides a general open preprint infrastructure that is connected to a range of preprint services. Importantly, it is not owned by a commercial publisher.  It supports a number of discipline-specific preprint services many of which use the ArXiv name under licence.

The list of preprint services is growing over time.
For further information go to: https://osf.io/preprints

In general, no matter what the discipline you can post to:

OSF preprints https://osf.io/preprints/

However, the OSF supports the following discipline-specific preprint services. Presumably, if your preprint aligns with any of these disciplines, then you would be better off posting to them.

Psychological Sciences.  PsyArXiv https://osf.io/preprints/psyarxiv/
Social Sciences. SocARXIV https://osf.io/preprints/socarxiv
Engineering. engrXiV https://osf.io/preprints/engrxiv
Agriculture and Allied Sciences. AgriXiv https://osf.io/preprints/agrixiv

More discipline-specific preprint services using the OSF framework are being added on a regular basis: https://cos.io/blog/public-goods-infrastructure-preprints-and-innovation-scholarly-communication/

Useful features of OSF-based preprint services

Strategy for long term archiving
Integration with Google Scholar
Integration with OSF projects which allows you to link other materials such as data, code, and materials
OSF is a not for profit entity run by academic researchers (contrast this with SSRN, Figshare, ResearchGate; i.e., no ads and goals aligned with academic community)
The functionality of OSF preprints is improving on a regular basis. See features road map
You can choose a licence
You can link to the doi of the subsequently published manuscript.


Is it reasonable for me to expect an official and timely response to my PhD application?

No, final decisions take a while. It is not the fault of the program, but rather an issue of funding. Programs tend to initially reject very few applicants. An applicant that seems weak on "paper" might get accepted if their proposal fits into a very narrow funding scheme that no other applicants are eligible for. There is no global rank order of the applicants, but rather the "best" applicant for each funding scheme is identified. Programs generally construct strategies which lead to the most funding. The strategy is constantly revised when the program finds out about successful/unsuccessful funding applications and whether the applicant accepts the acceptance. Basically the whole system is a nightmare for everyone.


What are the consequences of using Sci-Hub?

It's of questionable legality, but it's not going to lead to prosecution. For me personally using sci-hub has led to new research results in fields outside of my specialization that will (very likely) appear in leading peer reviewed journals. One problem I'm not sure about is whether it's wise to say in the acknowledgements: "I thank Alexandra Elbakyan for setting up Sci-Hub without which the research results reported in this paper would have been impossible", in an Elsevier paper.

Using sci-hub therefore has at least the consequence of your personal scientific enlightenment, and possibly even of many other people who benefit from research you have been able to as a result of using sci-hub.


Full scholarship and student advisor relationship

The main effect of external support on a student/advisor relationship is that there is less external pressure for production of short-term results.  Whether this is a good thing or a bad thing depends strongly on the individual student and advisor.

With less pressure on the student, there is more freedom to develop a unique research agenda but also more opportunity to get "lost" in the possibilities and waste time.
With less pressure on the advisor, there are fewer boss/employee dynamics in the relationship and generally less strain, but also more opportunity for the advisor to be distracted by other short-term concerns.

A secondary effect is that the student may have less opportunities to be apprenticed in grant-writing, since their support is already assured.

In sum: with a good advisor and a student with a mature outlook, the freedom of external support is a blessing.  If either of those two ingredients is lacking, it can be a problem to lack the forcing functions of external support.


Does FERPA apply to university teachers when they are working as private tutors?

On page 3, "FERPA applies to educational agencies or institutions that receive funds from programs administered by the U.S. Department of Education." Because you are a PRIVATE tutor and do not receive funds from the US Department of Education, you are not subject to FERPA. However, there is a fuzzy line on when you're tutoring as an agent of the University or when you are acting on your own. I would recommend as to not juggling the two, that you stick with FERPA laws and respect the student's privacy. Best would be to get written consent from the student to discuss his/her progress with his/her parents.


How economically efficient is the grant system?

I know of one such study: Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant.

The authors examine the full costs of the process used by the Natural Sciences and Engineering Research Council of Canada (NSERC) and conclude that it would be more efficient to simply give a base amount to every researcher who meets the requirements to submit a proposal. The costs they consider include the time spent preparing and peer-reviewing grant proposals. In addition, the authors argue that the current system is ineffective, in that it rewards mediocrity and safe bets over curiosity and innovation.

The same journal later published a rebuttal (The Real Cost of the NSERC Peer Review is Less than 5% of a Proposed Baseline Grant) and a reply to the rebuttal (Indeed: Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant).


What if clinical leadership refuses to protect research time?

Take a look at the rules governing the ombudsperson before you go there. Good rules will ensure confidentiality and that the ombudsperson won't take any action unless you say so. That will allow you to freely discuss your problem. If your institution offers an ombudsperson with good rules, then talking to an ombudsperson would actually be very useful in your case. I would not start with the idea of taking action, but just as exploring what is possible.

Also don't take this personal. The leadership has to make sure that all tasks are performed with the resources at hand: if you do less, somebody else has to do more. If your grant compensated your department for that in full, then that should not be a problem. Though even then, if the departments resources are stretched already, then the leadership will still be faced with impossible choices. It should not be the case, and solving those impossible problems when they happen is not your problem, but understanding it can help not to take those choices personal. If your grant contains no or only partial compensation, then the "protection" from the granting agency is very cheap: basically the granting agency is not spending its own resources but your department's resources. Your department can be forgiven for saying that that is not going to work.


How to cite in text a citation translated by me

Your suggestion "Name (2001, translated by me)" seems good to me.  Or else "Name (2001)" and then include translation information in the reference.

However, in a formal paper you would not say "translated by me".  Maybe "translated by the author" or "translated by AB" your initials, or even "translated by Alexis Brown" your name.

If there are several of your translations in the paper, maybe say once at the beginning: "Translations are by AB, unless otherwise attributed".


Will the bad grade in a proposed studied subject be a red flag in my application?

I don't believe there is a serious stigma associated with an undergraduate getting a B+ in a graduate-level course. It is generally understood that undergraduates taking true graduate-level work (with graduate-level course numbers, etc.) are taking exceptionally advanced subjects, relative to their own preparation. Therefore, it is entirely understandable that you might have an A-, B+, or even a B in a graduate-level subject without it having a strong impact on your chances for graduate-school admissions. Exceptionally weak performance (corresponding to "failing" grades—usually C+ or lower) would be an exception to this, but I see no reason here why you should worry too much.


Mentioning slipshod undergrad research or not in top graduate school applications?

As an undergraduate, you are not responsible for the scope and scale of research you are not directly leading. If a graduate student or PI is the one in charge of the work, you will not be "dragged through the mud" for having worked on it. In general, you are given the benefit of the doubt—you are asked to contribute to a project, and you do it.

I don't think any committee is going to take a dim view of having published two conference papers while still an undergraduate. (And any committee that does probably represents a department you don't want to be at.)

If you are concerned about the impact, though, I would mention but not emphasize it. If you don't mention it at all, and somehow it turns up later on, it will raise more red flags than if you at least mention it in passing.


What kind of assistance from graduate institution can I expect in transferring parole?

To answer my question based on my experience:

I did not find that any institution was particularly wary about my past. Of the many institution to which I was granted admission, only SUNY Stony Brook asked me to go through a review process. Most institutions found my past inspiring. I cannot say how the institutions that rejected my application felt about my history. However, my rejections came primarily from top 10 universities, so it is likely competitiveness of those programs led to my rejection.

I have accepted admission into a Ph.D. program at a University of California institution. In the process of transferring parole, the department of my studies has been very helpful. The chair of the department has provided a letter to parole, and the staff has assisted me in obtaining housing.

My experience was much less troublesome than I had feared.

Most helpful to me was:

Creating connections at my undergraduate institution. I have been an active student regarding campus activities. I volunteered often to help the department. I wanted to create a track record of assimilating into the campus community.
Being honest in my applications and statements of purpose. Many may believe that my history should not be highlighted, but I have found that having a unique story sets me apart from other students. Everyone seems to enjoy a good comeback story. (It has also helped me win scholarships.)
Letters of recommendations from professors with whom I have worked. These letters did not mention my history. They show that I am more than a good student with an interesting story; I have the ability to function as a productive student researcher.


Of course you can!

It is absolutely normal for especially young people that they do not yet know what their best and greatest interests are. Don't be afraid of those that try to spread fear with nonsense like 'straight carrer-lines'. Nowadays, job recruiters more and more value those that have the self-confidence, curiosity and intellect to focus on more than only one topic and demonstrate through this that they can work themselves in difficult topics even if those have nothing or few in common.

And to make a personal advice: It's your life, so do not forget to have fun besides going for a carrer. The decision of a Professor is absolutely individual; there might be some, that want to see some work in the field, maybe, that I heard about a lot of people that started writing about stuff they have never even heard about before they applied, so yes, it is not uncommon to change the topic for PhD work. I believe that they mostly much more want to see your effort and talent, oh, and it's about sympathy, of course, as you will see each other quite often (not in all cases, but at my university that's very common). If you are worried, simply go and ask your Professor of choice what his or her expectations are. If (s)he is fair, he will let you know very clearly what he expects and will give you a chance beside the master thesis you wrote to show your talents. A master work in the same field can of course draw the attention of a specific Professor beforehand if it was really good, but there are enough other ways to put yourself to be short-listed.


Lazy/Busy Professor does not give me my confirmation

I would address this by contacting the professor's administrative assistant or secretary. Usually, such "form letters" do not need to be actively written by the professor in question—just signed by the professor. The assistant can prepare the letter, and get the faculty member's signature; in some cases, the assistant may even have a digital signature available, so the professor's direct involvement isn't even necessary.


How should I know if my supervisor is deliberately ignoring my emails or he is simply bad in responding?

Your situation has the first thing I would try built in - ask your other adviser for help.  Your committee probably communicates with each other, even if they're in different departments at the same school.  Tell the adviser who is responding that you're held up because the other adviser hasn't replied, and see what they suggest.  If they are indeed in contact with them, then they might be able to nudge a reply.  They might also be able to inform you of anything going on that might be causing this, like an illness.

If that doesn't work, or if your responsive adviser is so far removed from the unresponsive one that they can't help, go to someone else in your department.  Do you have other junior committee members that might be able to help?  What about a grad student adviser?

The bottom line is that, while professors being bad at replying to emails is sadly common, it isn't professional, and you should keep at it.  With as much politeness and tact as possible, of course, since this person has a lot of power over your future here.


Why is Scottish BSc (Hons) 4 years while English BSc (Hons) is 3 years?

In Scotland, you can attend university after completing Highers, which are taken in the same year as AS levels are taken in England. Therefore, many Scottish students leave school a year earlier. Theoretically, the first year of university in Scotland is less advanced than the first year of university in England (although speaking from experience, I don't believe that this is practically the case). In recognition of this fact, it is often possible for English students to enter their course directly into second year, with a higher grade requirement.


Enhancing the plots from another person's research paper

If you don't like how they have plotted the data, or there isn't sufficient resolution in their graphic (e.g., they used a PNG rather than PDF so that blowing up the document doesn't help resolution) then the only real solution is to ask the authors for a copy of their data, as suggested in the comments above.

You also may consider that if this does not work, the ugliness of their figure is not your responsibility: really, you are only including it as a courtesy to the reader, in order to make your document more self-contained.


Accepted for Masters but Can Only Attend if I Have a Scholarship

Ask if you are eligible for student loan.

Scholarships are often not available for undergraduate and Master's degree. It is extremely common in the US (and UK) that students borrow money to pay tuition fee and stipend. My former flatmate didn't paid all the loan until he was 28 years old (his father paid his tuition fee, he only borrowed for stipend). You can consider this as an investment if you believe the degree could bring you a well-paid job in the future.

On the other hand, you don't have to go the US to do a Master's. Many EU countries, such as Germany, provide free education for foreigners, and many provide scholarships based on the household income.


Quality of an image for publication reproduced from another source

It is difficult to provide a detailed reply without knowing more about the figure, for example if it is a photograph or a line graph. I will therefore concentrate on the general aspects.

First, the best would be if you could get some form of original from the author (or whoever) has the copyright). Screen dumps are clearly not sufficient since printing requires high resolution (300 dpi in final reproduction size is a commonly quoted resolution in journals)

Second, if it is a line graph, and it sounds as if that is the case, I would argue that the best way is to put the image in the background of a vector-based drawing program such as Inkscape/Illustrator/Corel Draw and manually redraw the figure. This is done by placing the illustration in a background layer and then draw lines in the program to reproduce the background. This requires learning a vector-based software and is a tough solution for the short-term but one I strongly recommend for the long-term. If the plot is based on data, for example a scatter graph, then you could digitize the data and re-plot it as long as you think of the re-plot as a version of the original plot and not use data points for additional analysis.

There are of course numerous kinds of complicated plots where the second approach will not work so trying to get the source would be the first choice. Screen dump quality bitmaps will be rejected by most if not all journals.


How should I avoid someone patenting technology in my paper/poster?

You need not patent your invention. The requirements of a patent are that it is new, useful and non-obvious. To another person your published work is considered prior art. If someone else tried to patent your work the patent office would reject it as anticipated.

Of course this assumes the patent office finds your work. The inventor could fail to disclose it and the patent office could fail to find it in search. In such a case you can typically submit your work to the relavent patent offices to have the patent/patent application invalidated/rejected.


Institute affiliation link in google scholar

A scholar who wants their profile to link to an institute page needs to do two things

Include the institution in the profile's affiliation field, and
Verify an email address at the same institution.

The only place I've seen these requirements stated is if you go to an institute page (example) and click 'Learn more'.

Implicit in requirement #2 is that Google Scholar can recognize that the verified email address is related to the affiliation in question. It seems flexible enough with formats for use with university purposes, but maybe not for larger conglomerations. For example, under your link I can find a profile affiliated with GSK directly with a verified gsk.com email address where said link shows up. On the other hand, it seems that the system does not recognize that the same email domain is used for GSK's subsidiaries.


If I write an unsuccessful grant proposal with one PI, can I reuse those ideas on a different proposal with a different PI?

Generally speaking, it is fine to seek multiple sources of funding for the same project.  However, you cannot accept multiple sources of funding to do the exact same thing without permission.
You should check with the program managers of the funding agencies.   Program
managers say they spend much of their time looking for duplicate submissions and rejecting them.  However, if one application is to a government agency and another application is to a private foundation, that might be fine.  Or if the applications are to governments of different countries, that might also be fine.
The PIs should understand that it is normal to seek multiple sources of funding.  But tell them what you are doing and ask them if they are okay with it.


How should I compare my algorithm to others when their code is not available?

Asking the authors for the code is of course always an option, but from my personal experience this almost never works (there is a reason why they did not put it online in first place).

I don't know which area in computer science you are from but normally there is some quantitative measure to determine which method is better and those measures are somehow in the paper. Those can be things like run time or precision-recall curves on certain data sets.

If you want to compare on the same dataset, you can ask the authors for the numbers / plots themselves and then plot your own curves together with them.

If you want to compare on a different data set, you can ask the authors to run the code for you. In my experience, this works more often because many code is not published because its messy and needs a lot of parameter tuning - so it is unlikely someone else will produce good results with it.

If you have Bachelor/Master students to supervise, you can give the implementation as a project to them (although you need to give them enough time to do it).

In my personal opinion, it is not worth the effort to implement a method which is not described in enough detail anywhere. It will probably cost you an unreasonable amount of time without even reproducing the quality shown in the paper (for various reasons).


Applying to an Econ PhD program as a software engineer?

Disclaimer: I'm not in economics

You might consider applying for a MS degree first. I don't know about economics, but I know that in my field at my university, we are a little more selective about Ph.D. admissions versus MS admissions, having something like twice as many MS candidates as Ph.D. candidates. If you otherwise had good GPA and good test scores, you can probably get into an MS degree at a decent school, although maybe not your dream school.  If you can exceed at the MS degree, get a publication or two and network at a few conferences, then you've got a much better shot at a top ranked Ph. D. program.


Which US universities publish cohort ranking - position in class?

The US has no organized system of class rank comparisons. Some individual universities (or departments within a university) may track this, but at the university level the educational approaches are so diverse, even for different options within a single department, that direct rank comparison would make little sense in any case. It is for this reason that a number of high ranked universities (MIT being one example) explicitly refuse to create such ranking comparisons.


Leniency in journals' paper structure "guidelines" (required sections and divisions)

I hate it when a journal decides to stretch you on a Procrustean bed of arbitrary structure, since many research projects simply do not fit on such.  Some really want you to fit their arbitrary structure, while others will bend, and it's not really possible to know which is which and how much flexibility you've for unless you talk to an editor.

That said, I've often found that with a little bit of mental gymnastics in how you approach "results and discussion" you can generally make things work.  Consider, for example, this decently-cited paper of mine, which didn't really fit the "intro - results - discussion - methods" format desired by the journal, since it was about a (fairly complex) method.  Well, if you think of the method as being the result, then we essentially shove the whole paper as we wanted to structure it into the "results & discussion" section, with our preferred structure as subsections.  The "methods" section then contains all of the boring details about protocols for the validation tests that we ran.

Bottom line: often a journal really means it about its structure requirements, but that actually constrains you less than you might think.


Does a survey require an ethical approval?

The question of what sort of ethical approval is required is a complicated one, depending on the local laws, funding sources, university policies, and journal policies.  I don't think anyone can give a definitive answer without knowing these details.  For example, see these charts for an indication of the rules imposed by the U.S. Department of Health and Human Services.

  Since we have the forms of informed consent, aren't they sufficient?

No.  If ethical review consisted of nothing but saying "be sure to obtain informed consent", then it would be replaced by a simple rule requiring informed consent.  Even that is tricky (what exactly are the risks you need to inform participants of?), and there are other issues for a survey.  For example, are you following best practices to ensure anonymity of survey respondents?

  If none work out, is there a repository for unpublished work like ArXiv in epidemiology?

I don't know, but I can't really imagine the community would look kindly on using such a repository to avoid ethical review.

  The institute ethical committee denied a post hoc approval.

It makes sense for ethics committees to be reluctant to approve research after the fact.  One reason is that it puts a lot of pressure on them to approve research that's not perfect but can no longer be fixed; another reason is that if post hoc approval is an option, it creates an incentive for researchers to skip the initial approval in the hope of forcing it through the process later.


Let me assume that you already have listed in your CV the earlier article (the version 1) in the following way.

  Author Name, Title, Encyclopedia, Version 1, Dated online: xx-xx-xxxx; WWW: website

Now, you could just replace the above with the following:

  Author Name, Title, Encyclopedia, Version 2, Dated online: xx-xx-xxxx; WWW: website (Web version 1: website)

Though there is 25% difference, I would not go with redundant information in a CV.


In the UK is it acceptable for a lecturer/professor to join student societies?

In essence there is no problem, here in the UK, for the lecturers/professors to join societies. I experienced it first hand, both as a student and lecturer, and loved it. But you have the following ethical responsibilities:

Socializing and Not Dating: Most social clubs go out a lot. For example, they might go to some other part of the country to do hill walking, or pub crawling which involves loads of drinking. The bottom line is that you can socialize with students, but don't lose your mind and start dating a student while camping somewhere. Some social clubs are hubs for dating, so join them for the cause and socializing, and avoid dating altogether.

Close Friendships: Here in the UK, in my experience at least, some students are looking for an easy way out of studying. They are young, and therefore they just want to get by. Don't create a situation where they can take advantage of you and abuse your friendship.

Overall, know your limitations. Deal with students outside the university in a respectable manner, and don't get too comfortable. At the end of the day, you are the lecturer and they are the students.


How to negotiate salary at a school with a two-stage negotiation process?

While I do appreciate the concern related to the competitiveness of the academic market, I'm especially concerned at the idea of taking an offer to work at a place where unethical business practices are accepted as the norm and you are just supposed to take it or leave it. While I think you can be the only person to choose what's right for you and your family, if you are in the personal position to be able to say "no thanks", even if you might not get another offer - then I'd strongly suggest you not be manipulated into a sort of "just be happy you have a job" situation using strong-arm tactics. You can push back or walk away - or pretend to, as JeffE says - but I would not suggest you just roll over and take it if you don't have to.

Why is this a problem?

This Is Called Low-Balling

  First make what you want the other person to agree to easy to accept
  by making it quick, cheap, easy, etc.

  Maximize their buy-in, in particular by getting both verbal and public
  commitment to this.

  Make it clear that they are agreeing to this of their own free will.

  Then change the agreement to what you really want. The other person
  may complain, but, if the low-ball is done correctly they should agree
  to the change.

  The trick of a successful low-ball is in the balance of making the
  initial request attractive enough to gain agreement, whilst not making
  the second request so outrageous that the other person refuses. It
  nevertheless is surprising how great a difference there can be between
  these two requests.

The fact that HR specifically told you that you are in "full charge"? Yeah, that's part of the low-ball technique. They are all playing the same game, together. HR is the good cop, the helpful salesman who really wants to get a great deal.

  Guuguen and Pascual (2000) found it to be important that the person
  believes that they have made a free and non-coerced agreement to the
  first request. In particular adding 'but you are free to accept or to
  refuse' to the first request increased compliance.

First, they put out a feeler - asking for a range. That's ethical, honest. Then they get you to show interest, negotiate, spend some time - make a commitment. OK so far. Then you come to an agreed upon decision...that's where honest negotiations end.

The "gee, I'd really like to do that, but my [boss/sales manager/department head/dean/provost]"...that's normal for a used car dealership in Fargo. How about they offer you a clear coat upgrade to go with being tenure track - just 10% off your salary. It's a real steal, we don't normally do this, but you seem like a real smart guy. Please.

Let's Talk Payments

If they want to negotiate, by all means if you are willing and able to negotiate, have fun. Yes, you do need to be able to say no, and perhaps you need to get past embarrassment and contact that previous offer or stall so you can have the comfort to mentally know you can turn this offer down no matter what.

"Gee mister, I sure do like your school, but since I originally talked with HR  I've had to consider some very compelling other options [like telling you to shove it]. I feel bad about this - truly - but I think my original agreement with HR for X was lower than I should of been willing to accept. It seems like X+10% is really what I should have agreed to.

This is within the range we had originally discussed, and I feel bad about bringing this up now, but I wasn't aware of these other options at the time."

Maybe, you feel awful bad about this - but you suppose, if it would just be too terribly untoward to want more than HR originally OKed, the department being so great and the department head being clearly such a great guy, you'd be willing to accept something more like you originally agreed to with HR.

Or you can be angry and make it clear that you can't negotiate with such a thing on the table - the walk-away. But you have to be actually willing to walk away.

They seems to want to play games, and turn-about is fair play. But you have to be willing to turn down the offer and do something else, period, or it won't work out so well.

Still, I'd warn you that they are telling you now - far in advance of joining - that they are willing to negotiate all the way to playing unethical games with their offers and candidates, including wasting their time and reneging on phantom offers. If your facts are correct, this is not a accident - it's a design.

Personally, of all the jobs I've had I've only had one employer of any kind - academia, small business, or large enterprise - try to low-ball me like you describe here. And I didn't even try to negotiate that one - I just silently thanked them for letting me know they think it'd be OK to play games with my livelihood before I joined, and I got out of there with all haste, so I can't say how "winning" might work out.


Dealing with syllabus error as instructor

Well, you are polite enough to care about this deeply. I think one of your students might be polite enough to help you. As I understand, this "wrong" book actually is the course material in one of your other classes. You can ask in that class if someone who hasn't bought the book would like to buy that spare copy. You can incentivize it with a discount on the brand new book (something like 25 dollars) and you can pay the small difference to the student.


Is it safe to show my old advisor my new paper?

If you work in the US or Europe, intend to complete the paper and submit it for review somewhere soon, and have records that show the development work that you've done on the paper, there's little harm in showing it to people that you trust. If you don't trust your former supervisor, then I'd wait until you've submitted it or even have an acceptance in hand.

That being said, I'm wondering why you don't already know whether they should be a co-author and haven't already discussed the fact that you're writing a paper on which they might need to contribute. You should at least discuss this with them if there's any contribution of theirs in what you're writing up.


The department I will be getting my degree from and my research area have very little in common

No! It is NOT a big deal. This case is not so important because nowadays the research is interdisciplinary more than any time. Faculty members affiliated with a specific engineering department are even highly-involved in a vast variety of projects with their peers in other departments. The most important thing is being productive as a Ph.D. student within your studies. It requires interest in your research + coherent interaction with your supervisor.

You may have two plans for the future:

If you would like to involved in industrial positions: They actually do not care much about your major and degree's field, but your professional credentials and your practical capabilities. As an instance, assume that you're interested in working as a robotic engineer. As long as you show potential signals to be a right candidate for the position, MechE degree, SysE degree or something else would not hurdle your way.
If you're eager to work in academia: Just do your best to flourish your publication trace. As long as you both have a fruitful Ph.D. and show enthusiasm for research, most of vacancies related to your research in various departments (such as ECE, MechE, CS, etc.) will be open to you, POTENTIALLY (don't underestimate current competition for restricted tenure-track positions!)

Best


Will ISIS attacks hurt my PhD application as a Muslim?

Only indirectly.

Admissions committees have good incentive to get the sharpest, most hard working people into their programs. They will care about your excellent results, as they should.

But administrative procedures may hinder people coming from your part of the world more than other applicants. I am basing this on my experience of being a Serb who wanted to study at Western universities, while Serbia was screwing up royally on the political scene, waging wars and making enemies everywhere. Sanctions made it difficult to travel. A friend of mine was denied a visa even after being admitted into an academic program and obtaining funding. Tuition was more expensive for us (to study in the EU), but far less funding was available. Even though I obtained a scholarship that covered the tuition, it was paid to me in monthly installments while the university insisted that I (as opposed to EU students) pay the entire tuition up front. Nobody could employ me without massive administrative hassle, meaning I couldn't just work at a bar a few hours a week if I needed some extra cash. Phone companies would not let me have a contract with them, limiting me to expensive, pre-paid phone cards. And on and on the list goes.

So yes, I think your chances will be smaller, but not because of admissions committees within any given university. It could happen that academic staff are not sufficiently aware of the additional hurdles you're facing, though. On the other side of the equation, professors from your side of the world might be less experienced at writing recommendation letters, for example. So a number of small obstacles will accumulate, many of them stemming from recent and current world politics.

And my heart goes out to you. It sucks to be vilified by outsiders for things people you don't identify with are doing.


Can an online degree through an accredited institution affect admissions into masters programs abroad?

If you are seeking a BS degree from a United States accredited university through an online program, and wish to enter a Masters program with another U.S. accredited university, it should not be an issue on its own merits.

However, research universities may take a second look at your application if the online-achieved BS degree is not from another research institution.
To ensure your acceptance to such a Masters program, you will want to achieve a higher grade point average than expected. It would also help if you publish any articles during you progress towards the BS.

Other non-research institutions in this scenario should not have an issue accepting you with your online-achieved BS degree, so long as you clearly demonstrate in your application you meet all their requirements for admission.

Now, even with that said, non-research universities may even accept you even if you have defficiency in required undergrad coursework. In this case, a little real-world job experience as little as 1 year can help assure them you can do the work.

In all cases, don't underestimate the application letter you submit. I would make sure it communicates you have a goal in your education and career after the Masters. And it should demonstrate you are capable to meet their requirements, and to succeed in their program. That is ultimately what they are looking for.


(How) can I evaluate, whether a field has a future or not?

You have started well by looking for recently published papers. If there are none, it could mean your field is very small and you will find it hard to get future jobs and funding or that you are not searching in the best places. Maybe you could ask the professor if he can recommend any more recent papers for you to read to "understand the current progress and see if it matches what you want to do" or something like that. If he says nothing has been published more recently you can ask why.

You could also ask about or search for conferences or meetings. It may be a field that does not produce lots of papers but still has a large community of active researchers, so would not seem "dead".

If your University has cut funding in that area it will definitely be harder to get a PhD there after your Masters in the same topic.

But it is an important point that the topic of your Masters doesn't have to relate directly to your PhD or future career. It's a good chance to try out an area you might be interested and see if it suits you, and in any topic you will learn research skills that can be put to good use in a PhD. I know many people who started PhDs in subjects they had never studied before, but you must show that you can learn new things quickly and have all the other "soft skills" of research: writing and presenting, finding and citing good sources, data analysis, critical thinking, using any relevant software or machinery... these will depend on your subject area.

You would probably produce much better work in your Masters project by taking the option you are most interested in. You can then have time to get familiar with the academic community, let your supervisor know you are thinking about the future and want to find out what it is like, and if it is a dead end you can take a different subject for your PhD so long as you are not missing any core skills.

Good luck!


How to study for the GRE exam? (e.g.memorizing 3500 words, Math problems, AWA)

I highly recommend Magoosh. I used their vocabulary app while I was walking around campus for a couple months and by the time the exam came I was thoroughly prepared. They also have a pay-for-service learning course which is good to review the material you've forgotten since high school. I am a fairly math oriented person going into the life sciences so I did not do too much of the math portion of Magoosh but the writing section was fairly useful and the english section was great. Knock 'em Dead!


Can I help the impact factor of a journal by citing my own papers?

Since B is related to A, I will probably submit it to the same journal. Would this help the journal's metrics?

I fail to see the connection. One paper having one more citation is irrelevant to journal metrics (eigenfactor excludes self-citation, while JCR does not, if I'm not mistaken). Also, I'd expect that papers published in a particular journal would include citations to lots of papers on the same journal.

Or, lets say paper A currently has no citations. Would they be reluctant to accept paper B?

Very likely, no. I don't see as costumary for a referee to look at citation record of cited papers. But, if A is not being cited, maybe that's indicative that this research is not suitable to this journal.

... achieve a paper-to-citation ratio near 1:1 (is that good?)

No. Especially if it's a self citation.


How to politely ask a co-author to remove his/her name from my manuscript?

When a manuscript is ready to go, the way to deal with a lot of authors is to send an email along the following lines:

  Find enclosed the latest version of the manuscript. I plan to submit this version on xx/xx. If you have any comments send them by then, otherwise I will assume everyone is fine with its present form.


I ran one of these a few years back. Here's what we did:

Start by publicizing the idea with your friends/colleagues and setting up an initial meeting. You'll get a sense prior to the meeting whether there's interest. The more advertising you do here the higher chance you'll actually have a showing at the first meet.

At the first meet, re-state the purpose—group of people working through the ideas in the book—and decide the meeting cadence (weekly, biweekly, monthly). This is important; reading through books like this take time, and for the group to work it's critical that people actually read the content and come prepared to discuss questions. You need to give enough time to let them read, and not so much that they'll forget what they read.
On this note, we also split the book up by chapter (we were reading [Elements of Statistical Learning](http://statweb.stanford.edu/~tibs/ElemStatLearn/, chapter splits made sense there). You may decide to split by topic or whatever else. The main idea is to ensure that everyone's on the same page, and comes to the next meet prepared to discuss the same content.

During the break, read up on content. As the group leader/organizer you may want to take notes on what you read to prompt discussion (itemize points covered, questions you thought of, points for discussion). Send out one or two emails reminding them about it.

At the first meet, come with discussion points and be prepared to lead a discussion, as it's likely no one else will take the lead. You don't have to be an expert, you just have to lead the conversation and bring up talking points. If you're not comfortable in this role, find someone who is and make sure they come to the meeting.
I recommend you keep the meeting at 60 minutes or less. If the first one is a success the rest then just wash, rinse, repeat.


When do most students publish in a European PhD?

Probably, you have an incorrect picture of European PhDs.

There are significant differences in the paths that lead to a PhD in the US and in Europe. Several of these differences have been already covered by other questions, but let me highlight those I think are the most important for what concerns your question.

First, however, the usual disclaimer: Europe is not a single entity, and there are large differences among European countries. What I'm going to say below applies to many countries around here, but not necessarily to all.

Most European PhD programmes require an MSc degree for the application. Therefore, the common European PhD student has already done the coursework (or  most of it) that a PhD student in the US has to do during their first years.
Students in the US usually fund themselves through teaching assistantship, which keep them away from research for many hours a week. Most European students, instead, are fully funded by their institution and can work on research full time. Some institutions allow them to work as teaching assistants too, but with a lower workload.
If I got it correctly, US students are allowed during their first years to "wander" a bit to decide what topic they like most. European students are usually not allowed to do so: they start working on a specific topic from week one of their PhD.
European PhDs are shorter than US ones, but not that shorter: though in many European countries the canonical duration of a PhD is 3 years, the real duration is frequently longer, 3.5-4 years.

Given the above differences, you should not be surprised to discover that many European PhD students start publishing from their first or second year.

For your last point:

  Or do some people not even make that and wait till post-doc or
  something?

In some cases this would not be possible because some PhD programmes require students to publish at least one journal paper before the end of their PhD.


Should I mail my advisor concerning his attitude towards me, and possible re-use of my ideas by a colleague?

I have contacted already a third person about this (edit: an ombuds-person, who is also a professor at my faculty)

This ombudsperson is probably the person best suited to give advice about whether misconduct occurred and what your options may be. Given that you are already talking to an ombudsperson, I would not want to add my own speculation into the mix.

[I] am thinking about sending to my supervisor regarding my disappointments and questions about this issue later on, once I finished my exams and obtained my master.

Your instinct to wait until after finalizing your degree is probably a good one. As for the advisability of writing such a letter at all: well, I am afraid I do not see much point. Certainly it seems unlikely that your advisor will say "Egads! I have seen the error of my ways and am overcome with remorse!" Your desire to protect future students is admirable, but unless the ombudsperson recommends further action, I suspect your options will be somewhat limited.


To what extent is it acceptable to copy definitions from reference materials?

Is this acceptable if I include a portion of introductory matter of a source text if the source material is referenced?

There are two issues here.  One is whether you can be accused of plagiarism.  That's simple: you're safe if you cite the source and clearly indicate what was copied with quotation marks or a block quote, but you could be in trouble if you don't make it clear what was copied, even if you cite the source.  (Occasionally you can avoid quotation marks by saying something like "The following definition is taken verbatim from reference [3]:", but it's risky to try that with longer quotations.)  If you are not copying any text, then you still need to cite the source but you don't have to worry about plagiarism.

There's also the issue of whether extensive quotations are acceptable to your advisor, regardless of whether they are plagiarism.  Even if you cite appropriately and use quotation marks, your advisor might think you are quoting too much and ask you to rewrite it in your own words.  (But this isn't a matter of academic honesty, just of what constitutes a good thesis.  Relying on lots of lengthy quotations is honest but lazy.)

Students sometimes worry about how much text is appropriate to copy from a definition without quotation marks.  This is a little tricky, since there are certain standard phrases that get used repeatedly.  For example, the definition of a group in mathematics might start "A group is a set equipped with a binary operation".  I just wrote that myself, but a web search reveals that half a dozen people have used exactly the same wording (because it's a pretty standard way to express things).  If you read a definition that starts this way and later use this phrasing when defining a group, that's not a problem.  However, you shouldn't be copying elaborate definitions verbatim without attribution.

In particular, if a standard phrase sticks in your head and gets repeated when you write the definition, that's fine.  One test is whether you need to copy from a book.  If you can write a clear, correct definition without copying or looking at any materials while writing it, then you should do so (and you won't have to worry about plagiarism).  If you can't write a clear, correct definition without copying from a reference book, then you need to cite the book and indicate that the definition is copied (since this is clearly a complicated or subtle enough definition that formulating it well deserves credit).


Is it good practice to have hyperlinks in bibliographies?

Maybe I'm a bit late here, but I do think it is among the best practices there can be. I also can't understand why journals' names are abbreviated. IMO providing links is really important for many reasons:

It provides quick access to the cited material (either text or anything else).
If a link is available, checking that source is (normally literally) one click away.
If it isn't, it can be a challenge to get it. If the link is a DOI or other persistent link, it ensures access even if the final link changes. If the link is not persistent, it provides some transparency: the material was online at URL "x" at day "y", so if it's gone it's not your fault but you stated every information you had, and your reader now has some more info to work with when trying to reach that same source (looking for cached/archived versions, maybe looking for other people referencing the same URL who might quote some bigger part or even have an offline copy, who knows...).
A reason for deliberately using a not-DOI URL: "People click on URLs that they understand and view as authoritative", so depending on the domain or subdomain of your cited material's URL, it could be a (not so) subtle persuasive use of that information in one's favor (either a publisher's, a government's, an international body's or any other institution's domain).

And these are just the ones that immediately come to mind now. But I think all the reasons that justify all the efforts to create the idea of DOI as a persistent link and maintain a whole infrastructure around it apply here as reasons to use it.

Actually, the real question could be why not use them (DOIs first, but links in general), and there are as many reasons for not using it as there are for abbreviating journals' names these days.

As to formatting, reason 1 above suggests not using "doi:10.1234/abcd1234" as this is not clickable (unless you manually make each one clickable by formatting it as link etc.), but rather something (automatically) clickable like "https://doi.org/10.1234/abcd1234".

And providing the last date you had successful access to it is useful as well, for what I mentioned in reason 3 above. (Some styles suggest stating the date of your first access. I can't quite see why would this be more important.)


PhD manuscript with grammatical errors and informal phrases

Ok. Let the past be the past. You weren't perfect then, you are better now. Maybe not perfect yet, but neither am I, or anyone. The very fact that you can recognize past errors is a sure sign that you are now better at this than you were as a novice scholar.

As the comments note, there is little chance the problems will be noticed, or even that they will matter if the are noticed.

There is a phenomenon among writers that is worth noting. Many people, writers of all kinds, sometimes feel embarrassed by their older work. Even poets. It is a sign of growth, not of failure.

In Tai Chi we say "One day's practice, one day's progress."

A couple of additional thoughts.

It is immensely difficult for most people to proof-read their own writings. You tend to see what you thought you wrote, not what you did write. An external review is a great way to improve any writing. See, for example Ezra Pound and the drafts of The Waste Land.

Also, you would be in far worse shape if you ignored past errors and insisted, insisted, that they were PERFECT.


What's wrong with my e-mail to potential PhD supervisors?

The statements

  what are the chances that a student with a thesis in TOPIC Y would have his application taken very seriously into consideration by a group like yours?

and

  it will have a great impact in (sic) my application strategy and maybe in the selection of the advisor for the thesis

tell me you are not specifically interested in applying here.

Are you interested in working with this prof or just shopping around? Giving general application advice to strangers isn't high on the list of the average professor's priorities.

(My direct experience is with German and Austrian universities. Programms with centralized admissions are becoming more frequent in continental Europe as well, but in general professors have more leeway here over whom to hire or take on as PhD students than in the US.)


How to manage publications on a local computer

For the filename, I use a system that I plagiarised from my PhD supervisor:

aaaadd_xxxx_jjj.pdf

where:

aaaa: name of the first author (variable length)
dd: 2-digit year of publication (fixed length)
xxxx: first word of title, minus articles and other small words (variable length)
jjj: abbreviation of journal of publication (variable length, but short)

I then use the same without the .pdf as my bibtex key (with an added :).

For example:

T. Penguin et al, a Survey of Antarctic Leasure Activities, Journal of Improbable Results, 2025

would be

penguin25_survey_jir.pdf

with the bibtex key penguin25:_survey_jir.

I like this system because:

I'm used to it
Filenames remain compact and UNIX shell friendly
The encoded information is usually enough for me to identify the paper

It doesn't cover tagging or categorising.

This applies well to journal articles.  For conference proceedings articles or books, the journal acronym is replaced by an acronym of the conference or the publisher, or perhaps the full name of the publisher; I'm not fully consistent there.  But I don't usually have entire books as PDFs anyway.


What are the advantages for submitting my paper to demo or doctoral symposium sessions of conferences

My experience is with Computer Science conferences. Some have a multi-day Doctoral Symposium associated with them. The advantage of them is that you get both some experience in presenting your work and some useful feedback on it. The ones I was associated with have a review selection process so you get some feedback at that point and then were run symposium style, not presentation to a large audience. Other students and a few professors would listen to your presentation and try to give you feedback and ideas.

I don't believe that the symposia published the work of the students. This was pre-doctoral research in progress. The purpose wasn't publication, but advancement.

While I wasn't the symposium chair at any of these (part of overall committee), one of my close colleagues was the chair at one of them. I only heard of good experiences. Note that they aren't intended for finished/polished work, but for work in progress where additional ideas might be welcomed.

I'll also note that our doctoral program at the university used the same idea of symposium presentation with our own doctoral students. Once monthly, students would discuss their work with the other students and the advisors of most of them in an all day seminar. Each student would have a bit of time to report on progess and problems. This was very helpful, especially to those who were struggling a bit with the research as the ideas for progress were usually pretty helpful.

I see no reason that this wouldn't transfer to most other fields. Even when I was a student of mathematics, my professor had a weekly symposium for his own students. A few other faculty would also attend. But this, for the most part, wasn't student presentations, but rather discussions of mutual interest on which the (few) students were currently working.


My adviser threatens to kick me out if I am not to be a full time student

It is completely inappropriate for an advisor to send an email like that. The email makes it clear that this is an advisor that you should steer clear of. At a minimum a change in advisor is required. I would also approach the department head about the email. Faculty need to know that they need to behave better.


How to get into computer science research as a college student

The first problem you will have is coming up with a problem worth exploring. If you don't yet have much experience it is a very hard thing to discover. So, yes, talk to one or more professors, perhaps your advisor, about what sorts of problems they are interested in.

Perhaps they can get you started with some part of their own explorations, or give you a problem they have set aside for lack of time to explore it.

In your first time out, it may not be vitally important that  you actually come up with results. Learning the process may be enough. But who knows. Maybe you learn something that can be published.

In fact, some problems worth exploring don't really have accessible solutions. They may be beyond the current state of knowledge to solve. The same is true in math, of course. It is very difficult to predict in advance whether a problem is actually solvable with the resources available - including time.

Eventually - many years - you will probably develop the insight to see the problems that are unsolved, but solvable, and also worth the effort to explore. But like anything else, that takes practice. Start with someone who has already been there to help guide your initial steps.


How do postdoc proposal and PhD proposal differ?

It seems obvious that while some forward-looking ideas may have been included in the thesis and defense, a proposal to develop them should have much more than just a concept -- timelines, deliverable milestones, cost of equipment (for physical sciences and engineering) or travel or payments for volunteer research subjects, what approach to publication will be used, etc.  In short, mostly the same things that go into a grant proposal.

On the other hand, the methods of the thesis are not so important and should be condensed to an executive summary.  The only part that should really be common is the proof that an important problems is addressed -- if the resulting book will have no impact, there is no point funding the effort to finish it.

Disclaimer: I'm neither a social scientist nor in a postdoc.  But I do know what my employer would ask me to prepare in a proposal for funding for elaborating my dissertation.


Which page range do you cite in an article in IEEE proceedings?

If the proceedings actually have page numbers, cite the page range in which the article appears.

However, it is becoming more and more common for many conferences to not have bundled proceedings with page numbers (also in electronic form), and so all the articles have no page numbers or they have the same fictitious page numbers (e.g. with starting page 1 for all the articles). In this case, page numbers don't matter, but the reader should be able to locate the article: therefore, whether you don't put any page range or you put the fictitious one, try to add other identifiers like the DOI, if supported. This is especially important if there are two version of the article with the same title, a short one published in the proceedings and an extended one published in a journal.


How does research contribute to teaching, and vice versa?

Personally, I struggle coming up with good teaching materials (lecture notes, homework questions, et cetera). I had lots of teachers that were either way too abstract where abstraction wasn't necessary, or gave really wacky examples that didn't have much basis in real life, and I silently vowed not to do that to my own students. One way that I've found to present real-life and relevant material is to draw upon my research. For example, if I'm lecturing about a particular biological system that I study, I might walk the class through a particular experiment that I ran to test an aspect of the system. I find that students feel these lectures are the most interesting, and they seem to grasp the material better than if I gave a "standard" lecture.

On the flip side, I always get 1-2 questions per semester where I don't know the answer, and it turns out no one else in my field does either. As such, the questions I get while teaching are a source of research questions that I may attempt to answer. If I actually think the question can be answered, I almost always invite the student or students who posed the question to help me with the research, which is also another way teaching impacts research (i.e., I expose more people to what research is, and I get help doing it).


Short answer: there is probably no universal answer; in other words, you should check with the journal to see if there is prior precedent or guidelines in place. More specifically, you can check with: (1) the author instructions [it would be surprising if nothing is mentioned or this has not come up before], (2) the relevant section of a variety of recent, previous papers published by the same journal with a suitable number of authors, (3) an editor at the journal. From at least one of these options it should become clear what is expected of that journal for its author bios.

Aside from the specific journal, we could also more broadly consider the purpose of an author bio. It is important to preface such a discussion with the disclaimer that many journals don't even bother with such anymore in these days of Google, institutional webpages, and so forth. However, leaving that aside, we could consider that the author bio serves some of the following possible purposes:

Identify conflicts of interest: Were any of the authors employed (in some capacity) by a company whose profits could benefit from the results published? While such CoI's could sometimes be established from the institution, sometimes they could arise from secondary sources of income. Were, for example, some selection of authors paid for consultancy at a pharmaceutical company whose product could benefit from the new results? Did they serve on the board of a committee with a certain stance on a certain topic?
Establish seniority and background on the authors: Were the authors students at the time of publishing the paper? Or were they professors? Which authors held which positions? What is their main area of expertise or qualifications in said areas? Though such information should of course not affect the interpretation of the results of the paper, it may be useful to establish, perhaps, for awards purposes, or just to satiate the curiosity of the reader.
Contact information or disambiguation: If not already given elsewhere in the document, additional information may be necessary such that individual authors could be disambiguated and/or contacted by readers.

As mentioned at the start, admittedly the importance of author bios has declined in these days of the Web.

In summary, check with the journal guidelines, previous papers and/or editors to see what to do. My guess would be that you should include a brief bio of all authors with their institutions, roles and duration of employment at those institutions, and other paid or volunteer positions (past or present) that may affect (or be seen to affect) their impartiality in the context of the results of the paper (if applicable and not given in a dedicated CoI declaration). If there is space, you could include the principal areas of interest of the authors. I would imagine something along the lines of:

A and B are PhD students at the University of Z. C is a Professor at the University of Z, chair of the Institute of Y and part-time consultant for X. D is a Postdoc at the University of W. E and F are Masters students at the University of V. The principal areas of research in which the authors have worked are L (A, B, C), M (C, D, F) and N (E).


Can a conference paper be an extended version of a previous conference paper? Will it face copyright issues?

It would seem that you should contact the organizing committee of the conference and get their advice. To me it seems kind of low to write papers that have very similar content but it does happen.  If you are questioning it that much I would bring it up with the Organizing Committee and see what they say. You don't even have to mention names or specifics but just get their general opinion.


Should I take a tutor job or a research job in a company before going to grad school?

Personally I would choose the company position:

Prior experience in the private sector (outside of teaching) is a big advantage if you decide to look for a non-academic job later.
Python is a popular programming tool to use. Might as well learn now.
Data analysis is a big part of doing a physics PhD.
You will form better contacts (probably). Never underestimate the value of good connections.
You will get plenty of opportunity to do teaching later if you wish; and I do not really see what it adds to your position now. However, I never really saw the appeal of teaching, so perhaps my view is coloured.

A CV is just a way to get yourself an interview. It doesn't get you a job. Definitely send your CV in.


Is Australian Business Deans Council Journal Quality List 2013 a good metric to ascertain journal quality?

It depends what you mean by 'quality'.

I would argue the very notion of ranking journals as this list does is deeply unsound [see Brembs, Button, Munafò (2013)]. The quality of content in most academic journals is variable. Great articles can be found amongst the mediocre, and likewise mediocre articles can hide in issues full of high-quality articles.

Journals are a lazy proxy for the evaluation of 'quality' of content.


Healthcare in the U.S for foreign graduate students

Unfortunately the way you access to health care will be largely governed by the specifics of your situation and the institution which you are going to, so we can't answer your question with any degree of certainty. The general answer to this kind of question is that you will probably have access to good health care but you might pay more for it than you would at home. Make sure that you have some savings that you can rely on in the event of unexpected medical bills.

It is common for full time graduate students to be offered some kind of subsidized health insurance through their university, or even require graduate students to participate in a group health plan
The affordability of such plans (how much you pay) can vary a lot by institution
It is common that such plans have restrictions on how you access care, for example it might require that non-emergency care is provided at the campus health clinic
Since the passage of the Affordable Care Act (aka Obamacare) your health plan providers are generally required to cover any common illness or treatment. However, there are current political efforts to repeal or defund the ACA, so this may change in the future. In particular the ACA greatly expanded coverage specific to women, pregnant women, and children.

You should direct questions regarding health coverage to your university's international student's affairs office, as this will no doubt be a common question for them. They will be able to tell you how their graduate students access health insurance. Many existing students are more than happy to talk about their experiences as well- ask your future department whether there is a graduate student or international student group that would be willing to answer questions.

Edit: Update on how to plan for medical expenses. Yes, unfortunately it is common for major medical events to cost several thousand dollars in the US. Your friend paying $2000 for a broken arm is entirely possible.

The coverage of health insurance in the US is commonly expressed as three numbers: the deductible, the out-of-pocket maximum, and the coinsurance rate. These can give you a ballpark estimate for how much health care might cost you.

Deductible: How much you must pay, in a year, before your health insurance pays anything
Out-of-pocket maximum: How much you must pay, in a year, before your health insurance covers everything
Coinsurance rate: How much your insurance pays after you hit your deductible, but before you hit the maximum.

For example, my grad student plan was:

Deductible: $350
OOP Maximum: $7,150
Coinsurance rate: 80%

Suppose you break your arm and go to the hospital. The hospital sends your insurance a bill for $5,000.

First, you are responsible for paying up to your deductible without any assistance, so you pay the first $350.

After you have paid the deductible, your insurance kicks in and pays 80% of the bill. The remainder after deductible is $4,650 and your insurance will pay 80% of that, and you will pay 20% of that amount.

Your total cost would be $350 + $4,650*20% = $1,280.

Suppose later in the year you get sick and go to see the doctor. The doctor bills your insurance $100. Since you've already met your deductible for the year your insurance pays 80% of that $100 and you pay 20% ($20) for the visit.

Your deductible and out-of-pocket expense resets every calendar year (January 1st). If you went back to the doctor on January 2nd and they billed you for another $100 then you'd have to pay that entire $100 on your own, and you'd have $250 left on your deductible for that year.

So, how do you plan for medical expenses? If you have a medical crisis then you should assume you will pay at least as much as your deductible. If your deductible is $500 then have at least that much in savings (you should have 6-9 months of living expenses in savings anyway as a precaution).  If you have a really serious health problem, then I would assume that you're going to pay up to your out-of-pocket maximum, and that is your worst-case expense every year. Additionally, if you have a chronic health problem that requires a lot of management, it might be wise to assume you're going to pay your out-of-pocket maximum every year.

It is not uncommon for people in the US to go into debt due to a medical crisis. A lot of people can absorb a $500 medical bill, but not a lot of graduate students can absorb a $5000 medical bill. If you cannot pay your bill in full within a month or two, then the hospital will start charging interest as though it were a loan.

In a personal example, I had a health crisis about a year and a half ago that required a two week stay in the hospital. The hospital billed my insurance several hundred thousand dollars. I paid my out-of-pocket maximum out of savings, after which I am no longer responsible for the balance. After haggling back and forth the insurance finally paid about $150,000 to the hospital. So yes, health care in the US can be obscenely expensive.

Note that a lot of health insurance plans will cover routine care for free. Annual physical exams were paid at 100% by my insurance provider, and separate annual gynecological exams were covered at 100% for women. Same thing for routine screenings (prostate, mammograms, etc.) and immunizations. This is because preventative care is cheaper in the long run than treating acute or chronic conditions that could have been prevented.

Again- find graduate students in your prospective school who are willing to talk about their past healthcare experiences and how much it cost them. They will give you a reasonable expectation.


Finding non-REU funding for my undergrad math students

I'd also ask around your department. Many universities have various summer research fellowships available. For example, one enterprising student in my lab found money through NASA that was administered through the physics department but also funded math, science, engineering, etc.

Also, most funding organizations are happy to "pad" a research grant with 1-2 undergrad research positions. I usually add these to my budget when submitting. While other areas get trimmed, the undergrad positions have never been a problem.


Google Scholar has lumped two publications into one

You can edit it manually.

If you log in to your profile, there are several options to combine/separate articles.  You can also edit specific article details: click on the article title, then click on the pen icon in the top-right:


Why is it considered sub-par to re-test something that has been shown before as opposed to addressing a knowledge gap?

In short, a PhD is about something that has not been done before. If there is no gap in the literature, there is no PhD, and defining the lack of knowledge is the first step towards covering it. A PhD is about novelty and exploration, not tweaking, and even PhDs that improve existing methodologies need to fulfil that requirement in some way by showing theoretical or technical expansions, or at the very least an application from field B that is novel in field A (even that for many people is not enough). A PhD explores ground already covered is pointless because it does not show creativity and originality of thought, which are fundamental for a researcher.

On the other hand, academic papers can (and frankly should much more) deal with reproducibility and testing/verifying existing results. There is a strong tendency in modern research to present positive results and novel findings, so papers that deal with what has not been found or not has not been replicated fall out of favour. That is an important problem, in my opinion, and should have been encouraged by the practices of conferences and journal editors/ referees, but belongs to a different discussion (even commentaries are under extinction).