What are the necessary and recommended practices to cite a published picture of experimental result?

If the source is an open-access paper under a creative commons license, it's easy - copy the figure and attribute the source and license.

If not... most publishers have a system for this. The STM Association, which covers the majority of mainstream scientific publishers, has a set of guidelines for permission between its members, setting out what is reasonable to reprint, and importantly has a general reciprocal agreement that they will honour each others requests without charge. This covers both books and journals, broadly speaking.

The STM list has the appropriate links per publisher. Some have a blanket permission, others require a bit of paperwork. For example -

a figure copied from a Portland Press-published paper does not require permission to be reused;
a figure copied from a Royal Society of Chemistry published paper does require permission, but this permission will be automatically granted at no cost if you fill in the online form correctly.

You do not need to do this before submission (at least, not in the cases I've dealt with) - it comes after acceptance when you know where it will be published and you're sorting out the details.

In the majority of cases, because copyright is transferred to the publisher (or they are given a very broad license to authorise republication) you do not need to approach the author. However, you might want to anyway.

Firstly, it's polite, and I'm sure they'd be pleased to know you're publishing something building on their work. :-)

Secondly, and potentially more importantly, permission to republish doesn't mean that the publisher will send you the files. You might need to get hold of a copy of the master images rather than the version put out by the first journal, in which case you'll have to speak nicely to the original author and hope they can find them...


When listing faculty that I'm interested in, would it be a good idea to list faculty that are in a related department?

I would also agree with sending the email to A. You could also email B to see his view. He may have already worked with MS Stat in the past, for example.

Because the two subjects aren't that too far apart, you may likely also be able to work out something that is tailored specifically to you. I haven't met too many professors who like to shoot everything down, so it never hurts to try.


How do I reconcile this situation?

You don't.

It will be clear to the anyone reading you transcript that your university does not provide grades for preliminary stages of your PhD.  Most likely, what they're really asking for is merely proof that you have the degree.  If they actually want more detailed grades, that's too bad for them, because those grades don't exist.

  How does the grading of PhD work in other universities?

In the US, dissertations are not graded; you either get the degree or you don't.

Along the way to the degree, PhD students may take classes (either by requirement or by choice), and grades for those classes typically show up on the transcript just as they do for undergraduates.  US PhD students also typically sign up for research credit hours as a "class" during semesters when they aren't taking real classes, but those "classes" are almost always graded pass/fail or equivalent (for example, at my university, "satisfactory/unsatisfactory").  The actual dissertation and defense never shows up in the transcript, even if a student fails their defense.

I can't think of any circumstance where anyone (at least in the US) would even look at the transcript of someone's completed PhD program.  Proof of degree, sure, but grades?  Never.

  In this situation, why shouldn't a person see "Pass" as a C grade for a PhD!

Because PhDs don't have "grades".


How to find out the tier of a university in the USA?

Typically, when people talk about tiers in context of universities, the assumption is that they refer to levels of teaching and/or research activity within some standardized framework. As far as I know, the most well-known framework of this kind is Carnegie Classification of Institutions of Higher Education. Based on this question, I further assume that it implies an interest in university research tiers (which matches the traditional Carnegie Classification framework - the Basic criterion).

Thus, in order to find a research tier of a university, click LOOKUP link in the main menu of the above-mentioned website and enter your search criteria on the Institutional Lookup page. The request will generate a list of results or a single result, depending on your criteria. Click on the linked title of the relevant institution and browse the resulting webpage. On that page, find Basic classification row, which contains the target value. For example, performing the search for my current institution (employer), Georgia Institute of Technology (aka Georgia Tech), we find that it belongs to the category of Doctoral Universities: Highest Research Activity. This is what usually refers to as (the highest) R1 tier (for more details about the shorthand labels, see this page).

Note that, while level of research activity is the most popular classification criterion, there are other criteria (see Listings -> Standard Listings). Also note that Carnegie Classification is focused on the academic ecosystem in the United States. I am not familiar with similar national or international frameworks (but have no doubt that some exist).


It's important to define what reproducibility actually means and in what context it is used. Science deals with things that can be reproduced in principle: If you managed to re-create the exact same situation, you would be able to get the same result.
But in practice, that doesn't always mean that you can re-create the situation: You might have measured the seismic waves of a very large earthquake in Indonesia. Or you might have seen photons of a nearby supernova. Neither of these conditions can be created by humans, and so the experiment can not be repeated in practice, though in principle it could be. A related situation happens if it is impractical to do so: If the original experiment was done with a ten-billion $ machine (say, a particle accelerator, a nuclear fusion reaction), then yes you could repeat the experiment, but you probably find yourself in financial trouble if you tried. There are also valid research results that should not be reproduced, even if they could: Say, whatever we may have learned from the Tuskeegee syphilis study or the Stanford prison experiment might be scientifically correct, even repeatable, but one can only hope that nobody will ever try to repeat these studies.
Finally, there are often practical constraints: If you take a picture of turbulence in a pipe, you will not be able to recreate the same picture because turbulence is a chaotic process; similarly, if you try to do experiments on a single cell and count the number of molecules of a specific kind, you're likely going to find that it depends sensitively on temperature, time of day, etc. That doesn't mean that the science is wrong: In both cases, statistical assessments of the results may still be valid, even if you can't recreate the specific numbers.
Of course, there are also experiments that really can't be reproduced: Someone published the results of an experiment that seemed reasonable to them and to the reviewers, but the measuring device had a mechanical defect and consequently every number in the publication is just wrong and the measured effect does not actually exist. This of course shouldn't happen, but it does happen in practice. There are also common statistical problems in studies that involve a small number of human subjects where the random, involuntary, or voluntary choice of subjects suggested an effect that, if repeated on a larger and more random cohort does not actually exist.


Helping TA's creativity when writing exercise sheets

I'm not sure why you find this to be a special problem. We basically know how to teach people things. Just do it in the ordinary way.

If no framework for understanding how to do a task exists then you need to develop one. If you know how to do it, but are unique, then you need to capture what you do in some way that can be transmitted.

Then you "teach" it by presenting the framework and giving some exercises so that it can be practiced and giving some feedback on how people do.

It is a standard teaching problem.

If no one knows how to do it, then you need to do something like research to discover how it can be done and then operationalize that research. Again, a standard problem, with a standard solution.

But, one thing I would suggest is that you use some sort of team learning so that those who do it naturally can pass skills to those who struggle with it. Pairing is a good approach and one I often recommend for such tasks.

Beyond that, it will likely take the examination of good and bad examples, using discussion (by the TAs) of why some things work and others don't.

But it is practice and feedback that are the key to learning almost anything, hence key to teaching it.

Don't take the word "framework" too literally.

Also, the task itself is ill defined here. Expect that no one will be perfect at it and that the "examples" created will sometimes fail. But there are ways, such as pre-testing or other evaluative methods, to deal with that as well.


Will withdrawing from a graduate program, affect my future admissions applications?

Your transcript will very likely have a notation that shows you withdrew from the program; to claim that you are still enrolled when you are not would be dishonest (if either you or the university said so!).

And yes, this will be something that you will need to explain to schools to which you apply in the future. Just saying "it's not good enough for me" is a bad reason to withdraw from the program, because it suggests a "diva-like" attitude that is not particularly desirable (in just about any circumstances). If you're responsible for paying your tuition, and found you could no longer afford it, that would be a more tolerable reason.

But you will need to explain this, and it can definitely have an impact on the decision of future admissions committees.


When is it ok to cite handbook instead of original source?

This also depends on the journal, if they do not allow to cite a handbook and the page in it due to their citation style you are refering to, then the reader has not a high chance to find it this information within several hundred pages quickly.

In general your thinking is right and my rule of thumb here would be to cite a handbook if possible and necessary only as a primary source in a research article.

I don't agree so much with the comment of @Andreas due to the time factor. The point of a research article is not to teach the reader something or give an introduction and references, but to report on scientific advances. So brevity, non-redundancy is the most important goal. A case making this/your question/situation maybe even clearer are review articles. Here I could agree with his comment, but even in review articles you will not find many references on handbook.

Another reason for this is the difficulty to get a handbook, they are very expensive in comparison to an article, so putting several handbook references in an article might make it simply impossible for a reader to understand your research/he gives up. That is not good for you and the journal.

A place where handbooks are referenced quite a lot and for good reasons are bachelor, master, PhD thesis, because everything in a thesis is often explained from the fundamentals to the new scientifc advances in a thesis.

So the criterion is not laziness, rather think about who your audience is. If you don't have a special page in my mind citing a handbook and would have to look for hours therein on your own, it's also no good argument to reference it to save your time.


Leave Industry for Ph.D. without Burning Bridges

Be sure to consult your employment contract.

The professional thing to do is to give two weeks notice.  It is your manager's job to be prepared for the departure of employees.  You are not responsible for that job beyond giving the two weeks notice.

If the company treats you poorly during the two week notice period, all you can do is offer to leave immediately.  In that case you may loose two weeks pay.

Thank your manager for mentoring.


pdf or word of the article for the first submission

I recommend you submit PDF, for two reasons:

Only PDF gives you full control over the formatting of the document as received by peer reviewers;
Those who are accustomed to typesetting in LaTeX (of which I suspect there are a fair few in your field) may be biased against authors using Word. Admittedly a Word document with default formatting settings could not be mistaken for a regular LaTeX document, if only because of the characteristic typeface used by the latter, but a well designed document might almost be mistaken for a XeLaTeX-generated PDF. At any rate no one will be triggered from the production-neutral process of opening a PDF file, but some may resent having to deal with .docx.

The PDF image quality is a concern. Have you set image compression in the PDF export dialog to prioritize quality?


What are the pros and cons of multidisciplinary research?

This does not fully answer your question, but it is certainly one consideration.

Multidisciplinary theses are often examined by multidisciplinary committees.
Examining such theses is difficult, especially if the committee has no experience examining multidisciplinary theses.
 A consequence is that you will often be forced to conform to the conventions of different communities. In addition, the chemistry committee member may not see the thesis as a chemistry thesis and the sociology committee member may not see the thesis as a sociology thesis, because it lies somewhere in between the two fields and cannot be a complete thesis in both fields.


Physics Courses in Undergrad to Apply for Physics Grad Program

Taking chemistry courses is good, but there is no need to remove physics courses from your schedule to add chemistry courses.


“Contribution to technical achievement” in Australia for the purpose of applying for a Lecturer position

I suspect that "technical achievement", within the context of computer science, is a reference to the production and development of computer software/hardware.  Hence, "contributions to technical achievement" is a cue to allow you to give information on any contributions you have made to the development of software/hardware/computing problems (e.g., a program you wrote or helped with).  There is probably going to be some overlap with "creative achievements".


What open indexing services compete with Web of Science

I work for a biomedical literature database - Europe PMC, which makes citation data freely available. You can access it programmatically, via the articles API (https://europepmc.org/RestfulWebService#cites). This resource also tracks data citations for over 20 different public resources: https://europepmc.org/Help#trackdatacit


Is certified translation of diploma an absolute necessary?

Only they can answer the question as it is their rules that apply. But I think you propose a good solution. Send them a "faithful" translation that you can prepare at little cost. Offer to send a certified copy if necessary, but mention that the cost of such a translation is high.

But you might also be able to have your university provide an English language translation or even to assure the recipient that your translation is accurate.


Which tools should be used to produce charts in computer science research papers?

To add to other answers that will probably suggest some nice, specific software:

Use whatever you are comfortable with. I personally don't think this figure 8 is that special, and I don't even think it has any features that cannot easily be done with something as common as Excel. As also mentioned in some comments: even the potential graphical powerhouse Matlab will produce crappy figures if you use the standard settings. The same for some other "go-to" software packages. But you have to be able to use them.

In almost all of the mentioned software you can adapt (almost) everything, and some default settings look better than others (one of the reasons why Excel has such a bad reputation).

The most important thing is that you decide how a graph should look, and actually make it look like that. Don't settle for default colors / font sizes and line widths! Whatever software you use to get there is your choice.

If you're fluent in MS Office: probably you should just use Excel. If you like to write scripts and use commands instead of clicking everywhere: Matlab might be an option. If spent 3 years getting good at using Graphpad but don't like how the graphs look? Just adapt them to fit your tastes, don't be limited by the default settings.

And when exporting them use the right settings. Many journals accept vector graphics, which will always look better, but the journal has to accept those. Figures also need to be the right size. Everything can look perfect printed 12 cm wide, but when your graph has to fit one column (8.5 cm), the same graph will look too small with unreadable fonts.


Electronic Assessment / Submission for questions where each student should have a different correct answer

There is WebAssign, started at North Carolina State many years ago and now an independent company )http://webassign.com/corporate/about-us/), which provided
versions of problems from standard textbooks in physics and other fields with random inputs so that each student would have individual numerical inputs
(I had some experience with these in the early days -- the inputs were generated from Perl scripts with input constrained to be physically reasonable).

I have not been involved with courses that used these for ten years or so, but one issue that arose then was the appearance of spreadsheets that had the algorithms for solving the problems coded into the spreadsheet, so that students could simply plug their numbers into the spreadsheet and come up with the answers.

Your question suggests that you are using more complicated problems than those in elementary science courses, but perhaps you could use scripts (using Python, Perl or whatever) to generate unique inputs for each student.


How do I tell my advisor that I lost interest in the subject?

Assuming your advisor is a great person and someone who listens, could you simply say:

  I'd like to work in a new direction for my PhD.

Alternatively, if you feel it necessary to give some reason:

  I'd like to work in a new direction to differentiate my masters work from my PhD thesis.

Preferably in either case you have at least some idea of where you want to proceed so you can continue the discussion in that direction. A desire for some breadth is a fairly normal and healthy part of the academic experience.

If your advisor questions the change of direction, you can simply say that after working on topic ______ for ____ years you are more interested in pursuing another direction.

It's certainly possible your advisor will be somewhat upset if he expected you to work in your previous subject (and especially if he took you on as a student because of that expectation), but it won't serve either of you to be coy about it or to plod through, not enjoying what you are doing, until you decide to quit. Ideally, however, this should have been a discussion you had before you agreed to work on a PhD with this advisor.

Keep in mind that your new direction should still be a fit with your advisor's work; if your previous project was in ideal spheres and your new work is going to be in falling apples, your advisor may not be qualified to advise you. It sounds like in your case that is not an issue, but if you are receiving any grant funding through your advisor, those funds may be particular to the project you are undertaking - hopefully you have some awareness of whether this applies to your situation.

Note that in my suggestions I was careful to phrase things positively and prospectively: you don't need to say you are sick of your previous topic, only that you want to move into something else. By approaching it this way, you come across as forward-thinking and not at all negative about physics in general, and not negative of your past experience as a masters student.


Is an erratum justified for a weak result?

In my opinion, an erratum is an erratum. I mean you should use it if you really discovered a flaw in a result and you want to patch it when the patch is not evident.

In your case, in some sense you improved your previous result and this either necessitate a new paper if the improvement is substantial or just a remark in some follow-up paper.


Can i shift my subject from Chemistry to IT

Of course you can!  Especially since you have an IT related publication and it seems you have shown interest in the field. I would highly recommend finding a supervisor with a project that appeals to you. It's all about your relationship with them for a positive graduate experience. If they want you and have funding for you, you will have much better chances of getting into the school you want to work on a project that excites you.


Is it ok to ask ex-dissertation supervisor for any future funded phds

The short answer is Yes. Rather, the supervisor might be happy to take you in if she had such a project.

Since you have already worked under the supervisor during your earlier degree and showed some excellent outcomes with research maturity, the supervisor would be really happy to take you in as a research lab member.

If you had not shown any good outcomes during your dissertation, then she might not consider the request.

However, it is not a waste of time to write and ask. Since she knows you she may read your email. Many a time, professors do not read emails even, and that is frustrating.


What excellent university DSP programs exist and what makes them excellent?

Firstly, lets assume you're talking about graduate programs. X being such a specialized program would only be available at that level of study.

In a nutshell:

Large list of cross listed (undegrad/grad) or only grad courses in all areas of study. You still need to have courses that can advance your overall knowledge of engineering.
Large variety of courses in your area of study. (If your studying DSP, its not enough to just take a DSP class, you may find it relevant to study data compression, machine learning, Free-space laser communications.) This also means you wouldn't have to complete a large number of independent study programs.
Large Number of Faculty in your research area. If you are interested in studying music signal processing, you would want to do research with a professor who has experience in that field. If there are 10 professors, you could be more selective about who to work with or who will be the best fit for your research area.

As for schools with decent program: Binghamton University, while it is not well known outside of New York, its master's programs is well structured, large number of faculty in EE at least 3-4 DSP professors, 10-20 graduate level courses offered a semester and large number of those are DSP related.


What questions should I ask when I visit labs for potential post-doc employment?

Your list is a good start, but I would dig a little deeper into the "expectations" item than you may plan. "Postdoc" is maybe the least well-defined role in a research group, and what you are supposed to (and allowed to) do can vary greatly. You need to have a clear understanding in advance whether your vision of the position matches with the vision of your mentor. Concretely:

Ask whether you are supposed to write papers without your mentor. If yes, try to get a feel whether the mentor means it (very few will outright say No to such a request). Try to get a feel for what percentage of joint vs. individual work your mentor expects.
Ask whether you are supposed to write grant proposals. Ask whether you will be the PI of said proposals, or your mentor.
Ask whether you will be responsible for your own PhD students.
Ask whether it will be possible to work on topics that are of interest to you, but of less interest to your mentor.
Try to get a feel for the mode of collaboration your mentor expects. Everything from "you do your thing and ask me for input when you need it" to "I'll tell you which problem to work on, and you report back your results to me" is possible, and you will want to know which one it is.

In addition to that, also ask what your mentor has in mind in terms of your career plan. When you apply for assistant professorships in a year, will he fully support you, or will he want to keep you around for longer? If the latter, what can he realistically offer you?


Reasons to do MS before applying for US PhD?

I think you have already listed many good reasons for completing an MS before a PhD.

For one, it can give you an introduction to a field of study on a graduate level. That allows you to be introduced to many of the more prominent people in the field, some of which you might find out are worth studying under. In that case, it would only help you when it comes time to apply.

If you publish and then subsequently present at a conference, then you can meet with a lot of other faculty from schools you're interested in, and you can strike up a conversation. In turn, you can stay in touch with that person and visit them later when it comes time to apply for the program. They may in turn vouch for you during the admissions review.

It is common for PhD students to have already completed an MS, even if its at another school. And, virtually all programs will take that into consideration and credit you 30 hours of coursework towards a PhD completion, so long as the courses are directly relevant to the PhD program.

I learned halfway through my first year of PhD studies that as far as my university is considered, there is no differentiation between a MS and a PhD student, we are all part of the Graduate College. So all of the MS hours are in effect graduate hours, and thusly they are also PhD hours.


(Why) Is post publication peer review (not) taking off?

Most papers that are published are uninteresting.
The median paper has less than one reader not counting the authors and the reviewers.
The current reviewing system relies on a network of responsibilities that are independent of the author.  The editors have a responsibility to the community as a whole to get papers reviewed properly, and the community gives them esteem for performing this duty.  The reviewers have a responsibility to the editor to actually do reviews, and the editor is usually some influential person (and in any case will probably at some point be the editor for one of the reviewer's papers).
Suppose I have written one of my usual mediocre papers that is among the 70% (my estimate) of papers that are never read.  How would post-publication peer review be organized for it?  If I have to find reviewers myself, then everyone is going to say 'No' or do a bad job, because no one feels any need to impress me and it's not a very interesting paper to read.  Moreover, the best reviewers for my paper are people with a little higher status than me, and they would definitely say 'No' to me, but they might say 'Yes' to an editor.  (Keep in mind that, as the system is set up, some top people in a field do far more reviewing than they write papers, while many people write one write-only paper every several years (or grad students who stop doing research write one paper from their dissertation) and never review.)


Whether to use the author name with numeric references when describing a particular study

There may be slight differences between fields (I am in the chem-phys-mat. sci triangle), but the short answer is no, you do not need to explicitly name the authors.

Stylistically, the "the work in [1] proposed" sounds rather forced and exactly as long as "Smith et al.[1] proposed". Note I am not a native speaker, so I have no clue what I am talking about. On the other hand I would definitely would leave the name out if I am talking about the same work over and over. Also, if you structure your statements like "This problem has been approached using this [1] and this methods [2]", giving the name is actually more awkward than leaving out.

I think it also improves readability. Compare "our method outperforms the name-of-the-method method [1]" with your examples (name-of-the-method: you explicitly name what is the main difference). Assuming that the reader do not know the reference list by heart, this kind of reference is more explicit and more informative than the other two.


What should I do if my advisor won't give me input into my own projects?

I don't say this lightly, but it's in your best interest to switch labs. I think you know that already but it's a soul-crushing reality to face. Let's face it now, before it's too late.

I had many friends throughout graduate school in similar situations, and the spectrum of outcomes is telling. The students that stayed in their labs despite functioning primarily as a technician were miserable, for years, and fundamentally deprived of their opportunity to grow as a scientist. None stayed in science or academia. The students that joined new labs had a better idea of what kind of mentor they wanted to work for, were happier, and universally wished they had left sooner.

You are likely thinking to yourself:

1) You've done so much work already! How could you possibly start over?

I know, it stinks! But your job as a graduate student is to become an independent thinker, not push through projects already defined for you. Plus, you're not really starting over. You're TAing, doing coursework, learning to program, and hopefully learning how to assess the literature. You'll continue to build on all those skills.

2) You're still a junior member of the lab! As a senior more experienced student you'll get more freedom!

Advisors that promote independence establish that environment for their students early on (like first thing!). Based on what you've said, I don't think there's much room for growth.

3) You just have to talk to your advisor about your frustrations and maybe he'll give you more latitude.

I wish it worked that way. What I think you'll get is some small concession, enough to keep you hooked and doing his work. My pessimistic sense is there are very very few, if any situations where an advisor will have a change of heart adequate enough to improve your lot in lab. What you describe is a clash of philosophy: advisor knows best vs. allowing students to grow, make mistakes, and even deviate from the original trajectory. It's not that your advisor is a bad scientist, or a bad person, it just may be that he or she is better off running a lab of technicians rather than graduate students.

4) Your brother's advice: you just have to work harder!

I have to respectively disagree with that. As above, I think this is fundamentally a philosophical difference between what you want out of your education and what your advisor wants out of a student. No amount of hard work will change that.

5) This material is really interesting! There's nothing else I'm as excited about.

If the material is awesome, it makes it harder to leave. Nevertheless, I think you'll derive much greater satisfaction with a mentor who treats you more as a colleague than as a peon.

Lastly, I think your situation portends even more dire consequences down the road. This sounds like the advisor who you might have authorship problems with, who decides you need to stay another year after publishing 4 papers, or who doesn't write you the best of letters (how can he/she if you never demonstrated your full potential?).


How can I quickly retrieve the Semantic Scholar IDs of all my co-authors?

If you have a list of DOIs of your papers, you could do this using the Semantic Scholar API, or this unofficial Python interface for it.
For a query using the DOI, you get a JSON object (or a dictionary with the Python API) that contains the list of author names and IDs.


Catching small errors in lecture materials

If you catch this during teaching, this means that you probably should rehearse (out loud) and then similarly things should emerge. You already mentioned you rehearse, but maybe you need to rehearse in a more elaborate manner (in a different room, in front of a mirror, etc.) to change your mindset and then find new mistakes. If you rehearse in your head in front of your PC, you are stuck in the same state of mind and won't find mistakes.

Other typical approaches:

Typical proofread advice

Read from back to front and mirror images/figures to get a fresh view upon things. This helps finding misplaced labels.
Spellcheckers and other digital proofing tools (programs which check if borders are met, elements are hidden, etc.)

Teaching notes as bullet points, which you periodically check during the lecture, to ensure you are still on track and have told everything you want to tell (i.e. have not forgotten some points)

These should also uncover any kind of logical mistakes. If you follow your line of thought during rehearsal, this should help explaining correctly and in order.
Notes provide self-confidence, which greatly reduces being error-prone. If you are less nervous, things go easier and mistakes are not so disrupting.

Find someone to proofread (either mutual agreement with someone or pay someone until you are more experienced. A student could be a good choice)

Finally, things can and will go wrong. It is more about how you handle the mistakes. Maybe simply update your slides after the lecture and tell the student next week, that last weeks slides were updated, with comments where things were not explained correctly.


If a paper has been accepted at a conference does it mean that it will be published?

From the conference website:

  All accepted and presented papers will be submitted to IEEE Xplore (Digital Library) for conference proceedings publication and will be submitted to Scopus for possible indexing, IEEE Conference Record #45516. IEEE Xplore ISBN: 978-1-5386-7989-0.

Note that you are required to actually attend the conference and give a presentation (and pay the registration fee). With any conference, if you submit a paper which is subsequently accepted, you are expected to attend the conference and present the paper. If you do not attend the conference (barring exceptional circumstances which you communicate to the organizing committee), then the paper might not be included in the proceedings (i.e., will not be published).

Note that computer science is a bit of an outlier because it considers conference papers as publications. Many other fields do not consider conference publications as "real" publications as the review process tends to be less thorough. Many papers (even in computer science) which start out as conference publications are later published (in a more polished, expanded form) as journal publications.


Professor will not write a letter of recommendation because I have restricted access to my records under FERPA, is this legitimate?

David Z's comment is dead on: it is an unpleasant technicality that under FERPA regulations, one should not discuss the student's performance in any quantitatively specific way.  E.g., one should not say "Mr. X got an A in all my courses" or even "Mr. X was the top student in the course".  The exact rules are confusing to many faculty members, to the point where one feels like if one took FERPA too seriously one might not be able to write a suitable letter.

In my university there is, in theory, a form that a student can fill out to waive the FERPA regulations on a letter-by-letter basis.  In theory this means that if the letter is getting mailed to N institutions, one should fill out N forms.

(The above considerations apply to all students, not just those who have asked for special protection.  However, a student who places further restrictions on their records is precisely going on the record as being especially concerned about their privacy, so in practice it makes a lot of sense to take the FERPA restrictions much more seriously for these students.)

It may or may not be the case that Dr. Z is himself trying to access or view any of your academic records.  (I guess he must have done something to find out that your records are FERPA-restricted though.)  Whether someone would look up a student's grades in courses taken by other faculty members must depend on the people and the institution.  For instance, at my institution I have access to the grades of all undergraduate students -- and I have been informed of the FERPA requirement that I access them only for legitimate, educational purposes -- but I do not have access to the grades of any graduate students, even my own advisees.  So in practice when I write letters for students I speak only about their performance in my courses -- but again, if they were FERPA-restricted and I was being suitably conscientious then I would even then have to be extremely careful about what I could say and likely be forbidden from including a certain amount of positive information about the student.

Also:

  I have no reason not to remove the FERPA restrictions, but I hate the thought of removing them under these circumstances; this tastes a little too much like blackmail to me.

Even assuming that Dr. Z wants permission to access your records and not just to talk about them, I think you are not viewing this in the right way.  "Blackmail" seems ridiculous to me: one of the conditions for that is that the blackmailer must have something to gain!  What does Dr. Z gain if you waive or even entirely remove your FERPA restrictions?  The pleasure of viewing some of your academic records??

For my part, I am curious as to why you chose to place restrictions on your academic records at all: what are you protecting yourself from, really?  It sounds like you may not completely understand what FERPA restrictions mean and may have just taken them on as a sort of free insurance.  If I were you I would learn more about this.  In my opinion, one could argue that "I have FERPA restricted my records" and "Please write me a strong recommendation letter" is already a bit of a mixed message.


Can I mention my undergrad ranking in CV, when there is no official document about it?

If you can't prove it, I wouldn't put it in your C.V.

For one, anyone reviewing your application will have no way of knowing if you're lying or telling the truth. That's never a feeling you want a reviewer to have.

Even more importantly: what if you were actually wrong? What if you were 8 out of 60? Or 6 out of 60? I trust that when you say you're 7 out of 60, you have a pretty good idea of that, but you can't be sure if your school doesn't issue an official rank.

For what it's worth, if your GPA is high enough, I doubt rank will matter much. #7 is great, but #7 out of 60 students is different than #7 out of 600 students or 6000 students. For that reason, the rank itself is less valuable than your actual GPA.


The quintessence of the systematic review is that it's, well, systematic. That is to say, you have a system by which you do the review: a detailed protocol that you work by, just like when you run experiments. The protocol sets out how you will define your search terms, where you will search, what your criteria are for inclusion are, what your criteria for exclusion are, and so on.

The idea is that, just as with an experiment's protocol, it would allow someone else to reproduce your work: in this case, your trawl through the literature. It gives you and your reviewers and readers a basis for assessing how comprehensive your review is. It may include a detailed protocol for quantitative meta-analysis or qualitative synthesis.

Systematic reviews can be hugely varied in form and scope: I've got 3 books that each provide part of the answer to this question. Check your library (possibly in the medical / epidemiological section) - they should have at least one of these.

Systematic Approaches to a Successful Literature Review - Andrew Booth et al - encyclopaedic
Doing a Systematic Review: A Student's Guide  - Angela Boland et al
An Introduction to Systematic Reviews by David Gough et al


Discussing time limits in the limitations section?

No. It not common, nor should you do it! As paul garrett pointed out, this type of excuse makes it seem as though you didn't care or couldn't be bothered to do a better job.

I would add also that no matter how much time and effort you have put into developing an idea and writing your paper, it is almost inevitable that there will  be something that you missed or could have done better had you had/taken more time. Even the magnum opus on which you have spent your entire lifetime will be superseded by better or more complete thoughts; this is an inevitable reality of academic writing, and not one you should apologize for.

Perhaps especially as a student, one struggles to find the balance that represents maximum output for minimum time spent. Knowing when to 'let go' is a function of maturity and experience. When you've made that decision (or have had it made for you, due to time constraints outside your control), accept that this might be better, but don't apologize for the inevitable.


What are the differences between Peer Reviewed Journals and Refereed Journals?

To expand on Yuichiro Fujiwara's comment, "peer review" and "refereeing" are exact synonyms, and no differences at all are implied by the names.  For historical reasons, some fields are more likely to use one term than the other (for example, mathematicians talk more often about refereeing than peer review).  Publishing practices also differ between fields in other ways, such as the length of the reviewing process.  There might be a weak correlation with the use of terms like peer review and refereeing, since both issues are heavily influenced by which field you are looking at.  However, I'd bet that any correlations are small, and in any case this is not a productive way to investigate journal differences (since knowing the field would tell you enormously more than just knowing which term the journal uses for peer review).


How to send end-of-the-year wishes in academic environment?

There are many options which can be made by themselves or in some combination.

You can design a "card" to attach to the mail which could be informative or aesthetically pleasing (but do not make it a huge file).
You can, as I and my former adviser do, make a "Christmas letter" that summarizes the year both academically and private. You need to adapt to your audience here since the private section should not be too detailed if your are not really close friends, but comments on travels with a nice shot is never a bad idea.
You can divide the send list up into different categories but the backside of this is that if you group people and group them wrong (from their perspective, it can become embarrassing).
The previous point is also true for listing people in some order; so alphabetical, even in the way you list the e-mail addresses, is probably wise.

Do not emphasize Christmas and New Year per se since not everyone may be celebrating these primarily Western holidays. Use something more neutral formulation such as "Best Holiday Greetings" or "Best Wishes for the Holiday Season". Again, know your audience and adjust.

You can send a general more formal greeting to a larger group and then follow up with a more personal greeting to specific people you wish to share more personal greetings.

So, think about the options and combine to taste.


Courses outside colleges and do they count?

NPTEL is the best bet.
It is a MOOC by the Government of India, where online courses are offered by various Indian universities, including the IITs and the Indian Institute of Science. It is similar to Coursera and such in the sense that you watch videos and complete weekly assignments. You can register yourself as a student through this link and browse courses.
If you want your learning to be certified, you need to register for a particular course. Registration for courses happens twice a year (just like usual colleges). Unfortunately, I believe you have missed the registration deadlines for most of the Jan - April courses, there are only a few that are still available.
For example, this is the catalogue for the courses you can still enroll for during the Jan-April 2021 phase in Mathematics. Perhaps a course may interest you.
You can also wait for registration to open again for the July-November set of courses (this starts sometime in June-July).
How it works

You can browse for various courses using the Course Catalog tab.

Register for the courses you are interested in. Duration of the courses are typically 8-12 weeks.

Go through the uploaded video/text lectures (this depends on the course).

Complete the weekly quizzes and other assignments as applicable to the course.

Register for the final exam within the mentioned deadline. Without writing the final exam, you will not be provided the certificate.

The Final Exam

The final exam is usually written at designated test centres in March or April for the Jan-April courses, and in September or November for the July-November courses. Choose your test centre carefully.

All the final exams are conducted on Sundays, either in the morning slot (9-12 PM) or the afternoon slot (2-5 PM). If you are attempting the final exam of multiple courses, make sure they do not clash.

Note: You can attempt the final exams for a maximum of six courses per 'semester'. Also, there is an exam registration fee of ₹1,000 per exam.
Getting certified
There is a specific set of criteria that needs to be met for you to be certified. This may vary from course to course, and it is mentioned clearly in the course information. For example, these are the criteria for a course called "Introduction to Astrophysical Fluids".

Average assignment score = 25% of average of best 8 assignments out of
the total 12 assignments given in the course. Exam score = 75% of the
proctored certification exam score out of 100
Final score = Average assignment score + Exam score
YOU WILL BE ELIGIBLE FOR A CERTIFICATE ONLY IF AVERAGE ASSIGNMENT
SCORE >=10/25 AND EXAM SCORE >= 30/75. If one of the 2 criteria is not
met, you will not get the certificate even if the Final score >=
40/100.

Most courses seem to have similar eligibility criteria.
Transferring Credits
There is an option in NPTEL when you register for the courses to transfer the credits to your university. But you need to talk to the academic department of your university about this beforehand. I would suggest you talk to your university at the beginning of the semester in which you are planning to take the NPTEL course. You need to know if:

They even consider an NPTEL course to be eligible to be added to the official transcript (and if they do, the procedure for it).

Whether they will consider it a 'pass/fail' course where you only need to submit your final certificate to show you have taken the course and it will be marked as a 'Pass' or whether your grades in the course will also be shown in the transcript.

For example, in my university, NPTEL courses are considered purely for extra credits as 'pass/fail' courses, meaning the grade I have achieved in the course will not be shown in my official transcript.
The Value
I cannot comment with certainty about this since I am an undergrad student like you. My assumption is this (needless to say, take it with a grain of salt):

Under normal circumstances, an NPTEL will probably carry lesser 'value' than a typical university course since the assignments are online and there are no 'classes' to attend. But remember that since we are writing a proctored final exam in person (much like a university course), it probably carries more weightage than certified courses of foreign MOOCs like Coursera or Udemy.

Under the current COVID situation, I would say an NPTEL course is very similar to the online university courses (In fact, many of my professors ask us to refer to archived NPTEL courses i.e. courses that are not accepting enrollment anymore, for the material). We complete weekly online assignments and write a proctored in-person online exam, similar to a university course. I would say that in such a situation, an NPTEL course should be considered to have the same value as a normal university one.

Furthermore, if your university only accepts the NPTEL course as a 'pass/fail' course, there is no indication of your performance in the course, but only evidence that you have taken it. In such a situation, the course would not carry as much value as a typical university course.

Final personal thoughts
Overall, I would suggest you take an NPTEL course (or two). The best-case scenario would be that you do well in the course and it reflects in your official transcript. If not, you still have a certificate that you can add to your CV or mention in an interview.
With regard to transferring credits through an online course, NPTEL is surely the best bet for Indian universities. I highly doubt they take certified courses from Coursera/Udemy/EdX seriously enough for credits transfer.


Does a PhD give you global mobility in the job market?

There are two aspects to this question: the hiring process within an employer's institution, and the immigration policies which allow a foreign worker to move to another country and begin employment.

I think with respect to the first question—the hiring process and preferences of an individual employer—I think that in general, employers are looking for the best-qualified candidates, regardless of their origin. There are certain obvious exceptions to this (for instance, a foreign national will have a hard time getting a position at a National Nuclear Security Administration facility in the US), but otherwise, people will want the person best-suited for the job. I think this is true both in the US and Europe.

The other step is the national immigration policies. This is where things become more complex. For instance, if you are a non-European Union citizen, then your employer will need to certify that your experiences uniquely qualify you for this position, which can delay the hiring process somewhat. Similarly, employers in the US have to wait for you to obtain an appropriate visa, which can delay your start date significantly. This makes it sometimes less advantageous to hire foreign employees. (But this is a "speed bump," rather than an insurmountable obstacle.)


Include personal scripts & algorithms in scientific paper

Yes to both, though providing code through a service like GitHub may be preferable as you can obtain a citable DOI and your readers will know where to find updated code, if any. Figshare is another option. Providing code in your supplement can provide redundancy, especially if you would like readers to cite your paper when they use your code. See Rule 8 under these Ten Simple Rules for Taking Advantage of Git and GitHub for more details.


How did researchers find articles before the Internet and the computer era?

We depended on libraries and librarians. Grad students would spend hours in, say, the math section of a good academic library, going from book to book and taking copious notes (on paper, of course).

But, often enough, the next paper we needed to look at wasn't in that library at all, so you would go to the librarian and ask for a loan of the resource from another library.

But it was also an important technique to use the librarian as a 'knowledge expert' who could, and would, suggest things for you to look at and places to look. I don't know if librarians still get the training to do that.

And, of course, you could ask your colleagues for hints about which rocks to uncover to find the gems.


Transitioning from a PhD to Postdoc. Is it acceptable to stay with the PhD advisor for 6 months to a year after graduating?

In mathematics and in Northern Europe I have seen more than a few people do this. A grace period after graduation is not rare. But it is expected that you spend time elsewhere, preferably abroad, either employed or on long and frequent visits, or that you are very good. (Even if you are very good, there are probably other very good people seeking employment, so travelling is still a good idea.)

More importantly, going elsewhere gives you perspective:

New ways of teaching.
New fields and problems to solve and methods for solving them.
New contacts and collaborators.
If going abroad, usually a new language and a more-or-less new culture, depending on how far you go.

In most life situations, it is easier to travel now then later, even if you intend to come back. So if your situation allows, consider seeking for positions elsewhere. Current co-operators of your current research group would be especially useful, since that would probably allow you to contribute to the ongoing projects in some way, too.

Also, unless you specifically aim for it, you will never not have unfinished projects going on, though this is probably field- and personality-specific.


CS Master's admission after academic dishonesty

Based on what you stated, it doesn't really sound like this will follow you anywhere. You were caught, they gave you a token punishment, and everyone moved on. It's not as though you have to state your dishonesty on your resume or whatnot. I would recommend treating it as a lesson learned, and unless someone specifically asks you about it, don't bring it up.

To directly answer your questions... no, you really can't do anything to fix it. It's part of your history now. However, it may not affect your application, as they receiving university will probably never find out about it.

Note that all of this is based on the assumption that your dishonesty does not go on your official transcript, based on your having stated that in the question text. If it is on the official transcript—the one that one university will send to another when asked—then your situation is a good deal worse.


How to deal with a busy research partner?

As the comments have said, you need to go with your partner and explain this to your adviser face to face. It's not an incompetence issue and you need to make sure that you make that clear to your partner - it's a workload balance issue.

At the end of the day though, there are only two options available:

Either your partner reduces their outside workload or,
Your adviser reduces your workload to account for it.

This is something that needs to be decided between the three of you.

However, I'd strongly advise that after you've had the talk, that you put in place a very rigorous project plan for your next tasks with a strict timeline. Often, this situation ends up just repeating itself as your colleague says 'oh I'll find more time' or your advisor says they'll slacken off but not much happens, so a rigorous project plan helps highlight if the talk has worked or not.


How is the job market for Chemistry like?

Subscribe to your local job portal. It'll tell you more about what jobs are out there than most people can. Using Google for the term "uk job portal", I found these two sites: jobsite.co.uk and reed.co.uk (there are a lot of others). Search for positions requiring chemistry at your degree level (e.g. if you're applying for a PhD position, search for "PhD chemistry"). These job portals usually have lots of refine search options as well, such as sorting by location, salary, and so on.

I'd recommend subscribing and staying subscribed to these job alerts throughout your studies. Even if you never apply, at least you know what's out there, in case there's a change in market trends.


What employment can someone obtain if they were not given the PhD after studying and publishing?

Congratulations on the publications you have achieved thus far.

  If I change my advisor now, my present advisor will become vindictive. [...] A students fate depends on her advisor; higher authority cannot do anything.

It sounds like your best bet, if you want to stay where you are, would be to avoid conflict with your advisor.

  I am in my 3rd year of phd.

I don't know anyone who completed a PhD in two or even three years.


Should I do someone else's peer-review work?

No, you gain no benefit if it is you who submits the review instead of him. If you conduct a review on his behalf, you gain the advantage of his mentorship and advice. It will be good experience for you, as you will get to work through a work in progress and understand more deeply how submitted papers are evaluated. If you are concerned about credit, ask him to mention to the editor that he asked you to do the review and these are your comments. Ideally, he should ask the editor for permission before sharing the submitted manuscript with you, as it was sent to him under a condition of confidentiality.


Online resources for summer schools in software engineering?

I would say that one of the best online resources for Software Engineering is SEWORLD. You can browse their archives and look for summer schools there.

Note that their search engine is a bit weird, if you go through "search the archive", put Summer school in the subject and "2010-1-1" in the starting date (when I leave it blank, I don't get recent results). For future references, here is the result of this query:

ISSSE 2012 - 9th International Summer School on Software Engineering
Summer School Marktoberdorf 2012] Call for Application
LASER Summer School 2012: Innovative Languages for Software Engineering
CALL FOR PARTICIPATION - 4th RiSE International Summer School (RISS) - Next Generation of Software Product Lines
summer school VTSA 2011
Summer School on Technologies for Realizing Social Networks and Applications
CFP: 1st Insubria International Summer School on Open Source Software (IISSOSS 2011)
Summer School on Mechanized Logic for High Assurance Software
Canadian Summer School on Practical Analyses of Software Engineering Data
UPCRC Illinois Offers Summer School on Multicore Programming
3rd International CASE Summer School on Practical Experimentation in Software Engineering - July 11-15, 2011 - Free University of Bolzano-Bozen
Summer School on Programming Languages for Concurrent and Parallel Computing
8th International Summer School on Software Engineering (ISSSE 2011)
[Summer School Marktoberdorf 2011] Call for Application
LASER Summer School 2011: Tools for Practical Software Verification
[CFA] Summer School on Programming Languages PL2010
CALL FOR PARTICIPATION - 3rd RiSE International Summer School (RiSS) - Generative Reuse
Call for participation to the 3rd International Summer School on Adaptive Socio-Technical Pervasive Systems
CfP ADAPT Summer School
DSM-TP 2010: 1st International Summer School on Domain Specific Modeling - Theory and Practice - Call for participation
Call for participation: VTSA 2010 Summer School on Verification Technology, Systems & Applications
6th REASONING WEB Summer School "Semantic Technologies for Software Engineering"
Summer School on Mining Software Repositories - June 2010, Kingston, Canada
CfP: UPCRC Illinois Summer School on Multicore Programming
LASER Summer School on Software Engineering
TiC'10: Third International Summer School on Trends in Concurrency
Call for Part: CASE Summer School, Bolzano, Italy, 19-23 July 2010
CfPart: 6th TAROT Summer School on Software Testing
7th International Summer School on Software Engineering


Should one apologize in response letters to reviewers? If not, why not?

My rule of thumb, generally in life as much as any specific aspect of it, don't apologize for something you haven't done wrong. This is of course highly debatable but an apology is a formal acceptance of a mistake made, not a figure of speech to be polite. So I'd say don't apologize for something if you don't believe you "f*ed something up".

It does have a cultural component however, as a British friend of mine once put it:

  buying a bag of crisps in England involves 4 "Excuse me"s, 7 "Sorry"s
  and numerous "thank you"s.

In this scenario specifically, I think it'd be an insincere apology, and might even be taken as mockery to apologize in response of a comment made by a reviewer. I'd rather advocate for a respectful and appreciative response, something like:

  Re: "[blah blah blah] should be discussed and evaluated."

  We would like to thank the reviewer for pointing out the lacking
  discussion on [blah blah blah], this has been added in the revised
  version of the manuscript, see page X, paragraph Y.

or, if you disagree with the reviewer about that particular comment because it's not missing

  Re: "[blah blah blah] should be discussed and evaluated."

  We would like to thank the reviewer for pointing out the lacking
  discussion on [blah blah blah], however this topic has been covered in page X, paragraph Y.

OR, if you disagree with the reviewer about that particular comment because it's not necessary

  Re: "[blah blah blah] should be discussed and evaluated."

  We would like to thank the reviewer for pointing out the lacking
  discussion on [blah blah blah], this topic has been omitted because reasons A,B and C.

Of course these examples are grossly simplified and generalized, usually a bit more context regarding the proposed changes would be appropriate to give in the response. Remember the response is aimed primarily at the editor, not the reviewer. If you can convince the editor, you might even bypass a second iteration to the reviewer.


Can you appeal to the associate editor when given unreasonable requests for revisions?

Not a journal editor, just a researcher.

I would respond to the reviews directly. You don't have to accept all the proposed changes; you can simply say "We feel this fundamentally changes the problem structure...." and give a paragraph or two on why.

That said, I might also reply to the AE. This can be very brief, something like "Our updated draft and responses are submitted. Note, however, that the two negative reviewers requested significant changes that we do not feel are appropriate; we reiterated our objections in our response." That way there is no formal appeal (yet), but perhaps the AE will review more carefully if the reviews come back the same as before.


Journal requires to cite Arxiv pre-print of the same work – where and how do I cite?

Add something like this to your "Introduction" section:

  This paper has been published as an arxiv pre-print<cite pre-print here>

This is the approach I used when I published part of the research I had done for my thesis. It conveys the necessary information without cluttering the paper with verbiage that a majority of readers will find irrelevant.


How much seen material/questions should an exam paper contain?

If you hadn't included the "graduate school" tag, I would say this is both common and appropriate. My exams for undergrads are about half familiar material, that I've specifically indicated to them could appear on the exam. That way, most everyone who studies can at least pass.

But ideally, grad school should be more challenging than that.


How do I make a bad semester not look bad during my scholarship application?

They require a transcript, but do they allow any kind of supplemental statements as part of the package? If so, I would try to include some kind of simply explanation – something like:

  During the fall semester of my senior year, my grades slipped due to some personal family issues.

You might even try put a positive spin on it:

  During the fall semester of my senior year, my grades slipped due to some personal family issues. Even though my grades suffered, I learned a lot about priorities and biting off more than I can chew. Though my GPA might not reflect this, I emerged a better person because of that trying experience.


How to stop sexual harassment by teacher?

I suggest you should report it directly to the police.

Why, well, as he has been dismissed from the school they have no control over him, so reporting it to the school will only be for information.

You can choose to tell or not your parents but you may value their support.

I hope this sorts itself out. Best wishes.


Should I breach peer-review confidentiality if I suspect misconduct and the editor is not willing to pursue it?

That's a tricky question. I will try to give you my humble advice.

First, document every step and be sure that your statements are true. If you have some suspicion, you can also present that, but state that you only have such suspicion.

Second, write again to the editor telling him/her that in good faith you believe the study is fabricated, and it will undermine the journal credibility. If you do that after publication, the damage to the scholarly literature will be even larger.

Third, tell the editor your plan. For instance, you can tell him/her that if he does not act swiftly within 30 days, you will inform, without divulging too much details, of the situation, his/her insitution, as well as the authors' institutions and the publisher.

Fourth, if the above does not work (it should), then proceed and be ready to defend thoroughly your argument.


How should administration punish sexual abuse/trade for grade?

Initially, like xLeitix, my response to this question was "Say what?"

Then I did some reading. For those who are interested, here are some articles on the subject:

Sex, grades and power in higher education in Ghana and Tanzania
Kenyan tutor on 'sex for grades'
Teachers Demanding Sex for Grades
Liberian women battle against 'sex for grades' at universities
Sex for grades in Africa's academy

Given this context: if sex-for-grades is sufficiently "popular" in your department that it can "strongly weaken the quality of education," then you have a bigger problem then how and whom to punish the next time it happens.

  What should a head/dean do in this regard to preserve the education quality?

In a department where sex-for-grades is common, you can't stop it by punishing it in an ad-hoc manner. You have to create a comprehensive policy; educate students, faculty, and administration about this policy; and then enforce it.

If you don't have a university policy (or your university policy is not sufficient), you can create a school-wide or departmental policy, depending on the scope of your position.

Your sexual harassment policy should clearly describe:

Exactly what constitutes sexual harassment,
What the consequences will be for those involved,
and (the most important of all), How to safely report harassment.

In addition, you should then take steps to educate

Faculty, on how to protect themselves against sexual advances from students (steps such as: keep a strictly professional tone in emails and other communication with students, have meetings with students with office door open, etc.)
Administration, on how to respond to allegations against students/faculty with sensitivity and discretion
Students, on how they can report harassment without fear of retaliation

  Who to be punished? Student or professor? Or both ?

As for who to punish: any faculty or administrative staff member who

solicits sex from a student in return for grades, or threatens to fail a student who won't have sex with them, or
responds to an offer of sex for grades with anything other than a firm "NO"

should be punished.  Of course, it must say so in your policy and you must make sure to educate faculty about this policy.

Students are usually the disadvantaged group in this scenario, and punishing students could deter them from reporting sexual harassment. Therefore, I would advise against punishing students in most cases. I can think of a few exceptions, where it is appropriate to punish students: e.g., students who make repeated sexual advances, despite being warned more than once in an official capacity not to do so.

  How to punish?

depends entirely on what kind of punishment you can enforce, as a department head/dean. I have no idea what kind of power you have as a department head/dean in your educational system.

Typically in the U.S. it would be handled at a higher level, as   Nate Eldredge pointed out, because department heads in the U.S. don't usually handle disciplinary matters.


Why would a school prevent reapplying after declining an offer of admission?

I believe the issue here is that if a student has already been offered admission and turned it down, then the school has already given that student due consideration in reviewing the application. Reapplying in the following year means that the candidate was apparently unsatisfied with any of the offers of admission received, which included the school in question. So what would have changed in such a short period of time that meant the offer wasn't good enough then, but is good enough now?


Can graduate students be forced to leave graduate school under pressure from their advisers?

This is such a loaded question I'm hesitant to answer. While it might seem that a student was "kicked out" of a program for conflicts with an advisor, most departments (including ours!) have a procedure and policy for when students are asked to leave the program.

Usually, the reasons would be some mixture of lack of basic minimum grades and lack of satisfactory progress. if there's conflict between a student and advisor, there's usually some departmental mediator (a director of the graduate program) who should be able to step in and deal with the situation (either finding the student another advisor, or something like that).

But I'm not aware of it being generally possible for an advisor to fire a student and have that student then be removed from the graduate program: these two things are usually separate.


Are non-citizen Muslim professors and students going to be removed from US universities and subsequently deported by Trump's ban?

The current ban applies only to people who are outside the US.  Nobody knows what Trump might do in the future, though.

Edit: The situation keeps changing, and I will not be updating this answer.  Stack Exchange is not a news service.


"Under Editor Evaluation" to "Under Review"

My guess is that the editor felt the review(s) received were not sufficient to make a decision on. You can get some extra insight if you know how long the paper was in each stage. If the paper was under review for a long time (depending on how long it typically takes to review a paper in your field) and then went to under editor evaluation for a few weeks before reverting back to under review, that would be indirect evidence for this guess.

If this guess is wrong, then the next most likely thing is probably a more serious breakdown in the review process, e.g. the journal swapped editors responsible for the article. Either way, unless you want to withdraw the paper, there's nothing to do except wait.


Tenure-track offer with other applications in progress

I think what you are asking is if there is an ethical way to accept a position and then bail if you get a better position. Ethics are often very personal, but I think most people would conclude that this is unethical. That said, potentially the more important question, is can you get away with the behavior. From a legal standpoint, there is likely very little that can be done to punish you.

From a career standpoint accepting an offer and then turning it down tends to be a recipe for creating academic enemies. In your case, however, I think you can get away with it because of the Brexit and the fact you have a partner. If in the next month you get a better offer, you can tell the UK university that your partner has had a change of heart. Yes, I am advocating blaming it all on your partner to keep you from making enemies. Explain that your partner is concerned about moving to the UK because of Brexit and their treatment of foreigners. Yes, I am advocating telling a straight up lie. UK academics are generally up in arms about the Brexit. Having a change of heart because of the Brexit will be totally believable to them.


What is the difference between a research statement and a research interest?

This would depend on who is asking, of course. But I'd expect, generally, that a research statement would be more detailed with a plan for how you would go about things like obtaining funding and incorporating students, etc. A research interest might be as little as you area of special expertise, though it might be a mistake to make it too narrow. For example, in mathematics, Algebra might be a bit too wide, but not so narrow that only a few people in the world are interested.

But, it can vary. Ask the asker for guidance if you can.


Under review since 9 months. Shall I send another email

Yes. The person you contacted in the editorial office is paid to answer queries like yours. It's exactly why the publisher employs them! Feel free to email again, just don't be abusive (they do not directly handling your paper, and they cannot act without the editorial board's approval). I also suggest against threatening to withdraw your paper, because it's likely to be ineffective. At most the editorial office can only forward your message to the handling editor, and they're likely to say "okay, you can withdraw it" especially since they're evidently having trouble finding reviewers.

As for what to write in the email, it's up to you depending on what you want to know. You could ask them to chase the handling editor again. It's also possible they might be willing to tell you more details about the manuscript's status: how many reviewers have been invited, how many reviews have been completed (if any), when further reviews are expected (if there are reviewers who've agreed to review but have not submitted), and so on.


Getting a letter of recommendation from university

(transforming the comments into an answer)

The point your question seems to be missing is that professors give recommendation letters, not institutions. LORs are "personal" commitments from people that know you, know how you work, behave, etc. People that do not know you will most likely decline or send worthless letters.

That counts old professors that remember you, regardless of where they are at the moment. Track them down. And there is not that much of turnover in universities, I graduated 10 years ago, most of my professor are still there...

If no professor knows you, you won't get LORs. You don't need to "make friends" with the professor, good grades on his/her course should be enough. An undergrad research advisor would be better, but not necessary. It won't be a stellar letter, but for MS, it doesn't need to be. Just to reinforce: letters of recommendation are personal, not institutional.


Academic dismissal from PhD program. What next?

This answer is going to sting, but it's how I read the situation based on what you've written here. It sounds like there is something going on that you haven't addressed.

If a department wanted to keep someone who they felt was a promising student, who they thought could contribute with good work, I think they'd find a way to waive the GPA for another term, seeing that it's so close to the threshold. On the other hand, if they felt like a student was not worth keeping, they might be relieved that the student's GPA fell below the specified threshold, so they could use it as grounds for dismissal from the program.

As for the lab reports, there's a difference between being late and being unreliable. One is a fact, and the other is a perception. You emphasize the fact, but I suspect it's the perception that is behind their unwillingness to rehire.

As for the GRE score, those scores used to measure potential from an admissions perspective. Once you're in the program, GRE scores become pretty much meaningless; from that point on, you're judged by the work you do at the institution. (The fact that you even mention it makes me wonder if you have a habit of overestimating your own value in a way that annoys your professors and your peers.)

As for your options, I wouldn't recommend reapplying. That's an uphill battle; they seem to be sending pretty clear signals that they'd rather be done with you. That leaves transferring somewhere else. Given that your GPA is so close to 3.0, I'll bet you could find a school willing to accept you as a transfer student; however, they might have second thoughts based on some of the reasons for your departure. I would be very careful about who I listed as a reference from the school that is dismissing you now.

You might want to look in the mirror, and try to more accurately assess why you are being let go. As I mentioned, I think it has to do with intangible qualities such as personality, reliability, and teamwork – things that are hard to quantify, but easy to spot notice once you start working alongside someone, especially in an environment where the goal is to achieve a complex and long-term endeavor.


Is doing a 1 year MBA after many years of experience in the IT industry worth it?

It seems that you are unsure of what you want from a MBA, besides hoping it might kickstart your career. I think it's important that you first identify exactly what you want from a MBA - your goals. Do you want to gain connections with others in your field? Do you want a job that requires a MBA? After you have identify these goals, ask yourself if a MBA at a certain institution will help you achieve these goals. The degree itself is just as important as where you get the degree. Foreign universities might be cheap, but degrees that come with it might not be highly regarded in the States.

Studying abroad is not the optimal choice in your situation. As a native American, there are plenty of prestigious American institutions willing to diversify their graduation class and scholarships will be available to you - you just have to search or ask for it. Going abroad for only 1 year is definitely not worth the trouble of learning a new language - it will be a distraction to your studies.

I would also disagree with you that the economy in the US is slow. Are there particular reasons why you feel that way?


Politely decline an offer that I sort-of accepted

Dear [name],

  Thank you for your reply to my email of December [xx]. Please note that in that email I asked what documentation I need to send in the event that I decide to accept the offer to join your graduate program, but did not yet indicate a definite wish to accept the offer. In the meantime, I have considered the matter some more and decided to pursue other opportunities elsewhere. Thank you again for the generous offer, for which I am  grateful.

  Sincerely,

  [your name]


A blanket ban on bringing babies to class is probably not allowed at many institutions. However, I agree that if the baby is acting up, then the supervising parent should take the baby out of the classroom so as to minimize disruptions to the overall lecture.

This should be reached as an agreement outside of class time so that the lecturer is not placed in the position of having to stop lecture to ask the parent to remove his or her child from the room.


Self-Publishing or Academic Publishing (on Springer) for Mathematics books?

The problem with self publishing with Amazon or otherwise is that no one will be able to find your book unless there are some special circumstances. I've done this as well as published with large publishers, including Springer.
If you are incredibly well known in your field and have a valuable web presence and anyone who might want to find your book can find you, then it can work and you can get a lot of sales and retain more of the revenue. But otherwise the book will just get lost in the millions of others. Publishers actually, take some effort to advertise and promote the books they publish, but it is much harder for you to do so, since people know about Springer, but maybe not about Joe Doakes and what he does.
For text-book material, the big companies will travel to book exhibits at conferences that educators might attend and give their (your) materials some visibility. They might also help you attend and meet some of your potential audience. But for professional works there is less opportunity for that.
The down side of the big publishers is that they can be abusive in some ways and I found that their promotions of books was very time limited. Two years. If you had a popular book they will want a new edition in two years. If it isn't popular, then it will just disappear.
But one valuable service of the big publishers is that they can help you a lot with copyediting and such. It is very hard, I find to edit one's own work. When you read, what you "see" is what you thought you wrote, not what you actually wrote. You can pay people for this, but they need to be math "aware" for it to work out.
A minor issue, perhaps, depending on your material, is that the big outfits are likely to use better materials, such as acid-free paper, than what the in-house Amazon system does. The same is true for the quality of bindings.

I'm working a bit on a math book myself. But it is a labor of love, when I can find the energy. But I expect exactly zero sales. Mathematicians are a weird lot, I guess.


Should I respond to editors about unprofessional review?

Frustrating as it is, this is something that happens to many authors at some point, and the simplest solution is to shrug and move on.  The editor probably already knows that the review is sub-par, and has decided to move on anyway.  Arguing with the editor at this point is not just attacking the reviewer, it's attacking the editor's professional knowledge and judgement.  It's not impossible to have a good outcome from responding, but it's unlikely.  Even if you do get a positive response, the editor would simply send it out to a new set of reviewers, so even the best-case scenario has you starting all over anyway.  Find a new journal and send it there.

That's assuming that the review is genuinely completely useless.  From your description, I'm not convinced.  The reviewer may be wrong, but it doesn't sound as if their process is completely wrong; there is a specific reason for the rejection, it is based on something in your paper, and the fact that there is empirical support doesn't seem like a strong argument in your favor. Before you resubmit to another journal, you should seriously consider how to deal with that issue.


Is it possible to get into Psychology research after a PhD in HCI (human computer interaction)?

I've met people who were Computer Science PhDs and actually were part of Psychology departments.

If you did HCI, I think it gets harder to do Psychology, after all is a whole study area by itself, since yours was more specific.

My advice would be to find a laboratory that has both of them, and that way you can get involved in some projects so you can learn other things about psychology

I do not presume to know about the filed, but I'm guessing there are multiple laboratories that might have a psychologist as well as a computer scientists.

Essentially, build up your creed as a Psychologist by going somewhere where there is interaction between the two fields.


Google Scholar: How to search by author's email?

See my answer to a related question here. Basically, Google (and seemingly also Google Scholar) appears to strip the at sign from the search query.

Unfortunately, I think this means Google Scholar is the wrong tool for this kind of search. Some of the better paywalled databases (such as Web of Science or Scopus) allow filtering by affiliation. You can check with your university librarians what resources you have access to.


Why and how commonly are scientists concerned about open peer review?

This answer discusses a survey that indicates blind reviews are much preferred to open ones.  The main reason, from that answer, seems to be

Many people don't want to review non-anonymously.  I know many people on both sides of the fence on this issue.  Once concern is that authors are often sensitive to criticism and may harbor ill-feelings against a person who gives an unfavorable review (especially if the reviewers have not properly understood the paper).  Consequently, open reviewers may be biased (more so than blind reviewers) to colleagues they respect or want a good relationship with.

Fomite mentions a couple of other issues, but I see this as the main one (and it seems the survey does too).  Some other potential issues are

Certain "rivals" or "critics" can try to ruin your career by giving unfairly harsh reviews.
Some well-respect person could make a comment based on a cursory read of the paper that ends up heavily influencing the reviews, and maybe no one reads the paper carefully enough.


Are university counseling services usually able to help with the professional troubles that PhD students face?

In general, university counseling should be aware of how to deal with PhD student affairs as well as undergraduate issues. (Perhaps different staff or the two groups, perhaps not.) However, I'll focus on the "if they don't" part of your question.

There is usually a graduate "officer" in most departments, who is tasked with making sure that graduate students complete the requirements of their studies, and that departmental regulations and policies are being followed. This officer should be the first person to talk to if something goes wrong, and the problem can't be resolved between the parties directly.

Beyond that, the members of the thesis committee have an obligation to intervene in the case of severe conflicts that could disrupt the program. Ultimately, though, the chair of the department would be the last "internal" stop before you would have to go to the university-level administration (the office of the dean of graduate students, or a similar position).

If you are looking for advice from fellow students, perhaps you can get information from the student committee that is present in most departments.


How do I politely tell a student to take a shower?

Normally my advice would be identical to Buffy’s, to simply talk to the student. At least, I would have liked to think that we live in a world where that would be the correct, and obvious, answer to the question. However, the reality is that in today’s culture there is a great deal of sensitivity about certain topics, such that when a college instructor makes a comment to a student about those topics, the result may be unpredictable.* This is particularly true in matters relating to personal appearance and behavior, even more so when other factors like gender, race, mental health, disability status and perhaps other things get dragged into the discussion (which may end up happening whether or not you think it ought to), and even more so when the parties involved are of unknown temperament, sound like they may not be the most sensible people around, and cannot be counted on to react in a reasonable fashion even to the most benign and well-intentioned of approaches.

Considering all that, given your situation I should think that it would be a trivial matter to go to your department’s staff and/or faculty administrators such as the vice-chair or chair, and ask for suggestions how to proceed. Make it clear to them that the situation is untenable and that the student’s hygiene problem is impinging on your other students’ rights to benefit from a physically safe and healthy educational environment while attending your class, so that you feel that some action must be taken. And do not worry about being a busybody or wasting their time - this is indeed a tricky situation and it is perfectly reasonable even for a very experienced instructor to wonder how to respond and seek advice.

Finally, if your administrators suggest that you talk to the student — which is after all the obvious, and probably necessary, solution — well, then, at least you will be able to say that you followed the advice of officialdom rather than strangers on the internet, should your friendly suggestion to the student end up being ill-received.

*
Many discussions right here on academia.se, among other things, have opened my eyes to this reality - one memorable one involved an instructor wondering how to respond to a female student coming to class in a bikini top, if I remember correctly. I remember being rather taken aback by the diversity of opinions on what should be done in such a scenario, as well as by the judgmental tone of some of those opinions.


Is alumni success a valid parameter for selecting a group?

It is a valid parameter, but not the only valid parameter. It's absolutely justified to ask, and consider, "Where did people in this group go when they were done?"

  I haven't noticed MS alumni getting into top PhD programs. Does this say anything about the group's quality or could it be just because of the students?

You need more information than just "did they get into top PhD programs" - unless a research group is very large, it's likely that any patterns you see in the fates of MS students will be the result of stochasticity. For example:

Are they ending up in private industry? For many people, this isn't a failure, but a success. A group I was in sends many of it's graduate students onward to jobs, and this is considered a success by all involved. Masters programs are not just one step in a PhD conveyor belt. The same is true for "R1 Tenure Track Positions" etc. Many people don't end up taking what is conventionally considered the "brass ring" of their track because they don't actually want to.
Did they want to go to a top tier program and couldn't, or did they not want to? These are two very different things, and will be easier to assess by talking to members of the group, rather than just browsing their alumni page.
Is their alumni page actually accurate? Don't ever assume academic web pages are fully up to date.

It's a valid parameter consider when weighing choices, but I believe it would be a bad idea to eliminate a potential option simply because of their alumni page. You should also look at individuals. Where did the people who presented those important papers end up? Is there someone "like you" who had the trajectory you did? If not, it's worth talking to them about.


Graduate studies (phD & Masters) after a double degree

TLDR -- Yes.

Long answer -- A Ph.D. in Math is possible for a student who has double majored in Math and CS. A double major (at least in North America) consists of almost all the courses for both degrees. Taking some CS courses in undergrad is a good idea anyways for most math career paths.

With that said, Alexandros is right to point out that this is a bit premature. High school (and early undergraduate) math bears little if any resemblance to the math that a Ph.D. requires.


Submitting to a different journal after "Major Revisions"

Law is concerned with the actions; ethics is defined by the reasons and motivations behind those actions.

Unethical: Dr X employs an original method to improve his publications. Instead of spending a lot of time on literature review, improvement of his arguments and proofreading the manuscript, he simply prepares a first unpolished draft and sends it to a mediocre journal. The journals asks two or three experts to peer-review the paper; they voluntary spend their time to read Dr X's manuscript, spot the problems and suggest the ways to improve it. Dr X's collects the feedback, uses (some of) it to improve the paper, and sends the manuscript to a better journal. After a few iterations, the paper is accepted in a high-rank journal. Dr X is listed as the author, although the work is largely done by his anonymous peers.
Ethical: Dr Y has spent a lot of time on her experiments and manuscript, before sending it to a journal. She is a bit shy and she chose a mediocre journal because she was not sure that her work deserves to be published in a better one. Two of three reviewers responses are very positive; one reviewer clearly did not understood the paper and requested a lot of major changes. These changes are unlikely to improve the paper; the reviewer simply requires to compare Dr Y's method with his own weak results from far far ago to get fresh citations. The editor takes the reviewer's point and requests the major review. Dr Y performed the comparison, but it is clear that there is no academic benefit in publishing it - the reviewer's method is clearly outdated. Dr Y decided not to include this comparison in her manuscript and sends it to another journal.


Formalize the problem and identify any trivial cases.
Figure out where a result similar to your idea would be published and try to find it. Have a list of the places that you looked and where you didn't find your result. This will allow you to tell your professor something along the lines of "Professor, I checked ...noteworthy journals in your exact area... as well as ...famous textbooks in the area of study... And I didn't find this result."
Know why your idea is intuitively correct. Try to find counterexamples.
Outline your plan of action.
Be able to tell your professor why you want to work with him/her. Is it because you two work well together or because he/she is a major person in the field?
Bonus: State why your result would be (or could be) meaningful.


What to reply to your former supervisor that wrote that your paper "isn't worth much" before submission to a journal?

In the last months, I wrote a paper about an aspect of my thesis, with
  the collaboration of my former supervisor.

That means that the paper is not 100% yours. Do not add or remove co-authors on the basis if you like them or hate their guts.

  Having the paper accepted in this special section may be the best
  thing that could ever happen to our our paper

Sounds like excellent advice. Special issues are more focused, have shorter response rates and usually easier acceptance for more focused papers.

  Writing this request to the editors may cause a lot of problems"

Also excellent advice. You want to contact the editors to do the review of your paper sooner just for you? This is simply stupid.

  should focus on how to improve the paper, instead of inventing new
  ways to create problems

You have four months to improve the paper. Are you sure that it cannot be improved? Are you afraid that your competitors might publish sooner? If yes, submitting to the journal now, will not save you anyway. Could you not upload on arxiv? You should also discuss this with your advisor.

Conclusively, cool down. As a PHD graduate and not a student anymore, you must behave always as a professional. Perhaps your paper is not that great (perhaps it is). That is not an insult - it is the sincere scientific opinion of one of your more senior peers (who contributed to your success). Do not burn bridges with your supervisor, just because he expressed his honest opinion (even if you do not agree with that).


How important is the keyword section in a paper

The number of keywords you should use depends on the journal you will submit your paper to. They usually require 3 to 5 keywords so they can direct the paper to relevant reviewers and editor.

It also makes it easier to get recognition since search engines utilizes keywords instead of scanning whole papers.

In short: No, you definitely should not ignore it. You should write down related keywords but do not exceed the number of journal.

Additionally each journal has a "Author's Guideline" documentation. If a submission fails to meet these guidelines, your paper is most likely to be rejected even before evaluation.


Authorship Dispute: Soft threats from funders to cancel project unless they are listed as coauthors

Moo You need to get a new job, and you need to submit this work for publication the second that these people no longer have any power over you. It sounds like they have copies of all of your things, which unfortunately means that if you just leave and don’t do anything you could wind up with them publishing your paper(s).

If they don’t have the ability to publish your work, you have more flexibility. I have no idea what your professional situation is like or if your work is time-sensitive, but you do have the serious option of delaying publication until you’re further away from them. There are pros and cons to each option, it’s pretty context dependent, but if you can take the hit for not publishing, letting the paper languish they might drop it. On the other hand racing and publishing it without them might make them give up. It depends on the psychology of the handlers, but if you can guess the lengths they’re willing to go, you might able to get out of the situation without having an authorial dispute. Both choices could also lead to further conflict: either ten hounding you about it indefinitely when you don’t publish the paper or them contacting the journal and trying to formally dispute the paper.

Your main goal for an authorship dispute should be to get as many walls between you and the handlers as you can. Straight up don’t talk to them as much as you can. They’re already in violation of their own policies and of the EU University policies (it sounds like there’s a partnership between the non-profit and the EU University), which is a great start. Contact the ethics office at the EU University and explain the situation, including providing any documentation that you have of what work they did or did not do. From then on, you can forward any angry emails to the person in the ethics office working with you. If the non-profit has an ethics office, then you can use them for this purpose too. You should also talk to the ethics office at your university and feel out how receptive they would be to helping you out. This kind of filibustering is incredibly effective in all kinds of disputes.

However, the best wall you can put between you and these people is the journal itself. Submit your paper(s) to journals that have clearly defined authorship definitions, or even better require submissions to document authorial contributions. At the end of the day the journal is the final arbiter of who gets on the paper and who doesn’t.

Another option would be to fake conceding. Split the work up into multiple papers and divided it such that the stuff they’re claiming they touched is all in one paper and the core concepts are all in the other. It’s easy enough for the joint paper to languish in revisions while your other paper gets published. How effective this is can wildly change depending on the exact circumstances though.


The title "Dean" is by no means restricted to the leader of a faculty (or college, or other similar unit). For instance, most US universities have a "Dean of Students" who is responsible for student services, discipline, etc. Some have a "Dean of Residential Life" who runs the dorms. My alma mater had a "Dean of Student Activities", popularly known as the "Dean of Fun".