Rule #1: Always try to pin these types of things down before performing the work.
Rule #2: Understand that academia (graduate school) is run on an implicit pecking order:

Departmental pressures and requirements > Advisor > PhD Student > Master's Student

This makes complying to Rule #1 very difficult in practice. Every early career researcher runs into the issue you have described in some form. (Not that this makes such practices right). People higher than you in the pecking order will use administrative leverage to get what they want.

Advisor: "I am the first author on this paper." (And if you disagree, you'll have to find a new advisor and lose a year's worth of work).
Department: "Give Professor Smith what she wants or we will not sign off on your degree."
PhD Student: "Collect this data for me. (And then try to convince someone that you actually did the work and not me)."

The order of attribution should be based on the order of contribution in most CS-based fields. Equal contributions are noted by alphabetical order of the authors' surnames, sometimes with a footnote indicating equal contribution.
I would bring the issue up first with the PhD student directly. I would then speak with his/her advisor. The advisor is essentially the court of last resort. An advisor also will be able to help with the navigation of what actually constitutes authorship for each party. At the very least, your own advisor should (hopefully) be able to help you obtain credit for your work in the form of a chapter in your thesis or something.
Going forward, I would be firm in establishing what the authorship expectations will be on any work you do. You will at times be forced to balance fairness in authorship and expediency in obtaining your degree.
I will note that I take the pecking order things into account when I interview applicants for a job. I care much less about author order and much more about what the person actually did for the paper. Thus, if the OP applied to a job with me, I would likely give his research the same weight whether he was first or second author. I fully understand that superiors sometimes take advantage of their underlings.


What to do about a proposed research idea during the waiting period after submitting a grant proposal?

Start the work if you can.  Acknowledge the grant if you get it.

If you don't have the necessary resources to start the proposed research without the new grant, the only thing you can do is wait for the new grant.  Yes, your idea could become obsolete after six months; in fact, your might already be obsolete.  Nothing you can do about that.  Let it go.

If you do have the necessary resources to start the proposed research without the new grant, go right ahead.  (Those necessary resources definitely include your time and expertise; they might also include specialized equipment, money for research assistants, money for publication costs, money for travel, ethics board approval, and/or other things I didn't think of.)

But while you're waiting for the grant decision, remember that developing a research idea into a publication also takes several months.  You have to do the actual research; you have to write the paper; the paper has to be reviewed and edited.  All of these steps take significant time.

If you can get a paper all the way to print before the proposal decision, you don't need to acknowledge the new grant, because it doesn't exist yet.  But this seems rather unlikely; any idea that you can get to publication in only a few months is a weak basis for a grant proposal.

On the other hand, if the grant comes in before your paper is actually published, pat yourself on the back and then acknowledge the grant.  Even if you are already revising the galley proofs.  ("Research by this author is partially supported by XXX under grant ZZZ.")  You have nothing to lose by being generous to the funding agency.


Professor behaving oddly, but I don't want to persecute him

Without going into legal definitions of what this is exactly, the bottom line is:

This is inappropriate, discriminatory behavior, and you shouldn’t put up with it.

It seems like you’ve already done your best to politely stop these kinds of comments with no success. The fact that you documented everything is really great. You should approach student affairs/ombudsman/Graduate studies division and report this. Keep a record of the report.

I’m willing to bet that you’re not the first student that encountered this behavior. One could hope that you’ll be the last if you report him.

I want to tell you that your school will make sure that your grades won’t suffer and that the outcome will be that the professor will face disciplinary action. In cases like this it’s unfortunately not always the case. Even more severe cases (eg outright sexual assault) have been covered up by university officials because of their bad press repercussions. I hope your university will do better.

I’m sorry this happened...


Question about listing postdoc on NSF biosketch

Why not just contact the division rep to see if you can update the application, or if it is necessary? Obviously there will be a discrepancy among your CV and your application professional appointments sections. If this exists and a reviewer sees this error of omission, it may (sub-)consciously bias their review.

Call one of the reps, I bet they're lonely in their D.C. office and would love to hear that phone ring XD. Rep names and ph are listed on the section webpages (e.g., there are two for Biology).

Perhaps there is a way to request edit/update or add comments to the application in FastLane (although you probably already tried this...)?


Contact a professor to agree a research proposal for a post doc position that he is advertising

A postdoc application process is not a competition to find which person can magically understand the PI's objectives, it is there to find the best fit for the job. On the other hand, a postdoc is the start of independent research. You should devise your own research agenda(s) and ask questions about the suitability of your ideas to get a better feel for the project.

In my direct experience and experience of people in a similar position, it is entirely normal to ask questions about the position beforehand. Have a look at the advertisement, it may even explicitly mention to email any questions. My recommendation is to email the PI with a very short description of yourself (research area, where you got your PhD from, etc.) and very short questions. If - this - job is not suitable, the PI may even have you in mind for something else.

In my case I emailed asking if there was scope to do X (there was) for a job in an entirely new field, it is the best position I've ever applied for and I wouldn't have if I had not known it was possible.


What does it mean if my advisor decides to remove his name from a paper we co-authored?

Please ask your advisor politely. There can be numerous reasons he wanted to have his name removed:

The quality of your work is too bad and the paper might affect his reputation. I do not believe that this is the case. You worked together on the paper for the first submission where he agreed to be on author list. Why should he remove his name when there is better content, now?
No right of authorship: He may know that all of the work was done by you and he has too little contribution to the paper. So he is friendly by declining authorship of your work. This might be quite likely, at least this has happened for me. However, if this is the case, consider including him in the acknowledgements.
He wants you to become more independent. You may have worked rather closely on the first paper but now he wants you to take the lead and do most work on your own. This may be due to a limit of time on his side.

All in all, just ask him, you need this answer/feedback to continue your work.


How to obtain a copy of my own article from an APS (American Physical Society) journal?

You could ask the journal editor directly to send a copy of your publication. I will help to clearly summarise your situation. This will be something they encounter on a regular basis and if the editor replies with a strict "no", you can still ask a colleague for the download. It is your work, so the editor will likely be understanding. Hope this helps!


I think this is very unlikely, but it would depend on the educational resources that you have access to. If you have a local university you should talk to them and maybe to one or two faculty members there as well as the department head. I assume that your relocation options are currently limited, so that is where to start. If you have a lot to contribute they may make something possible, but expect it to take a long time. But it will likely require a formal relationship.

On the other hand, there are places at which the on-site requirements are short term. You might have to spend weekends (or one or two a month, at least) at a university remote from you. Such programs aren't part-time, however. It is just that most of the work, even team work, is done remotely. This might be a better option for you, though the travel costs (time and money) might not be small. They can also be just as intense as a residential program.

Some of these programs, while they are doctorates, may not be PhD programs, though. They may require the same level of research or not. They may or may not be suitable as the basis of an Academic career. They may be intended as more practical/applications based than theory based.

An online search might turn up something that interests you.

However, if you seek a career in Academia in the US, you almost certainly need a doctorate that the NSF recognizes as a Research Doctorate. Anything that isn't may get you a job initially, depending on the market, but you will very possibly run in to trouble when it comes time to apply for tenure.


Typical turn around time to write recommendation?

It is insane if they only gave you 3 business days to respond, particularly if they didn't tell you, but even if they had.  I don't check all my inboxes every day!  Normally I'm given a few weeks, and the deadline is in the email requesting the reference.  If there's no deadline, I write immediately something like:

"This is one of my former students and I can say off the cuff that you should probably hire them, they were great with me.  But I've got a lot of writing deadlines on my plate at the moment.  When exactly do you need a formal reference by?"

They can then respond saying:

that's enough, we just wanted to be sure you knew who this person was, thanks!
the actual deadline.
asking to phone you because they need advice quickly and are very sorry to disturb you etc.

I've had all those responses.

I would be suspicious in the case you describe that there may have been discriminatory hiring, e.g. of an internal candidate.  You may want to let your referee know that this is not normal.  Lawsuits are seldom worth the time, but I hate to ignore unfair hiring practices, and do at least try to scare firms when I think I might have seen one.  On the other hand, your referee may have known there was a fast turn around needed and forgotten to tell you.  But the HR office really should have told you.


Are PhD supervisors responsible for informing students about legal issues pertaining to research?

Good research practice (which I would argue is not country specific), requires an independent ethical review of any research that involves human subjects. A university can make blanket determinations that certain types of research do not require individual review (e.g., interviews).

It is generally considered academic/research misconduct to not have proper ethical review and follow the recommended guidelines. Failure to obtain informed consent, when necessary, definitely falls under research misconduct. In the US and UK, it is the responsibility of the supervisor to make sure that the proper procedures are being followed.

In your case, your supervisor should have told you to get informed consent. The problem, however, sounds way bigger then you just not being able to use the data. The problem could be as large as PhD students not being properly trained regarding human subject research and faculty not following good research practice.

You need to work this out with your supervisor quickly. It should eventually escalate to your department chair and the IRB/ethics board. Not getting informed consent, when needed, is a huge deal.


Avoiding Working with a Potentially Arrogant Researcher

Dismissal of previous research in the field is not problematic in itself. As you concede in the question, you may even share this assessment. The possible problem, which you can't really assess from one general comment like this, is whether the researcher lets that opinion drive his research in inappropriate ways. I'd say that's a question of emotional maturity. Does this person need to be right where everybody else is wrong, in order to feel fulfilled or successful? That would be a big problem. But, being overly risk-averse, and "going with the flow" too much, could also be a problem. In science, the main thing is to look at evidence dispassionately, and draw conclusions based on the scientific method. Any character trait or emotional immaturity can threaten one's ability to do that.

TL;DR: It's not a problem in itself, but it could lead you toward some worthwhile inquiry. Focus on the person's ability to manage their strong opinions or emotional dispositions and integrate them into appropriate scientific techniques, not so much on the specifics of what those opinions or emotional dispositions are.


How free are you to take mathematics courses as a computer science graduate student?

This is frequently very easy: the boundary between mathematics and computer science is pretty blurry, especially for the more theoretical side of computer science.  In many universities, you will even find classes that are shared between math and computer science departments.

I suppose that If you are a masters' student, you might run into problems fitting in the classes that you want to take if there are a lot of other program requirements.  For Ph.D. students, however, there are typically less constraints.


Authors' contributions statement to highlight contribution of an undergraduate student

In mathematics, the default assumption is that all authors contributed more or less equally to a project, so the main reason I see to describe individual author's contributions in a mathematics paper is that the authors want to attribute credit of certain aspects of the paper to individual authors.  (This can also be done with appendices by subsets of coauthors.)

It does not make particular sense to me to highlight someone's contributions just because they are a student. You are free to do so if you wish, but it will be weird if you only describe one of the authors' contributions.

  To avoid opposition from coauthors who may question listing a student as an author.

This is completely ridiculous.  I have never heard of any co-author complaining that someone should not be listed as a co-author just because they are a student.


What is the downside of not pursuing postdoctoral fellowship position?

The purpose of a postdoctoral fellowship is simply to gain the skills detailed in this answer to a similar question, notably:

Get involved with obtaining funding
Build an international reputation
Start collaborating with external parties
Learn how to manage projects and a lab
Start to devise a strategic research plan
Improve your publication record

If you have all those things from your work as a graduate student, then you should have no problem finding employment and furthering your academic career immediately after you earn your PhD. Most students don't, which is why they try to find a postdoc position to help them  gain these skills before attempting to run their own lab.


Thesis: what is the difference between discussion and conclusion?

Can someone supply a more descriptive or formal definition?

There isn't a common definition. Furthermore, how you're supposed to define formally a humans' texts.

  Is this right?

It depends on a field, country, journal, etc.... I'll give a more general and brief explanation.

Discussion unrolls the main results, explain their meanings. Put there the new questions and perspectives, describe the most interesting points for the entire field. Define the possible answers, write down why and how and what for, your suggestions.

Conclusion is a summary of the discussion or the whole work. You can put there the main points and results, their factual meaning for the field and a possible further direction. I like to describe this as "discussion's points and facts without the discussion."


Is it reasonable to cite published computational results rather than reproduce them yourself?

I treat computational results as in silico experiments. They have been published in a peer-reviewed journal, so I trust them by default, unless I have a reason not to. I cite them without a need to recompute them.
Sometimes, I have a reason to doubt them: they don't match my intuition, or they don't match my own results in a related case; they seem incoherent; they don't match experimental data; etc. Then, I redo them, possibly in more than one way (different software, try checking the effect of some of the assumptions, etc.). If I learn something from it, I consider publishing this study.


Can I only submit my graduate transcript for a second-master/PhD application?

The general answer to this question is no, your undergraduate transcript is required as well.

The reason is that for master's degree programs where coursework dominates, undergraduate success is usually a good predictor of graduate success. While for PhD admissions, they don't have as much predictive value (since PhDs are about research, not classwork), it is still important to have a baseline for judgment.

In addition, the schools will want to check if you have the necessary prerequisites to undertake PhD studies. This usually requires your undergraduate transcript.


How many US institutions use letter-grades without + or - indications for GPA?

There is quite a lot of variation. Some don't even use 4.0 as the top. In some places the grade assigned is a letter grade, not a number. The numeric conversion, then, doesn't involve rounding. It is just the number equivalent to the letter. The numbers are used to compute overall GPA, but do not relate to numeric grades in and individual course. Some courses (mine) have numbers between 0 and 1000, with letter grades defined by a table, but the university only sees the letter grade.

Other places the grade assigned might be a number such as 3.67, though I think this is fairly rare in the US.

Plus and minus grades is a fairly recent refinement (50 years??). One university  in my past had problems when they started to give A+ grades since graduate schools then considered the place to have a 4.5 scale, not 4.0. This effectively downgraded gradates with "perfect A grades". The had to rethink the system in a hurry.

But to find out which for some set of universities you need to do the research. Contact the registrar's office if you want the true picture.

And some parts of your question suggest that you are confusing an individual course grade with an average over several courses, each weighted differently. The weights come from the "credit hours" assigned to the course. Thus a course that meets five hours a week might be "worth" 5 credit hours and an A there contributes 20 "quality points" toward the GPA. A course meeting one hour a week would "count" less toward the GPA.

I took a writing course once in which the prof defined his grades thus:

An "A" on a writing assignment means that it is written as well as it can be written. A "B" was assigned if it was written as well as any college student could expected to write it. Etc. I forget the rest. The course was 3 credits so an A gave you 12 points toward your GPA, since the conversion was the typical A = 4.0.

Add up the "quality points" and divide by the number of credit hours completed to get the GPA. But there was no "average" in a given course. Just a grade.

If I had to guess, I'd suggest that more places use plus and minus grades now than don't. Before ubiquitous use of computers it was harder to have a more nuanced system, but now, the prof just needs to check a box for each student and the computer takes it from there. And some older, more conservative university systems want to stick with tradition. Why change what ain't broke? So, if you got your degree from CMU in 1960 and your grandkid did in 2015, your grades are on the same scale. Nominally, at least.


What would be a good approach to make sure my advisor goes through all the report?

I would strongly recommend against putting a "trick" sentence into a report, because it looks immature and unprofessional. Remember that your advisor is someone who may be writing recommendation letters for you in the future, or helping you find a job. You want to leave a positive impression on him, and you do not want to appear ungrateful for the time and energy he has invested in you so far (even if you wish he would invest more). That can only backfire on you.

You wrote in a comment that your major concern is,

  his all focus is on writing and he never gives me feedback on the main content, which is the primary thing to validate

As a general rule, a good way to get more useful feedback from someone who is very busy is to focus their attention on the specific points you are uncertain about.

For example, when giving your advisor something to read, you can ask him specifically:

I'm not sure about the way I motivated the problem. Can you suggest any changes to that section?
Do you think the assumptions I make at the beginning of Section II are reasonable? Did I do a good job of justifying them?
I'm not completely sure if the results strictly support what I wrote in last paragraph of the Discussion section, what do you think?

By directing your advisor towards your specific questions, you are likely to get much better feedback. (Almost certainly much better than you would get with a passive aggressive approach like putting "trick" sentences into your draft.)

This approach also means that you are taking responsibility for identifying and trying to correct your own weaknesses, which is a very good quality in a student.

Also: if he suggests corrections to the writing of the paper, fix the writing of the paper. Then come back and ask him to read it again, and offer feedback on the contents. Sometimes when the quality of writing in a paper is poor, it becomes very difficult to extract the technical content. It's reasonable for an advisor to ask a student to make a paper readable (by fixing writing issues) before the advisor reads it more thoroughly.


Is it usual for finished PhD students to send out physical copies of their thesis to unknown persons?

This is not uncommon in the country where I did my PhD (the Netherlands). There you have to print a reasonably large amount of hardcopies anyway, typically people get around 200-300 copies in my field. It is not uncommon to send some copies to researchers that you genuinely believe may be interested in the work, usually people that you have been in contact with before, or are in contact with your advisor.

The cost of the thesis printing and mailing is generally reimbursed by the university (of course, all within reasonable limits). In countries where printing the thesis is not so common, I can imagine that the practice of mailing around copies is not common.


Drawing Lines when Giving Ideas to Undergraduate Students

The purpose of teaching, which includes both your lectures, later guidance on their projects and also includes evaluation, is for them to learn new skills. So, the question you should ask yourself is: what skills do I want them to learn, and how do I achieve that best?

Typically, it seems to me that (if you have enough time for it), it is very important to teach them not only to read, filter and digest information, but also to search for it (Information Age and all). So, you might want to make “searching for relevant information” a required skill. But that doesn't mean you should help them acquire it. In fact, you probably should:

advertise it as an important part of what they are expected to learn
help them learn it, i.e. show them how it's done
evaluate them based on their performance

However… even if you do all that, it still doesn't mean you can't help them if they miss something. After all, if you are teaching them how to best look for information, they might realize it's a good idea to come to the expert they know in that particular field… you, their teacher. So, maybe they will come asking

  here are the relevant events I found about X in the archives… do you think I missed something?

or even:

  I see a spike in the data around the fall of 1974, and I have searched but couldn't find any event possibly related to that company, do you know of anything that might explain it?

in which cases you might want to answer them, if it seems they did their due diligence.


Sounds like Applied Math.  In terms of a specific PI doing quantum information*, I don't know which school.  But when you mention your course interests and wanting to collaborate with people on real problems that is applied math all the way.

Here is a list of top programs:  https://www.usnews.com/best-graduate-schools/top-science-schools/applied-mathematics-rankings  Not passing judgment, but list gets you started.  I would look at some of their webpages and reach out via email to one or tow and just start educating yourself on what they're like versus what you want.  Maybe do a visit if one near.

You could also consider statistics grad programs.  That is a wonderfully applied field and one where there is some connection to industry, the sciences, etc.

*Music on CDs as opposed to vinyl?


How to figure out timing for working on and submitting independent research?

I can not give you a fully fledged answer at all, but some things to take into consideration:

Where do you want to place your article? This determines the amount of time you will have to spend on it. This has to be in-line with your idea about being short on papers (because it might not help the issue if noone reads the journal).
I personally would find it a tad rude to publish alone, if the idea has spawned from something connected to your work for your insitute (and might also not be allowed depending on your contract).
If you are not pleased with option 1 with respect to your ideas about the paper's benefit for you I would go with 3. You could also think about finding a PostDoc position which includes the work on this subject. If you do this intelligently, you could also use this as a selling point for yourself. Ideally this also would be the general idea of a perfect PostDoc position, allowing to develop your own ideas and research. You could try doing so with a research stipend while going abroad.


How can I get involved with applying my expertise in a specific subject?

In academia, the best way is to attend research seminars in the fields that interest you and connect with people in there. If there are other universities/institutions in your area, you should start doing that. (Hopefully this will become possible in the Fall, but perhaps zoom options may provide even more opportunities?)
Another (much more expensive) way is to attend professional conferences. Most active researches to that, so you'd be able to make some connections.


Should I send a letter of recommendation directly to a student?

In general, this is a generous thing to do, if you are comfortable with the student.  I would make sure to ask what school/program it is being sent to, and then you can double check (and decline if it's fishy). You can ask this question without acting suspicious, just say you want to tailor the letter for the position.

I have had to include my letters for a few postdoctoral positions I applied for (in Italy and Croatia), and I cannot be more grateful for the fact that I had some senior researchers who were willing to send the letter directly to me so I could include it with my application materials.


You certainly can publish without an official affiliation. One of the advantages of the anonymous peer-reviewing is that reviewers should be concerned only about the content; Not the author information. Even if it's not an anonymous submission, your name and affiliation should have nothing to do with the quality of your submission.

I have seen affiliations like this:

Author Name
Independent Researcher
author email.

Some even with only the name and email address.


CV heading to include participation in scientific/organization commitees?

"Service" activities are usually listed under a heading such as "Professional Service" or "Professional Activities." However, this does not apply to simply attending or presenting at conferences and workshops, but rather to organizing or scientific committees.


How to write a objectives section in undergraduate thesis?

There is a difference between what you intend to do and what you hope to achieve or learn. The doing part is about the procedure you expect to follow.  The objectives part is about what you hope to achieve or learn from it.


How to develop your own argument in a literature review?

Damien Igoe's answer is very accurate, however, I would add that I think it is possible to interpret what someone wrote in a different way than others have previously interpreted. However, your arguments should not be confused with the other authors' arguments.

Originality in analysis is often welcomed. However, originality in structure should be done very carefully. Common structures exist for a reason. In my field, it is common to switch between the reviewed author's points and your own:

  Jones (1991) claimed that the primary motivator for workers was public
  recognition while Smith (2004) believed that workers were more
  concerned with monetary compensation. I will show that both were
  correct by showing that workers really care most about their
  compensation being publicly higher than the average for their
  position.


What makes a didactically effective lecture?

Unless you put a lot of thought into your lectures, it's hard to adopt the mindset of a student who knows much less than you.  You may take certain concepts for granted, and you've long forgotten how you learned them, or what originally confused you.  At the time you learned them you were probably much more well-prepared than the average student, so common stumbling blocks for students were never issues for you.

This means there are a lot of professors who are good at giving talks (to people well-versed in their field), but poor at giving lectures (to people with little or no background).


How should I decline a referee request for the paper which I refereed before?

I recommend against declining. You've already refereed the paper once, which means you can referee the paper again much quicker than a fresh set of eyes can.

Instead, send your original comments back. If the authors have updated the paper, send an explanation of why it's still not publishable as well. Then write in the "confidential comments to editor" box that you've reviewed the paper before, you still recommend rejection, and your original comments are attached. The editors will know what to do.


Please carefully read your school’s policies concerning academic dishonesty before you do anything.  Follow those rules carefully so that the students won’t be able to get away with their cheating on appeal.  For example, at my school you’re expected to talk directly with the student to give them a chance to defend themself before you decide on a punishment, and you’re required to submit an official report which allows the school to decide on any larger sanctions.

I’d also recommend having a third party (e.g. course coordinator, director of undergrad studies, or TA) present for the conversation.  This makes it clear that it’s serious, makes me feel safer, and prevents the student from lying about the meeting.


What does this Elsevier revision report mean?

My reading is that the associate editor has rejected the article and it just has to be formalized by either the editorial staff or the editor-in-chief.

Prepare for an email with bad news :-(


Is there value in posting a video of my paper presentation online?

You need to be sure that you are allowed to record presentations—as one of the comments indicated, many conferences prohibit such behavior.

If you are allowed to do so, it's usually for personal purposes, and public postings may be limited.

On the other hand, it may be possible for you to create your own version of a "podcast" with the talk using screen capture software. You can talk through your slides in greater detail than is possible in a typical conference presentation.

That said, I don't think there will be a huge demand for such a presentation.


How to talk to a project advisor as an undergrad?

If you think your advisor made an error, then I would suggest you figure out how to prove he made an error. This is the first step to showing someone they've made an error without being ignorant or arrogant (the rest follows from general customs about politeness, but you absolutely must do this first bit. He supposes, presumably in good faith, that he proved something to you; the "burden of proof" that he's wrong now lies in your hands). Besides, this is a good exercise. Lots of things don't seem like they make sense until you yourself figure out how to make them make sense to you. This can be a lot of work. This act of "hacking" someone else's grand idea until it makes sense to me is how I spend most of my time. Thankfully this often leads to totally new ideas and directions that the first guy didn't see (or thought too trivial or obviously wrong to mention, yes that happens too...)

The problem is that, in very many fields, undergraduates are actually extremely frustrating to work with. They don't yet speak the language, or have the baseline knowledge that all of your colleagues share. But nonetheless, this person is not the ideal advisor if he lacks the patience to put up with a lot of questions -- this is absolutely normal behavior for an undergraduate advisee, totally to be expected and many advisors find the interactions quite rewarding!

On the other hand though, you have some hard questions to ask yourself. Basically, you say that you want to ask questions without sounding lazy, but you must be honest with yourself about whether or not you are in fact asking lazy questions. The research process (again, at least in fields I'm familiar with) is most emphatically not "do exactly what some famous guy told you to do." It generally involves painfully slogging through material that no one really understands and proving everything you think you know to yourself repeatedly, and then to others, and then occasionally having it pointed out that you made a really silly assumption, or that some obscure paper already solved everything you had set out for. Again, the point is to create new knowledge, and so you have to know your tools inside and out. In fact, if your advisor is explaining anything at all clearly and to your satisfaction, what he is explaining is, by definition, old knowledge.


Can I publish a research paper without notifying my supervisor (the corresponding author)?

No, you absolutely may not do this.  Every author must consent to the publication of an article.

If he finds out, he could have the journal withdraw the article.  They would typically publish a notice about this, which would effectively inform the whole world that you had done something unethical.  That is a potential career killer.  Additionally, a serious breach of academic ethics like this could cause you to be expelled from the university where you study.

Many journals do directly contact every listed author, to prevent this sort of situation.  (For instance, in many cases every author has to sign a copyright form.)  Others will ask the submitting author to certify that they have the consent of all other authors.


As a part time volunteer, how can I ask my advisor to let me work independently, so that I can have a chance at first authorship?

In general, you should explain to your advisor that you are really interested in taking the lead on a research project, and ask if there is any way you can do that in the scope of your role in the lab.

Some suggestions:

Have this conversation sooner, rather than later. It's easier to sort out before too much work has been done on the project.
Ask "What do I have to do to..." rather than "Can I...". As in, "What would I have to do to be able to be first author on a paper coming out of this project, or another project?", not "Can I be first author on this project?" (He may say something like "I think that to submit a paper by December, we'll need to put in around 60 total hours per week of work" - and then you may decide that you can't do that, but that second authorship and a great letter of recommendation is better than no paper. Or not.)
Don't assume that your solution - working independently - is the only one. For example, your professor might suggest that multiple papers are expected to come out of the project, each with a different focus, and you can "specialize" in a certain part of the project and be first author on the paper on that part, even while collaborating on the project as a whole. Be open to other suggestions.
Don't assume that you have the full picture. For example, this grad student may be working on the project with you for a few weeks just to get you started, or on the side while also pursuing another project. Etc.

Note that just like you have goals and want to put your time towards them as efficiently as possible, so does your supervisor. Supervising one student per project, especially when that one student is a temporary part-time student without much research experience,  may not be an efficient use of his time. (That doesn't mean he'd never agree to it; it does mean that you may have to be flexible about what kind of solutions you'll accept.)


Which is more important for PhD applicants — Quality or quantity of research papers?

I disagree with the assumption that top journals with slow turnaround times are more highly regarded than top conferences with quicker turnaround times.  In most (all?) areas of computer science, the most competitive conferences are at least as highly regarded as the top journals.  It is also not unusual for longer versions of conference papers to later be submitted to journals.

As David Patterson (UC Berkeley), Larry Snyder (University of Washington), and Jeffrey Ullman wrote in Evaluating Computer Scientists and Engineers For Promotion and Tenure:

  The evaluation of computer science and engineering faculty for
  promotion and tenure has generally followed the dictate "publish or
  perish," where "publish" has had its standard academic meaning of
  "publish in archival journals" [Academic Careers, 94]. Relying on
  journal publications as the sole demonstration of scholarly
  achievement, especially counting such publications to determine
  whether they exceed a prescribed threshold, ignores significant
  evidence of accomplishment in computer science and engineering. For
  example, conference publication is preferred in the field, and
  computational artifacts —software, chips, etc. —are a tangible means
  of conveying ideas and insight. Obligating faculty to be evaluated by
  this traditional standard handicaps their careers, and indirectly
  harms the field. This document describes appropriate evidence of
  academic achievement in computer science and engineering.

Your research advisor should be able to provide you advice more specific to your case.

I agree with amirg that having any publications when applying to a PhD program (especially based on undergraduate research) makes you exceptional.  Your advisor's recommendation also counts a lot, especially if he or she is well known.


How to start a startup based on university research?

This will heavily depend on the specific country you are talking about. We have a so-called Innovation Lab that aims at encouraging "entrepreneurship and innovation by identifying, supporting and providing guidance for potential high-tech startups and spin-off companies originating at TU/e." Specifically, they guide researchers along the entire process: from checking whether the idea can be patented to actually establishing a startup / spin-off company.

With respect to copyright: lion's share of our research is being published so there can be no problems for companies to use the ideas presented in scientific papers. Using unpublished results might be more tricky but I can imagine that the university will agree to formally keep copyright and allow the company to benefit from it under some restricted conditions.


Is it true that many people study psychology in university level originally for self-help reasons?

Even psychologists joke that we study what worries us. (I am one).

And that doesn't pass as we go through the ranks.  Our interest might move on though.

What does happen is that we are firmly told that speculating about 'cases', ours or anyone elses, is not what psychology is about.

Psychology is the -ology (study of) psyche (Greek word).  Psychologists are rigorously trained in research methods.  We are expected to be able to frame inquiries, conduct inquiries and evaluate inquiries.

As we go into the profession, we will learn other skills as well but we never leave that insistence on thinking methodically about the question we are asking and sticking to evidence.

Hope that helps!


Are journal papers really viewed as strictly inferior to conference papers in Theoretical Computer Science?

I understand that in CS, conferences are generally preferred to journals

I disagree: Conferences are preferred for earlier, smaller results, journals are preferred for more mature results. Journals can be considered more prestigious, given that journal articles are typically derived from earlier conference papers and are subjected to more scrutiny, e.g., multiple rounds of review (conference and journal reviewers) and discussion (after talks, for instance), and they've survived some test of time.

my advisor told me he would prefer to submit the paper to a journal...right away, rather than to a conference.

Your advisor is confident that the paper is already sufficiently mature and the typical conference-journal route isn't appropriate.

assuming that the CS theory paper gets in, would
I be disadvantaged during the grad school application process against
someone who has, say a SODA, paper?

I'd argue a journal article is superior. However, the turnaround time for a journal article is longer than a conference paper, so you might be in the position that your paper is under review, whereas a competing grad school applicant may have had their conference paper accepted. An article under review at a top journal is a good sign, but an accepted paper at a top conference is perhaps better for an evaluation committee - a bird in the hand is worth two in the bush.

Are journal papers really viewed as strictly inferior to conference papers?

I don't believe they are, but I don't think there's an absolute consensus.


Roadmap and possible pitfalls for a first-time software author to publish a paper on a Python package?

I published a paper on a Python package myself.

Finding a journal

My main recommendation is to start looking for a journal now, even before you start writing.
Unless journals in your particular subfield of choice is very open to software papers, there are likely only a few journals you can choose from and those may have special requirements.
These requirements may not be obvious and if you do not fulfil them on your first submission, you may not get a second chance, which in turn is particularly bad if alternative journals are scarce.
Depending on the requirements, you may need to write your paper completely differently.

I would proceed as follows:

Find a journal whose target audience are potential users of your software.
Does the journal clearly state that it accepts software papers?
If yes, do they clearly state the requirements for acceptance?
Are there any precedents of software papers in the journal?
If yes, is any of them comparable to what you are going to do?
Comparable here less refers to what the software does, but on how it is “sold” and what the paper does beyond software.
For example, it could be that a software paper only got accepted through featuring new algorithms and yours may be rejected because it doesn’t.
When in doubt, contact the journal briefly outlining what your paper would contain and ask them whether they would consider publishing a paper of this kind.

In my case, the journal had a clearly stated policy for software papers and there was an existing paper for a competing software.
Still, I encountered problems with one of the reviewers recommending to reject the paper on account of being a technical manual.

Consult field experts

Going by your question, you may not belong to the typical target audience of your software.
If that is the case, try to solicit assistance from somebody in the target audience (if you do not have one at hand anyway), as to what they consider important in your kind of software or what they think about features of your software.
You do not want to focus on a part of your software that the majority of your target audience doesn’t care about.

Also, by all means let somebody from the field who has not used your software review your manuscript before you submit.
(There is even less need to worry about plagiarism here since you probably already published your software it this point.)

Writing process

Getting inspiration

There are many variants of software papers.
I have seen some without any code (despite the software being a code library) and those with a lot.
If the previous did not yield any clear recommendation in this respect, look for well-received software papers and let them inspire you.
(Beware that a crappy software paper may be well cited because the software is popular despite the paper.)

Examples

Whether with code or not, you are likely to feature some examples.
These usually only belong in one of the following categories:

Didactic examples that demonstrate how your software works.
I found it very helpful to choose these with extreme care.

For example, for me it was pretty clear that I needed five didactic examples that could not possibly be combined, but each of which could be chosen from a wide selection of use cases.
I optimised some of these cases to be as simple as possible.
I chose the remaining ones to exemplify other things as a side effect, so I would not need separate examples for these.
(On the other hand, you do not want to leave the impression that everything is a special case requiring tricks.)

Do not blindly take the examples from your documentation, because these are aiming at readers who are familiar with Python, have your software installed, and can directly test things.
Also, your target audience in the journal is different.
For example, it also includes professors who have last programmed twenty years ago in Fortran, but who may make some supervisee use your software.
Importantly, the reviewers belong in this category.
For instance, in my paper I took care not to use any advanced, non self-explaining features of Python in my examples, unless absolutely necessary (and Python is rather benign in this respect).
Impressing examples that demonstrate that your software is capable of handling particularly difficult cases, e.g., ones that no software before could handle or that are considerably better in your software.
It may also be cases that show that your software can actually further science by doing facilitating novel results.
It strongly depends on your software and the journal whether you need this, to what extent, and what to optimise for.
Either way, again this example should be carefully chosen.
If you show code in your paper, you also want to make sure that the example is not overly long.

Selling your software

Make it very clear why people should use your software as opposed to an existing one or doing everything by hand.
Do not forget that usability may be a relevant feature.

This is also crucial for the review process: You have to convince the reviewers and journal that your software is something the readers have to read about.
If the journal does not require a significance statement upon submission, consider to volunteer one anyway.


If you were writing for a journal, you would want to check the journal's style guide. If it doesn't cover that issue, then the next step would be to check previous publications and see what the norm is.

For an internal report with no applicable style guide, one should write for the intended reader/s. If your advisor is going to be the main reader for this document, then write it in the style that he requests.

To me, this change seems unnecessary, but it may help to consider this story from the development of the computer game Battlechess:

  The producers of the game were known to demand changes to the game, presumably to make their mark on the finished product. To this end, one animator added a small duck around the queen piece, but made sure that the sprite would be easily removable. Come review, the producers, predictably, okayed everything but asked for the duck to be removed.

In my experience, this is a very broad tendency among managers/advisors, and now that I'm a manager myself I understand the temptation to micro-manage. Even if a document is quite good enough as-is, if we don't suggest changes we don't feel like we're doing our job.

It may be that your use of "we"s is the sacrificial "duck" shielding you from more annoying change requests.


My immediate reaction is to put them both on; It is not unusual to have two affiliations. I then mean to state "A and B" to show a shared affiliation. That way both departments could benefit from your publication. The question is then how to get the different departments to losen up their purses. In my system no such funding is typically given out by departments/university, one has to apply for money from different sources oneself. I could possibly convince my head to provide the money if the reason was particularly well deserving. So I cannot comment on how such support would be provided.

I would suggest communicationg with both univesities stating that you will publish the paper with them as an affiliation to see if anyone would provide funding. I would obviously put any funding source as my first affiliation afte the fact.

Finally, to get a request to put an extra name on the paper in order to get money sounds terrible, in fact unethical. It is of course easy to say that when you are not facing the situation so thumbs up for standing up to that behaviour.


Letter of Recommendation for Business Analystics from Satisfied Client

Would a reference like this be acceptable?

It would certainly complete your application and would likely be considered appropriate (though this is not my field and I cannot say for sure).

  How would this option compare to a third academic reference?

It really depends on who the client is. If you built a website for a non-technical person, then they really couldn't say much other than "they did a nice job, were professional, etc." This reference won't count for much.

On the other hand, if this person can say "I'm the CTO of a company and deal with dozens of contractors per year; this one is the best I've had and displayed specific skills X, Y, and Z, etc.", then I don't think anyone will care that this person is not an academic.


Can I perform psychological experiments at home and be taken seriously?

Publishing papers about psychology experiments does present an additional issue, human subject research ethics. A reputable journal is likely to require assurance that the rights and welfare of the research subjects were protected during the research.

If you were working or studying at a research university in many countries the university would have some provision for reviewing the ethics of planned research, and monitoring it in progress. US research universities each have an Institutional review board. A journal could rely on IRB approval to know that the research subjects were protected.

You need to find out how that is handled in your country, and make sure you are following procedures and getting reviews that will make your research acceptable for the journals in which you wish to publish. There are enough pitfalls in doing human, or even animal, experiments that one should really not attempt them without guidance.

Usually, a psychology researcher starts their research career as a graduate student with an academic advisor supervising them. They will learn how their supervisor, and other researchers, prepare and organize experiments. Their supervisor will guide them in selecting ethical experiments, getting informed consent, preparing paperwork for independent review, etc.


How do I identify predatory and low quality journals? With Beall's List gone, how can I tell if a journal is spam?

I heard about Beall's list several times on this site, but I'm amazed about its significance to some people.

When you start doing research, you need to know which papers are important in your field (your advisor or google scholar will tell you). Then you need to know who is the big shots, and not so big shots in your field. Then you need to know where those guys have published their papers (where your advisor published his/her papers).

Then follow the masters, submit to the conference/journal that they published. If it is a new conference/journal, you need to know some people in the PC members, editors.

If you know none of them, it's not a good idea to submit your paper. In the best case, they are not in your field. Even if you don't know them, you can check if they are from reputable university, if they have well-cited papers to become editors?

Another way is to check 5 papers published by this journal 5 years ago. If none of them has any citations, that journal is spam.

TL;DR: You don't need any list.


How to export and cite Google Ngram Viewer result?

I suggest you download this python script https://github.com/econpy/google-ngrams

This allows you to download a .csv file containing the data of your search. Then you can plot with your favourite program in your favourite format to be embedded into latex.

Concerning the .svg, it's perfect for latex, especially if you have Inkscape
https://tex.stackexchange.com/questions/151232/exporting-from-inkscape-to-latex-via-tikz


Publishing results that were trimmed from another paper

I suppose you could.  When submitting the paper with the "leftover" results, you'll probably want to explain in your cover letter what's going on, so that the editor doesn't think you're double-publishing those results.

However, I don't think it's a very good idea.  People usually expect a one-to-one correspondence between preprints and published papers.  Having results from a single preprint going in two separate papers will confuse people and make it harder for them to find and properly cite your work.  So if you are going to have two papers, I think you should have two preprints.

So first, decide how you are going to split up the results among papers.  Update the preprint of your current paper so that it matches the content (and title) that will be in its published version.  Then submit a new preprint with a new title containing the leftover results, corresponding to your second paper.

In your current paper, you can then cite the second preprint.


What is the difference between graphical abstract and graphical table of contents?

If you upload the required image and text, the journal staff will figure it out and it will be fine.

Image:  This is the TIFF or EPS file.
Graphical abstract:  This is the text.
Graphical table of contents:  This appears to be an error.  Perhaps you can upload a file containing both the image and text in this category, but there is no need to do that.


Are GRE Practice Guides Easier Than the Actual Test?

Assuming you are referring to the GRE General test: It would depend on what materials you are referring to, but the popular ones, particularly those from ETS, closely match the difficulty level of the actual test. However, note that:

To get a more accurate impression of difficulty, try to mimic test conditions as closely as possible (e.g., practice online tests if you are giving the computer-delivered test). Even if the questions seem easy, time could be an important factor, and familiarity with the interface helps. ETS offers two free online practice tests that use the actual test user interface.
The difficulty level is adaptive based on the section. So, if you perform well in one section, you can expect more difficult questions in the next, and vice-versa. However, the scoring is weighted based on section level difficulty, so ideally this should not adversely affect the final score.


I am struggling due to insufficient background in a graduate course and feel like a moron. What do I do?

Sounds like my Physics II course decades back.  The effort on that course was greater than the effort on all other courses combined.  Little did I know that I took it from Paul Chu, who at the time was a Physics Superstar, and he wasn't going to "just pass anyone".
Somehow I managed to get a B.  To me that B was worth more than all the A's I obtained combined.
Hard material is not a sign of you being a moron.  Perhaps you're not ready for the course; but, the entire idea of taking a course is to challenge you with new material.  The harder the challenge, the more you will learn.
Take it easy on yourself.  Try to do as much as possible without over involving your professor, but do use an hour of their "office hours" to go over problems you have difficulty with.  Be very well prepared for this hour, showing them what approaches you've tried and failed at, and can they teach you "how to approach the problem" instead of "how to do the work".
For support, find others in your class that seem to be bright enough to warrant working with, and form a study group.  If the group starts to look like an unbalanced "share the answers" group, get out of it, as it will do nothing to prepare you for the exams.
Rearrange your schedule for the reality that you'll be spending six to eight hours a day doing this class's work, until you can gain enough mastery to cut it down to a mere four hours a day.  Remember, it won't last forever, you only need to keep up the crazy schedule till you get out of the class; and, should you have to repeat the class (which is common for such classes), you'll not be under as much of a burden due to your gained familiarity with the material.
In short, hang in there; but, hang in there smart.


How to apply for a PhD scholarship in USA if I'm European?

In general, the process is to apply for admission to PhD program at a particular university and ask for financial support in the application.  In most STEM fields in the US, nearly all PhD students do receive financial support in the form of a 20 hour per week teaching or research assistant job.

To answer your specific questions:

Application procedures vary from department to department, so you'll have to check out the web sites of programs that you're interested in to learn about the application process.
No, there aren't spots reserved for ethnic minorities.  In any case, as a foreign student, not a citizen or permament resident of the US, you wouldn't be classified as a minority student for most purposes.
Financial aid in the form of teaching and research assistantships is nearly universal for PhD students in the US.


Transcript of records is full of grammatical/spelling/formatting mistakes and the issuer gets angry when I inform them

I suggest requesting a copy of the transcript in whatever language the issuer writes best.

For some purposes, such as graduate admission to a foreign university, you may need to pay for a certified translation by a professional translator.


How to concentrate during conference talks where the quality of the presentation is poor?

When I attend talks where the quality of the presentation is poor, I like to use it as an opportunity to learn about what not to do in a presentation.

I have an ongoing list of "things not to do in a presentation", with examples from talks I've attended. I just take out the list and add to it whenever I attend one of these presentations. I find it helpful for improving the quality of my own presentations - more helpful than just reading tips others have written about presenting, because when I refer to my list I am reminded of exactly why and how a presentation is made worse by [insert bad thing here], from personal experience.

Usually as a result of taking notes on the presentation technique, I end up also paying attention to the content of the presentation, which is a nice side benefit.

P.S. I also have a list of "effective presentation techniques" and I add to it whenever I attend a talk where the quality of presentation is very good.


If admissions are handed in by email, they will probably have a dedicated email address for admissions.  Just title your email with your name, the programme you are applying for, and an indication that it is an application, such as:

  Application of Shahryar Rah for the PhD programme in Unicorn Ethology

The rest doesn't matter, as soon as they start processing your application they are unlikely to record the title of your email.  All relevant information should be contained in the content of your application.


Is it normal for professors to hold their graduate students "hostage?"

Pretty much everything is according to his/her will and they also get to determine if they want to "let their students graduate."

This is how it works in the U.S. also.  However, the proper behavior is for the supervisor to have a collaborative working relationship with PhD students.  I think Germany is similar.

In Australia, and I think Canada, the award of the PhD is decided by an external committee.  Members of the committee all work at other universities.  This substantially reduces the power of the supervisor.

Practices vary by region, and even among universities.  For example, some U.S. universities require a committee to approve the PhD thesis, with one member being from a different department.  At other U.S. universities the committee does not have this external member as a check.  Generally the committee does what the supervisor recommends.


Why transcripts instead of degree certificates?

Most applicants for positions at US universities will have been educated in the US, so US hiring practices are based around the sorts of records that US universities provide.  And US universities don't really have such a thing as "degree certificates".   The paper diploma from a US university is considered purely ceremonial and not used for any official purpose; it often doesn't even have complete information about the degree (major, honors, etc).  For most US universities, the only official academic record they produce is the transcript.  Hence, that is what a US university expects when hiring.

Note that in some cases, a hiring decision may be based on more specific details about your education than the simple fact that you have a degree.  There may be formal requirements, coming from university regulations or accrediting agencies, that you have a certain amount of coursework in certain areas, and the transcript is the only way to verify that.


what do you do if your PhD advisor publishes a solo paper on your topic?

You asked,

  Is this normal?

The answer is no, it's not normal. If two people work on some research together, the "normal" thing is for them to write the paper on it together, and for both to be authors on the paper.

It's possible that you seriously overestimated your contribution to the work and don't actually deserve authorship. Even in this case, it's clear you were involved in the research and it's not normal for your advisor to go ahead and publish it without discussing it with you first.

(When I publish work that involves students whose small contributions do not warrant authorship, I always discuss it with them first. I explain why I don't think they can be an author, give them a chance to state any disagreement, and also tell them what additional work they could do in order to merit authorship.)

However, the latter (your contributions did not merit authorship, and your advisor failed to discuss this with you) is somewhat more forgivable than the former (your contributions did merit authorship and your advisor published without you anyways). (You do say your advisor is new, and probably inexperienced in advising.)

To answer

  What do I do?

You should talk to your advisor. This is the only way to really understand which case you are dealing with.

You can bring this up in a non-combative way without upsetting your advisor; for example, you can ask "What do I need to do in order to deserve authorship on future papers?" This gives your advisor an opening to discuss why he thinks you didn't deserve authorship on the conference paper, and for you to respectfully state your perception of the situation.

There may still be a chance for you to get some credit for this work, if you come to agree with his point of view that you didn't do enough to deserve authorship on the conference paper. For example, once you and your advisor have come to an agreement on what it takes to get authorship, you can propose that the two of you work together on an extended version of his conference paper for a journal - on which you will be an author :)

Unfortunately, it's also possible that after this conversation you believe you did deserve authorship, and that your advisor published your joint work without you for no valid reason (i.e., committed misconduct). In this case, the best advice I can give you is to start looking for another advisor.

Finally, the lesson for the future is: talk to your collaborators about authorship early and often.


Should I include a paper published in a non English language in my CV?

If you have published a paper, you should include it in your CV.  It does not matter what language the paper is in.

For the aid of people who do not speak the language, however, you may wish to include a translation of the paper title as a note, e.g.,:

  J. Caesar, Commentarii de Bello Gallico [Commentaries on the Gallic war], Caesar House Press, 49 BC, (in Latin)


What habits should I build in the first part of my PhD?

To get the ball rolling, I will offer an answer.  I will invite others to edit my answer to improve it, or write another answer.

In the early part, spend about 5 - 10% of your time looking at journal articles and other scientific literature (if you are on top of your coursework).
Form one or more study groups, if for no other reason than to get practice communicating about your subject area.
Attend seminars.
Visit office hours.
Try to keep your notes organized.
If there are foundational exams in your program, get some old exams and start looking at them, as time permits.
Find fun ways of getting exercise.


What to tell students who want to know how to succeed in your class

Actually, in the US, in modern times, it really is your job to help them develop study skills. Many students arrive at college with hardly any skills at all, having coasted through their previous education, often with few learning burdens put on them. Many don't know how to take notes, or summarize them, or separate the important points from the rest.

More important, in math, they may not have an attitude that it may take more than the minimum to get by and that memorization isn't going to carry them very far.

I've discussed the teaching of learning skills here in other answers, so won't repeat it (search: Hipster PDA, for example).

But there are two things that might work. The first is to require more practice and make sure that students have some way to get feedback on that practice. A text book usually has more exercises than you want to require, but you can suggest that more (even all) be done. You can even hand out supplementary problems that are graded or not.

The second thing is to have a daily quiz, taking up the first 5 minutes of your class. Ask questions based on the previous few lectures (2 or 3, say). The quizzes don't need to count much toward the grade, but should count for something. Students can swap papers and grade each other for a short quiz, so your load doesn't need to increase. But an additional advantage of this, other than the goad, is that you get feedback every day on how they are doing.

I can't say that the students will love you for this, of course. They will likely grumble. But you will learn who most needs your help and it won't be much of a burden on those who don't need additional work to succeed.

I once became something of an expert on rational functions and could look at a definition and pretty much know what the shape of the graph would be. I learned this by graphing hundreds of them, by hand (1960s) using derivative information.

Two specific links you might want to examine for Hipster PDA are one here and one at CSEducators


Paper accepted for poster presentation in IEEE, what are the chances of it being published?

It depends on the particular conference and the field.  In computer science (where the main publication venue is conferences), many conferences divide the published papers into "talks" and "posters" (eg NIPS, AISTATS, ...), and there's no difference in terms of publication.

In most other fields, however, acceptance at a conference means nothing, and you have to get published in a journal.

TL;DR: ask your advisor.


How important is being in a good institute for a theoretical physicist?

It depends.

A good student who is very self motivated can rise above. That means you would need to be doing a lot of work in addition to the work assigned in class. If you can do that, consistently for your entire degree, you can come out knowing as much as you would in a "tough" school.

It's a two-fold challenge.

First, there is doing it and keeping it up without somebody to drive you.  If you are that sort of person then GREAT! More power to you, I wish you well. But you won't need my good wishes, you will be too busy creating your own good future.

Second, there is getting recognition for this extra work. Eventually you will want to do something after undergrad. Whether that's grad school or industry or whatever, you need an entrance that allows you to get some credit for the extra work.

Sometimes, a possible solution to the second part is to publish something in a research journal. Lots of undergrads publish a research article. Of course, it's a small fraction of undergrads overall. But if you can publish something it will go a long way to helping you in whatever your plans are for after undergrad.

Sometimes it's extra-curricular projects. Are you technologically gifted? Build something keen. Are you software creative? Write an interesting and useful computer program. Are you the gifted writer? Write a web site that explains some interesting physics topic. Are you a good video presenter? Maybe something for the Khan academy.

https://www.khanacademy.org/

If you are fortunate in the "summer jobs" you get, that can be very helpful also. One of the undergrads I met at a "cow college" was doing some interesting work with a local research company. They were doing a thing with testing microwaves for therapy in sports medicine. He got to do some of the mundane measurement work. It looked good on his resume, it taught him a lot about microwaves, and it paid the bills.

Sometimes a nearby school will have enrichment opportunities. If you were at a small school in Southern Ontario, you could consider managing to get some time at McMaster University.  They have a pool type nuclear reactor. You could get training on that for a few months. That would look pretty good on your resume for certain jobs and grad schools. Many universities will have some kind of lab or facility that you can do some kind of exchange program.

From the other side of things, a gifted student in a "tough" school may not achieve maximum results. Tough schools can sometimes be very regimented and by-the-regulation-book. "My way or the highway" kind of thing. It does not always nurture the creativity of a young student who has just come from a high school where he was top-of-the-pops while hardly trying. And tough schools might not have a friendly environment. Students might be far more competitive minded, angling for scholarships and such.

The right school for you is a difficult choice. And it's one that, once made, is difficult to unmake.


Should I recommend accepting a manuscript with major revisions because of a strong topic, but quite poor content?

Jeff Offutt has a very insightful scheme for calculating the final recommendation based on technical, presentation, and omission grounds (source):

The fields in the matrix correspond to different types of problems:

  Technical Problems
  Minor: Mistakes in background, related work;
  Moderate: Does not affect the key results;
  Major: Changes the key results;
  Critical: Negates the key results.

  Presentation Problems
  Minor: Typos, spelling, grammar;
  Moderate: Make understanding the paper harder  (organization, notation, repeated grammar);
  Major: Prevent understanding of part of the paper;
  Critical: Prevent understanding or evaluating a key result;

  Problems of Omission
  Minor: Omitted background, related work;
  Moderate: Not part of the key results;
  Major: Missing in the key results (proof or experiment,
  lack of control in experiment);
  Critical: Must be in the paper to evaluate the result
  (experimental study, etc) or not enough results.

The source also provides additional information and context.

Based on this scheme, I think the appropriate recommendation in your case would be a major revision.


Do graduate committees in math decide to not take students based on lack of knowledge of specific topics?

Mathematics as a whole is very broad. It has been about a hundred years since any individual could say s/he knew all of it. Mathematicians are specialists - often extremely so. So, if you are working in a different area, having little knowledge of an unrelated one is not considered much of a disadvantage.

On the other hand, it is possible in the US to gain admission to doctoral programs, even very good ones, with only an undergraduate education. In the US the undergraduate education is very broad with only a little specialization. A math major also studies history and philosophy for example. So, the undergraduate math education, while, itself broad, can't cover everything.

However, if you are interviewed for a doctoral position the interviewers will decide on the questions. You need to make sensible answers, of course, but most interviewers will be looking for general math ability, not expertise in everything. That would be different, of course, if you are interviewed by a potential advisor who will want to know about you background in a particular specialty.

But from your description, your lack of specific knowledge in a few areas isn't likely to be a handicap. However, the competition for any slot will be intense at the level for which you aim. Nothing is guaranteed.


Grant from private company - conflict of interest

I don't see this as a conflict of interest, but the issue itself is deserving of careful attention from both a contracts perspective and a scientific perspective. I would advise against any such funding source that puts restrictions on the publication of findings.  In particular, you state that the business is "hoping for a particular outcome."  Are you still allowed to publish results that are contrary to their expectations -- or, does the contract specifically state they have authority over what can and cannot be published. You will want your grants management officers to carefully scrutinize the contract.

Science is really about answering questions through an open, replicable and systematic process.  It is not about providing evidence for an expected outcome.  I think this type of funding will be more problematic than helpful for a scientific career.


Is there any dedicated, academic channel i could use to establish contact with other universities on an international scale?

Summarizing the comments: the primary form of communication and dissemination of information among academics is e-mail, for better or worse.  But perhaps more towards what your end goal might be, a Slack channel might be appropriate.  You will still need to solicit participants via e-mail and advertising on ResearchGate or listservs dedicated to your research field.  But once you get a core group, you can put everyone on Slack and give them admin permissions to add additional participants as the group grows.


How can I compile a study material of a course in this case?

I suppose you are obliged to prepare what some may recall as a minimum learning material. It is what a student might need to get the a broad knowledge of the subject before s/he is to delve into the details.

If you are concerned that the original source ought to be referred due to its importance, then you might include this sentence...

  The provided study material is by no means a complete replacement to the prescribed textbooks/sources on the subject.

...somewhere in the beginning of the material, such as the preface section. It what I usually do when compiling such notes.


You can do whatever you want.  If another school accepts you into their program and you'd rather be there, I don't see a problem.  Of course, there exist circumstances in which switching might have downsides, but you haven't told us enough about your situation for any of us to judge them.  Sounds like you just want someone to tell you it's OK to switch, which I'm fine with doing.


What is the purpose of getting good grades once in college?

The other answers give the standard practical reasons why one should aim to get good grades, but I prefer a more idealistic explanation, which is that good grades are not the real goal one should focus on, but rather a side effect. If you focus on the real goal of learning the material at the highest level possible, good grades will follow automatically. So, good grades do have their practical uses, but philosophically speaking, they are just a distraction.


I've worked as a waitress. Should I indicate this in my PhD application?

That sort of employment is unnecessary to include and will be of no benefit if you do. I suggest only doing so if you need to account for a long gap. Even then, you should say why that was necessary to do. And, if you are in mathematics, as the "handle" implies, write about anything you did that was productive in that field.
It might even be better to describe it as "short term, non-academic employment" without describing its nature.
Most people will find this sort of employment irrelevant, and those that don't would be more likely to consider it a negative. You want your application to be positive-focused on how and why you expect to be a success in doctoral studies and thereafter.


Are authors identified by the chapters they contributed to in multi-authors books

It seems so to me. YMMV by the field, but I can't recall reading any books cited like that, except for compilations of essays where the "chapters" are really papers that are functionally distinct from each other.

Presumably you read a lot of works in your field. Go grab 10 books with multiple authors and see if any of them have a capter-by-chapter authorship breakdown.


Secure backups of PhD and journal-research

Backups, short-term and long-term storage of research material is actually something we have to address whenever we apply for a IRB for a research study or an IRB exemption. We have to spell everything out in great detail including when we are going to destroy or get rid of the acquired research materials (since they usually contain personal identifiers like name, address, email etc.)

This is our approach:

We have our own encrypted lab server on a RAID configuration. Access to the server is restricted to myself and my adviser.
We store generalized, public versions of our scripts on github. The previous answer has very good specifics on github so I will not go into the details here.
Periodically, we backup our lab server to another externally hosted server (not physically located in the US). This backup script is encrypted and password protected.
Physical interview questionnaires, survey instruments, interview transcripts are stored in a locked file cabinet with access to my adviser and myself in our lab. Entry to our lab is through keycard only.
Interview recordings, videos and audios are also stored and backed-up according to the procedures in 1 and [3].

This approach seems to have worked so far.


"Warning signs" that candidates should be aware of during an academic job interview

One thing to consider is tenure rates. Some departments are much more difficult to gain tenure in than others. My undergrad institution is well known for tenure cases that end in litigation. Similarly, I am aware of a department (small liberal arts college, not MIT or the equivalent) that denied tenure to something like six assistant professors over the course of a decade without granting tenure to any of its hires.

Additionally, it's worth considering whether the department has autonomy over the hiring process. If the meeting with the dean is not largely a formality, this might be an issue.


Is publishing a graduation requirement in many master's programs?

I've never heard of a publication requirement for a masters degree in the USA or UK.  There is not even a novelty requirement for a masters dissertation, that's what makes it different from a PhD.  Obviously publishing is a good idea if you want to continue on to a PhD, it makes your CV look much stronger and shows your promise as a researcher.  But frankly, in the UK at least there is no time to publish before you finish your dissertation (Masters degrees are very compressed one year degrees) and most publications follow the formal completion of the degree.


Is it alright to thank my Master's thesis advisor, via e-mail, for getting a good grade?

Instead of thanking her for your grade, I would thank her for the time and energy they spent with you during your thesis, as well as what she has taught you. You earned your grade, she did not hand it to you.


While it is indeed bizarre and there are many ways in which a school director would not be the same as a boss in a traditional workplace, it is technically correct. An academic unit director such as a department chair, head, school director etc is technically the supervisor of everyone in that unit. Faculty are still employees and have someone above them (a person they “report to” in traditional-workplace lingo) in the organizational chart. If the employee misbehaves, the director would be the person who would need to handle the situation; if the employee has some special life situation or a request that needs accommodating, the director is the person they need to see; etc. These are all functions of a boss or supervisor.

Two notable aspects of an academic director’s work that make them rather different than traditional bosses are:

The academic supervisor does not have as many powers as a traditional boss, and is constrained in many ways by the institution’s policies and by the academic culture of shared governance. In particular, he/she can’t usually make hiring and firing decisions. And faculty members with tenure cannot get fired anyway, so the workplace dynamics and psychology of how people relate to their “boss” are much different than in other places.
In many academic units the directorship rotates every few years. This results in a situation where the person who is your boss today could be your underling tomorrow. Again, this frequent change in the organizational hierarchy drastically changes people’s perception of what it means to be the boss, to the extent that the word “boss” no longer sounds very appropriate to describe the role of the supervisor. But as I said, it is technically correct.


I suspect an author of a paper I'm reading was listed improperly - what to do?

Can? Yes - the comments already give you some hints: Look at the prof's website, try asking him a question about the paper.

Should? Probably not. If there is really something going on, then it would the business of the professor, not yours. If you proceed as above and ask him something, and there is really something fishy, he can decide by himself if something needs to be done.


How to find out which math departments have a research group in mathematical logic?

I guess some logician is me. I don't know of any list of schools that have programs in logic, and it would be hard to keep such a list anywhere close to comprehensive---very few schools have more than one or two people in mathematical logic, so the list would change frequently based on whose hired/moved/retired recently.

Steffen Lempp keeps a list of logicians which, while not comprehensive, is pretty large, so the institutions those people are at is a good place to start.  Another idea is looking at whose spoke at recent logic conferences (for instance, the program for this year's ASL annual meeting, or the European equivalent, the Logic Colloquium).

Always, of course, if you know any faculty who are familiar with your interests (not necessarily logicians themselves), they may be able to point you towards some schools.

Also, note that there's no school with anything like a "generic" logic program---anywhere you go, your specialization within the field will be limited by whose present there. You likely have some narrower idea than generic logic that you're most interested in, so looking for people working in that area (or who've done work you think is interesting) is a good way to find schools. (You shouldn't obsess about this, though; you don't have to work in exactly the same area as your advisor anyway, and your interests are likely to shift at least a little over time.)


Effects of financial burden on PhD research

I had an almost identical situation. Due to financial commitments and the lack of grant, scholarship etc availability - I had to do close to fulltime work while completing my PhD (experimental physics).

I can assure you that I got through it, it was exhausting but very much worth it.

What I did:

As you are doing, keeping the advisor in the loop, informing them of what is required for work (time, energy etc), but at the same time, discussing and setting short and medium term goals.
Set yourself weekly goals, make these achievable and unambiguous.
Give yourself some evenings off to rest, and occasionally a weekend (I did this every 5 weeks).
Keep the sleeping, meal and exercise patterns - can not emphasise how important this is.

and possibly a weird one (but it worked):

keep a notepad or a small printed copy of a task in your pocket.

But, still seek the possibilities for grants, related jobs or scholarships.


I am not aware of any journals in my field (physical sciences) that would pay cash to authors for research papers. There are some obvious edge-cases:

Some major journals such as Science/Nature contain a certain amount of non-research content, e.g. 'science news' and commentary on policy matters. I presume that the authors of this material get paid fairly directly for their efforts to produce it. However, one might argue these individuals are acting as 'journalists' rather than 'academics' when they do so.
Some journals carry book reviews. I think it is fairly common that the author of the review gets to keep their review copy of the book. For a major textbook, this may have non-negligible financial value.
Some grants/awards, especially those from professional societies, may come with some obligation to contribute a report to one of the society's journals. However, the award is not (in any case that I know) expressly claimed to be payment for the journal contribution.

Researchers in certain areas have opportunities to profit from private consultancy arrangements with industry/commercial enterprises. In some cases, this may entail conducting and publishing studies with a particular focus (typically, to prove that the company's products are safe/effective/better than the competition). Anecdotally, this is particularly prevalent in medical fields. Of course, there are many potential ethical issues here.
Otherwise, the general assumption in the physical sciences is that authors do so in the course of their employment at a university/research institute/company, or as students working towards a degree (for which they may receive some scholarship/grant). Of course, there is a big difference with the humanities here, due to the relative abundance of research funding for the sciences.
That said, it is interesting to note that publications are (largely) required only to get or improve a job, rather than to keep it. An academic who habitually failed to show up to teach their assigned classes would likely find themselves facing disciplinary action. However, an academic who fails to publish rarely sees any personal consequences until the next time their employment falls to be reviewed  (either as a tenure/promotion/contract renewal case, or because they've applied for a new job).
I presume the premise of your question is that many academics have teaching-only contracts, and therefore any research they do is 'in their own time'. The issue here, as I see it, is that people who want one career path (academic research) are being encouraged to take a different one (academic teaching) and view it as a 'stepping stone' to research. This is a huge problem, but I'm not sure that either the blame or the solution lies with the publishing process.


How often do professors accept new graduate students?

There is no way to guess how many students an unknown professor is likely to accept, because professors vary wildly in the number of graduate students that they accept each year.  Reasons for this variation include, among others:

Amount of funding varies, from professors who are totally broke to professors who need lots of warm bodies to feed into their research machine.
Personal taste and scholarly style vary, from some professors who love to be in charge of a big lab with lots of things happening, all the way to others who would prefer to have just an occasional disciple or two.
Career and life events vary: a professor about to go on sabbatical may not want to take any new students, while one in the fresh excitement of an opening line of research may want many.
Program structure varies, from some programs that admit students almost entirely without reference to professors and the students don't even link up with professors for their first year, all the way to others where the individual professor is almost entirely in charge of admission.

The best way to guess how many students a particular professor is likely to be hiring is to look at the web pages of their students and see when they started their programs.  Even that, however, only gives you some indicators about the past, and not the likely near future, given all the sources of variability.


I would like to ask a counter question; what it the main motivation in you wanting to publish your contradicting results and your disagreement with the authors of that one paper?

I think the main motivation of a publication should be to add something to the literature, not the discuss results back and forth. That's what conferences are for.

Without knowing the specifics of your particular case at hand I see the following possibilities:

Experiment presented is not the best way to test the hypothesis

If your reasons for refuting the article originates from the approach presented in the paper, then you are merely proposing an alternative approach to  solve the same problem.

That's the easiest scenario, in my humble opinion, since you can easily refer to Smith et al. and say that your approach is superior/more accurate compared to theirs because X,Y,Z. That would essentially be a standard "original research" paper.

Incorrect results

if you have tried to replicate the experiment by Smith et al. and cannot come up with the same results, then you can adopt the following steps in that order:

Redoing your experiment, once more, retracing your steps to make sure you have done exactly as explained by the authors.
Contacting the authors to tell them that you cannot replicate their results and whether or not there might be a key step that you might have overlooked. This is a sign of good faith for your fellow researchers.
In the case where despite all your efforts there is something just not right, you can try contacting the editor with evidence on contradicting results, which may lead to a correspondence type paper. This approach might come across as a more or less accusatory approach however.

Misleading conclusions of results

If you think the specifics of the experiment (or equivalent) are solid but the conclusions drawn and presented are misleading, you can write an opinion piece, or a commentary and send it to the editor.

Be sure that the discussion (i.e. whose conclusions is more accurate) is actually relevant to the general audience in that field. Otherwise it's just scientific banter which can be carried out by email.


Is Excel-generated chart acceptable for publication?

Excel can produce high quality charts, but it takes a lot of work. The biggest difference between Excel and other systems is the quality of the defaults. I suspect some people are using excel charts, but they have gone to a lot of effort to tidy them up.

In the example chart, you will, for example, definitely need to deal with the x-axis labels overlapping the y-grid lines. In fact the y grid lines are too strong - in fact I'd put some more consideration into the gird lines in general - why y lines, but no x lines - there might be a good reason, but you should think about it?

Limit the y-axis to make 0 the minimum (I'm assuming a negative flux makes no sense).

I would personally also add a y axis and x-axis border line. You are almost certainly going to want tick marks on the axes. And markers on the lines/larger markers if they are already there but too small.

Your axis titles need to have the same font size (the y looks bigger than the x to me at the moment) and the difference in font size between the labels and the titles is probably too big. I probably take out half of the x-axis labels and make the remaining ones bigger.

One thing that Excel is bad with, and isn't easily fixable is consistency. Getting two plots looking exactly the same, with exactly the same size plot, same size text, with all the elements in the same place is really difficult because it relies so much on the mouse and manually moving/sizing things.


Lack of confidentiality for a letter of recommendation

As I understand it, although job applicants, grad school applicants, and so on, can nominally "waive their right to see the letters", in most states this seems to be not enforceable, in the sense that it is not legally possible to genuinely waive this right.
When I've written letters, I construe peoples' waiving of "rights" to be an expression of intent, plus, an acknowledgement of the actual state of things. Yes, I've had people (misguidedly, in my opinion) refuse to waive these rights, which makes me wonder about their perception of things, and who's giving them advice.
And, yes, if someone is of the turn of mind to explicitly refuse to waive, I am much more guarded in my letter... ironically, usually because there are concommitant awkward issues as well.
And, yes, letter readers certainly understand that (in the U.S., in academic math, anyway) there is an expectation of at least pretending to not plan to ever demand to see the letters.
Yes, if we imagine that letter-writing should be fair and unprejudicial, then the issue of non-confidentiality might seem an unhelpful complication. However, decades ago, and, still in many scenarios, information is passed and decisions made in some sort of good-ol'-boy network rather than on a level playing field. That was, and continues to be, a bad thing, and needs pushing-back-against. (My own dept's faculty hiring has traditionally been a sort of star-chamber proceeding, and only this last year some of us have objected to it...)
So, yes, ... complications. :)


Two criteria often I consider in making a choice between approaches are based on the value proposition/ addition and the uniqueness of the approach.

Ideally, you don't choose.  A "unique" approach that doesn't add value isn't worth much.  Solving a problem using off-the-shelf techniques also isn't worth much.  What you should aim for is a unique approach that adds value to the research landscape in your field.

But if you must choose, work toward your strengths.  Do you carry a hammer and look for nails, or do you carry nails and look for hammers?  If you're better at finding new tools to attack hard problems, then you're more likely to come up with unique approaches.  If you're better at finding hard problems to successfully attack with a small suite of tools, then you're more likely to add value to those tools.  I know lots of successful researchers in both camps.

  Which one among the two help in quicker publications or
  acceptance rate?

You are optimizing the wrong function.  Your primary goal should be to produce the highest quality, highest impact research, not to maximize the number of lines in your CV.  One good high-impact paper is worth far more than a pile of publications that nobody cares about.


How to politely tell the PI I'm working with to use the vector format for images

From the comments I gather that you are afraid to criticise your PI for producing low quality images, which is natural.

I think that a good course of action here would be an e-mail where you tell your PI that your journal requires vector based images. Then you say that you know that he is a busy man and that you are willing to reproduce his images in Illustrator if that is okay with him (assuming the pictures are easily reproducable). That way he will probably thank you for going the extra mile and taking work off his shoulders.

I would refrain from telling him to make better pictures himself, because he has probably done it the same way for decades and it is hard to change such habits.

Good luck with your publication!