Whom should I ask for letters of recommendation?

Ideally, you do want letters of recommendation from academia.  That being said, graduate schools (especially for PhD programs) are all about research and not so much about coursework, so you would want a letter to describe how you have the potential to succeed in a research setting.  The industry connection may help you do that, but you haven't provided too much detail on how you worked under that person.
I mentioned this in a comment above, but have you done anything outside of research where you interacted with professors (including TA'ing a course)?  That is also a valid source of getting a recommendation letter.  In addition to this, who would you be thinking about for that third recommendation letter from what courses and why?  It's never too late to try and send a quick e-mail and/or have a conversation in their OH to try and see if you/them remember each other.  Maybe talk about how interesting their class was, what your plans are in the future, or maybe how interested you are in their field/research.  (As a recent graduate, I occasionally try to send a quick e-mail to get advice from professors, especially since with COVID things are largely virtual, and maybe see if I want to ask them for a recommendation down the road, since I am also in the same boat)
When would you be applying for graduate programs?  Maybe you could try to TA a class or get an additional research experience in before you do so, and by extension, that third recommendation letter that you need.


Can a paper directly be written on a new application developed rather then an algorithm from existing research results or algorithms?

This is something that I have been doing.  If I understand your question correctly, you are looking at a new product using existing algorithms and techniques. If this is the case, the answer is yes: many journals will welcome this, as I have found.  I have also taken an existing technology, aspects of existing algorithms, based on existing research and developed a brand new technique.

A couple of caveats though:

You will need to make the specific context to which it will be used crystal clear, this must be the focus.
You must give full credit for the prior information and techniques.
You must fully justify why such an altered technique is useful, what are the implications and benefits of such a product.


How important is it, exactly, to use a rubric for grading undergraduate lab reports?

Having a rubric will make your own work grading fairly simpler, in particular if what you are grading are reports/essays. It breaks down your mental process of coming up with a grade. For example, if you don't have a rubrik, you may have to think about whether as a whole the report should be worth 70 or 75 points. There are many dimensions involved, and you will find that you are juggling too many balls when trying to assess how 3 or 4 reports compare to each other. It's easier if you only have to assess them on one dimension, e.g., spelling/grammar, use of examples, clarity of exposition, correctness of formulas used, adequacy of citations. You would then assign a grade for each report for each of the categories in your rubrik, and the task of computing an overall grade is only one of adding up the points.

A rubrik will also make your life easier when students (as they always do) come to your office hours and ask why they got this grade and not that. If you grade based on a holistic view, it's often difficult to articulate how you arrived at a particular grade. It's easier if you can break the grading down for the student into individual categories. You make your argument why you gave the student a 70 instead of a 75 a lot easier if you can explain why they only got a 10 out of 20 in grammar, etc.


What affiliation to put on an academic paper for alumni authors?

The standard practice is to list the affiliations under which the work was performed. If you performed the work as an undergraduate at your undergraduate institution, then you should continue to list it in work related to that effort. However, you can "update" your address by listing a "current address" along with the old affiliations.


Applying to more selective programs after having been diagnosed with a long-term mental condition

It's certainly a huge relief to finally know, after years or decades of struggling, what the underlying problem is. But people with ADHD tend to assume that a diagnosis and treatment is a magic bullet that will suddenly make them like everyone else. I think part of this is ADHD tendencies and part is internalizing the erroneous belief that if you just tried harder you'd stop screwing up. I don't have any first-hand experience with ASD, but the issues seem to be similar.

So here's my first observation: A diagnosis does not "fix" ADHD. A diagnosis together with medication and therapy or coaching does not "fix" ADHD. Right now you're at the starting point and you've been pointed in the right direction, but it's probably going to take some time and experimentation to find out exactly what you need to successfully manage advanced academic work. Expect that what you need might be really different than what is ordinarily offered in an academic setting. Don't beat yourself up trying to be like the neurotypicals the work is designed for.

My second observation: As you can see from the answers already given, many professors and programs take the attitude that learning disorders/differences are the student's problem and it's not their job to deal with them (except maybe in a very superficial legally-mandated way). This attitude might vary by country--my own experiences in the US have been pretty dismal. So even once you know what you need, and even though the law is on your side, you might find yourself fighting a losing battle against these attitudes to get it. So it's also important to be sure that you're entering an environment that sets you up for success.

I honestly don't know the answer to this second problem. I might post a related question here later to see what the ASE community thinks. I don't mean to sound pessimistic, but the fact is that the academic community is on the whole not particularly welcoming to people with learning differences, and ADHD is particularly misunderstood. The trick here is to find the exceptions who will provide the conditions you need to flourish.


What is the likelihood of getting tenure?

This question was the topic of a recent article in Science. Briefly, around 50% of tenure-track faculty will actually remain to become a full professor. This varies with gender, discipline, and year (e.g., its harder to obtain tenure now than it was 20 years ago). I strongly recommend reading this Ars Technica article, which explores the aforementioned Science paper in depth.


Are religious invocations in academic presentations appropriate?

I think this is a good question.

Let me propose some guidelines:

1) A religious invocation should occur at the beginning of the talk or the end of the talk, but not in the middle of the talk.

People often begin talks with material that is unrelated to the topic of the talk itself, e.g. thanks to various organizers; comments about the weather, the venue or the town; jokes; and so forth.  It seems to be clearly asking too much for someone to speak only about their scientific field during the entirety of their talk.  However, at a certain point you get down to business and the "talk itself" in the narrower sense begins.  One should not (of course this is an opinion, but a strongly held and easily defensible one) mix religion with the material of the talk itself.

2) A scientific talk is not an occasion for proselytization.

To me whether religious material is appropriate depends a lot on the purpose one has in bringing it up.  If you include religious material as an attempt to convert audience members to your religion, I think that is really problematic and unethical.  If you include religious material for other promotional reasons, then I still have a problem with it, just as I would be with someone promoting their not wholly scientific company or product.  (Even wholly scientific promotion might not be so great, but that's a different answer.)

On the other hand, it is a totally standard thing to have the last slide of a talk give thanks to various people and institutions.  If you feel deeply grateful or thankful in the religious sense, then it seems natural to want to express those feelings, given that other speakers are thanking people and things (e.g. the US government) that, in your sincere opinion, have not helped you out as deeply or fundamentally.  At any rate, it does not bother me if someone ends a talk by thanking some theological entity.

3) One should not express religious sentiments in a scientific talk in a way that encroaches on anyone else's religious sentiments or lack thereof, nor which implicitly or explicitly invites or requires participation or complicity from the audience.

Thus "Alhamdulillah" is probably okay; "Now Thank We All Our God" is probably not.

In general, in (e.g.!) an academic context, one should be respectful of others' beliefs and views, and one should not be controversial or exclusionary in anything without a specific intellectual purpose for doing so.  One should also be respectful of others' time and realize that speaking in front of a group is a privilege.  On the other hand, academics are human beings and can choose to say things which are not strictly necessary.  In my calculus class last week, I had students identify a quote about mathematics being someone's worst subject followed by a careful and insightful consideration of the reasons for this.  The quote turned out to be from Malcolm X.  What calculus reason could I possibly have to quote Malcolm X?  None.  But I thought it was interesting and perhaps important in its own way.  I enjoy my freedom to do that, so it is not a hard sell for me to give leeway to those who want to make some kinds of religious statements, so long as they are in line with the above guidelines.


Is there a journal that publishes slides together with the text?

I don't know of any such journal.  The closest I've come to this is that often after I've listened to a talk, I've asked the speaker for his slides.  I can't recall ever being turned down.  Alternatively, if you can't attend a talk, you might still ask the speaker for his/her slides.  This request will likely be a bit more successful in person, but even via email it can't hurt to try.


Best search engines for scientific books

There are a number of non-commercial meta-catalogs that cover the stock of various (often national) libraries. For example, Germany, Austria and Switzerland have a common cross-library interlibrary loan catalogue called "Karlsruher Virtueller Katalog". In the United States, there is the Catalogue of the Library of Congress, which probably has the largest coverage in the country. Italy has the "OPAC SBN" of the "Istituto Centrale per il Catalogo Unico".
In terms of coverage, meta cataloges like these represent the submerged part of the iceberg that Google Books only sees the tip of. However, only small parts, if any, of the inventory are accessible for full-text search.
The use of these catalogs is free of charge, but small fees are charged for checking out books or for ordering copies of book sections, journal articles, or other documents.
In general, it's always a good idea to talk to a librarian for particular queries or about search strategies.


Ways of developing non-core skills during PhD studies?

My goodness, but this is a tough one.  We all learn and maintain our skills in our own unique way.  Especially in industry or when operating independently, so it's difficult to say what would work for you.  I'm in a similar situation except that I'm a developer first and I've been tasked with 'just making security happen'.   Much like with you and bio-med, there is an awful lot that is changing in the landscape of info-sec and staying sharp in both domains is a real challenge.

That said; your mileage will vary but here are some techniques that work for me.

Find overlapping areas:
When I started to move toward developing a new aspect of my skill set I looked for areas where the old and the new overlap.  Luckily for me; this was a pretty easy thing to do with infosec and software development.  The benefit here is that it allows you to leverage your existing skills in a new area.  If can can find areas where you can turn two jobs into one you can ease your way into it, rather than just sitting down one weekend and deciding "I'm going to learn X.".

Sit down one weekend and decide "I'm going to learn X.":
Sometimes there is no easy overlap to ease your way into a new tech or topic. In those cases I've found that a couple of days in power study mode can be a real benefit.  Strap on the headphones, coffee up it that's your thing, and just read the literature & work problems.  If it's tech then do tutorials.  If it's topic then vacuum up as much as you can.

Find mentors: Maybe you can't find the all encompassing guru of everything you want to do, but that's OK.  Someday that guru will be you.  In the meantime find people with expertise in your subject areas to help you fill in the gaps.

Keep it fun:
If at all possible and whenever possible. If you hate what you're doing then you're not going to do it well. At least that has been my experience.

Don't give in to the temptation to 'dumb it down':  You're a smart person.  You've taken the time to learn a new skill. You've actually read the materials.  You work hard to develop and maintain a system that crosses a number of subject matter domains.  Don't let people off easy when they ask hard questions; give them hard answers.  My approach is to ask them 'do you want an answer or a response?'  If all they want is a response that's OK. I give them a short and succinct response.  If they want an answer then I do my best to provide the most exhaustive and thorough explanation of what I do, that I can.  When I work hard to learn a new skill I don't need to show it off but I won't let it be taken for granted either.

Well, that's what I've got. All the best to you in your endeavors. If you ever need Java help feel free to grab me on chat and I'll get you an email address.


Does a professor respond to my request to work with me?

A decent professor will not submit your article under their name if they only read it.
You could ask.them if they want to work together with you on something (but you shoupd probably not contact them out of the blue, especially if they are higher ranked as you).


Is it okay to ask for a letter of recommendation more than a year before applying to a master's program?

Explain this situation to each of the few professors you plan to ask for letters of recommendation from, and ask what they would prefer. Some of them would probably prefer to write you the letters now, while you are fresh in their memory. Others, (ones who are very well disposed to you, or very generous people) might like to wait until you are applying for specific programs, because then they can tailor their responses to the specifics of what you are applying to. Even in that situation, you will feel less awkward if you have already broached the topic with them. Also, you learn if someone you are expecting a recommendation from is actually not willing to write one for you, or feels that they can't recommend you strongly. This will be better to find out now than a year from now.

Plus, your professors might have advice on what kind of job to take in the meantime in your field, or even a connection for a job. You won't know if you don't ask.


What are the benefits of getting a PhD in statistics over a MS in statistics?

Actually, this greatly depends on where you get your degree from. Sometimes people who have done just MS are able to get to the bottom of the thing and can use their knowledge of statistics on a practical level. It depends on how solid your concepts are. Once you are in some position earned through your sound academic record you can grow quite fast.

So, if you have good record (not just grades but grasp), you may be able to get to the same level of salary as a PhD would. This is because statistics is an applied branch and is in demand.


A reason for some is because LaTeX will do this.
If you have Floating figures, and the layout engine can not work out a good way to place them, as to balancing the amount of whitespace, and other rules for an "good looking document" (eg No Figures on First Page is a rule for IEEE transactions) it will shunt them to the end.

The rules LaTeX uses to define what is a "good looking document" can (and often should) be adjusted. See for example this, where the rules for the various fractions of text etc to figure are adjusted.
Positioning can also be forced some, eg with !.

A lot of detail into how LaTeX placed figures can be found in this TeX.SE question.

Obviously this only applist if the thesis was prepared in LaTeX (or some other system with automated rule based layout, that prefers figure only pages to squeezing a figure in to a page badly).

In other cases, it could be because the page was inserted from the output of another program. Eg a simulator output printed to PDF, merged in. Or a scanned hand drawn diagram inserted as a full page image. This is not a good or attractive why to do things, but it is fast/convenient.

In general, as a undergraduate thesis is not heavily judged on its appearance, its often not worth the time to do better. I know when I was writing mine, I had 3 final year (and thus difficult/timeconsuming) coursework/project based units to do at the same time. I had better things to do, like ensure the wording was clear, and I didn't exceed the word-count. Placing figures well is hard, I was satisfied once I got FloatBarriers working, to stop the figures from floating all the way to the end -- FloatBarriers can be used to force figures not to be shunted beyond the current section (etc).

The undergrad thesis will likely be the first serious academic writing of that form they have done, and writing it comes at the end of the hardest work they have done, during or just before their final exams. Don't hold any up as perfection in method to judge yours by.

There is a quote (I believe from someone on this site) which basically said:
"Your PhD thesis will be the worst academic writing you have ever done; because anything written after will be better as you will now be more experienced."
This goes double for an undergrad thesis.


Reapplying to PhD program after Master's

Your masters program experience will likely give you a boost if it will make your letters less generic and you can demonstrate research experience. It's possible some programs will not think you worthy, I don't know how self-absorbed those programs are in physics, but in biology a commitment and talent for research are prized above classroom performance.

I wouldn't stress so much your former poor application and instead focus on your recent successes, and use your personal statement/whatever equivalent is available to make clear your goals, and you could also use that space to reference your goals for your masters. Paraphrased, "In my masters program I set out to accomplish _______. Now I would like to continue/add to/expand towards ________."


Does anyone know a good resource for statement of purpose critiques?

One might believe that one of the best ways to assess a SoP, in view of technical affairs and coverage of the necessary cases, shall be:

Composing based on the best practices, have which been accessible within the web. Such advice-driven clarification will paves your way to consider the stuffs within your SoP, are which necessary in view of the target reader. A handful of typical resources could be tracked like this one, this one, this one and even this one. By taking such approach into account, your SoP will have been checked according to those guidelines, indirectly.
Presenting the SoP to the fellows, who have been already admitted to the competitive programs in your field. Obviously, That person had composed a decent SoP to become successful and the feedback from such person shall be, noticeably, constructive for you.

Best


E-mailing a paper under review to a prospective PhD advisor; a co-author wants all co-authors to be CC-ed. Is this OK?

I asked my co-author which is my advisor for a permission

Here a better move would have been that of asking all your coauthors for permission.
I'd now:

Inform all your coauthors, cc'ing your advisor, asking if they are OK with that.
Inform your advisor that you would not feel comfortable in cc'ing the coauthors in the discussion with the prospective supervisor.
Write to the prospective supervisor without further copying your coauthors. At most, if your current advisor insists with that, use a blind cc.


Two professors teaching the same course, should they unify their exams?

For advanced courses, I've never had such a policy imposed or used, but it likely happens. For first year courses, it is common for students to have the same exam, but to take it at the same time and be graded together by the (large set of) TAs. First year Calculus, for example.

But it might be a mistake to give the same exam to different groups at different times or days. It is an invitation to cheat. So, if such a policy were in place, it would seem to be a requirement that a common exam time be made. That may be possible and desirable. Coordination between professors is probably desirable, even if they each use their own questions and deviate a bit.

This is a US view, where grades overall are normally given for somewhat large ranges of achievement. It isn't desirable if a student can do well in one section but would do poorly in the same course taught by another professor. And even using the same exam is no guarantee of equal results if they are graded by people with different philosophies.

I'll also note that two such courses may not proceed in lock step for a variety of reasons, such as the teaching skill and/or philosophy of the professor or even differences in the ability of the students in the sections. Even with random selection of students to sections there can be differences and, in some situations, there can be large differences. So, some judgement is needed about how to conduct the exams.


What's more important in choosing a PhD program, advisor or institution?

Obviously one needs a competent advisor with whom one is compatible. But assuming that both professors qualify, I think what matters most is the quality of the students who will be your peers. You need to surround yourself with students who, from day 1, expect nothing less of themselves than to produce novel scientific research of the highest caliber, present it at top meetings, publish it in top journals, and forth. Ultimately you will learn more from your peers than from your advisor. A sufficiently talented and ambitious cohort will hold the bar high for you and push you to excel whereas a sufficiently talentless and unambitious cohort will help you make excuses for your own failures to reach your potential.

In my experience, top schools with top graduate programs have the sorts of students you want to surround yourself with. Second tier regional programs may, but I have yet to see it.


How to help reduce students' anxiety in an oral exam?

The following assorted suggestions stem from standard procedure at my department, which has a long-lasting experience with oral exams, and positive experiences reported by fellow students suffering from anxiety.

The exam begins with the student giving a brief elaboration of a topic of their choice (within the subject of the course). They can talk uninterrupted for a while, and then the exam gradually shifts to question-and-answer mode on this subtopic, probing whether the student actually understood what they are talking about. This has several advantages:

The student knows how the exam will begin and they can prepare the first few minutes. This avoids anxiety due to uncertainty.
The student is not dropped into interactive mode instantly, but gradually.
The student knows which topic will be examined first, they can prepare for this, which boosts confidence.
Not related to the question, it allows the examiner to estimate how well the student can structure the chosen topic (which usually goes hand in hand with understanding) and put it into the context of the course’s subject.

Do not ask questions that require long and elaborate answers, but go step-by-step, guiding the student if necessary, but only if necessary (so they have room to shine). For example, do not ask:

  Please tell me about [central result of course].

Instead ask a chain of questions, allowing the student to answer each of them, and adapt them depending on mistakes the student makes or similar. For example, the questions could be as follows:

  What does [central result of course] state?

  Why is it so important?

  Under which conditions does [central result] hold?

  Why is [some necessary condition] necessary?

  Why does [some sufficient condition] suffice for [central result]?

In a typical case, these questions are raising in difficulty with the first questions being something that every serious candidate should be able to answer without much thinking. This allows the student to get some confidence and get tuned to the topic before the questions become more difficult. Also, this avoids the impression of time pressure and the student knowing that they have to get to that bit which they are not confident about, even if they can score by explaining a lot of basics before that.
If you ask questions where the student shall apply their knowledge and which require some thinking time, do this after they succeeded with some simpler tasks and announce that this is a advanced task and that they have some time to think. This avoids fear of failure and gives an extra boost of confidence if they succeed.
Give positive feedback whenever you can. This does not mean that you should be drowning the student in praise, but rather avoid fuelling their anxieties by forgetting to let them know that they are correct when they are.
If the student makes a mistake in their elaborations, let the student finish first, assert what was correct and then remark or possibly ask about the mistake. For example, if the student is elaborating on some equation and made a sign flip, do not remark upon it right away, but let the student finish. Then praise what was correct and ask them to elaborate their reasoning for that sign again. This has the following advantages:

It doesn’t break the student’s flow by interrupting their elaborations and lowering their confidence due to the mistake.
It gives the student an opportunity to detect the mistake themselves, e.g., by detecting it due to a follow-up problem.

Announce the examination mode beforehand as much as reasonable, to reduce any uncertainty due to an unknown situation as far as possible.


Should one mention multiple, albeit somewhat unrelated research interests?

If you can convey your enthusiasm for the overlap of these two somewhat distinct areas, you will be ahead of the game. A PhD candidate is expected to extend the limit of human knowledge, and one of the better ways to do so is to research within the overlap of two (or more) disciplines. I would tend to see having more than one area of interest as being an advantage rather than a disadvantage. Of course, as your question implies, a multiplicity of interests can backfire by causing a candidate to appear unfocused. Focus on the overlap, and make your application shine!


When is it proper to add someone to your research paper?

You should discuss the issue with both faculty members.  I would bring it up with your primary advisor first...if only for linguistic reasons (i.e., the meaning of the word "primary").

When you say that the project is "going to be published", do you mean that it has already been written and accepted for publication?  (If not, how do you know?)  In general it is a good idea to discuss issues of coauthorship as early as possible.  If you are already writing the paper it is on the later side, and if you have already submitted it then it is very late (but maybe not too late).

That's all I can think to say on general principles.  It depends a lot on the field and what kind of work has been done.

tl;dr: As an undergraduate, you can't know the subtle expectations regarding coauthorship in your discipline.  So err on the side of graciousness and inclusivity.  The worst that can happen is that you get a "Aw, how cute: he thinks I want to publish with him" type of reaction.  If so, you will definitely not have offended the faculty member and you'll probably engender a lesson about how publication culture works in your field: no problem there.


The bad reference is given to prevent you getting the position, it is a warning to whoever might supervise you. From what I have seen, it is quite common for far more subtle and hidden negative messages to be put into an academic reference than what you have described. In these cases the references are not used because the letters are there to convey a warning. That's not to say I know the right answer, but my feeling is that a bad reference gives you no chance whereas a single good reference gives you at least a shot.


Is it better to do undergraduate research in the summer, or during the school year?

I think the main question is a false dichotomy. Most students don't have a choice between either doing research over the summer or doing it during the year. As long as it doesn't interfere with your grades or other activities, more research is always a good thing, no matter when it happens.

That said, in my experience you should simply have a conversation with your professor (or direct supervisor, who will often be a grad student or post-doc) about time commitment and expectations. No one expects you to do the same amount of work in 10-15 hrs/week that you might do in 30 hrs/week, and no one expects you to work full-time while taking a full course load. As with many things in life, just make sure to communicate about expectations.


Is it absolutely necessary for a researcher to have an institutional email?

Every employer, including universities, should create email accounts for their employees/students to use for official purposes related to their jobs/studies.
There are many reasons that using private emails for these purposes can be a problem. Depending on what country you are in, these can include government records requests laws that would allow the public access to your private communications if you're using that private email for public purposes (in practice, this isn't quite as dire, but it's potentially a massive pain).
Not sure why your institution has not provided you an email address, but this seems very unusual. It isn't that uncommon for your institutional email to be used to authenticate that you are indeed the person you say you are and that you have some association with that institution.
I won't go so far as to say it's "absolutely necessary" but I'm having a hard time imagining doing any of my own work without an institutional email, and I would find it very very weird to work somewhere that wouldn't give me an email address.


I wrote a major report and our client put it online. How to present it in a CV?

It sounds eminently sensible to put that into your CV to me: it shows you can write articles for a technical audience, and get the articles past some kind of review process, which in some sense is a researcher's job.

There's no law on how to express it, it depends how the rest of your CV is arranged. I might adjust your "Presentations" header to be "Selected presentations and reports", and then right at the top,

  I was the leading author on 100-page blah blah report for a commercially vital client of $xyz billion dollar turnover company; report available at www.xyz.com/


Being invited to present a paper or give a keynote is an honour. It shows that the community recognizes your work. Of course, it is also a way to further advertise your work, or to reflect on what you have done. Generally, the audience is larger for invited speakers.

One accepts the invitation if one has time and prestige of the conference matches one's reputation. If you have a small reputation, an invited talk at a workshop is an honour. If you are super-famous, you'll tend to only accept invitations to prestigious events.

The cost may depend on how much money the conference has in its budget, which will often depend on the sponsors. Sometimes the conference will waive the registration fee, often they may provide accommodation also, and sometimes they may even cover airfare. Bigger conferences will be able to cover more of the costs. Small workshops may not be able to cover any of the costs.


Are there any positives/negatives in this rejection email ? or, it is just a desk rejection?

This is a desk rejection. There's not much more to say about it - I suppose you could say that they haven't outright said your paper is incorrect, which is a positive; on the other hand they did also say that they are not considering your paper and you should submit elsewhere, which is effectively the same as rejection and certainly a negative thing.
There's nothing to do but submit elsewhere.


Will working as a Teaching Assistant as an Undergrad help for Graduate Admissions?

Here's my opinion, based on being a faculty in a math department. When you apply to a graduate school, it's really a two-in-one application, i.e. there are two questions to be decided: will you be accepted or not; and if yes, then with or without financial support.

Having or not prior TA experience probably won't have any effect on your admission to the program. But getting financial support is a whole different story. If you have existing connections with a research professor in the department where you're applying, then he/she may be able to support you out of their research grants. Otherwise, especially for departments with a lot of service teaching — such as math or computer science, for example — having teaching potential can be decisive when it comes to awarding graduate assistantships. Of course, prior TA experience would be a huge plus for that.


I am assuming you mean a turn-it-in type similarity index. There is no acceptable similarity index. Even a 1% similarity index could be the result of an entire paragraph being the same in a long paper. That is not acceptable. It could also just be random matches and not an indication of plagiarism. Even a similarity index of zero is suspicious since it would be surprising for sequence of words to match in a paper and therefore suggests the authors may have intentionally hid something. In other words, algorithmic detection of plagiarism still needs a human to look at it. At the upper limit, a similarity index in excess of 50% is almost always indicative of something wrong.

The key is that plagiarism and copying other people's ideas is not allowed regardless of what the similarity index is.


To whom should the letter of motivation be addressed?

Usually, you address your letter to the contact mentioned in the advertisement.

As last resort, you can always used an undetermined Sir, Madam.


The most important detail that you need to check is if those Universities that you want for your PhD will accept an IT MSc as entrance for an Engineering PhD. As long as they do, you can continue your research now, get the MSc then move on. If they don’t however, then you’d have a lot more thinking to do about your direction. It's excellent that now you actually do know what you are indeed passionate about. Research interests change all the time and be assured that it's completely natural.

Source: My fiancé has an MSc in Mechanical Engineering but now is keen on doing his PhD in Theoretical Physics and has also approached potential supervisors  and so far the response has been positive.

Good Luck!


Email to a professor after long time for recommendation

After a decade of teaching, I get these quite often. While people use a variety of styles, the one that I am most responsive to is:

Initial formal e-mail asking me if I remember them (with hints such as "I was the student who wrote the thesis on faster-than-light dog walking"), then telling me what they've been doing for the past X years (with a recent CV or resume as an attachment), and transitioning to their desire to move on to a new career or grad school and asking me if I could write a letter of recc for them. Close with an offer to talk on the phone (or come up to campus) to help refresh their memory of them.

Once you get the ok, make it as easy as possible for me to write the letter. If there are things you want me to emphasize, be blunt about saying it ("Please don't mention the folly of FTL dog-walking" or "Please emphasize my familiarity with temporal dilation and astrophysics").


How to list "Visiting Student" on my CV?

I have my visiting student experiences listed individually as if they were education segments or professional appointments. I just make sure that my current appointment/school is listed first. I use the format:

XXXX - present: University of Somewhere, B.Sc. (Major in interesting subject, minor in cool subject)
  Cool blabla I did here. Credits earned, etc.

ZZZZ - ZZZZ: University of Elsewhere, Visiting Student
  Cool blabla I did there. Credits earned, etc.


should I go for a Ph.D.in electronic/electromagnetism engineering?

There is no question that stress can kill you. But there are ways to reduce it. One of the big stress factors among students - especially high achieving students - is pushing too hard and never taking a break.

One advantage you have over many others is that you now recognize the issue and can learn to take action before the level becomes unbearable.

One problem with learning is that you are trying to change your brain - physically. To learn requires rewiring the synapses that connect the neurons. But the brain doesn't work as well as it might if you force it to work too hard all the time. You need to give it periods of rest. If you try to force it to learn it will work less efficiently. But that may just induce some people to try harder, increasing the problem and adding stress, but not learning.

To give your brain a break you just need to do something different. It may include physical rest or not. In fact it may include intense physical activity. In grad school I used bicycling as an outlet. 50-100 mile rides. Maybe 35 if time was tight. I rode in a group, fairly fast, but not so fast that we couldn't chat as we rode. As an undergraduate I practiced judo on a college team. I was terrible at it, but it provided a break from studies. Nowadays, I use Tai Chi which is a mind-body fusion exercise. An hour several times a week will make a change in your outlook. Some academic departments actually have groups that regularly do some activity. Tennis. Racketball. Swimming. A computer scientist I know (very high level person) once joined a theatre group.

Moreover, when you are trying to solve a difficult problem, pushing the brain harder may be counterproductive, but giving it a rest lets it work differently. Many researchers have gone to bed with a nasty problem unsolved, only to awake with the solution. It might even come in the middle of a bike ride. Your brain doesn't turn off in these situations, but the overall body structure (including the brain) will work differently.

My advice, then, is to find a way to deal with stress. If you are at a university or similar institution, there may be some "counseling" office that has short courses on such things or people skilled in teaching stress reduction. If you can find ways to manage and reduce stress (you probably can't avoid it altogether) you can function at a higher level whatever you do.


Writing a recommendation letter as an employer for a student applying to programs in a different field

In the letter, while you describe his duties, you could explain (and provide specific examples if possible) about skills that the former employee has developed and demonstrated that are transferable across all fields, including:

analytical skills
writing skills
interpersonal/collaborative skills
work ethic
initiative

Also consider if the person has written any published work, have they the potential for innovative research that could be a source of grant funding.


If my research is applying methods from field X to field Y, should I do my PhD in field X or field Y?

A PhD is meant to extend the knowledge within a field. It's obvious that you can contribute knowledge to Y, Z, and W, at least if you apply the X methods to solve some research questions in these fields. It's less clear what you contribute to X.

You state that you don't contribute to the theory of X, but maybe you extend or generalize the X methods alongside applying them? If you do that, you could get a PhD in X. Otherwise, Y, Z, or W would seem to make more sense.


How to Get Over Feelings of Being a Failure in Engineering/Academia

It is not helpful to compare yourself to who you aren't.  There is an interesting concept in economics called "opportunity cost", which is essentially the cost of not doing something because, due to limited resources, you chose to do something else instead.  In your case, you left your program and focused on yourself rather than your academics.  Essentially, you chose to work on your internal issues at the expense of your first masters program.  You couldn't do both ,and you had to choose one.  No problem with that.
A better question to ask yourself is: "what do I do now?"  You clearly have a goal in mind for who you feel you need to be in order to be a) successful and b) an academic.  Whether there is overlap between those two or not is debatable, but for now let's assume you want to be both successful and an academic.
You also feel that there are parts of yourself that need work still, and I'm assuming this involves at least academics and personal, internal stuff.  You won't be able to fix it all by posting to stack exchange.  Instead, I think that there are some low-hanging fruit problems that you can start to tackle.

You compare yourself negatively to the person you want to be.  Instead, use that as motivation.  So instead of "I can't organize my research project" say "My best self can organize their research projects.  They do that by..." and then list the things you feel you should be able to do but aren't doing yet.

You seem to be comparing yourself to your colleague who has taken a different path than you have.  Again, motivate, don't discourage yourself.  We compare ourselves to others all the time.  It is totally fair, and probably true, to say that we'll never be "as good" as everyone we look up to.  That doesn't mean that we can't be good at things, and it doesn't mean we can't use those people as examples of how to achieve our own success.

Whether you're starting later or not doesn't matter.  I personally remember thinking that I'd be "so old" when I graduated from my undergrad that I wouldn't be able to do any more learning or growth.  I have since come to understand that what I was really afraid of was being too inexperienced, not too experienced.  I didn't think I had enough time to gain the experience I needed, but I've since realized that a few years here or there to work on things is perfectly acceptable.  How many people go back and do PhDs in their fifties or even later?  Just because it's not how it's usually done doesn't mean it can't be done.
Finally, you appear to be planning to fail.  I think that you are giving yourself an unfair safety net here.  It's easy to say that I won't start because I will fail anyway.  It's much harder to start and fail.


What to do when you found something new, but don’t have motive/application to justify it?

This is hard to answer without more information about the actual problem, but in general it is all about finding the correct publication venue. It does not necessarily mean a venue with lower impact, but one with another focus.

If you really can not think about any practical application, it might still solve an interesting problem and might find an application in other areas.

For example, it might be the case that you found a new method to formulate process scheduling as a graph problem that you can solve in an interesting way. The resulting schedules might not be better than the state of the art scheduling algorithms, so you get rejected by journals about process scheduling. Still it is an interesting graph problem so it might be better suited for journals with the focus on  graph theory.

But the most important aspect in this context is to tailor the paper to the publication venue. If you now try to submit to the graph theory journal do not write "This paper presents a method to improve process scheduling" but "This paper presents an efficient method to solve the minimum dominating set problem under the constraint .... It has, for example, application in the area of process scheduling".


Etiquette in asking for funding proposal example

First: Good approach to looking at successful proposals first. You cannot write a winning proposal if you don't know how winning proposals look like.

Second: Most people will probably be loath to share their proposals with anyone they don't know. But at the same time, most professors will (or at least should!) share their proposals with those they mentor in one way or the other. In fact, they may also take the time to walk you through the process, look over your proposal, give you feedback, etc. So ask your superiors, your department head, or others in similar position who look after your career development to help you with proposals that have been funded.


If I was on a graduate committee, I would want to know

How long you held the job.
What your responsibilities were: e.g. if I was an aide in an undergrad class, did I grade homework? Did I teach the class sometimes? Did I have contact with students? Did I write tests?
How did this job prepare you for admittance into the graduate program. What relevant skills did you obtain?
If the person that oversaw you in the said job is known to the application committee, perhaps say who you worked for. Or if it is a company, say who the company is. There is a huge difference between "Software Engineer" at a company with 5000 employees and "Software Engineer" at a start-up in someone's basement.


My paper was retracted – how can I handle this in my future career?

In the following, I may misinterpret what happened.
In this case, please correct me.
I just don’t want to append “if I understand correctly” to every second sentence.

Let’s first consider whether you did anything wrong:
As your “collaborator” designed the research underlying your paper, he was entitled to authorship.
You understood that he waived that right, which may be correct or at worst an honest misunderstanding.
However, when submitting the paper, you did not disclose this situation to the journal, and as a result, they could not double-check that your collaborator waived the authorship, etc.
Thus I can understand the journal’s reaction.
This failure of disclosure is the one thing others can truly hold against you, but I would not consider this to have career-ending severity, in particular given your collaborator’s abusive behaviour.

Second, how bad is the retraction note?
If I were to read that note without knowing anything else about it, I would primarily be confused, asking myself things like:
“How is overlapping and being based on unpublished research a bad thing?
Why was that research not published?”
It’s nothing which clearly says that you committed misconduct.
In particular, I have no idea what actually happened and would not judge you without hearing your version of the story.
Of course, others may jump to wrong conclusions, but then you probably do not want to work with such people anyway.

Now, how can you handle this situation in the future?
I strongly suggest to be upfront about it.
Should you not mention it and somebody will find it, this can get you into big trouble.
Keep in mind that as long as your collaborator is around, they may inform any of your employers about it.
Also, sitting on this ticking bomb will not be good for your psyche.
For example, mention the paper in some special section on your CV, noting that it was retracted due to “misunderstandings/disagreements about waived authorship” (be careful not to present it as an achievement).
This is accurate and explains the retraction note.
Hiring committees and similar may ask you about it, but then you can tell the entire story, presenting your evidence if applicable.
When you do so, make clear that you are aware of your mistakes, but also that your collaborator was far worse.

Finally, follow the journal’s recommendation and contact your collaborator’s university about this.
If your abusive collaborator was officially discredited, this could substantially strengthen your point.
Whether this is feasible depends on how strong your evidence is, and I strongly recommend that you seek professional help with this (your current university may provide some).


Longer PhD with a deeper result vs a shorter PhD with a sufficient result

There are several considerations regarding whether to graduate now.
I'll go through them from most to least important (in my opinion).

Thesis readiness:
You can't graduate unless
your advisor and your committee feel your thesis is good-enough.
For some departments, you need to have 2 or 3 separate projects
which are in advanced enough state or even published.
Research readiness: As @seteropere noted,
if you feel that you are able to do research independently,
and your advisor agrees, then you are ready to graduate.
Future job situation:

If you can get a tenure-track job or post-doc in September 2015,
then go ahead and graduate in June 2015.
If you can't get any academic jobs in September 2015,
then maybe you should stay one more year.

Job prospects this year vs next year:
For some fields, getting a good job requires a student
to have papers in advanced stages of the publishing pipeline,
i.e. submitted is good, under second or third round of review is better,
and accepted is best.
If you have a great paper but it is not yet ready,
waiting until the next year before you apply for jobs
may allow you to have that great paper
in a more advanced stage of the publishing pipeline
which can't hurt your job prospects.
Funding from advisor:
Is your advisor willing/able to support you for an additional year?
Some advisors limit their support to 4 or 5 years,
and students who wish or need to stay longer may have to carry heavy teaching loads.
Research environment: Are you learning from your advisor,
and doing good work with the other students/professors in your current institution?
If so, leaving for another position becomes more risky
because the situation may be worse than your current situation.
Financial situation:
Usually, a PhD salary is less than a post-doc salary,
which is less than a tenure-track job salary.
For some students who may be supporting a family,
earning more money as soon as possible is an important consideration.


Can I add dropbox links to my resume for graduate school applications?

Your CV should stand on its own.  Admissions committees are likely to have stacks of material through which to look, and will almost certainly make a decision based on what you send them.  It is most unlikely that they'll be willing to hunt around to find things you should have told them directly, and even less likely if they have to download documents from Dropbox instead of just displaying them.

Spend your time making your CV as good as you can instead of spending time trying to take shortcuts, because that's what those Dropbox links will look like to the committee.


Writing two papers on two different topics with the same data = two protocols?

Data sets can, should and are used many times over. Your two very different research questions appear to be candidates for two different research papers, since the one is methodological (instrument accuracy) the other is not.

Even if you keep them very separate in your protocol, lumping them together in one document may indeed be detrimental.

It also appears to me that the methodological question should be worked out first, since the conclusions/findings from this front will qualify positively or negartively the findings related to the other question.


What preparatory steps should I be taking for admission into med school?

Speaking from (1) experience applying and talking to applications officers, and (2) knowing doctors who take part in the admissions process, I would suggest that the ideal medical student would appear as follows:

Any major, but very high grades in all pre-med courses
Very high MCAT score
Experience working in a hospital or medical research lab, with demonstrated results (good recommendations from doctors and published papers, respectively)
Very personable during the interview, well-liked by all interviewers

None of these should be a surprise; they just want awesome, academic students.


For a long theory paper in image/signal processing, you could try IEEE Transactions on Information Theory. The papers typically run about 20 pages, but this classic runs 45 pages. Note that the two-column format can condense a one-column draft by 25% or more.

Trans IT is a very well-regarded journal in my field, with regular contributions from math-y engineers, statisticians, and engineer-y mathematicians.  To quote the aims and scope (emphasis mine):

  The IEEE Transactions on Information Theory publishes papers concerned with the transmission, processing, and utilization of information. While the boundaries of acceptable subject matter are intentionally not sharply delimited, its scope currently includes Shannon theory, coding theory and techniques, data compression, sequences, signal processing, detection and estimation, pattern recognition, learning and inference, communications and communication networks, complexity and cryptography, and quantum information theory and coding. IEEE Transactions on Information Theory papers normally contain a strong conceptual and/or analytical contribution.

The "strong conceptual and/or analytical contribution" means theorems and proofs; don't submit here if your paper doesn't have these. I couldn't find any stated page limit, but if your work is unnecessarily long for its contribution, the reviewers will definitely complain.

Another option is the SIAM Journal on Imaging Science.  There is no hard-and-fast page limit there, but the policies do state that "papers exceeding 30 journal pages, excluding the supplementary material, will be reviewed more closely to ensure that the excess is fully justified."

For both of these journals, expect a very rigorous review cycle.  I suspect that, unless the results are earth-shattering, you will still hear complaints about the length.


I feel that my professor didn't notice a mistake I made on an assignment. Should I have informed the professor of my mistake?

Whenever I've taught, I would find no problem an action like yours.  You might have pointed out a mistake (in which case it's honest and respectable to point it out), and you might have benefited from partial credit (in which case, it's easy for the professor to tell you or to ignore the correction).

I personally would have also found it a delightful breath of fresh air and a break from the students grubbing and grinding for a few extra points, and would feel warm and fuzzy feelings toward such a student.  Anybody who teaches ends up with a distorted view of the student population because most of their time is spend dealing with the most problematic and annoying students, while the vast majority of the student body who are having no problems are entirely invisible to them.  A reminder of the honesty and integrity of the mostly silent many may thus be quite appreciated.


Is there a way to search for papers such that the data used are also published on google scholar?

Not through Google Scholar. Instead, see repositories of open data, including Google Dataset Search, Open Science Framework, and others specific to your discipline.


Can I reuse a recommendation letter that was given to me a year ago for PhD applications now?

Would you send a CV that's a year old?

You have hopefully been doing something in the time between when your professor wrote the letter and now. Your reference letter should reflect that. If you can, ask them for a new one, otherwise find someone who you've been working with more recently to ask.


What does the path to professorship in maths and computer science look like?

My ultimate goal is to be a professor and spend my life researching math topics in computer science, or just math.

Not really. That is, it seems you are not seriously committed to any kind of research, you just like the idea of you being a professor. That is not good enough of a motivation. Don't presume to become a professional life-long researcher before you've done some significant research first. And you won't get such research done before you find a particular research subject (or a few subjects) which fascinates you, which is important to you enough emotionally that you want to spend a large chunk of your life exploring it.

When you tell us that you "want to research X. Or maybe Y"." - what I hear is: "I'm not particularly attached to any research problems."

So - your question is premature right now.


Using a github code for my journal paper

It would be plagiarism only if you don't cite the source. There's no plagiarism issue if you properly explain that you use this source code as a basis for your implementation and make it clear that it's not yours (preferably by citing a paper from the original authors if any, if not just give the github link).
Whether this will be considered an original contribution by the reviewers is a different matter. It might be ok if your motivation and data are significantly different from what the original authors did.


"Storytelling" in the introduction: Math papers

I propose the following guideline as a basis for answering your question: what is "appropriate" is for the author(s) of the article to try to write the best paper they can write, and for the journal editor and reviewer to make helpful suggestions about small changes the authors can make to improve the paper even more. In my humble opinion, the editor should generally not require changes to the paper unless they feel that they are seriously necessary to keep the quality of the paper at the standards of the journal. Thus, there should be a bit of room for authors to impose their creative vision on the work, which also includes the freedom to make wrong judgment calls that annoy some readers.

If you accept the premise above, it follows that if the authors of the paper thought the story with the wine bottles makes the paper better, the editor should let them include it, even if he/she personally disagrees with the decision.

TL;DR: within reasonable limits (and half a page sounds reasonable to me), it is the authors who should decide what is appropriate. Some readers may be displeased, but that is true about almost anything that one writes.


Pursuing a master's in mathematics with eyes on a PhD: Will a D or C in graduate Analysis 2 ruin my chances?

Sorry, I think I have to be blunter than the other answers.

Unless there are extenuating personal circumstances that have led to your poor performance, a C or D in one core graduate course combined with a C in another core graduate course (even if you will retake the course, presumably with a better grade) should make you seriously question your goal of getting a PhD.  Keep in mind many lower-ranked programs admit students in part so that they can have cheap labor to teach classes, while hoping rather than expecting that the student will be able to earn a PhD and get a job using their degree afterwards.  This means you could easily be admitted to some programs without necessarily having a high expectation of success.

Most PhD programs in (pure) math will require you to take comprehensive exams in analysis and in algebra.  Generally speaking, the problems on these exams will be like the most difficult problems in the final exams for your courses, although you will not be expected to solve all of them to pass.  Unless your current professors are exceptionally tough graders, or you have something else going on that indicates your performance this year is not indicative of your mathematical abilities, or you have some sudden gain of insight that significantly improves your ability to solve math problems, you will likely have great difficulty passing these exams.

Moreover, while there are quite a few exceptions, generally speaking, your ability to learn graduate level mathematics is correlated with your ability to do research.  Therefore, difficulties with your courses suggests that you are likely (but not certain) to have difficulties writing a dissertation.  (Since you might be doing a research project next year, you might have more information about this then, so I wouldn't give up yet, but keep this in mind.)

Finally, the job market in pure mathematics is quite dismal and likely to remain so for the foreseeable future.  Someone graduating with an average or mediocre dissertation will not get a postdoc.  If you are a good teacher (and you presumably have some idea by now of whether you could become one or not), you can get a teaching-oriented position, but you can (in reality, not just theory) get most community college positions and many lecturer positions with a Masters degree.  There are almost zero industry positions that you can get with a PhD in pure math that you could not have gotten with a Bachelor's degree (and an undergraduate record that can get you into graduate school).


Is it ethical to reach out to other postdocs about the research project before the postdoc interview?

For every job I've contemplated I have gone out and done what I consider to be the necessary due diligence. If you have connections, use them. If it involves cold-calling a person or two to ask questions, do it.
Fun story - I was considering moving from technical staff to management and an interesting position opened up. My due diligence consisted of answering two questions for myself. (1) Did I really want to be a manager, and (2) was this position the right position to step into management. In the course of a week I talked to about 10 different people, some staff, some managers, some trusted confidants. I decided the answers to (1) and (2) were affirmative, so I applied.
The day for the interview arrived, and I walked into a room with 6 people, the interview committee. I had talked to every single one during my process. Not surprisingly, the interview went very well.
So, yes, go and ask. There are no ethical issues at all.


If during revision process an author discovers and corrects errors not detected by reviewers, should the author inform the editor of these changes?

This is a straightforward question with a simple answer: correct whatever you find is wrong, even if it has not been raised by the reviewers.

I have an experience of more than 600 publications (see Google Scholar for instance) and have reviewed even more manuscripts as peer reviewer, editorial board member or editor, and it is commonplace to have the need and opportunity for improvements in a manuscript during the revision process.

Be candid, disclose the correction. Possibly don't say it was a mistake in the first place, but present it in a positive fashion, saying it is a correction or improvement in the paper.

In most cases reviewers and editors will be pleased by your self-reviewing effort.


What does "signposted" mean in the context of figures in a paper?

In short, it sounds like they are saying they are just getting lost in your figures. As such, they request "signposts", or some kind of further instruction on how they are supposed to traverse your figures and writing to see the point you are trying to make. In my experience, especially with complex figures with multiple panels, readers tend to get lost and don't know how they are supposed to make sense of what you are presenting. Are the panels in some kind of important order? Is there some progressive meaning to each panel which requires comparing between panels, or are they independent?

Signposting can take the form of a more descriptive figure caption, better panel/figure titles, or further instructions in the text. For example, in a figure with 4 panels I thought the most important takeaway is that the points on the graphs got farther apart as you moved from left to right across the figure, showing increased dispersion between methods I was comparing - but readers had a problem figuring out what the figure showed at all, and why I thought it would be important. So I added some descriptive text, along the lines of "the panels are ordered by increasing effect size, and show an increased in dispersion between conditions" - and then I expanded upon that in the text, explicitly referencing the figures. Sometimes it is better to remake the figure entirely to make the key point more clear, and then use additional figures or an alternative design to show the less-central findings.

This is especially important with complex panels, as we who have built the figure have likely spent many hours staring at the results and see them as pregnant with meaning - but to a reader who is just encountering them for the first time, they don't see it the way we do. Even if there are supposed to be many important observations in the figure, at least 'signpost' - describe - a single, clear main idea that is most important. You can then reference it further in the text, returning to it for additional findings, but you have to make at least one key observation relatively obvious or most readers will give up on the figure entirely.


Advice and etiquette for building up collaborations

You sound very optimistic that having met a senior colleague at a conference and having a desire to work with them, will automatically lead to a collaboration. You should consider that they may have other constraints on their time, and may not be able or interested to engage in more collaborations.

Before jumping into the details such as travel arrangements, you should first find out whether they are interested in a collaboration and, if the answer is yes, how they would like to go about it.


How to work in academic research as an outsider/experienced software engineer?

Yes, it's possible, though the opportunities are likely to be somewhat rare, and might require specialist knowledge within software engineering just like you'd expect in your industry jobs.

Your work would likely be in more of a support role, though. Rather than driving the research project you'd be using your software expertise to write custom software or manage data. I disagree a bit with @Buffy on the scope of project that would hire software engineers; there are much smaller projects that can make use of programming skills, and in the past my small research group has had a share of a programmer's time.

I would recommend you start by looking at job postings at universities near you (or where you would like to live).

Expect salaries that are below what you would expect for your level of experience outside academia, and that many positions will be fixed-term.


How to equitably divide the economic benefits of a licensed patent among academic inventors?

(Expanding a bit on Buffy's answer)
Short answer: Use some math to make everyone happy.
This is actually a well-explained problem in economics for which there is a solution.
It is possible to mutually assess everyone's contribution, without anyone unfairly boosting their own contribution, so that the proceeds are distributed in a way that everyone is likely to be satisfied with. This is, as Buffy said, a type of cake-cutting algorithm.
A Tool
If you'd like to skip the theory and go straight to a solution, check out spliddit.org/apps/credit. They provide a web app for everyone to subjectively assess everyone else's contribution and computes the fair proportions. The theory behind it is pretty clever, and you will likely find that everyone finds the splitting to be satisfactory.
A Theory
If you're looking for a more principled answer (other than "try this tool"), here's the paper that describes the theory and method used by Spliddit in rigorous depth: Impartial Division of a Dollar - Clippel, Moulin, Tideman
The method satisfies two formalized criteria:
Impartiality - no one assesses or covertly influences the assessment of their own contribution
Consensus - the ultimate division is compatible with every individual's assessment of others' contributions
Good luck!


What are some good ways to take a break during the academic workday?

Getting back into "The Zone" always takes some time. Relax, while nervous it just won't happen. Walking seems to do the trick for you, perhaps warm clothes help when taking a stroll. Socializing doesn't for you (and I doubt it would work for me). Perhaps read a chapter of a book (not technical, a novel or so). Or try meditating, or yoga. Or go to the gym for a half hour or so.

And don't get all worked up if it just doesn't click one day. In my case, when nothing works, I just give up and do "chores", like chasing after references to complete bibliography entries, check it there are new versions of documents/software packages out, edit my notes. Or do my course-related work (invent homework/exams, ...).


What are potential PhD funding sources for international students in UK?

Most universities in the Russell Group provide a scholarship for PhD students in natural and mathematical sciences. Nevertheless, they tend to be very competitive, and, for obvious reasons, there is preference to UK and EU students. Usually, a professor/lecturer writes a project, and if it is approved by the department, a PhD student can be fully funded. It may be the case that your potential supervisor does not want to do this as it is time demanding or the project is not a priority in his/her agenda.
Another way of finding a fully funded PhD studentship is to look for projects that fund an international PhD student. These tend to be less restrictive in terms of your nationality. You can find hundreds of opportunities at:

https://www.findaphd.com/


Can I include a Table/Figure which is mentioned on the "discussion" section, after the Conclusion section?

Unless you are submitting to a journal that expects "camera-ready" copy, it doesn't matter. They'll reformat it anyway. Put it where it fits in the narrative, to make life easy for reviewers.


PhD dropping out and funding reimbursement

This will depend on many things including local law and the details of anything signed. In the absence of some rule, it is unlikely that there is any need to repay. In particular, many funding agencies have no real way to accept money paid back. The reason that the person dropped out may be very complex, and actually a shared issue with the institution.

But this can differ widely. Read the fine print if any.


Making a joke in an email asking for a PhD vacancy?

TL;DR: Women rates funny guys as more intelligent. Are professors the same?

No, not really.  In ordinary conversation, nobody is expected to say anything deep or knowledgeable.  Making a joke at least shows more cleverness than many of the alternatives (such as chatting about the weather).  On the other hand, in a context where you might be expected to say something with real academic content, just making a joke instead suggests that you don't have anything else to contribute.  I think it would be better to try to engage with the subject matter, even if you are clearly not an expert yet, than to look like you are deflecting the issue with a joke.

The worst case scenario is making a terrible joke and seeming overly proud of yourself for making it.  Don't write to someone doing gene editing and say "Your recent papers are really impressive and have been getting crisper and crisper (get it? LOL!). I guess mi Cas es su Cas, am I right?"


What can be done to bridge the gap between amateur and professional mathematicians?

First, I can't help but notice your complaints are extremely vague and the language is evasive. You don't like "sociological culture usually shared by professional mathematicians", but it's hard to guess what you mean by that, and what are specific "aforementioned issues" you have problems with. Put it into plain words, please.

However, I can give a general comment. Amateurs might indeed have brilliant ideas, and this is true for all branches of science from history and linguistics to maths and chemistry. Amateurs can write papers and submit it to journals/conferences as we at universities do.

The problem is usually in, as you say, "lack of technical knowledge and methods", which in practice means that these papers are often poorly written (I had to review some) and aren't ready to be published. Your idea of "bridging the gap" by effort of retired professionals is rather popular among amateurs: we might have brilliant ideas, and all we lack is just knowledge of some technicalities, so we just need someone to take care of them, so we can focus on the big things.

Unfortunately, working in science is a full-time job, and dealing with "technicalities" takes most time. I would go as far as saying that understanding the methods and being able to write a decent paper is as important as having bright mind full of cool ideas.

Potential "gap-bridgers" should 1) be good in several wide areas (while academics usually specialize in narrow fields); 2) devote a lot of free time to find grains of brilliance among 99% waste generated by amateurs; 3) do the hardest and least rewarding work by turning mere ideas into something publishable; 4) neglect own interests in favor of pursuing someone else's agenda.

Summing up, an amateur doesn't necessarily have to undergo a formal training and get a PhD. However, having good understanding of methodology and paper writing is vital. There are books devoted to this subject -- take your time and acquire the necessary knowledge rather than waiting for someone to do the job. If you still need help, try to collaborate with people having more experience and write a joint paper.


Theorists facing tenure track faculty interviews

If you don't need lab equipment or space to do your research then just say so and explain what, if any, support you do need to conduct your research (e.g. travel funds, a desktop computer, a chalkboard, coffee, etc.)

If there is an expectation that you will bring in external funding to support graduate students, then you need to be prepared to respond to questions about possible sources of funding and how you will involve graduate student research assistants in your research in a way that will be considered appropriate by both the funding agency and your future institution.   Not being prepared to answer this question could very well cost you the position.


Making latex sourcefiles publicly available by default

If you upload your papers to arXiv, then your Latex source is already publicly available there (click "other formats" and then "download source").  So the only difference is that the source would also be available on Github.

There is no legal issue with this unless you sign an agreement that forbids it.  In that case, the publisher could ask you to remove the manuscript from Github.


My research area has very few research positions, would it still be possible for me to stay in academia?

I wonder if it is still be possible for me to get a postdoc (possibly in one of the two places) and later go to a top-ranking school for tenure-track positions?

Yes, this is possible. But, unless you are making definitive progress on famous open problems which are well-known to everyone in your field.... then it is very unlikely and you should not count on it. (And perhaps even if you are.)

Most academic jobs involve both research and teaching. For example, I work at a research university with a Ph.D. program and a 2-2 teaching load. I definitely have time for research, but teaching is a big component of the job, and if I didn't enjoy teaching I would not want to do this job. (Moreover, if I wasn't good at teaching, then the hiring committee probably would have picked up on this and not offered me the job in the first place. Most people who are good at teaching, enjoy it.)

I think you are wise to investigate your other options. I've known people who decided not to pursue (or continue with) academic careers, and for the most part they were able to find good jobs. Software companies like to hire mathematicians, and you might learn programming if you don't know it already. Some mathematicians successfully go into finance (and make boatloads of money doing it.) Actuarial work is another possibility. In any case, these sorts of jobs don't generally just "happen"; you have to proactively think about what you do like and look for opportunities.

Good luck to you!


Sharing an unpublished paper but retrieved from a third-party site?

Disclaimer: I am not a lawyer. This is not legal advice, just educational information.

As the owners of the copyright, you face no restrictions over what you can do with your own material, even if it was downloaded from a third-party site. Frankly, there would be grounds for you to have the material removed from Scribd, since they never got permission to use it! (On the other hand, academic information should generally be shared as widely as possible... and there's always the possibility that you lose your copy again!)

Whether or not Scribd has embedded a tracker of some kind is largely irrelevant, since they have no legal interest in the material. The worst they could do is close your account. Of course, there are plenty of ways to scrub out any such watermark; I'd ask in the Information Security stack exchange for that.

As an amusing anecdote tangentially related to your situation, several years ago Nintendo released their "Virtual Console" for the Wii. This was an emulator that allowed people to play selected old SNES games on the Wii. Of course, in order to sell their old games in this form, they needed copies of them... and it seems they didn't have them. Disassembly of the Virtual Console app shows that the included version of Super Mario Bros. was downloaded from a pirate site!

This is interesting and amusing, but there's no copyright problem here. In order for there to be one, they would have to bring suit against themselves, and they would lose that suit because they have full rights to use their own game.


Does membership of academic honour societies carry any professional weight / recognition?

Does membership of honour society carry any professional weight?

No, not in general.  At a very early stage in your career, for example when applying to graduate school, it may be useful as a quick indication that you have received high grades.  However, the grades themselves are more meaningful than the honor society membership, and in any case grades only matter so much.  It's worth mentioning the honor society on your CV, but it won't make a big difference.

Once you are more than a few years past undergraduate studies, neither grades nor honor societies matter.


Am I missing something or is submitting from the ArXiv really that unfeasible?

I think you are not really missing anything at all, except that there is not compulsion to make the set-up as minimalist/efficient as you seem to argue it should be. That is, while you and others may not find this feature useful, it's probably harmless, no? And some programmer somewhere might've thought it would be interesting to implement this, and proposed it to whatever authority, it was approved, and so on.

But, yes, there are common situations for many people (in math, familiar to me) in which the submission to arXiv is essentially simultaneous with a submission to a journal, whether or not they make use of a literal submit-from-arXiv feature. So, yes, a paper might be considered ready without-change-from-the-version-submitted-to-arXiv. Why not? (Sure, one might realize things later, perhaps upon referee reports...)

As to whether one "has to wait until arXiv publishes..." Well, apparently, yes, since your paper won't have been processed. Perhaps someone who knows the inside workings of the software at arXiv (which surely could change from time to time) knows a trick to interact with the system prior to that, but I've never heard of anyone finding a need to do so, given the quick turnaround. But I can't help but wondering why a day-or-two delay would matter...

So I think you're right that it's a fairly useless feature, but it wouldn't be the first.


Is it ethical to contribute to a workshop one is organizing?

I've helped organize several minisymposia (MS) at conferences that are built entirely out of them, and it's basically expected that we submit to our own MS. Out of three MS organizers and 8-10 expected speaking slots, 2-3 will be from the organizers. A few workshops I've attended at more prestigious conferences have been similar. The conference wants its events to be full, and if the subevents are peer reviewed, especially double-blind, then there's no possible conflict of interest in my view. Even for single-blind review or no review (abstract-only submission) as long as you don't review your own work, there's no problem and self-submission is practically expected in the fields I publish in.


Is first authorship a big deal (in terms of highlighting it on CV, etc.)?

As mentioned here this is field dependent. Given your former advisor offered you the first authorship and assuming that if ordered alphabetically he would be the one to be the first author, then yes, it is something to be excited about.

In my opinion better than highlighting in a CV that you were the first author it would be better to describe what you did in that paper yourself and what was done by the other author(s). And maybe even better that putting this to CV would be to put in to a motivation letter (or any other text accompanying your CV in an application somewhere).


Submitting paper to journals and/or conferences in different fields

Two important things that you need to consider:

If the papers share any substantial amount of text, then you would be guilty of self plagiarism.  If this is discovered then its likely that one or the other or both papers will be rejected before publication or retracted after publication.
In submitting to most conferences and journals a condition of publication is that your article is an original contribution.  If reviewers become aware of a duplicate publication of essentially the same research (even if the text is distinct) then they can and should reject the paper as not being an original contribution.  Some editors might retract a paper after publication if they discovered that you'd published essentially the same research elsewhere.

It might be reasonable to submit two different papers to journals or conferences in different disciplines as long as the papers really do contain different material.  However, it's utterly inappropriate to reuse text or even to submit two papers that report essentially the same results.

Statements by various publishers about duplicate submission/publication don't include any exception for publication in journals from different disciplines.   In short, the answer to your question is "no."

Some statements on publication ethics that discuss duplicate submission and duplicate publication:

http://www.icmje.org/recommendations/browse/publishing-and-editorial-issues/overlapping-publications.html
       http://www.oxfordjournals.org/our_journals/jpepsy/for_authors/multiple_publications.html

http://www.biomedcentral.com/about/duplicatepublication


What merits acceptance for rapid publication in letter format?

From my understanding of the term, it seems to me that your job is to evaluate two things:

Is the manuscript in "good enough" shape to publish without a proper, more rigorous peer-review process? As you say, there's no opportunity for a back-and-forth with the authors, although presumably they would have an opportunity to incorporate your feedback. So you'd need to be confident that the manuscript will be publishable with just one round of revisions.
Is there a clear, urgent need for publication that warrants circumventing the traditional peer-review process? I think the editor is looking for your recommendation, given your knowledge of the field and your assessment of how timely and significant the contribution is, as to whether to publish the manuscript as a letter, rather than as a regular research article. I imagine the authors won't make an argument for rapid publication specifically in the manuscript (due to lack of space), but perhaps in an accompanying cover letter or something similar (as indicated in this answer).

Regarding your specific question about a submission that is "original and novel, but may lack investigations or results," I think it is your job to judge:

whether publishing the manuscript essentially "as is," without such investigations, will sufficiently spur further advances in the field such that it's worth not waiting for those results; and
whether there is significant risk of similar, cutting edge work being published elsewhere earlier if this manuscript is subjected to a full peer-review, that would undercut both these authors and the journal you're reviewing for.


Should I include the names of my Master's and PhD supervisors in my CV?

Additionally, your supervisors might have written you letters of recommendation for grad school (or could in the future for other grant applications). Thus, mentioning your former supervisors is a form of acknowledgement and transparency for other researchers or research institutions.  I totally agree with the former comments that in 90 %, it won't harm you.  In case you are completely unsure, you could ask your former supervisors whether they are okay with it (but I would be surprised if there is an academic scholar who says no)


Reproducible research and corporate identity

My university has had enforced its "corporate identity" since the 1990s. It is described in details on a web site and available in a series of templates. Although I get a sense of tiredness when I read the material surrounding the "identity" I can also see benefits, to recognize the university "products" (sorry) among other materials at a congress etc. But, the question was about reproducing material.

As I see it I would want to have the logo on material such as posters or presentations so that people can identify my affiliation. I am free to post presentations and posters or other materials on my university site with the logos on them. If I want to put some material out that is mine I simply would not use a unversity logo. An example: I have written several hopefully useful booklets on scientific writing to be used by students. This material is my initiative and is not the result of the university asking for it. These booklets are distributed for free using our web-page and I would gladly distribute them more widely if there was demand. So from this perspective I can see two different "products" where one benefits from the logo and one where I do not want it.

Now the rules of my university says the logo is copyrighted which means others cannot use it. this still means I can post material with the logo in public places. The problem arises if someone takes my, say, presentation and uses it as their own. Then they break the copyright and make themselves guilty of a kind of fraud by associating themselves with an organisation to which they do not belong. I still have done nothing wrong, posting material is fine and even encouraged. The copyright also prevents people from the taking the university logo and adding it to their own "product" fo rexample showing it on their web-page or using it for commercial uses.

So now, the content. You seem to indicate that you will be prevented from displaying your work without the branding. I do not think this is correct. The laws on copyright and particulary intellectual ownership in my country is very clear. If you have created something it is yours. In a commercial company you may end up sign off this right by becoming employed so that the things your develop within that company belongs to them, not you. That is how research in pharmaceutical companies work, for example. My university system has made attempts to gain rights to lectures etc. but this has so far failed miserably due to the strong laws. You need to check these laws that apply to you since I do not know how they may vary internationally; I would expect them to look fairly similar.

You mention "proprietary fonts". This means the university has selected fonts and bought them from a font foundry so that you can use and copy them for free within the university system. This does not mean other cannot use them, they must simply buy them first so providing copies to persons outside of your university would be illegal. Since fonts are not included in Office templates or in pedfs resulting from your templates there is nothing illegal about distributing such documents. If you were to take the fonts and produce a product that you were to sell for your won personal gain, you will, however, break the law.

The bottom line, then, is that you can put your  material in the creative commons as long as you avoid the logo (ater all who would want to use a figure with somebody elses logo in it?). I cannot see the university preventing you from doing this unless they explicitly ask you to waive your rights. Material with logo has its place when you want to make sure your afficilaition is clear. If you do not want that, then I believe you are free to post things in another style.

Finally awareness of the laws and regulations concerning intellectual rights are important and I strongly believe it is good to carefully look at whatever applies in each of our cases so that we can react if someone tries to infringe on such rights.


Do US Graduate Admission Committee review and assess International Applicants country-wise?

I doubt that there is any widespread effect of this. In fact, most grad schools would want, and many would require, a "level playing field" for admissions. But the GRE is not the main determinant of anyone's admission. It is at most an indicator, among many others, that might indicate success in a program, or not. Letters of Recommendation are relatively important in US.
Your application needs to give strong indicators of your likely success. But you don't need to be "perfect in every way" to gain admission.


Is university teaching better than high school teaching experience in applying for teaching-funded PhDs?

If there is an option definitely university teaching is more valuable as it is at the same level as the teaching you will experience while doing your degree. However, you should consider that PhD is a research-based degree and teaching obligation is not primary concern. So you might get the position without having any teaching experience and finally get your PhD being a year or so younger.


Ph.D. work seems like a drag sometimes, is this normal?

This is quite normal - it is possible to be passionate about the topic, but at times, to be not so enthusiastic about the work involved.  This could be a sign that you are need of a bit of a break, or in the worse case, heading towards a burnout.

A few things to reflect on:

Are you getting enough sleep, exercise and eating well?
Are you making time to visit and go out with family, friends and other like-minded academics?
Are you giving yourself some time out to pursue other interests and hobbies?
There would have been times that the greats of the topic felt the same.

These greats of the field more than likely had days when they also could not be bothered.

Specifically, why not consider the following:

The days when the mathematics is very difficult, take these as challenges (rather than hurdles) to accomplish (rather than just overcome)
Teaching the class could be opportunities to refine your mathematical (and mathematical communication) skills and similar type of skills.
Is there anything you can change to make your situation more enjoyable?

It is very normal.


Starting postdoc before getting PhD. Is that possible?

Yes, it is possible. I and many others started a postdoc before officially obtaining the PhD. However, your chances may depend on country, postdoc position, and field. For example, in some countries before the official defense the PhD has already been examined by the committee and hence there may be more trust from a potential postdoc PI that you will not still be focusing on your PhD.


First, your titular question:

  What is the value of participating in proposal-writing efforts, for a postdoc researcher?

Especially in Europe, and when applying for faculty positions, the value is huge. Successfully playing the grant game is nowadays what keeps the lights on in many European universities, at least research-wise. Having a track record in this dimension can easily be viewed as even more desirable than a great research track record (although, of course, you will still need at least good publications).

  should I highlight this experience in my cv (i.e. provide more details about the bids in which I participated, my role, the outcome etc)

Yes, you should definitely highlight this somewhere in your application (not sure if the CV is the right place, though). Your letters may or may not be a good place, if LoR are considered important for the job you are applying to.

  If I have the chance to avoid being involved in proposal-writing efforts, should I?

This is an interesting question, and mainly depends on what your grant and research track records look like at the moment. If you have not actually been involved in grant proposals, I would certainly recommend getting this experience. If your research track record is lacking, I would focus on research. Realistically, you will need a good record in both dimensions to be competitive for faculty positions.

  Moreover, how can one's claims be verified? How do you prove that you are telling the truth and not over-selling yourself, regarding your participation and experience? Isn't this part of your cv a part that is less verifiable?

In the optimal case, you have won some grants in your own name. But even if this is not the case, the experienced recruiter knows what to look for and who to ask to figure out whether you are overselling yourself. Keep in mind that researchers are connected and EU projects are large - somebody in the hiring faculty will know somebody who was involved in your project and give them a ring to ask them whether you actually did what you claim you did. If that's also not possible, the recruiting faculty will just ask you a few questions regarding the claim they are interested in, and observe your reaction.


Doing research outside of academia, without a PhD?

As Nunoxic noted, doing research as a part of your job is possible. Also, doing research at a graduate program that isn't at a top school is possible. But doing research on your own, and hoping to bring innovations to a field... is highly unlikely to work, in my opinion.

My opinion is based on experience with a bad schooling system (undergrad and Masters in Serbia) where publication is mostly irrelevant to survival of the teaching staff. Access to research journals is also severely limited, and, as a consequence, access to international conferences, international collaboration and all that. Essentially, supervisors would offer minimal guidance, and students are always free to choose their research topic. This is still more guidance than you would have on your own.

Then I got myself into good schooling system (a second Masters - to catch up - and now my PhD studies), in The Netherlands. Neither of the two Dutch universities I've been studying at are top schools in the Shanghai sense: their rankings fall between 100 and 150. Still, in comparison with Serbia, the difference in what I've learned and achieved since being at these universities is staggering.

I don't spend months of my time sifting through articles in order to slowly begin comprehending which papers/names are the most relevant ones in the field.
I have someone to immediately tell me if a research question is worth pursuing.
I have someone to immediately point out similar research.
I have someone to immediately correct small mistakes that would prove important at the end of data collection
I meet important people in the field, and get feedback from them, with no cost to myself
I work with technology that costs a great deal of money, with no cost to myself

The essence boils down to having access to people who know what my work is about. This speeds up my understanding of the subject matter by an order of years. Science is so fast-paced nowadays that it's very difficult to make breakthroughs without collaboration.

In sum, my advice for someone in your position would be to give priority to non-top graduate schools, if it doesn't work put with top ones, instead of trying to be a solo researcher.


How to mention paper that we withdrew and another paper under preparation in CV?

I would avoid mentioning the bad-quality conference and the withdrawal.  Mentioning it may send a negative message about your  planning habits, and your willingness to waste peoples' (reviewers') time due to those planning habits.

After re-submitting the paper, you can mention it in your CV if you clearly label it as "submitted". The other, unsubmitted paper can be mentioned as well, with the note "in progress" rather than "submitted".


In computer science, what does winning a Sloan research fellowship say about an advisor?

The Sloan research fellowships are distinguished awards for early career faculty.  This means that your prospective advisor is considered a very talented young researcher.  However, it also means that your prospective advisor is not very far along in their career.  There are some cons to working with a young assistant professor as an advisor, including the risk that your advisor might leave the institution or not get tenure (not terribly likely for someone talented enough to get a Sloan fellowship but more of a risk in the generic case of working with a new tenure track faculty member.)  I think that most people would recommend picking a more experienced and well known advisor.