How to evaluate a software implementation for master thesis

The goal of your thesis was to create a tool that meets certain requirements. Consequently, your evaluation should show that your tool satisfies these requirements.

One way to organize your thesis is to have a section called "Requirements", where you walk through all requirements detailedly. For example, you could have following requirement with sub-requirements:

R1: Generate 3D cat models: the tool can generate 3D models from 2D cat images

R1.1: Brown cats: the model generation works for brown cats
R1.2: Black cats: the model generation works for black cats
R1.3: Checkered cats: the model generation works for checkered cats

Then you have another section called "Validation" where you walk through the requirements a second time, this time discussing for each requirement how you satisfied it.

R1: The cat model generation was implemented in the catgen component of the tool that uses the XYZ algorithm to build the cat models.

R1.1: for 4 sample cats, the tool was able to produce a model (see Fig. 1)
R1.2: for 5 sample cats, the tool was able to produce a model (see Fig. 2)
R1.3: for 3 sample cats, the tool was able to produce a model (see Fig. 3)


What is the standard way to include introduction and references parts to a masters thesis?

You mix up two things: Thesis introduction and Chapter introduction.

From what I observe, every thesis has to have an introduction. It makes sense after all: You need to introduce the topic of the thesis etc. You can't simply start a math thesis by Theorem. For all X ... -- you need to start somewhere, and that's the thesis introduction.

The chapter introduction is a nice thing to do, and there are more options. It can be a short text before the first section, a separate section, some people even provide short (3-or-so-sentence) abstracts to each chapter. However, this is mostly part of your writing style, and it can't be so much enforced (well, it can, but that is IMHO ridiculous).

As for references, there should be guidelines for them. If there's no, then I advise to include full list of references at the very end, since that's what people expect by default, but it's only an advice, not a rule.


What, if any, roads are open to graduate schools for athletes with borderline grades?

I'll answer based on the U.S. (which is where these issues are most relevant, I believe).

There is no special consideration for athletes in graduate admissions.  Undergraduate admissions are handled by admissions officers who often use all sorts of non-academic criteria, and recruiting athletes to play for the university is a specific goal at many universities.  However, graduate admissions is done by departmental committees made up of faculty, and the non-academic criteria that play an important role for undergraduates (well roundedness, extracurricular activities, athletics, etc.) are irrelevant.  If anything, a continued desire to participate extensively in high-level athletics could be considered a disadvantage, since it would take time away from academics.

If Derek Jeter wanted to go to graduate school, I'm sure some faculty would be impressed by his fame, but they would also be careful and skeptical in evaluating his qualifications.  In any case, there certainly wouldn't be a special admissions slot designated for an athlete.


Should I chase up confidential feedback not being "sanitised"

At most institutions in the United States, instructors are given their course evaluations in toto, only stripped of names. It's up to students to not write anything which would lead to deductive disclosure. But there's plausible deniability, so you could have feigned ignorance when she approached you (which was an entirely unprofessional thing to do).

If you are worried about retribution then speak to your chair or at the very least send an email note so that you have a paper record of your concerns.


Is it acceptable to require a post-doc to teach a course?

In the UK universities, the pressure to teach is very significant. Postdocs employed on RCUK grants / fellowships are often given an "opportunity" to contribute 20% of their time to teaching. This is not a formal requirement -- they can, of course, reject the opportunity and focus on research. But focusing 100% on research would not necessarily be wise, since their next University is likely to look for candidates with some teaching experience already (unless they move to a different country / sector).

Since it is your fellowship, you can set your own rules to a certain extent. I have heard of PhD studentships with attached duties, e.g. to staff a University museum for a week, etc. It is not unusual for a fellowship / bursary / studentship to come with some strings attached, and it is may be even a good thing to help selecting "right" candidates for the fellowship.


In choosing a postdoc, how should I prioritize mentorship versus research opportunity?

I think that the choice of mentorship versus. research opportunity* entirely depends on your own way of working/your preferences.

If you are very good at working independently, enjoy working on your own and have the ambition to become a full professor then I would pick research opportunity over mentorship.

If you need or desire a lot of guidance, or flourish when you have lots of discussions with someone 'higher up' and you don't really care whether you do cutting edge science or just good science then you might be better of going for mentorship over research opportunity.

*As a sidenote, mentorship and research opportunity don't have to conflict necessarily. There are small research groups with excellent mentoring that do very cutting edge science


Inquiring about the possibility of a job

Is it appropriate to email my former advisor and ask to be notified if/when they choose to fill that position?

It’s generally appropriate to ask about job opportunities and to express potential interest. However, I wouldn’t rely on the former adviser to remember to notify you of something several years later (for me it’s hard enough to remember what someone asked me to do last week), and asking for such an open-ended future commitment to notify you might come across as a bit insensitive. It might be better to phrase the request as a question about whether they anticipate that there would be openings soon, and if so, what would be a way that you could learn about them.

As a general rule, people will show more good will towards you and willingness to help you if you show yourself willing to do things yourself (like keep track of job postings at a place you’re insterested in) instead of asking them to do those things for you.

  How should that email be phrased?

Since it sounds like it’s been some time since you’ve had contact with your undergraduate advisor, I suggest starting by saying hi, reminding them of who you are (there’s a good chance they’ll need their memories jogged, even if that may sound unlikely to you) and updating them about what you’ve been up to. They will probably be glad to hear you are now beginning a career in academia.

After that background, you can get to the point and simply say you’re writing to inquire about job opportunities that might open up in the immediate or near future. It’s okay to mention the professor retiring, but I should caution you that the way you’ve phrased your question suggests an implicit premise that departments always fill positions of professors who retire with new faculty who have similar expertise or are qualified to teach similar classes as the retiring professor. In my area (math) that is usually false. So keep that in mind when you mention how your own expertise overlaps that of the other professor.

Good luck!


My master's thesis is extremely similar to an article that had already been published. Is that okay?

I had this same question when I began writing my concept paper for my dissertation. I was alarmed when I found similar articles related to my dissertation topic and I almost changed topics in a panic. My advisors told me that finding related research was to be expected, but that I had to prove that my research would add value that was missing or limited within the findings of the prior studies. To provide proof, I created a matrix of all of the related material from my literature review to show how the others sources were similar or different to each other and how my research would fill the gaps.

I think it is very important to show that you are aware of the related research and that you have a clear understanding of what you are adding. One place to get a clue of this is to look at the Recommendations for Future Research that will be in the closing of the related research.

Good luck with your thesis.


Is it appropriate to register a girlfriend with "companion registration" for an academic conference?

In the conferences I am aware of, companions are people not attending the conference, but coming along with some of the participants for tourism or company. Depending on the venue, they may or may not offer some alternative activities for them (anything from visits to the city to a heap of maps and sort yourself out).

If this is the case, your girlfriend would fit right in, as long as she is not interested in the conference itself.


Can a penetration test write-up be used as a bachelor thesis?

Sorry, but the only valid answer will come from the professor. It is acceptable or not based on their views only.

But be aware that a penetration test on a real system can come with legal implications. Claiming to be a white hat may hold little weight with authorities. Gaining permission, as you suggest, might be very difficult as institutions running real system have a lot of concerns beyond the obvious. Their own legal department might nix any such project.

A simulated system is fine, though seldom has sufficient protections in place for a valid test. An iterative, competitive, duel between two teams (Red team, Blue team) might be interesting.

The answer to the general question, though, is yes, such a test can be used as a thesis, but only with the consent of the advisor. The general answer to the question has exactly zero impact on your case.


How can I avoid learning secrets at a research internship that would block me from legally pursuing research interests after it's over?

You should take the internship - congrats on that. Yes, you may learn some stuff that is proprietary to the company - it will be quite specific, and far more application oriented than anything you are likely to do in grad school. Working there will give you some good ideas about how things work in the real world (the fanciest ideas don't always produce good results). Finally, they know you are an intern - the probably won't have you working on the deepest darkest proprietary stuff.

You are not now, and will not be, the first or last student intern at a company that has proprietary information. Just be clear, before you go, what they consider as 'theirs'.


Intellectual theft by a colleague, how to respond?

It sounds like your adviser is already on the case -- let her handle it. She may know the colleague better, may know better how to handle such situations, and is in a position where she may not care about consequences any more if she calls out the colleague about the issue (because she already is a professor). You, on the other hand, do not have this luxury and consequently would be better off letting someone else handle this as long as you think that it is handled in a way that goes in the right direction.

So, rather than being involved yourself, let her handle that and keep you updated as to what is happening.


How to write good Response Letters for the reviewers

If the reviewers are in error, yes you should show it to them, but you should often also take the opportunity to revise your paper, so that your readers don't fall into the same error.  For example, suppose reviewers say that you could use such and such an approach to get a better result.  If they are right, then you should either do it, or explain why you're not doing it.

But if the reviewers are wrong, then maybe you should address this idea in your introduction.  In one paper I wrote, we included in our introduction a false one paragraph proof of the thing we took 10 pages to prove.  Afterwards we pointed out the error.

For one paper we submitted, we got conflicting referee reports.  Essentially, the referees both wanted us to revise the paper, but in different directions (to oversimplify: one reviewer said "shorten and simplify" and the other said "lengthen and elaborate").  We agreed with one report, and disagreed with the other.  So in our response, we pointed out that we couldn't do both .  We explained why we preferred the choice we were making, and our paper was accepted.

You don't have to do everything the reviewers suggest. But if you don't, your response letter should explain why you have chosen to do otherwise.


Have you considered using ebooks in situations where they're available and reasonably priced (and don't have Digital Rights Management)?

A few years ago when I went to Los Angeles for a sabbatical leave, I made it a point to get electronic copies of as many of my frequently used books as possible.  I bought a few, but mostly I was able to work with freely available copies.  This dramatically reduced the number of printed books that I had to take with me.


Should I add descriptions of courses taught on my CV

A brief description of the courses you've taught is never remiss, as it helps reviewers place your teaching work into context. This is especially important for teaching-primary positions. However, for many positions, you also have the ability (or requirement) to submit a "teaching statement." This would be a place, for instance, where you could discuss your unique projects.

What I would certainly want people to know about in the courses I taught:

Full course name
Whether they were required or elective
The intended audience (e.g., "freshmen" or "upper-year undergraduates and graduates in the major")
How long (how many times) you taught the course
Did you have sole responsibility, or was it co-taught
Format of the class (lecture, seminar, laboratory, etc.)
A brief description of the course, if its nature cannot be inferred from the title (for example, "Introduction to US History to 1865" doesn't need an explanation; "The Critical Period" would.)

Other information could be listed on a "courses taught" appendix, but I might not necessarily include it directly in the CV.


How to Cite an IGO Document in Chicago style

A report is referenced in the following format in Chicago style

  Last name, First name. Title of Work. Publisher city: Publisher, Year
  of publication. Accessed Month Date, Year. URL.

In the case of your report you have 2 authors and an unknown place of publishing so Bibliographical note would be;

  Cullen, Dr. Patrick J., and Erik Reichborn-Kjennerud. MCDC Countering
  Hybrid Warfare Project: Understanding Hybrid Warfare. N.p:
  Multinational Capability Development Campaign (MCDC), 2017. Accessed
  September 26, 2018.
  https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/647776/dar_mcdc_hybrid_warfare.pdf.

As you can see N.p is used to show that there is no record of place of publisher. This can be seen in this guide and this question.

Your first footnote should look like this;

  Dr. Patrick J. Cullen and Erik Reichborn-Kjennerud, MCDC Countering Hybrid Warfare Project: Understanding Hybrid Warfare (N.p:
  Multinational Capability Development Campaign (MCDC), 2017), page number.

Your subsequent footnote should look like this;

  Cullen, MCDC Countering Hybrid Warfare Project: Understanding Hybrid Warfare, page number.


Are there any tools to automatically search and download literature in a given .bib file?

In contrast to the freemium/proprietary tool suggested in the answer by andreas, I propose a FOSS solution that works reliably for this specific task.

Assuming you are connected to a network that provides permissions to legally download the required content, the cross-platform reference manager,JabRef has integrated fetchers to download full-texts for the entries in your library. Import your bib file into Jabref (maybe just start a new library for this task to keep things clean) and select the desired number of entries for which full-text PDFs are needed. Then, from the Quality pull-down menu, select Lookup Fulltext documents.

However, you still have to manually confirm all downloads. From the user's perspective, this requires just a bunch of clicking the OK button in the same on-screen co-ordinate (for pop-ups that appears sequentially for each citation entry). Jabref does all the heavy-lifting and correctly downloads the desired PDFs of the full-text and link each of them appropriately by matching to their relevant citation entry in the library.

The latest master build of Jabref is recommended, since there were some recent fixes to its IEEE fetcher (i.e. if IEEE matters to the OP).


Why do people say you shouldn't do a PhD unless you want a career in research?

Research is not just the most important aspect of any PhD program worth the name; it's the entire point. Everything you do as part of the program (teaching duties aside) is to prepare you for a career as a researcher. So getting a PhD without any intention of putting this research training to use would be like spending years as a baking apprentice without any intention of becoming a baker: maybe not a complete waste if you really like baking (but not enough to make it a career?), but almost inarguably not the best use of your time.

Lots of people get PhDs and don't become researchers, but if these people had known beforehand what industry they would end up in, odds are they could have gotten a better jump start on their career by getting a  Master's degree focused on that industry and entering the workforce after one or two years (rather than 5+ for the PhD). There are exceptions to this principle, but they are relatively uncommon, and usually involve industry jobs that somewhat resemble research anyway.

I can think of only two other justifications for getting a PhD: learning for learning's sake, and prestige. The former is a noble goal, but if all you want to do is learn without contributing to the body of knowledge in your field, this is contrary to the spirit of (good) PhD programs as stated above. Furthermore, you can learn all you want in your free time without entering a PhD program. Find out what the standard graduate-level textbooks are in your field, and work through them. If your knowledge gets up to the research level in a particular topic, you can start reading recent research articles. (Your local library will likely have access.) As for prestige, this may be subjective, but spending five years of your life for a piece of paper is unlikely to be satisfying in the long run. And, speaking as someone who has a PhD, you'll soon learn that most people will not really want to address you as "Doctor."

Having said all that, if you do like (or think you would like) research, but are put off solely by the expected competition and stress, I urge you to be more open-minded. Academia is certainly competitive and stressful, but so are most careers worth having.


Have I given my PhD supervisor enough time to react to serious issues before raising it above their head?

Your university has a responsibility to provide you with adequate pastoral care. If these issues are related to your well being you should talk to your student support services. If they are related to the managemt of your project and the progress you've been able to make as a result then keep emailing your supervisor and reviewer. If it's both, do both.


“Theories”/“frameworks” for how multiparadigmatic research should work (in the context of interdisciplinary research)?

Interesting question. My suggestion would be to look in the social and historical sciences for advice how interdisciplinary research can work fruitfully. The standards of methodology and reproducibility can vary very strongly from fields like engieenring to psychology so that researchers from both fields have a very hard time to find a common denominator apart from common vocabulary or measured quantities.

In the social psychology/historical sciences branch I'm aware of very fruitful interdisciplinary projects/collaborations and results that have been published.

Even phycisists study social systems, nonlinearity of complex systems, population growth models etc. So often interdisciplinary research seems to be worthwile to understand which and how distinct quantities in complex systems are scaling. Multivariate statistics is a common method here to understand the structure of complex systems by different perspectives and methods. But a common scientific language or method seems necessary, even if it is as simple as counting things in both disciplines and relate quantities to distinct phenomena. While machine learning algorithms are not very smart, they can show at least whre possible correlations or dependencies from perspectives of each discipline are.

There have been many tests by researchers to publish nonsense articles in journals of other disciplines, e.g. Sokal affair. So rather falsifications of multiparadigmatic/interdisciplinary research.

I think a good place to look would be EU funding calls requiring interdisciplinary collaborators and setting up clear requirements and goals for the project results to get a picture what modern interdiscplinary research standards are.


Is it okay to work in a very old research area (in TCS)?

You have discovered a fundamental trade-off. If you work in an obscure field and do something significant it may be harder to get recognized, but you have the field to yourself and a few colleagues. But if you work in a popular area you might just get lost in the crowd and even get scooped in your latest findings. Neither is ideal. But either can be a path to success.

However, you need a base from which to work. But so does everyone. In looking for an academic job you need to match yourself to requirements and also show that you have the potential to stand out, at least a bit. If you are competing with 40 other people just like you in background and research interests it will be difficult to stand out. But if you are unique you will raise questions about how you will fit in. It is, however, your case to make.

It is easier, of course to do what you want when you are already well established (tenured). But you have to do what it takes to get tenured. But I don't think you need to defer doing what you like. You just need to do it well.

Personally, I find your interests intriguing. But that is because I studied math but worked in CS. I'm certainly not unique in that. Being able to collaborate across departments might be seen as a plus in some institutions. So might joint appointments between two departments. Everything is a tradeoff.

But spending your working life on things that don't much interest you just because they are "hot" seems like a waste of talent. Since you don't seem to be one of those fighting to get into one of the top ten institutes in the world, but can, perhaps, have somewhat more modest goals (top 50?, 100?) I think you can do fine.

So, yes, you can be a successful researcher, but you will have to make that success yourself.


Is a German Hochschule able to offer a Ph.D.?

One further note to clarify is that using "Ph.D." to denote doctoral degrees in Germany is somewhat nebulous, as many of the doctoral degree-granting institutions in Germany do not award Ph.D.'s. Instead, the range of doctoral degrees is somewhat broader. For instance, the institution where I work offers the Dr. rer. nat. and the Dr.-Ing., but not a Ph.D. In fact, we are not even allowed to use the term "Ph.D." in our advertising of our doctoral degree programs.

So, if you are asking "can German universities award doctoral degrees," Pieter's answer above is correct. However, if you mean literally "can German universities award Ph.D.'s," I'd have to say the answer is essentially "no."


What does it take for a lower-ranked university to compete with a top-ranked one?

Money can indeed buy a lot of things that will move you up in rankings, though probably not all. It's true that you will be able to attract good faculty with money -- spent on salaries, research infrastructure, beautiful offices and spacious labs well equipped with machinery, several postdocs attached to each professor position, and maybe money to support (grad) students and travel. For this, you will actually need a lot of money -- take a look at the budgets of the really good universities in the US and UK, and you will realize that you will need an operating budget in the $1+B region per year. So $10B will be spent quite quickly.

But that by itself will not be enough. Faculty will generally only go to places where there are also good students, and the best students go where they can historically expect to get an excellent education. To find out where these places are, they look at, say, the top 20 or 30 universities in the world -- so you're caught in a catch-22 if you want to move up. In other words, you have to have a long-term strategy to move up: things can't be achieved within a few years, but it will take 10, 20, 30 years of big spending if you really want to get high in that list.

There are some examples of relatively new universities who have really tried this, and you can look at the press coverage to see what they have achieved and what they haven't:

The King Abdullah University of Science and Technology (KAUST) in Saudi Arabia
The Okinawa Institute of Science and Technology (OIST) in Japan
National University of Singapore

There are other examples in China and in the gulf countries of universities that have (tried to) significantly rise in rankings in recent decades.


What does 0/3, 1/3, 1/4, 1/11, etc. mean in the context of assigned reviews in a journal management system?

My intuitive guess is that it's the number of reviewers who have completed their reviews / been invited to review. The journal invited 3 reviewers in the first month. Two months later, one reviewer finished the review, but the other two either didn't accept the invitation (more likely) or didn't submit a review. The journal's policy is to have at least two reviews per paper, so they invited more reviewers, to the current count of 11.

If this guess is correct, then there's nothing to do except wait. You can also write to the publisher asking what the number means - it can cause no harm.


Should I ask colleagues of my mentor for internship opportunity?

I think it would be perfectly reasonable for you to a) ask your mentor which of his colleagues might be accepting students and b) mention his name when contacting his colleagues, AFTER you've first made sure he's ok with this plan.

I don't think you need to be worried about a conflict: he's opened the door by saying that he's too busy to take on students this summer. As to whether he'd give you a good reference, that's quite hard to say, which is why it's best to ask him. Paper rejection in and of itself doesn't mean he doesn't like your work.


Applying for a mathematics PhD in the US after getting a BSc degree from Imperial

Most US students enter doctoral studies after "only" a bachelors degree. It isn't a reach at all. But expect there to be coursework and exams. The coursework is something like what you would get in a masters, but is intended primarily to prepare you for the qualifying examinations. Serious dissertation research often starts after you've done a couple of years of other things. But you aren't likely to finish in three years from where you are now. Expect something like twice that.


What will happen to Academia in the future when it takes too long to become an Academic?

There is one thing that you are leaving out and it is critical to understand it. Researchers work at the frontier of knowledge, the frontier is vast and growing, but an individual only works (concentrates) on a very small part of it. Getting to the "research edge" has always been hard, but no one knows everything within the known bubble of a field if the field is at all advanced.

For example, it is no longer possible for any individual to know all of mathematics. The last time it was possible was early in the 20th century. Henri Poincaré may have been the last. There is too much there. But no mathematician worries about that. You can know a bit about a lot of things, but to work in mathematics you need to know a lot about a few things. So we specialize.

It is also the fact that the path taken by a researcher to reach the edge (say, in mathematics) isn't the same path that was taken 50 years ago, since much of what has been learned in the past hundred years has been abstracted into the courses that fresh students take. That compression wasn't available in the past when a sub-field was fresh.

What you describe as the necessary path isn't wrong, but you don't need to learn everything that it is possible to know in order to be effective in extending the frontier of knowledge. A researcher's path is narrow and deep. You focused on the deep, but it is the narrow that makes it feasible.

For completeness, however, I'll also note that there are parts of academia that value the broad as much as the deep. There is room for the people who know a lot (broad) and can synthesize it for students and for the creation of the learning materials that students use to guide their own path. Such people may not be state-of-the-art researchers, but they understand the edge of the known universe well enough to describe it properly.


Is it common to work concurrently on projects with PIs other than your advisor?

It very much depends on your relationship with your PI, funding sources, etc. For example, a PI might discourage this kind of work if you are solely funded by one of their grants, wherein they need most/all of your research output heading toward a specific objective. On the other hand, it might be necessary to work on other projects if you have a gap in funding and need to take a research assistantship elsewhere for a semester or two.

In my own experience, even within a given department (or even a given PI), there's also a component of how interested a given student is in pursuing other projects, and how well they balance their time.


How can I develop leadership skills in graduate school?

Actually, I am surprised your graduate school doesn’t offer these kind of trainings. Graduate schools prepare PhD-students for their future life, whether in academia, industry or entrepreneurship. My graduate school offers for example also trainings on: leadership, group dynamics, teamwork, effective negotiation, autonomy and self management.

You probably have some room for ‘electives’ in your curriculum. Maybe you can use that room and follow your prefererred trainings in another (nearby) graduate school or in private sector. It may bring some additional costs and your department should be prepared to pay for it.

I would certainly contact your graduate school about your needs because these are legitimate and in line with the objectives of a graduate school. In my university graduate students can also contact an HR advisor to talk about their future career development. I would be highly surprised if your graduate school or HR advisor could not / would not help you in shaping your future path. Maybe your request even helps your graduate school to improve or expand its curriculum.


What must an international graduate student do before arriving in the US?

Some key things that any international student will typically need to do before arriving in the USA:

Obtain a student visa.  Your institution will be able to support you, but you are likely to need to lead the process yourself, including going to a US consulate in your country.  This can take a long time, so it is important to start many months in advance.
Make sure you have any required vaccinations and health certificates (I'm not sure whether this is part of the visa, or separate; your institution and the US consulate can advise)
Find housing.  Some universities will help with this, many do not.  For example, MIT is notoriously bad about this, and the Boston rental market is insane.
Ensure that you will have health insurance.  The US (still) does not have a national health system.  Your institution will likely provide insurance, and may assist you in enrolling, but not all institutions will.
Ensure that you will have access to money from your bank accounts, if needed.  This can sometimes be a difficulty, and many things in the US are much more difficult to do without a working credit or debit card.
Ensure that you will have a working cell phone.  The US does not use the same standards as most other countries, though this is slowly changing.  Just changing to a local SIM card may or may not work.

Caveat: I might be missing some things from this list...

Regarding scholarships: the USA does not have any organized system of scholarship exams.  In many cases, however, graduate programs in STEM fields ensure financial support for their students through TAships or RAships.  Any reputable Ph.D. program will do this, but Masters programs are much more mixed. Check with your particular program to find out what they advise.


How can I document depression for later reference in grad school applications?

Your transcript should be all you need. Presumably, your transcript shows that you studied at a foreign university, and that things did not go well. If you are back to 100% next semester, it will be pretty obvious that the problems were related to studying abroad. You may then want to write something in your statement of purpose when you apply to assure them that attending grad school won't cause problems similar to what happened when you were studying abroad. This should be an easy sell, especially if the exchange program was in a very far away country and the grad program is in your home country/region.

At any rate, graduate school admissions people certainly do not want to see documentation about your health or personal relationships. They just need a believable reason for why that one semester doesn't indicate you are unfit for grad school, and the transcript showing you studied abroad far away and had some problems should address that. The only place you may run into problems is if your application is automatically filtered out before it reaches the committee -- but no way to avoid that.

The question posed in the title is a bit more challenging. You are able to attribute your difficulties to having studied abroad. For students who suffer mental health challenges at their home universities, graduate school admission is more challenging. Even in this case, however, I do not think they are interested in seeing medical or other documentation.


I would recommend against it. I've been bitten by this in the past: A famous quote attributed to a certain person, that after some investigation seems to be mistaken.

Specifically: Many sources claim that Newton referred to "The Great Principle of Similitude" in regards to dimensional analysis, but having searched all through his Principia and other writings and not finding it, I'm now pretty sure the phrase comes from Rayleigh in a letter to Nature (No. 2368, Vol. 95; March 18, 1915). There's even a class at Stanford by that name, which recently changed its description to attribute Rayleigh instead (link).

In summary: If you can't source it, then you probably shouldn't reference it. I feel pretty bad about saying something to several years of math students that turned out to be incorrect. Make a commitment to not distribute misinformation.


How to deal with if you found someone is using your research proposal?

Could that topic have been a relatively "generic" topic or a topic that is now fashionable? In which case it is not unlikely that people come up with similar ideas. Fashionable topics are unlikely to be exclusively yours.

However, if it is an exotic idea, you may have been very unlucky. In which case, cut your losses and move on.


What would be different between two years of graduate admissions?

In the US, if you get admitted to a funded PhD program, often they will let you defer a year. If for some reason they are unable to let you defer, then the next year your application would be looked at fairly. A lot can change in a year, so it is no guarantee that you would get in again. The quality of the competition can change, the allocation of students to supervisors, and the amount of funding can all influence chances of admission. Sometimes faculty leave and the admission committee changes from year to year. Admissions can come down to a single vocal advocate.

If you get accepted to multiple programs and decline the offers (you can only really defer from one place), your application may not be judged fairly the next year. Admissions involve some politics and trying to judge if a student would accept is part of that game.


Is it unethical to accidentally benefit from online material in a take-home exam?

I suggest that you don't lose a lot of sleep over something that happened several years ago. While you may have crossed a line, your description suggests it wasn't a bright line. Assuming your description is honest, you started out (probably) appropriately looking for alternate explanations of the material, not solutions to the problem at hand. But, rather than the internet it might just as well have been a different textbook.
But if it bothers you, then, assuming you are an academic, make sure that your own students get more explicit advice about what is and is not permitted.
It would have been better, of course, if you had pointed out the situation to the professor. But let the past be the past. Make the future better than the past if you are able.


It is completely acceptable to display this kind of information on your CV and I can't think of any situation where it can hurt you professionally or socially. However, I would not recommend putting this kind of information on the resume you send out for specific positions (or even proposals) unless it is important to the job (or proposal) you are applying to.
I say this because your CV is a more complete profile of your professions and abilities and listing another language (preferably near the bottom somewhere above hobbies) will not be deemed as a bad thing and in many cases it can actually have a positive effect on how others perceive you. However, a resume is more tailored for specific needs and listing irrelevant information can always have a negative impact on the opposite person.

EDIT: In my personal line of work/study (computer science), speaking another language usually does not help you directly, but is is seen (by many) as an indication of your potential abilities. Speaking another language (and speaking it well) is not an easy task and those who are capable of doing so, show above-average motivation and determination.


How much comparing to another paper is too much?

1) Is it bad to compare to one single paper often in a paper?

Not at all. It happens all the time. If it represents a significant improvement of the paper in question, especially one that opens up new possibilities, you don't have to hide the fact that this is what you have done. The same answer applies to your question 3). Whether or not it is a significant improvement of the paper (and thus the answer to your question 2) is exactly the sort of thing that peer-review is supposed to address. Trust your instincts. Resist the temptation to inflate what you have just to get a larger paper.

As far as the second set of questions go, you could write two papers and submit them simultaneously, the second referencing the first. It isn't uncommon for researchers to cite unpublished but submitted work.


Which one is more valuable in a postdoc application? a full paper in a B* conference or a short paper in a A* one?

A short paper at an A+ conference is better on your CV than a full paper at a B+ conference, because readers will pay attention to venues and will most likely ignore paper lengths (even if you include them -- which you probably won't, because they take up room).

But, it seems like you're trying to decide upon a venue on the basis of only the immediate impact on your CV, you should take a broader, longer-term perspective.

Backstory: The OP's paper was originally ten pages and it has been accepted at the A+ conference on the condition that it is reduced to six pages.


Can I include images licensed CC BY-NC 4.0 in a conference paper?

Summary: Is it ok for you to include the CC By-NC 4.0 image in your paper?  Yes.  Is it ok for the paper to go through a particular process at the conference? Maybe (see below).

The answer to this question is not clear-cut.  There is no general agreement as to what constitutes "commercial purpose" with CC licenses.  There has been much discussion on the CC pages which has resulted in guidelines, but they are still not black and white.

The best approach is to contact the person who owns the copyright for the image and ask them for permission.  That is the non-ambiguous approach.  If that is not possible, the next best approach would be to discuss the issue with the conference in question.  Depending on how aware they are about licensing issues, they may already have an option in place to address your situation.

A separate issue is the one of copyright transfer.  You are free to transfer your own copyrighted content to another body, such as the conference.  But you cannot assign another person's copyright to them.  Usually there is a line in the copyright transfer agreement that requires you to specify that you own all of the material being assigned to the new owner.  Regardless of the outcome above, you do not own the copyright on the image, even if you have permission to use it.  These are separate issues.  Once again, you should discuss this issue with the conference organizers.

My personal experience has been that many conferences request copyright transfer as a blanket process without realizing that it's often not necessary.  When I have contacted such conferences and told them that my work is published under a CC license and that I will NOT assign the copyright to them but WILL give them permission to use it as they see fit, they usually accept and have no problem with it.  Sometimes, however, the conferences get stuck on procedure and try to force a single process that doesn't fit modern publishing constraints such as the ones you describe.


How to explore Physics research as an undergraduate, keeping in mind the ever increasing weight on publications?

It would be amazing for you to get 2-3 publications before you enter PhD.  Maybe it’s just the semantics of what is meant by “getting 2-3 publications” but just participating as co-author in one publication in first- or second-quartile journal is not that common, and it’s extremely unlikely that this would be “your” publication, i.e. that you would be the major contributor to this.

It is not easy to publish original work in a mature field like cosmology: the low-hanging fruits have long been picked.  In other words, all the easy work has already have been done by current researchers or their graduate students or their undergraduate students, or by the generation before them.  Rejection rates in well-recognized journals are generically above 70% of submissions, and these are submissions by authors who considered their work sufficient good to submit to those journals in the first place, i.e. the rejection rate would be much higher if it weren’t for a significant self-filtering of submission to good journals.

I recommend students not to play it safe at the undergraduate level, i.e. if they would like to learn about cryptography then take a crypto course rather than some other “safe” topic which might narrow rather than expand their expertise.

There is this nice article published in the NYTimes which makes a similar point, although in a the context of students obsessed by grades and from a more “dealing with failure” perspective.


Should I notify students that I've interacted with after getting sick, by email?

Either you infected them, or you didn't. Sending an e-mail about it will not change that (enough time has passed that telling them to wash their hands now will make no difference).

Therefore, it only makes sense to send an e-mail if it turns out to be something where early treatment can make a big difference, or where ignoring it can do harm. (IIRC, this year's flu is an especially bad one, and students might be tempted to dismiss it as just a cold. It's good to remind people that the flu kills and that they need someone to check in on them every few hours.)

Technically, an early warning might also let them avoid people until they are sure they aren't infectious, but in practice that is unlikely to happen as "I was in the same room as someone with fever earlier" probably won't be accepted as a valid reason to skip class...


Personal Statement(s) for two similar masters courses

You want the two statements to be unified, so that a person reading both isn't confused. And especially, doesn't think you are playing to the audience rather than being honest. As you suggest, the programs may share faculty, and hence admissions committee members.

But especially, don't say things in one that are inconsistent with things in the other.


Deal with academic failure as an undergraduate

Allocate time specifically to prepare for your tests
This might seem like a waste of time, since you would rather spend it studying the course material more deeply. However, this is a trade-off you should be willing to make in pursuit of your long-term goal of entering into research. If 100% of your studying time is currently spent on learning the course material deeply, you may need to reduce that to 75–80%, and spend the rest of the time doing test preparation. I understand that test preparation can be extremely boring and feel completely pointless. But, as you've noticed yourself, you need to score a minimum amount of marks to stay afloat in the system. There is no need to judge yourself by your course marks, though; feel free to think of it as just an arbitrary number that you need to display in order to apply to graduate programs.
Furthermore, to the best of my knowledge, a few failing grades will not disqualify you from applying to the graduate programs of any university. I believe you have options to take the failed courses again, or at least their final exams, so make use of that. If you plan to apply to graduate programs in India, in particular, as long as your overall grades lie above the cutoff and you perform well in the interviews, you should be fine.
Finally, your attitude towards your education is commendable, but at some point the effort involved in going through the system may end up not being worth it. Several talented classmates of mine found this to be true for themselves, and chose to take other paths. You will need to choose your path, too, and possibly very soon. But try your best to fulfil at least the bare minimum requirements before deciding that this system is not for you.


How to withdraw from an application process in a polite manner?

Just send a polite email stating that you found another position or that you simply prefer to take a different direction. Be sure to thank the professor for the time he has put into you. The email does not have to be long, but it should give a reason. You do not need to be overly elaborate, though. And don't forget to be polite.

The thing you do not realise is that the professor wants to find a student who will be committed to his topic for several years to come. If you are not such a student, it is best for the professor to know that before taking you on as a student. In a sense, you are doing the professor a favour by withdrawing.


Is it recommended to invest in stocks as a typical broke graduate students?

Don't even think about investing until you've saved an emergency fund enough to cover at least 3 to 6 months (and perhaps a year) of living expenses.

Due to exponential growth, investing earlier does have huge advantages, but for PhDs in many fields you make more than enough after PhD that you will be able to invest enough to retire comfortably even if you save nothing before you get your PhD, so there's no reason to be stressed about this until you graduate.  And you may need your emergency fund for the time between graduation and your first job.  Once you have your first job out of graduate school and have saved an emergency fund then you can think about this.


Methods for Assessing The Performance of an Exam

The most common analyses I've seen are generated automatically by scantron grading software, and are thus only used for multiple choice questions. But a motivated person could perform the analyses themselves.

I've read a few articles on test analysis over the years, and this summary of a particular scantron software's results seems like a good overview of test analysis in general. A quick summary to improve searchability:

Item statistics:

Item difficulty - percentage of students answering correctly. Desirable = above chance.

Item discrimination - how much item correlates with test as a whole (students who did well on the exam get this right more than low-level students). Uses stat like Pearson Product Moment correlation. A "good" question has a score over 0.2.

Test statistics:

Reliability coefficient - A general measure of test length, breadth and its intercorrelations. Scores above 0.8 are considered excellent for a classroom test.

Some other interesting measurements are used more in standardized testing, rather than classroom testing. These definitions are taken from this overview.

Construct validity - does the exam actually measure the subject, or some other variable like reading skill. Generally uses a panel of "experts" or feedback by students.

Split-half reliability - measures whether different test items that purport to test the same concept produce similar results within a single exam.

Criterion-related validity - measures how well the new test correlates with a known exam, like an ETS field test or GRE subject test.

If you don't get a basic output from scantron software, is there a department on your campus that will analyze your exam for you?


How to ask professor to let me audit lectures at university I am not enrolled in?

First I would check if the school has a formal procedure for auditing. For example, my school wants auditors to pay as if they were attending the class, and they also have insurance concerns if, e.g., a student is hurt in a chem lab and it turns out that they weren't enrolled. You can get this info from the school's web site or catalog.

If that's not an issue, then I would just send a brief email and ask permission. There are unlikely to be any objections, but it would be polite to ask. Some conceivable problems:

There might be a shortage of seating.
In certain subjects (e.g., languages) or in classes using certain teaching methods, it might be expected that students will participate actively. The quality of the discussion or activities might be worse if there is an auditor who isn't taking the course seriously.
The professor might want to talk to you for your benefit to see if you have enough of a background to get anything out of the class.

Personally it doesn't bother me if an auditor's attendance is irregular.


What are the negative effects to the first author when adding coauthors?

I think for some people, the principle is important: they didn't feel that the person whose name has been added contributed enough, and humans hate the feeling of giving up something unfairly.

That said, there is a very real cost in terms of credit.  This will not be consistent across different people looking at your record, but every new co-author decreases the chance that the important part of the work will be attributed to you.  There was actually a recent study about this which found that women pay an especially large price on this score: when they do joint work with men, the evidence suggests the men tend to get the credit (the actual observation of the study is that their chance of getting tenure do not improve).  You'll note though, even for men a solo paper improves chances of tenure by more than a jointly authored paper with anyone.


Can a PhD thesis in computer science have two major parts?

This is a question for your advisor. In general, what is acceptable in a thesis is what your advisor and committee will accept. If the division into parts makes everything clearer then all to the good. If the two parts complement one another, say theory and application, then it should be fine if the advisor agrees.

But also, what is a "Part" is also a function of the writing style. In CS, for example, one "part" might be new and necessary algorithms and another part might be how they are applied, or evaluated, or ...

But a thesis that tries to solve two different problems is likely less useful unless they are tightly bound. In such a case, focus on one "part" and save the rest as future work.


How to calculate overlap with a previous publication

Your problem is that you need to show your paper is sufficiently original to merit publication.  Calculating a measure of overlap will not help you achieve that goal.  Instead, you need to:

Clarify the original aspects of the paper.  For example, you might write in the paper "Previously we showed [minor progress]" and then "but we did not solve [major problem in the field]" and finally "in this work we achieve [important step towards goal]"
Justify to the editor why some overlap is necessary.  For example, "This paper is about x, which is well known to experts but may be unfamiliar to some readers of this journal.  Therefore, we repeat our introduction to x from our conference paper."
Remove unnecessary overlap.

The editor will be looking for meaning, not quantity.  Don't invent metrics where they are not needed.


What sources of information are there to find suitable congress, reunions, convention and other scientific gathering events?

A quick search at the CORE conference ranking website produces the following:

Tier A:

IEEE Computational Systems Bioinformatics Conference (CSB) [can't find a link! WikiCFP seems to think it hasn't been held in a while either]

Tier B:

Asia-Pacific Bioinformatics Conference (APBC) Perennial website
Workshop on Algorithms in Bioinformatics (WABI) 2018 website

Tier C:

Bioinformatics Visualization (BioVis) 2018 website
IEEE Bioinformatics and Bioengineering (BIBE) 2018 website
IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) 2018 website

An alternative venue for searching for relevant conferences is WikiCFP, which gathers Calls-For-Papers of a great many conferences.


Sourcing lecture notes instead of publications

I firmly believe that one should cite what one has used... and possibly more. To use a source and not cite it is simply dishonest and fails to give credit where it is due. At the same time, yes, one also wants official credibility, which usually entails citing refereed-journal publications (although the latter is not a promise of correctness, either). If nothing else, citing refereed-journal publications is expected, so doing it is doing what one is expected to do.

(Lecture notes are not always mere echoing of textbooks or journal articles.)

So, cite both the actual source you used, and find "cite-able" sources to accompany, so you'll be both honest (and explanatory) and "formally correct".


Are non-degree courses a viable option to offset a low master's GPA?

This wouldn't hurt, but whether it helps depends on the admission process at that university and how competitive it is generally.
Another possible benefit is that the faculty (at least a few of them) will become familiar with your work. It also shows some seriousness of purpose.
The letter of recommendation may be possible.
But, have you explored the option of just applying. You may be making assumptions about how important your GPA is in the process. Many things are considered, including letters you might already be able to get and how strong your background is generally, and even undergraduate work.
If you can discuss your current situation with someone at the university, do so before you make decision.


Lack of congruence in mathematical abilities versus writing abilities in faculty

Writing is part of your everyday life and an essential job skill, as a STEM academic. The comparison between your writing skills and the basic math skills of a humanities professor is only valid to the extent that these math skills matter for the humanities professor's job. By all means, if their mathematical inability is hindering their research or teaching, they should brush up. But frankly, I trust them to make that call, and to seek out the many resources that are already available for that purpose, if necessary. If they need "encouragement" to do this, I question whether it would be all that helpful. You could teach them to add fractions, but if they didn't use it regularly, they'd forget again. If your only reason for why they should know math is that you as a STEM academic know how to write, I think it's a stretch. It would be like a physical education professor coming to the math department and saying "I remember geometry, why can't all of you lift weights?"


Is it better to start the paper title with a verb?

I see two issues here. The one is the stylistic sense that some people have developed over their life and that is not necessarily always to be generalized. The other is the strictness of such "style advice".

For the first issue: Everybody develops some kind of preferences about stylistic things they like or dislike and things they believe to be (or have worked) better than others. This personal preference does not necessarily coincide with what is generally considered to be good style, which means it could be true in the special environment of this person but it could also be some anecdotal experience that has no broader foundation. Therefore I would be somewhat cautious to take such advice too strict when it comes from a single person and you cannot find it anywhere else.

For the second: Let's consider this rule exists (which I don't know and didn't check), you shouldn't take it as a strict "law". If you have a title that fulfils the rule and you feel good with it, then go for it. But don't try to twist your formulation just to meet this single criterion as the confusion that you create with it might outweigh the "beauty" that you win by starting the title with a verb.

TL;DR: Be careful with possibly subjective "style advice" and don't take style guides as strict "laws".


As a student, is it appropriate to use my university's letterhead for a letter I write, to give it extra weight?

Do not use any professional letterhead when you are not speaking "on behalf" of the entity it comes from.

Using your status, like explaining who you are or whatever, is fine. However, the sole fact of using entity's letter head, implicitly involves your employer and can only ends in a bad situation.

If you are writing to another department of the same university, like in case of an internal matter, this can be deemed acceptable, but otherwise I would refrain from doing it.


This answer is about the US.

  Are there any for-profit schools that have achieved a good reputation in academia?

As far as I can tell, the answer is (1) we don't know, but (2) probably not.

The reason it's difficult to know the answer to this question is that although there is a variety of mechanisms for judging the quality of education at non-profit schools, such mechanisms either don't exist or aren't working well in the for-profit sector. US News and World Report doesn't rank for-profit schools. There are accrediting bodies, but the ones that handle accreditation for for-profit schools seem to be lap dogs of the industry.

Because of the lack of data, people in the federal government who have been trying to crack down on fraud have been forced to use various proxies as measures of educational quality. For example, they look at the percentage of graduates who default on the government-sponsored loans that they used to go to for-profit colleges. People have also tried to figure out what percentage of students at these schools actually end up employed in their field of study. All of these statistics are at best indirect measures of quality, for-profit colleges tend to come out very low on these measures, and the colleges tend to give out fraudulent numbers to try to make themselves look good by these measures.

You can try to try to pick out a specific college, or a certain program at a certain college, as a success story. I didn't have much luck at that when I googled. One article mentioned Microsoft certifications as an example of something reasonable that you could pay a for-profit college to help you prepare for. But when I started looking up information on Microsoft certifications, it basically sounded like a scam in which the instructors are really not vetted at all, and the purpose of the program is to achieve sales and vendor lock-in.

Another example I've heard about is that often community colleges don't have enough capacity to handle the demand for certain programs like nursing. In theory, it would seem to make sense for the private sector to take up the slack. As private, non-union businesses, they are more agile. But the reality seems to be that these programs are of extremely low quality. For example, stories abound of students taking a semester-long nursing course in which five or six different instructors come and go before the course is over.


If your professor really doesn't want you to leave, he needs to offer you a permanent position. It may be that keeping your association going would be good for you. But you need to leave the nest eventually and fly on your own.

But it sounds like you are in a good position to finish your doctorate early. I suggest that you do that, at least. Accelerate anywhere you can.

There is no reason that you can't explore a position elsewhere as you get closer to the end, to see what is on offer. It is good to have options.

To maximize your future, stay as helpful and cooperative as possible.


Can lowlighting less important text improve readability? Are there alternatives?

Yes, there is an alternative to de-emphasizing the less important parts (which might possibly impair readability): Emphasize the most important parts. Something you can do is to use clearly outlined boxes with "take-home" messages, like in the example below:


writing a paper as an independent researcher

First point - don't force it. Getting ideas for academic papers comes over time and has to be a natural process. The more you try to get good ideas for papers, the more unnatural the process can become and the less likely you will be to come out with something worthwhile.

The best way to get a good topic is just to carry on reading around in your field as you normally would. At some point you may well come across a topic or a research gap that needs to be filled and one which excites you and stimulates you at the same time. That is the point where you can start planning your research.

Bear in mind that a good research article topic can take time to discover. It can be weeks - or months - before you come across something worthwhile and that you feel you can turn into something research-worthy. You don't necessarily need anyone else to do this with, but you do need natural drive, enthusiasm and acumen in your area. If you have these, you will come across a topic and be able to write about it and conduct research effectively. But don't search too hard: writing academic papers should be a natural process and you'll find that something will present itself soon enough.


Do researchers study topics outside their field for fun?

Fundamentally, a researcher studying a different field "for fun" is in no other situation than anybody else studying "for fun". It's a hobby, just like reading, going to the theatre, or sports. Some engage in this hobby, some do not. Whether they "have time for that" is really the same question as whether they have time for any other hobbies - some do, some (especially on the tenure track) are maybe a bit crunched for time, and choose to use their little spare time on something a bit farther removed from their daily work grind.

  Is there any known case of a researcher who, by studying a topic outside his/her field for fun, had an insight for a novel approach or solution?

I am sure there is. Note that "having a an insight" is not a particularly high hoop to jump over. My students "have insights" all the time, the question is whether they are important, work well enough, and are generally more useful to pursue than the myriad other ideas they could use.

My gut feeling is that you rather meant whether somebody had a big breakthrough in a different field as a "hobbyist". I think this used to be more common in times past. I can't really think of a recent example (at least in the STEM fields), as plenty of time and resources (both of which a hobbyist definitionally does not have much of) is required for major breakthroughs.


Do measurement protocols belong anywhere in the scientific publications?

There are a bunch of journals coming out for methods now, e.g. Methods in ecology and evolution.  Methods work is increasingly seen as a contribution in its own right.

On the other hand, it sounds like you may be writing quite an excellent review paper, and in that case you might include (unusually!) a methods section in your review article, and mention your methodology as one of the contributions in the article's abstract, intro, conclusion etc.

You should regardless of whether you publish the method be sure to include it as an appendix or part of the methods sections on your papers you use it on.  All papers need to be reproducable.  If you haven't published the paper featuring it yet, you will need to describe the full method in the first paper that uses it.  The editor will tell you whether to put this in electronic, appendix, or methods, don't worry too much on submission.  If you have already published it, you can just cite that publication and any differences / improvements since the publication.

Go ahead and blog it too.  Different people read blogs from papers.  Some people prefer to wait until they've got it published and past peer review before you go public on a blog.  But unless I thought the method itself was going to get me into a journal with an embargo (e.g. Nature / Science – unlikely!) I would probably blog it now.  I'd do that with the caveat on the top of the blog post in bold that it hasn't been published yet, and then another caveat at the bottom of the post in italics asking for feedback.  When your papers get published, be sure to go back and edit the blog post, edit out the caveats, and link to the new paper(s) so people who find your blogpost will cite your papers.


How can I anonymously store supplemental research data that I submit with papers?

If an author is very concerned about keeping their data private and anonymous until the last moment before publication, the workflow would be like this:

The authors deposit their data in a private repository while they are finalizing the manuscript, before submission. They ensure that the documents and files they upload to the repository do not have their names on them.
The authors obtain a 'view-only' link from the repository. This link will give anyone access to their private repository in a way that hides the repository metadata so that the authors of the repo are not visible to people using this link.
The authors insert this view-only link into the text of their manuscript, for example in the data availability statement. Then they submit their manuscript for peer review. Their data remains private on the repository.
Anyone with the manuscript, such as the editor and peer reviewers, can click on the 'view-only' link in the paper to download the data. The peer reviewers can anonymously inspect the data on the repository, and they do not see the names of the authors on the repository.
Once the paper is accepted, the authors switch their data repository from private to public, and the 'view-only' link is removed from the manuscript, and replaced with the DOI to the public repository of the data. The editor or copyeditor checks that the paper now has a DOI, because the 'view-only' links typically expire after a few months.

The repositories that I know support this workflow are:

Open Science Framework: https://help.osf.io/hc/en-us/articles/360019930333-Create-a-View-only-Link-for-a-Project
Figshare: https://knowledge.figshare.com/articles/item/how-to-share-cite-or-embed-my-data
-Dataverse: http://guides.dataverse.org/en/latest/user/dataset-management.html#private-url-to-review-unpublished-dataset
Zenodo, not exactly as I describe above, but very close: https://ineed.coffee/5205/how-to-disclose-data-for-double-blind-review-and-make-it-archived-open-data-upon-acceptance/amp/

There may be others I don't know about!


Failed undergraduate research project: does it belong in my CV?

I think for an undergraduate student, it is quite valuable to show that they have experience working on a diverse range of problems with different people, even if some of such projects do not lead to anything substantial.

Usually for grad school application and other fellowships there is an essay component. It may also be useful to mention such projects (briefly), and how such experience clarified your research interest/taught you how to do research/provided cross-disciplinary/cultural experience, etc. The exact messaging of course depends on what you think the program is looking for from the applicants.


What to do when journal comments to rewrite the article?

Obviously, the editor felt that your manuscript has too much overlap with another publication of you(r group). This may simply be indicated to them by a computer program which checks for literal overlaps with any source.

Often papers from the same authors suffer from such overlaps, in particular in the introduction section. However, this self plagiarism should be avoided, even if only by rephrasing the text. Duplication of content (even if rephrased) elsewhere (than in the introduction) is less acceptable and should be limited to the necessary minimum.

In any case you should add an appropriate reference to your previous work, for example "see also paper 1, where we have explained all this in more detail".


Changing from molecular neuroscience to ecology after PhD? Ecologist perspective needed!

I am not an ecologist, but I work with several, and if you squint and don't look very hard I might pass as one.

It will very much depend on the type of ecology you're interested in doing, and what kind of skills you have now. "Ecology" is a very wide open field, which can involve anything from fairly advanced mathematics to lots of field work, and everything in between. It's certainly possible (a lab I know has taken several postdocs from fields further afield than your own), but it would help if you could find a way to either apply your current skill set to an ecological problem.

Failing that, while it's likely still possible, it may take more time and be something of a rougher path.

Short version: "It depends."


From thesis text to slides. How to ease the process?

You have to cut down brutally. You will have a half hour or so to show the work of a year or more, that is hard.

Explain what this is all about. A short introduction/reminder (depending on your audience!) is probably needed.
State your objectives clearly. One slide for this should be enough.
Summarize your main results. You won't be able to cover everything, but make sure you show enough to cover the stated objectives. Perhaps highlight some tricky point, or a neat technique.
Summarize your objectives again, explaining how they were met.
If pertinent, point out possible future fruitful work building on your thesis
It might be useful to have a slide with publications resulting from the thesis, both already published or in the works (submitted and waiting for approval).

You might consider having some "spare" slides with more details, on which you can fall back when asked to elaborate.


How to deal with inappropriate comments during interviews for academic positions?

Although the comment was absolutely inappropriate, it wasn't directed toward your friend and had nothing to do with the selection process.

The department chair took notice of the comment in your friend's presence.  We could hope the department chair will have taken appropriate action.

I think that's sufficient, especially since your friend is a candidate for a position.  If your friend believes he or she must do something further, your friend could write to the department chair, saying something like, "I couldn't help but hear Professor X's comment.  Have any students complained about his comments or demeanor?  Should I report his remark, and to whom?"  That puts the department chair on notice that you took notice, didn't like it, and are prepared to go further.


Submitting a crude working paper in a Ph.D. application

It's been a few years since I've reviewed applications for math grad school, but I don't remember ever looking at "mathematical writing samples" of candidates. (I'm not even sure if this is an option at our school.)  As discussed elsewhere on this site (e.g., https://academia.stackexchange.com/a/67732/19607), actual research outcomes are not typically a major determining factor for admission (though a great letter from someone based on your research experience may be).  Thus, I don't think it will make too much of a difference, provided the rest of your application is solid.

That said, if you do decide you want to upload a writing sample (it could make some impression), my advice is don't upload something unpolished.  That almost surely will not make a good impression.  However, you could write and submit a summary/expose of your paper, which will take less time to write.  If in this case, you should try to have one of your professors look over it if possible.


How to cite an aside article in a bible MLA format

It is possible that your department at your university could provide some further guidance on this as they would possibly have a stylesheet developed that would deal with this type of publication.

That said, after reviewing the book at the link you provided and as per your question said it is impossible to cite the individual contributors to the book.

Because of these circumstances I believe the most appropriate way of citing this work would be as follows. Citation below is for International edition so you may need to amend based on what edition you are using.

  Kaiser, Walter C. Jr., and Duane Garrett. NIV archaeological study Bible: an illustrated walk through biblical history and culture: New International Version.. Grand Rapids, Mich.: Zondervan, 2005. Print.

This is similar to your second suggestion but drops the article title. This should be appropriate as the articles in this book appear to be half page further information pop-outs rather than full scale academic articles.

A useful site as well as the one you linked to in your question for creating citations is Citation Machine


This answer will be a little different from that of JoshuaZ.

Yes, such a position is intended for people wanting to build a career as teachers/educators, rather than theoretical researchers. But there are caveats.

First, the job may not come with a tenure track leading to eventual traditional tenure. Instead, as at Duke, after a probationary period the holders get long term (say ten year) contracts that are renewable. The ones I am familiar with also come with various ranks. You don't get a lifetime employment commitment, but you do get security. I know people who have held these positions over a long period. (I actually don't know of a situation in which traditional tenure is offered.)

But it isn't quite correct to say that there are no research expectations. The professors of the practice are expected to contribute to the profession and, normally, to publish and have a presence at conferences and such. But the research is more likely to be in pedagogy than theory. This is the situation in computer science at several very good universities. The people are very active professionally and may be text book authors.

These positions exist when a good university has both a commitment to research in a field, but also to high quality undergraduate education. Holders of these positions relieve the top theoreticians of teaching lower level courses, especially to large classes, but still provide high quality instructors for the undergraduates. Of course, such people are also able to interact with the more traditional research focused faculty.


What kind of design freedom can you permit yourself in academic writing?

I read papers, I don't hang them on my wall. That is the main objective, and your design should subdue to it. I enjoy a well crafted book, but I get extremely annoyed when some unnecessary decoration gets in the way of usage.

In your case, the font of the titles requires a mental effort from my part to read them, which I find unacceptable, and thus, annoying. When reading a paper, I usually skim through the sections to get a broad picture of it; with Pacifico, I need to waste neurons in deciphering it while constructing my mental idea. I also find that the numbers in the text stand out a lot, probably more than they should, as they are not information I would like to get while skimming.

On the other hand, I have encountered a few unique and very nicely crafted documents, and those made a more long lasting impression. If not for anything else, I remember the general image of the article.

Bottomline is, if your design is good, it will be welcomed; but if it has flaws, some picky people like me* may get displeased and cause a worse first impression. A standard template is a safer option; but more difficult to stand out.

*To give you an idea of how much, I find several citation styles to be rather annoying because they are clearly inferior to others. For example, anything without DOI in the modern times.


Should a CV have footnotes containing links to proof of achievements?

When I look at someone's CV, I don't plan to verify the details. Often, I have a printout and am not close to a computer anyway. I just want to see the information. And the typical vita does not include links or other documentation, it just lists the information.

So, adding footnotes to verify things would make your vita seem unusual, and I suspect it would make the document more cluttered as well. It could also have the unfortunate effect of making a reader wonder why you are trying so hard to give proof - perhaps you are compensating for something else?

If the person reading the vita wants documentation, they will ask for it. Until then, don't worry about it.


Is this ethical: "I like your paper and if you submit it to Journal X, I will be the reviewer"

If we replace the word "reviewer" with "editor", this would typically be seen as normal behaviour. I.e., editors often have pre-submission discussions with authors about the suitability of a manuscript for their journal.
In the case of editors, it is a standard part of their role to have discussions with authors about submissions and in some cases encourage authors to submit their work to their journal.

In addition to "editor in chief", many journals have associate editors and the like who act as editors for submissions related to particular topics. They also often have some scope, although typically less than the editor in chief, to encourage submissions.

Finally, the person you mention sounds like they might be a very active reviewer for a journal and quite often get asked to review submissions on a topic related to your paper.

I think the ethical issues relate mostly to whether everyone is acting honestly and in good faith, and that conflicts of interest are not perceived.

Editors are allowed to solicit submissions, and they almost always know the identity of the submitting authors. They are meant to be well-regarded members of the academic community and are trusted to make publication decisions based on academic merits and not based on friendship or other bases.

Reviewers are a little different. Reviewers are meant to review in good faith and base their decision based on academic merits. For journals that expect double blind review, I think that encouraging authors to submit to a journal where they are likely to be a reviewer is problematic. For journals that only have single blind review, the issue is more one of honesty. Specifically, the reviewer should generally inform the editor if they encouraged the authors to submit the paper. That way, the editor can integrate that information into the assessment of that reviewer's review and assess it for bias.

More generally, the implications of the reviewers comments are problematic. A more appropriate comment would be "I think your paper is good and it would be a good fit for journal X." or "I know that the editor of journal X would be interested in your paper." By focusing on the idea that they might be a reviewer, it implies that they might give a more favourable review than a random reviewer, which from some perspectives implies a biased review process.

If you are submitting the paper to that journal, you could remove most ethical issues by acknowledging in your cover letter that your colleague and potential reviewer recommended that you submit the manuscript to this journal. This would allow the editor to consider whether they want to let your colleague be a reviewer, and if so, how their review should be treated.


Should I submit an expression of interest for another position although I still have 1.5 years left in my current contract?

Is it a common practice to submit an expression of interest although I will only be available 1.5 years from now?

I wouldn't say it is "common practice", simply because it seems relatively pointless. While starting dates for academic jobs are usually flexible, 1.5 years of delay for a postdoc seems like a stretch. Many postdocs are hired on specific projects, and the project in question would be half-over before you even begin. Even for postdocs paid by some sort of fellowship, the start date usually isn't that flexible. Of course this does not stop you from asking, but I would not get my hopes up too high.


Why does a university course become defunct?

Some reasons we've eliminated courses in my department:

The professor who created the course is no longer at the college or is no longer interested in the material.
College-wide requirements have changed, and the course was created to meet a requirement (such as for interdisciplinary work).
As new courses are added, other courses have to be removed, unless the size of the faculty grows.


Is there a metric for the impact in teaching?

TL;DR: yes there are metrics that evaluate standards of teaching, but there are many and they vary widely. For the UK, the Higher Education Statistics Agency (HESA) collects performance indicators that include teaching outcomes. Because of these differences, the impact of these metrics vary, too.

There are two crucial problems. The first is: how you define impact? A good teacher can impact a student by inspiring to do great things- inside or outside of academia. If students leave university, how do you know what they do is a function of the teaching they have received? And even if it was that straight-forward, how do translate macro-level successes onto individual teachers? The second is: how do you compare such measures across institutions, disciplines, countries?

Most measures that try to evaluate the quality of teaching tend to be on the macro level. For instance, university league tables approximate quality of teaching using student-staff-ratio, teaching satisfaction and course satisfaction. See for example the Times Higher Education Ranking for US universities or the UK Guardian league table 2016. The THE explains here:

  the Teaching metric is measured by five performance indicators: a reputation survey, the ratio of staff to students, the ratio of doctorate students to undergraduate students, the number of doctorates awarded per academic staff, and institutional income

All of these are approximations and make some assumptions about what is affected by teaching. For example, the number of PhDs awarded per staff: is this a function of teaching? In the US, where PhDs usually encompass 1-2 years of classes, this makes some sense. In the UK, where PhDs are much shorter, this is already a problematic measure.

Internal feedback mechanisms

Many UK universities use internal systems: at the end of each course, every student receives a feedback form with questions about how well they though the course was run.

This differentiates lectures from seminars/classes/labs, differentiates Teaching Assistants (TAs) from lecturers (if applicable) and includes questions on how quick the feedback on homework was, how well-prepared classes were, whether or not the TA made the subject interesting, whether they felt engaged and so on.

In my institution, every lecturer/TA gets sent their evaluations after each term, in addition to the departmental average. This way you can gauge how well you are doing according to your own students, and how well you do in relation to your teaching peers. As with any questionnaire or survey, methods are imperfect (students that don't turn up don't get to take the questionnaire etc) but it serves as an approximation. How well you do does impact your chances of promotion (this is anecdotal, however- this will likely differ from place to place).

External measures of teaching

The UK government plans to implement the Teaching Excellence Framework (TEF), akin to the Research Excellence Framework (REF). See here the House of Commons report (Green paper):

Inside the report, page 5 reads:

  There is no commonly agreed definition of what constitutes good teaching in higher
  education. In a diverse higher education environment, we heard that excellent teaching may
  look very different across different subjects and across different autonomous institutions

Instead, the government wants to introduce metrics that can approximate the quality of teaching. The more recent white paper reads:

  We define teaching broadly
  - including the teaching itself, the learning environments in which it takes place, and the
  outcomes it delivers. Such things can be measured: students assess their satisfaction
  with their courses, retention rates are a good proxy for student engagement, contact hours
  can be measured, employers choose to sponsor some courses, or work with some
  institutions, because of the industry-relevance of their offerings, and employment rates
  can be measured

The TEF is not implemented yet and reactions have included many concerns about the usefulness of the proxies and the bureaucratic burden that collecting these measures will imply. The consequences of TEF include for example that universities can raise tuition fees if they do well.

Practical issues collecting teaching data: the example of retention

Since retention and drop-out rates (especially among minorities and working-class backgrounds) are very important in measuring teaching quality, the easiest way to collect that data is by recording student attendance. Both manual and electronic measures have their pitfalls: manually calling out 150 students in a lecture is time-consuming, electronic systems prone to failure or abuse.

Assuming that this is not a problem, the next question is: what to do with students that have missed classes? Recently, my institution has been obstructed to see to it that every student that misses two classes in a row, will have a personal meeting with their tutor. This has created huge pressures on tutors who have to see up to 60 students per week. A common problem of this system for example is that students missing classes due to illness are not recognised as such. Another question this raises is that perhaps vulnerable students drop out not due to lack of teaching engagement, but rather due to reasons that are beyond university control.

This example illustrates how difficult it is to 1. define measures of teaching and 2. to collect data on said measures. As with all measures, like the impact ratings of journals, they often serve a narrow purpose and should be used in addition to other pieces of information, and not replace them altogether.

Further difficulties arise from different types of universities (for example the difference between Universitaeten and Hochschulen in Germany, or Community & Liberal arts colleges in the US), and the differences between subject areas. A computer science class with many lab hours will require a different set of standards than the philosophy lecture accompanied by seminars. Many university rankings differentiate between subject areas, regions and age of university to counteract some of these issues.


Generally, startup funds cannot be used for moving costs unless you are moving an existing lab. Even then, mixing personal belongings into your lab equipment is pushing the envelope.

It might be for buying a computer or a tablet or some teaching technology. If it is a one year position, you should expect the university to keep the technology at the end of the year. It might be for buying teaching materials and/or office supplies. Some school offices have a supply closet, others do not.

They may also realize that while your job does not include research, that you may still want to travel to a conference. They might allow travel, but they may not.

It is not unreasonable to ask what the constraints are on the money, but if the answer does not affect if you are going to take the job, you could wait until you start.


Authorship: This one is messy. The JAMA instructions say Authorship credit should be based only on (1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; and (2) drafting the article or revising it critically for important intellectual content; and (3) final approval of the version to be published based on the acknowledgements, I think there is a case that Matthew Fiedler, PhD, and Jeanne Lambrew, PhD could be authors for their contributions to planning, writing, and data analysis while those who only edited the manuscript fail the test.
The difficulty is that the JAMA requires written permission from everyone named in the acknowledgements. For whatever reason, the contributors did not feel they deserved authorship. It is possible that they were bullied out of authorship. Universities, and I am hoping the White House, have systems in place to handle this type of bullying. In the absence of any evidence wrongdoing, I think we need to assume that credit was fairly given.

Political papers: This is also a little messy. I think good scholarly journals should include non-research papers (as long as they are clearly mark something like special communications) that likely have broad appeal to the readership. I think journals should strive to keep readers up to date on important issues in the field, even if it is not original research. I also think journals should actively engage in activities that will bring wider attention to their respective field. I think the specific paper falls well within the scope of JAMA which includes all subjects that relate to the practice of medicine and the betterment of public health worldwide. What makes things messy is that in addition to Special Communications JAMA also publishes Controversies in a point-counterpoint and Health Law and Ethics, both of which may have been better fits. Given the partisanship surrounding obmacare a Controversies may have been a fairer way to present the issues.

Conflicts of interest: The JAMA instructions say A conflict of interest may exist when an author (or the author's institution or employer) has financial or personal relationships that could inappropriately influence (or bias) the author's decisions, work, or manuscript. and I don't think that being the originator of an idea counts as a personal relationship that would qualify as a conflict of interest.


Is getting admission as a foreigner to a PhD program through a position within a research project of a principal investigator mostly hopeless?

Most PhDs in the bio-molecular subjects in the UK are awarded through the "job-like" route (although that is changing in some places). For most of these the position will only be open to those that count as "Home" students. Until we leave the EU in October, that includes people from the UK or the EU (after that it will just be people from the EU).

The reason for this has nothing to do with already being part of a network etc, but simply because these positions might look like jobs, but they are not. They are usually government funded PhD scholarships (where the PI has been selected to stand proxy for the government in selecting the student). For better or worst (worst in my opinion) the government has decided that its job is to educate native students (and is forced to include European students by the EU).

However, such studentships will almost always state in the advert "Home/EU applicants only".


Is there a "place" to deposit and, or publish reports produced in grad school?

It makes sense to share your work online as long as you make sure to do some quality check. Students can benefit from availability of this type of material and it can indeed improve the online presence of the author.

Quality check

Check for English correction as best as you can. I would strongly suggest languagetool.org as an excellent tool for this.
Do not copy direct parts from other authors, make sure not to plagiarize. This is something that takes time and is often overlooked. Clearly point out where you are quoting and where words are your own. Always give author's name, date and page where the information was obtained. Here is an excellent source in the subject: Melbourne University Student Skill manual
Conform to one citation standard and check correctness of the citations (provide a doi whenever possible).
Use an open science tool, so to permit transparency of the contents. This is particularly important if your report includes statistics. Have a look in the Knitr R package or my own Mighty_Make.

You can list any material you want in your ORCID page. However, do that clarifying which material was peer-reviewed, and which was not. Graduation level reviews goes in the group of non-peer-reviewed scientific contributions.

Where to publish?

This is the easy part, a very effective tool is zenodo.org. Once you feel your document is ready for submission, you can upload it there, and you will have a doi for your material so it can be cited and tracked.


What to do if my professor won't give me a grade for a test?

In my assessment, the professor acted somewhat negligently here. (Albeit maybe not lying).

I find it odd that he claims that he had a few blank scantrons without names, so he just gave people 0 points on the test. Really? He doesn't even have the presence of mind to email students and ask if there had been a mistake? This seems incredibly lazy. (Not to mention the fact that he waited until the end of the semester to grade the tests). I'm not sure it would be too far beyond the call of duty for him to have at least email students to verify if what he is seeing is correct. I would have done this for students I have, especially if they were turning in the homework and completing other assignments.

I do wonder how in the world your testing center would return blank scantrons to a professor. At every school I have ever taught at or attended, the testing center produced scantrons with student names computer printed on the top. And the testing center always scored the scantrons. Does this professor have his own scantron reader?

Moreover, every testing center I have ever interfaced with kept records. Surely your university keeps digital records of which students have taken the test, right? I'm pretty sure my undergrad institution kept computer-based testing center records even in 1996.

As Buffy says, I would stay away from accusing the professor of being a liar. But make this professor account for testing records recorded by the testing center. I'm of the opinion that this is actually part of his job description (implicit or otherwise).


Should I share course notes from my previous university with my students?

If these were my notes, and you asked if you could share them with your students you would get permission in a heartbeat. In fact, if I had continued teaching the course, and thus continued to develop them, I would probably sent you the most up to date version of those notes. I am not alone in that, I remember that several associations have been trying to set up a repository of such teaching notes, which struck me as a good idea, but I don't know what came of that. However, I have come across people who take a more restrictive view on their notes.

So, I think the best thing you can do is ask. Best case is you get the most up to date notes and a potential reference writer gets reminded of you in a positive way. Worst case (s)he says "thank you for asking, but I don't want you to release those notes". If you don't ask, release the notes, and (s)he finds out, things could get a lot more ugly.


Why do companies sponsor academic conferences?

Advertisement.

  is there any evidence that these hopes are fulfilled

Yes: if it didn't work, companies would slowly stop sponsoring.


The appropriate way to address someone is with their proper title. In your question, it seems you know what the title should/should not be. If you know, use it. If you don't know, it's generally safer to err on the side of formality.

While I personally prefer (and request) everyone to refer to me by my given name, I do feel it a little strange when someone I do not know / have never met addresses me in writing by my given name. Perhaps I am old fashioned but I expect introductions to be formal (and better to be too formal than too familiar) and then quickly get to preferred ways of addressing (i.e., to use my given name).

When corresponding (in writing or electronically) I would look to the signature. If they wrote:

Dear Professor Schmoe:

Blah blah blah

Sincerely,
John

-----
Dr. John Doe
Agri-science Department
University of Whatchamacallit

Then I would write back

Dear John:

Thank you for your letter. Blah blah blah.

Sincerely,
Joe