What day rate should I set for consulting work?

No, do not ask the professor to choose a rate
Speaking as an academic who has recently obtained his PhD and who earns his living from freelancing and consultancy, I would not recommend bouncing the question back to the professor. If he/she already had a particular rate in mind, he/she would have said so at the time of offering the work.
Instead, I would advise doing your own research into the "going rate" -- in other words, what other freelancers of comparable credentials and experience charge for the sort of engagement the professor is proposing. Many freelancers have websites or online profiles, and these will sometimes give an indication of what they would charge. You may also want to ascertain discreetly how the work will be funded (is the professor paying you out of his/her own pocket, or does he/she have funding from another source, and, if so, what?).
In the last few years, I have charged figures in the range £70-£240 for a day's freelance work, depending on the "going rate" for the type of work, how much time and skill I think it will demand, whether I have to travel (and stay overnight away from home), whether the assignment is funded by a private individual or by an institution, how well I know the customer (and how much work I have done for him/her in the past).
Discussing the price
Deciding upon a quotation for freelance consultancy is tricky, especially if you are doing it for the first time. You could avoid committing to an exact figure too early by asking to discuss the project by telephone in the first instance. It is perfectly reasonable to say that you want to know more about what sort of work is required before quoting a day rate, and discussing it by telephone may allow you to get a better sense of what the customer wants. A reasonable customer will see this as a good sign that you are interested in doing the work and have a professional attitude.
When it comes to actually agreeing a price, always put it in writing (electronic mail is fine), reiterating what was discussed by telephone. That way, you avoid misunderstandings later.
When you give a quotation, you could qualify it with a statement such as "I am assuming that ____. Obviously, the rate would be different if ___." or "Based on what you have described, my day rate would be around ____, but I would need more details on ___."
General pointers about freelancing

If you are doing unglamorous but highly skilled 'grunt' work (i.e.: if it is a so-called 'support' role), you can charge more. This applies especially in fields/endeavours where the 'headline acts' work for so-called "exposure" or volunteer for a "good cause". Last month, I provided a highly skilled 'support'-type contribution for a project where the 'headline acts' were not getting paid, but where I did get paid. Basically, if your name is going to be a tiny footnote in the acknowledgements, you should charge more than if your name is going to be on the list of authors (realistically, a couple of days' consultancy work is unlikely to be enough of a contribution to qualify for authorship/co-authorship).
As a freelancer, you have no job security, and this should be reflected in a (significantly) higher day rate than for a permanent employee. A good analogy can be seen in mobile telephone service providers, where 'pay-as-you-go' costs more per minute/SMS/MB than a 'pay a fixed monthly amount for a fixed allowance', but would be better value for those who do consume relatively few minutes/SMS/MB.
As a freelancer, you are responsible for your own pension arrangements, and this should be reflected in a higher day rate than for a permanent employee (who usually benefits from employer contributions to a pension scheme on top of his/her salary).
As a freelancer, you are responsible for collecting payment and declaring your income to HMRC in a tax return (assuming you make more than £1000 from all freelance work/enterprise in a tax year). Making an invoice, chasing up payment, and doing your tax return are time-consuming administrative chores that a freelancer has to do but an employee does not have to do (then again, the bureaucracy of some big organisations is even worse).
Be careful not to underestimate the difficulty of the job -- it is awkward to increase your fee significantly above what you quoted originally (unless the customer has made substantial extra requests). Speaking from personal experience, I have often found myself wishing I had demanded more money for an assignment after realising it was harder or more time-consuming than I had anticipated.
As a freelancer, you are responsible for your "continuing professional development" in your own (unpaid) time and at your own expense, unlike a permanent employee (whose employer will cover the cost and allow the employee to do it during salaried "work hours").


Editor not replying to emails long time after submission

The way I see it these two scenarios are the most likely:

They feel they're being pestered by you and so are ignoring your emails. This would apply if by "many" times you mean you wrote them so many emails that they got annoyed. It's also more likely to be the case if, in your field, the average review times are up to 1 year (e.g. mathematics).
The other possibility is that the editor is busy/inactive, and isn't paying much attention to the journal.

Your options are:

Wait and see what happens.
Write to the journal office and ask for a status update. Check the journal's website and see if they have a contact email. If they refer you back to the editor then the chances of #1 having happened increase (although it's also possible that the desk editor is simply not very motivated and is passing everything on to the editorial board).
You can also ask the editor-in-chief instead of the handling editor.
Withdraw and submit elsewhere. If you choose this route, look around at the editorial management system and see if there's a withdraw option.


Contacting a reference for verification as an editor

I think that since the authors are making a claim that will eventually be public if the paper is published, you can do this certainly.

If you have any suspicions of misconduct then due diligence might also require that you verify the accuracy of the translation, but that is a different issue.


I am a Re-Applicant for MS/PhD program,can I copy snippets of my previous SoP for my new application

It's a common practice among students to do so. I applied to two schools and used almost the same statement of purpose - I just made sure that any specifics like school name and programs were tailored correctly. You should be okay, just be sure that your new essay isn't an exact duplicate of the one you sent before.


Toxic colleague talks about me to Professors

A campus is a complex social environment that not everyone can adapt to, which is why most campuses have a free, confidential consultation office regarding harassment and personal issues. I'd recommend discussing this with that office before trying to engage with this troublesome student directly.

It sounds like you have gone out of your way to avoid confronting this student, and you don't want professors to know about your negative feelings towards her. When you consult a third party, there is no need to cover up such details. Let the campus staff specifically know that

This person was making you feel uncomfortable.
You tried your best to avoid conflict by disengaging with her.
She is now complaining about you to professors, even though you are no longer communicating with her.

The professors apparently don't understand the full story with this student. It is wrong for them to ask you to confront her directly.


How should I reference my own previous work in a talk to a general audience?

If the list of authors is short, just write all of them:
For example: Lagrange, Cauchy and Carnot, 1800, Journal of Mathematics
You may want to put your own name in bold.
If there are many authors, then a pretty standard way in many disciplines is to write as FirstName et al., see here: https://www.scribendi.com/advice/how_to_use_et_al.en.html
But if you are at the middle, you need to choose. Maybe something link:  AAA ... YouName et al.,
Or you can still put your name as first and the rest as et al.,


How to decide which university to study for PhD

Choosing a place to do a PhD is a hard task, but one that needs to be completed before you start. I would call your attention to three main points that you need to consider to choose well.

First point is alignment of research interests, methods, and schools of thought. Different research groups have distinct ways of thinking even when looking at the same research topics, therefore, it is important to carefully look whether you fit or not with the research they do, and how they position themselves towards that research. This you can see in the research papers that are published (or not) by them.

Second point is the personality and ways of working of the professors and colleagues. The time you spend in a research group will shape the way you think about and approach research. In some way, you will level your conduct through the examples of the ones around you. For this reason, I would advise you to look for a group that works in an professional, collaborative, open, and ethically sound way (in your opinion). This you can discover by talking with other PhD students and with people that used to be in that institution.

Third point is what you want to do next. If staying in academia is important for you, it would be important that the group publishes in top venues in the area. If going to industry is a path you would prefer, maybe you should look for a place that already has many connections with companies, or that enables you to do some part of your studies while working in a company.

These points are the most important for me.

I do not think that you have to be in a top-5 university to be successful during or after your phd. In the end, it is all up to you. Of course the environment helps, but you will be the one driving your papers and manuscript, so it is up to you.

Top students will be top everywhere, but it is important that they have people around them that can recognize and foster their talent. Look for someone that understands what you want to do and that trusts you from the beginning to take it to another level.

good luck!


Will going to an university in UK be profitable for me in the future?

Personally, I think it is to early to think about graduate school if you haven't even started undergraduate. I would go with where you want to live, and where you think you will have the most research opportunities, and where you think you will get the best grades. Most of all, I would go where you think you will be happiest in life, and not academics. It is infinitely harder to do good work, no matter what field, when you are not happy.


Unexpected long delay to start review process and withdrawal of article

Today it is very difficult to find reviewers, especially good and timely ones, unless the journal is very prestigious or rewards them highly (eg with editorials).

Having said that, this journal seems to be handled poorly. Thus, I would suggest you to pursue another scholarly venue.

If your email was clear in stating that you were definitely withdrawing the manuscript, then you can submit it wherever you want already.

Be prepared though that they may try to dissuade you stating that the revision process is already quite ahead (which could be true but not necessarily).


Why upload to academic preprint sites like arXiv?

In mathematics, there are several reasons to post to the arXiv:

It provides free access to papers that might otherwise be hidden behind paywalls.  Of course you could achieve this by posting on your web page, but your web page may move or disappear, while the arXiv is far more stable.  This means it's better for archival purposes and it's better suited for citations.  [Note that this is not just about preprints: it continues to be relevant long after publication.]
It attracts readers.  Many people pay close attention to arXiv postings in their area, in a way that doesn't happen as much with journal tables of contents.  I don't have statistics, but my impression is that a substantial fraction of the people who learn about my papers do so through the arXiv.  If you can get noticeably more attention for your research with almost no additional effort, why wouldn't you?
It establishes priority.  Submitting to a journal does not: if you submit to a journal without circulating your work publicly, then you may still end up sharing credit with anyone who makes the same discovery before your paper is made public.  The way to establish priority is to distribute your work so widely that any competitors cannot credibly claim to have been unaware of it.  Submitting to the arXiv is the easiest way to show that you have done so: it's widely read, and it preserves all versions of the article with time stamps.
It's conventional.  This varies somewhat between subfields, but once arXiv use reaches critical mass in a given area, it becomes the standard way of announcing to the world that you have completed a paper.  At that point, not posting to the arXiv looks strange.

Compared with other fields, mathematics and physics are anomalous in making heavy use of the arXiv, with physics even more so than mathematics.  As I understand it, in high energy particle physics the arXiv replaced an elaborate system of paper preprint distribution that was used in the late 80's (and it rapidly became popular since it was obviously better than the paper infrastructure).  Usage spread to other areas of physics, from physics to adjacent areas of mathematics, and then further into mathematics.

Things are trickier in other fields, because many of the advantages depend on network effects.  If nobody in your field pays attention to a server, it's not conventional, and it counts for little or nothing regarding priority, then there's less reason to post to it (although it still has some value).  I'm not surprised that it catches on only slowly and spreads primarily to adjacent fields, but I expect green open access servers like the arXiv will become more popular over time.


The value of preregistration for a retrospective study is pretty marginal. Preregistration works best for prospective studies where the primary analyses and hypotheses to be tested are finalized before data collection begins. It is worth noting that preregistration does not prevent data fabrication or many other types of scientific misconduct. The main benefit of preregistration, beyond making the process more open, is by preventing p-hacking and HARKing. This only works for new data, or at least for new aggregations of existing data.

The worse abuse of preregistration I have seen is a study where the hypothesis and planned analyses where changed 6 months after data collection was completed. The paper then talked about the planned comparisons from the updated version of the preregistered study.


How can corresponding authors protect themselves from academic spam?

We all deal with this curse. Sad as it is, I suspect that your only option is to endure it -- my take is that papers ask you to provide an email address of record in some sort of official way, and playing games like the one you suggest would look inappropriate in this context.


A tuition waiver is when no tuition charges are paid at all. For instance, at my university, graduate students on research or teaching assistantships are not charged any tuition, nor are their advisors. In this sense, they have been granted a waiver for their tuition.

Note that even partial-year tuition waivers can be significant. For instance, during the 2017-2018 year, MIT would charge over $16,000 for summer tuition for graduate students, unless they're only enrolled in research!

I have yet to see any commentary on the issue of advisor-paid or department-paid tuition counts as a "tuition waiver."


Taking break/vacation during graduate studies/PhD

The answer is of course, yes. In fact, you need to take a break to recharge your batteries.

The answers to the other questions will depend on what the rules are regarding holidays (which is country dependent). I think that our guys get six weeks annually (where as other countries only offer one or two weeks). Our guys can take them in one chunk, but this is sometimes problematic if there are deadlines that need to be met, or tutorials, etc.

The way to deal with your advisor is simply to ask him with a concrete proposal. It is better that you have not bought the plane tickets before you ask, because that will be perceived as an attempt at manipulation by your advisor, which will damage the trust relationship.

When my guys ask for a vacation I simply ask whether it clashes with anything. If not, I grant it.

The pros of taking a couple of holidays is that you will have time to recharge your batteries. The cons of not taking a holiday is that you can burn out.


How do I address research gaps in my Thesis (Research article)?

I have not written an expansive issue such as a Ph.D paper or article. But here is how I would approach the problem:

Identify the current literature on the topic in question, in effect a literature review. Is the gap even a gap? Was there discussion in the past, but not now? Depending on your findings then you can claim that

  Based on my findings, I believe that there is a gap based on the following...

How would you approach in measuring/defining/articulating this gap? Is this a conceptual gap that is not discussed in detail, therefore there is not sufficient interest in it, or it was stipulated as a closed-case?

  Based on John Smith, et.al, this [topic] was discussed in length and defined as the following... using these metrics I introduce an alternative means of measuring its effects and impact on the field...

What do you ultimately wish to do once you identified the problem? Procure more research funding, collaborate with experts?


What is the best alternative to plotting a figure with colors in an article?

If you don't want to use colors, you could use patterns instead. Here is an example:

Image Source


What is equivalent degree of Masters by research degree in the USA?

In my experience, there isn't a separate degree in the US for achieving your Masters degree through research. In fact, in many places, that's the only way to do so. At the university where I received my Masters degree, you had three options, all of which granted the same degree:

Coursework - Take something like 30 course hours.
Coursework + Project - Take fewer hours (around 20 - 24) and do a larger project than a normal project course.
Coursework + Thesis - Take fewer hours (around 20 - 24) and do a smaller thesis than a PhD.

Many universities don't have of the options and just have #3.


Low quality postdoc application and deadline extension

Contact them, explain yourself, and ask if it is OK to resubmit your application. (And make sure that you can submit a significantly better application before the new deadline.)

This has the added advantage of bringing you in contact with the PI, and putting yourself on their radar.


Approaching faculty members I don't know well to solicit career advice

Send this person a brief e-mail, explaining the followings:

How you found out about him/her, and give a 2-sentence introduction of yourself.
That his/her career path and/or research interests overlaps with or inspires yours very much.
Ask if you can have a phone conversation for 15 minutes to answer some questions. You can also ask for a meeting if he/she is nearby.
List the brief questions that you plan to cover. Don't be too broad. Think if these 15 minutes are really the only time that he/she will be willing to talk to you, what would you like to get out from this?
Provide 4-5 dates/times for him/her to pick, and invite them to suggest some dates if none of them works.

Avoid asking for reference letter, inside contacts, or any kind of favor beyond just formal career advices. He/she may not feel vested enough to do that, and if you push, he/she may close up. Also, don't attach any CV/resume; that would look like you're looking for a position.

And also don't ask "How did you get a job at an institution like this one?" Zoom out and ask for the job search process he/she went through. Ask him/her to elaborate on the thought process and how the pros and cons were weighed. Once the topic gets going, you can probe a bit further, but the focus should be on the faculty member, not the institution.

On the date, be on time, and honor the 15 minutes (or whatever you both agree upon) limit. At the end of the meeting, ask if you may ask for his/her opinion very occasionally through e-mail in future, and then establish the mentoring relationship from there.

When you got home, follow up with a thank you e-mail.

The tricks are:

Don't ask them to write back. Replying e-mail on this kind of issues takes a lot of time and thought, plus he/she may not know you well enough to know if the recommendations are suitable for you.
Make it low stake. At most they'll lose are 15 minutes.
Make it thoughtful by listing highly relevant questions. This shows that you really did look at their work and know something about it.


How to sort issues over authorship in my manuscript with PhD supervisor?

It's unethical to include the name of a collaborator who contributed nothing to a particular paper as a co-author. However, as you said, it can be difficult to confront your advisor about including someone else as a co-author.

If you are the person responsible for submitting the manuscript to the journal, one alternative you might have available is to ask your advisor is to have an explicit assignment of duties in the cover letter for your paper. ("Author A did activities Q, R, and S, while author B did T and U, etc.") The tasks of each author would be provided in such a manner—and in principle it would be hard to justify the inclusion of someone unqualified to be a co-author when you have to "certify" it to the journal, rather than just providing a generic statement of authorship.

If the advisor is unwilling to come up with such statements, then you could make the argument that since it's typically a requirement of journal submissions nowadays, that you're uncomfortable including an author whose contributions can't be clearly delineated.


What references must be acknowledged in a paper?

This is a question of academic honesty and due diligence.

If you did not arrive at the result yourself, but got it from someone else (either on SE or a homeless man on the street) then it is your responsibility to not claim credit for the result. Of course, in the case of the homeless man you can get away with claiming credit, and in most cases for SE, too. However, it is simply not honest.

If you arrived at the result by yourself, then as a research you should provide due diligence and check if the result is already known. This usually consists of checking the standard sources (i.e. published papers, books) and the communities which you are a part of. "Folklore" in mathematics is vast, and MO, math.SE, and cstheory are all becoming part of it. If you are aware that others arrived at a result before you then you should mention it in your paper (either with a full citation, if applicable, or with an acknowledgement).

However, just like you are not expected to search the back-log of every journal ever published, you don't have to scour the whole internet, either. If you want precedent of this: consider all the results that were published independently in the west and the soviet union during the Cold War. It would have been unreasonable of the scholars on both sides to be fully aware of the work of the others.


How do some researchers have such beautiful figures in publications, while their homepages look simple?

There are a few reasons not to waste time with web design:

academic web pages are read mostly by other academics who are looking for information;
the information a professor needs to put on pages is about group members, papers published and talks, courses, books and none of these seems to require sophisticated web design skills;
learning proper web design skills is time taken away from research. Most professors don't have that time. But, it can happen that graduate students or postdocs are capable of making nice web pages, so the professor asks them to do that.

The beautiful figures that appear in journals, are most often the work of postdocs and graduate students. Again, most professors won't spend time making them, unless they can't rely on anyone else. It was quite common back in the day to have someone else from within the university or research institute make figures and typeset, but now, there are plenty of great software packages one can use to make figures.


working on an open problem for the master's thesis, without any guidance or help

First of all, your English is quite good, but as a fellow German I am well aware of the jokes about Germans excusing their poor English skills in high level prose. xD

Now back to topic:
I myself had to deal with an open problem during my master thesis, so here are some points I learned during that time that might help you:
(Disclaimer: As I wrote my thesis somewhere in between linear algebra and algorithmic number theory, some points might slightly differ depending on your field).

Mathematicians are only human. Yes, after sitting in lectures, with professors telling you all the brilliant results, it might seem as if a professor, someone who finished his studies in mathematics, might be some omnipotent entity that is always right. But that is not the case. That the problem you are working on hasn't been solved yet does not mean that it is impossible for you, it just means that the people trying it up to this point where not capable to do it. Maybe they hadn't enough time, maybe they hadn't gotten the right ideas, maybe it just wasn't tried by so many yet.
It seems to me that you are expecting your advisor to know the answers and just withhold them. But I'm rather sure he does not, he just doesn't know and wants to learn about it.
Even if you can't solve the problem, you can develop methods to help with it. For example you might implement efficient algorithms to compute many, many examples, which might then help you (if you have the time) or others to see a pattern and solve it. I don't know your topic, so I don't know if it would be best to use algorithms, plots,... to show results, but I'm sure you can come up with something.
You stated that your advisor does not expect you to completely solve the problem. That is in fact good. That means that even smaller contributions might be helpful. Can you get result for certain subclasses of the problem, can you solve some cases that are easier? Can you give relations and reformulations, e.g. "Problem A is equivalent to problem B, assuming condition C (thus I devote a whole chapter to the question when condition C holds)".
Find structural results related to your problem. For example say your problem is of the form "We have structures of type A and want to find the automorphisms between them" and you are not able to find these. Then it might still help to study the structures of type A, find other ways to see/write them, get any results on them that might then help someone else to find the automorphisms.
Prepare a time plan and discuss it with your advisor. For example you could say "I try to find results on problem A for another two weeks, if I don't find anything I will write down results on the structures (to at least have something to present) and after that look at these special cases: ... At (date) I will start writing down what I have up to this point, no matter how much it is."
If you have a well worked out plan, your advisor might be able to tell you what is important to him, which of the points should maybe get more attention or less.


How do open science practices affect tenure and promotion decisions?

Based on my limited experience, I am not confident that open science practices affect tenure decisions directly, at least at the moment. However, there are many indirect benefits.

Making the paper publicly available increases the citations. See this article by Kurtz et al. from 2005. This blog post provides a nice summary and critique of this literature.
Making the data publicly available increases the citations. See this article by Piwowar, Day, and Fridsma from 2007. This blog post provides a nice overview.
I am confident based on my own experience that a reproducible workflow is a much more efficient workflow (e.g., much easier to pick up and make progress after an invitation to revise and resubmit). Efficiency should then lead to higher quality output, higher quantity output, or both. And both quality and quantity contribute positively to tenure and promotion. Further, one important step in encouraging other researchers to use your data is allowing them to easily reproduce the original findings. This step is automatic for reproducible research.
I'm less optimistic about the incentives for pre-registration (at least in my field of political science). In my view, there are still strong incentives to not pre-register studies. The culture is changing, but somewhat slowly. Here's is a blog post discussing some of these pros and cons.

Indeed, this article from 2013 by Ebrahim et al. titled "Effective Strategies for Increasing Citation Frequency" lists many practices that are also open science practices, such as self-archiving papers, publishing in open-access journals, placing papers in open-access repositories, and making the data publicly available.


How to make sure one understands each and every detail while reading a textbook/research paper without leaving any gaps?

I will give a separate answer for textbooks and for scholarly papers. The difference is that textbooks normally come with exercises to help solidify the understanding of the material.

For a scholarly work in a technical field, however, a proven method is to read the paper three times, but with a different focus each time.

The first reading is something like a deep skim. You are looking for an overall, not a detailed, understanding at that point. Take notes as you go, but don't just try to copy things. The notes should capture the main points of the paper. What was the methodology, what are the main conclusions. But also take notes about what you don't get from this reading.

Wait bit, a day or so, before the next reading so that the ideas have a chance to settle in your mind.

The second reading is deep. Here you are trying to follow the arguments of the paper in detail. Use the notes from the first reading to guide you. Think about how the paper extends the field. Think about what it does that is new and interesting. Take notes also. The notes include those things you don't yet understand. Different colored note cards are very useful for different kinds of notes.

The third reading, again after a short wait, is to solidify the second, if needed, but also to look for ways that the paper can be extended. What future research does the paper suggest, explicitly or implicitly. Again, refer to your older notes and take new ones.

Then, after the third reading, summarize your notes. What is most interesting about the paper? What is incorrect in it? What are the important things to retain?

Note that not every paper requires this deep understanding, but those that relate to your own research probably do.

For textbooks, you can do the above, but it may not be necessary for two reasons. First, a scholarly paper is directed at a small group of specialists and you may not yet have the skill and experience to understand it quickly, but the textbook is supposed to be written for people still learning. So, it should be more accessible, using more complete arguments, say. But you can also, intersperse your readings with the exercises. Ideally you should be able to do every exercise in the book. (There are exceptions, in which research problems are hidden in the "exercises", but these are rare.) If you don't have an obvious solution to an exercise, seek feedback on your attempt. Even if you don't have time to do every exercise, you should read them. Think about how you would attack that exercise.

Time is obviously an issue if you adopt/adapt this method. One way to handle that is to make sure that you don't waste time, not that you spend longer hours. If you take notes on notecards and paper then you aren't tied to your desk. If you have periods of inactivity, say on a long commute by bus, make sure that you always have a copy of the current paper and a few note cards. Even if there are only a few moments, waiting in a line to buy coffee, you can review your note cards and jot down a few ideas if they come.

There is a learning theory behind all this. Deep learning requires reinforcement. You don't "learn" something by reading or seeing it once. Feedback from exercises is also an important element, but harder to get for papers. One way to do that is to read a paper as part of a study group and have a discussion after, say, the second reading. Discussions with the professor for students can also work if it is available.


asking for CS coauthor as an undergraduate

Yes. Implementing part of the algorithm, running it and producing the figures, and especially writing a significant portion of the text of the paper, are all contributions that should count for a listing in the authors.

We can't exactly know whether your contribution to each of these were "significant" without seeing the paper, but it is very likely. So, ask.


What are some bad effects of bullets in presentations?

TL;DR: A bulleted list onlys show one kind of relationship (either sequence or membership in a set). If you want to show another kind of relationship, it's better to use something else. If you want to show sequence/membership AND something else, you can either use a different visual tool (not a list) or a list + additional dimensions.

Bullets are useful to help speakers remember what they wanted to talk about, but they're not a powerful way to visually convey ideas and relationships between ideas.

To quote Edward Tufte in The Cognitive Style of Powerpoint:

  By leaving out the narrative between the points, the bullet outline
  ignores and conceals the causal assumptions and analytic structure of the
  reasoning.

He in turn quotes the Harvard Business Review:

  Bullets leave critical relationships unspecified. Lists can communicate
  only three logical relationships: sequence (first to last in time); priority (least to most important or vice versa); or simple membership in a set (these items relate to one another in some way, but the nature of that  relationship remains unstated). And a list can show only one of those relationships at a time.

Bullets may be OK when you want to convey sequence or membership in a set. But even then, lists often have more than one dimension, in which case there are almost certainly better ways to present this than just as a plain text list with bullets. For example, take this slide showing an outline of a talk by Tom Rondeau:

and compare it to the classic way to show an outline with a list:

The point of this example is to show that the "plain" list, which is a fairly standard way to show an outline, conveys one dimension. The list version conveys sequence, which bullets can do fairly well (the parenthesis attempt to add another dimension, but it's subtle). The graphical version shows the sequence of the talk and also adds a color dimension to show the content of each section and its classification.

You could of course add extra dimensions to the list, too. This image was contributed by Eddie:

But if you are just listing points and not trying to show order, priority, or membership, all the more reason to stay away from lists.

Also see Bullets versus sentences in posters (I hate bullets in posters).


Is it proper to cite a web page using embedded metadata for an APA paper?

Some large websites, assign responsibles for each page, so in the case of a question or need for update that person would handle it. This does not mean authorship in its academic sense. So if the page does not contain a scientific claim and you refer to that just as a web-page then it should be attributed to the university (or department?), I guess.


Getting into the Computer Science Industry

As "computer science" covers anything from front end web development to artificial intelligence so I recommend you try to go in a direction which utilizes your mathematics background. Look into more advanced computer science where your PHD will mean something. In that case you will probably want to take courses rather than the 3 month cram sessions. Those teach you to get a job coding even though you were previously in house keeping. I know because I've worked with them. Some are really good coders. You don't even need a B.S. anymore to do most programming. Do something that is at your level.


What is the academic approach when the supervisor attacks student's religion?

No matter what the advisor's beliefs are, it's not OK to discuss a student's differing beliefs AND criticize them. It's the criticism that takes this from honest exchange of views into a more dangerous territory: your advisor is in a power relationship with you by definition and it's impossible to have a discussion "as equals" while this relationship is active.

If you think that the relationship and his continuing advising would be beneficial to your career, then you might try to have a chat with him where you indicate that these topics need to stay out of bounds. And I'd erect a high bar for "beneficial".

But if your assessment of value does not cross that high bar, then I'd follow JeffE's advice and run.


Many review processes are single-blind rather than double-blind (that is often the reviewer knows the identity of the authors but the authors don't know the identity of the reviewer).

One of the arguments in favor of single-blind review is precisely the one you outline: its almost impossible to hide the identity of authors, particularly if the field isn't so large, even if the names in the author list are blanked out (and how can you review a paper properly if you can see the references).

Single vs Double blind review is a topic of some controversy, with much written about the pros and cons of each. But I think its fairly clear that there is no good solution to the problem you outline.


You said, "MAY raise a questionable ethical concern". So, you might possibly misunderstand what they did, perhaps because they might have explained things poorly. I think that you should give the authors the benefit of doubt and let them defend themselves: recommend a major revision, acknowledging the potential value of their study, but make it clear that you insist that they document that they have followed ethical procedures in the method of concern. If they cannot provide satisfactory evidence of ethical methods, then you would be justified to reject the article for ethical problems.

And, as many other comments indicate, you should clearly explain your concerns to the editor.


How does a prospective applicant fail to qualify for RAship, but fit the bill for TAship?

In the US, TAships and RAships are generally assigned by the department. There may be a rule about first year students (ours was that 1st year students could not be assigned TAships). You should also not assume that the division is made by a committee. RAships can be grant-related, or funded by generic department funds. The PI would usually make the decision if a student is considered especially appropriate for the project (unless the PI has a lousy department that doesn't give him/her much autonomy). Depending on the level of democratic sentiment, either the chair decides on the allocation, an admissions / funding committee does, or the whole department faculty does. TAships are also subject to university rules, if any, or department policy, about language competence, so it may be impossible to grant an incoming student a TAship if their English isn't certified for oral proficiency.

Generally speaking, an RAship is better than a TAship from the student's perspective, but the department might either have a particular need for a TA (prehaps in a specific area) in that year, or it might be advantageous to have a year's teaching out of the way so that in your second year you can do something else. I would say that you should not over-interpret either outcome, if you checked the "both" box. "Prefer" means prefer.


Review response to quite positive review comments - first grant

I assume your question is about one of the UK Research Councils, probably EPSRC. If that's true, then 5555 is currently considered quite a low score, and such a proposal is not likely to be put forward for funding during the Panel meeting (unless you have a year with unusually low competition level, or someone in Panel is really keen to fund your research). In fact, the competition levels in EPSRC right now are so insane, that even proposals scored 6666 are not always supported.

The fact that you have "lazy" comments from Reviewers makes your situation even more difficult, as you are not given a good chance to stand for yourself by answering the questions. Your mentor is right that at this stage you have to write a really brilliant Response to Reviewers to make your proposal fundable.
Good luck with it.


How to request a professor who has moved colleges to acknowledge project work?

If he is personally available (different College, same place) then go see him with an update as usual. If not, then email him with the update as an attachment.

But, in either case, also ask him if he is willing to keep advising you on a less formal basis and tell him that you are continuing work and value his feedback. It may be possible for him to continue or not. If not, ask him if he will write you a letter of recommendation then or later.

Actually, it is pretty simple. "Just ask" is usually the right move in these situations. You don't learn unless you ask.

Welcome to Academia.


What suggestions should I make when reviewing a poorly written paper?

To comment on language is fair, to suggest improvements and even making corrections goes beyond what can be expected, depending on the degree of problems. There is of course a fine line between when something can be salvaged with a little editing and where things start to lose meaning. Many journals and publishers provide services (albeit often at a cost) for non-native speakers. What you can do is to try to help the author(s) if possible by providing examples and making minor corrections. But, it is not your job to be a service. You should state your opinion about the paper, clearly separating the scientific aspect (indicate if your think the science holds) and the language issue. It is particularly potent to state when the language obscures the scientific message. In the end it is the editor who should decide what must be done.


Is it ok to use Github code by having explicit permission from author for Thesis but without license mentioned on the repository?

There are both legal and academic aspects to this. The the single most operative question here being "permission to do what?":

If your thesis quotes significant portions of the original code then you need permission to reproduce it (very small portions are likely to be covered by whatever fair use/fair dealing defence the relevant jurisdictions allow).
If you are distributing the code online (e.g. by creating a public GitHub fork with your modifications in it) then you also need permission to distribute it.
If you are expecting your changes to be used and modified by others (which is generally thought of as a good thing for both knowledge and reproducible code), then you probably want to release it to them under a specific licence yourself, for which you will again want the permission of the original author.

All together, if you are literally only citing the code (e.g. "Plots were created with a modified version of Library X [https://github.com/foo/libraryX] under special licence from the author." ), then you don't need to do anything more. If you want your work to be useful to others in the future, then you should encourage the author to pick a licence and update their repository, then do the same with your version.


Any verbatim copying of a long block of text, including if that block of text is an algorithm, would be plagiarism if it is not attributed. However, you can avoid plagiarism by stating explicitly that your description of the algorithm is copied verbatim from another source, and citing the source. Then you cannot be accused of plagiarism, although it may still be considered poor or lazy writing if a substantial amount of your review is copied from other sources.


Article published in a conference has several technical flaws in it. What should be done?

When I was in graduate school my group found a major flaw in another group's work, and another group found a flaw in one of our papers. Beware that it's worth it to be sensitive about these issues- academia tends to be a small world, and you don't want to hurt people's egos or make enemies. Everyone makes mistakes, even in published and peer-reviewed papers. Bear in mind that once a peer-reviewed paper is published with a methodological flaw it becomes a failure of the entire community rather than a failure of that author.

I think the most productive way to handle this is to first contact the authors of the paper directly. If you feel as though you've found an error then you should be able to provide specific evidence or (for theoretical work) a counter-example to some proposed theorem. Approach them gently, and remember that you might be the one in error or that the error might be a simple like an unstated assumption. If the authors are responsible academics then you will have a dialogue with them that identifies the error or points out the flaw in your argument. If your claim is substantiated then it may be an opportunity to publish a joint correction or they might opt to retract their paper, depending on the severity of the problem. This is how good peer-reviewed science is supposed to work.

However, if the authors are unwilling to talk then and you feel like you need to push the issue then you'll have to escalate. Get in touch with the editor of the publication, but be sure you can substantiate your claims of an error in a way they'll understand and agree with. If they determine that you are correct then they may unilaterally retract the paper or provide the authors a chance to publish corrections. Depending on the severity and circumstances of the issue it may be appropriate for you to publish your own analysis of the topic.

Done correctly, finding a published flaw can be a great way to start a new relationship or collaboration with other people intensely interested in the same topics as you are. If you allow them to fix the problem with their published work in a way that allows them to save face they will be grateful. If you make a public debate out of the issue or go above their head to the publication editors too quickly you'll engender some bad feelings. If you make a public fuss about something and you end up being wrong then you'll look like a stupid jerk. Remember that academia is a small world and your reputation will follow you, so think about how you'll be perceived.

Above all else just remember that the purpose of the exercise is to correct the scientific record and you should be OK.

Edit: I wanted to echo John's comment to another (now deleted) post, which is that the probability that you are wrong or have misunderstood the paper is very high. Let the paper sit for a few days, and then read it again carefully. If you're still convinced there's an error then go to your adviser or a colleague and ask them to review your analysis. If everyone agrees that there is an error then it is time to humbly approach the authors.


PhD student and postdoc statistics related to relationships

This study has "postsecondary teachers" divorce rate at around 14%, and "Other education, training, and library workers" at 15.6.

For reference, "Computer scientists and systems analysts" were at 15.64.

Both were below "verage US Divorce Percentage" of 16.35.

Most occupations typically associated with financially secure lifestyles (doctors, engineers, CEOs) seem to fall <= 10%.

Most occupations not typically associated with stability or prosperity fell >= 20%.

Predictably, it appears that financial stability, on average, brings an order of magnitude increase in the stability of marriage. So all the girls looking to marry a doctor or lawyer (or engineer??) really do seem to be statistically more likely to live happily ever after ;) Likewise for all the boys looking to marry up.

In my relationship, we went through a total of 3 graduate degrees, for 2 of which we were both in school at the same time.

That definitely helped, as each of us had first-hand experience of living below subsistence level while in grad school. We were able to mitigate the inevitable adverse effect of financial insecurity on a relationship by being understanding and patient with each other; developing judicious spending habits; living below our means; and understanding that, in the long run, a relationship of the kind that we have is more important than a job, a salary, or a lifestyle.


How should I deal with my groupmate's unprofessional behavior as a TA?

Being nice is nice, but you also need to set your own priorities. You are not the TA for that course, so you are not obliged to answer any questions. If you happen to have time and feel like answering a question (notice the singular), then fine, answer it. When not, just politely say you don't have time and that they should go see the TA. Also, you are not responsible for (bad) advice given by that TA. Instead I would focus on getting your own research done, or do the TAing of some other course.


Applying for a postdoc with degree from different fields

In my experience, people are much more interested in your publications and research specialty then your previous degrees.

A previous degree in a separate field is more of an asset that can open new doors; you are a credible person for any possible cooperation between your current and previous field (about which I know little; maybe creating or investigating materials that might be of use in aerospace engineering). Interdisciplinary work is difficult unless someone knows both of the fields and understands their concerns and languages.

I suppose someone might see a positive or negative signal in you having changed a field (learning an entirely new field in your PhD studies is certainly impressive, or maybe you lack some fundamentals in your new field, and almost certainly you stand out from among many other candidates whose master's degree is in a more usual field), but this could go either way and depends on the person doing the hiring. I would not be worried.


There will be some flexibility for the assignment(s) due around the closing / travel / quarantine times - all you have to do is talk to your professor.

However, you need to do this as soon as possible - if you wait 2 months it may not be accepted as people are making exceptions now.


Becoming a referee if authoring mostly in large collaborations

Being asked to be a reviewer means that people think your scientific opinion is likely to be valuable.

Authoring papers in an area is only one of several ways to be noticed in this way (and, in my experience, not the best way). Other ways of being noticed include:

letting people in your professional network know that you are interested in reviewing papers
asking your supervisors to delegate sub-reviews to you
participating in conferences and workshops
organizing scientific events
giving seminars or other talks

In most areas, there is always a need for more prompt, thorough, and constructive reviewers. Thus, if you are at an appropriate point in your career to begin reviewing (e.g., at least a senior graduate student or postdoc), then people who know you will likely be interested to start delegating work to you as soon as you express interest, and performing a few good reviews will start more and more people looking your way to provide input, as your reputation spreads through the network.


Is it against the rules to see someone's exam answers after the exam?

Certainly it wasn't illegal in the technical sense and it is very unlikely, though not impossible, that some local rule would prohibit it. In fact, it ought to be entirely permissible for one student to aid the learning of another in this manner.
Even working together on "possible" exam questions before the exam should be permitted, even encouraged, IMO.
The point of it all is learning, not grading. There shouldn't be secret information.
On the other hand, there are some things that are best learned through struggle and not by reading answers. On a math test, for example, seeing the answer is very different from generating it. As a learner, you want to strive, as much as possible for insight, especially in those subjects that you are most interested in. That insight comes from hard work.


How do you (digitally) catalog the books you've read over the years?

I use a wiki these days! I've been using a personal wiki to collect notes about everything I learn, read and watch since last year and it's great. I've installed a DokuWiki on my personal website, and it's like my micro-wikipedia.

Installation is not complicated and anyone willing to tinker with tech should be able to find a way to get it working in a couple of hours.

Before that, I've used Evernote, and also note taking capabilities of my kindle for that.


Structure of research statement for a tenure-track position

Discuss your past experience only to demonstrate that you are the correct person to carry out the ambitious program of research which you are proposing. Your CV, letters of recommendation and sample publications will already speak highly of your prior work, so your research statement should be almost entirely forward looking. Good luck!


Help and opinions about difficult PhD choice

Some general points I will address.

It is much easier to get a PhD in one topic, obtain a faculty position somewhere, then pursue a new niche field of research, than it is to obtain a PhD in the niche field in the first place. I did a dissertation on a topic I am not passionate about. But I was passionate enough about it that I could spend four years thinking about it then move on. In my current position, I do not do any research on my dissertation topic. I have shifted towards something that interests me more. All of this was facilitated by the fact that I already have a PhD. I can control my funding and research much more now that I have a PhD.
This is based just on anecdotal evidence, but I have found that students who want to find a topic they are extremely passionate about usually end up unfunded and take several additional years to complete their degree. And often, in the end, they end up writing a dissertation on a topic they are not mind blowingly passionate about.
If it is stability you are looking for, topic B may be where you need to look. You will need to decide between pragmatism or passion.
Be aware that if a field is extremely niche right now, it likely still will be in ten years. This means that funding and opportunities will be harder to come by if you pursue faculty positions after getting a PhD. Unless it just happens that somehow your topic all of the sudden becomes in massive high demand, niche subjects tend to sort of stay just that: niche.
I cannot give you relationship advice. But if you are going to be in a relationship, her feelings do need to be taken into account.


tl;dr: You want a letter from God.  Until then, do not work with God.

Reference letters for promotion and tenure cases are supposed to be impartial evaluations of the quality, importance, visibility, and impact of the candidate's research, their standing in the research community, and their promise of future intellectual leadership (or in the case of full professor promotions, their proven intellectual leadership.)  So the people who write those letters must be credible independent judges of those qualities.

Here are the rough guidelines applied at my university.  Specific standards my be different elsewhere, especially outside the US — Ask your senior faculty mentors, department chair, and/or dean! — but I suspect the general principles are common everywhere.

Referees must be familiar with the candidate's research.  Promotion letters must discuss the importance and impact of the candidate's research in detail.  It is especially helpful if the candidate's work led to a breakthrough in the referee's research.  (Obviously, you can't dictate the letter; you have to choose a referee that can write such a letter.)  It doesn't matter whether the referee knows the candidate personally.
Referees must be experts in the candidate's research area.  For successful cases, this criterion should immediately imply the first.  However, "research area" must not be defined so narrowly that there are only a dozen experts in the entire world, or the impartiality of the referees is not credible.  Editors-in-chief of major journals, committee chairs of important conferences, and officers in relevant professional societies are all good choices, but for the most part, the expertise should be visible from the language of the letter.
Referees must be obvious experts in the candidate's field.  Here by "field" I roughly mean "department".  The letter-writers will be scrutinized by faculty committees at several levels (department, college, and campus), most of whom don't have the expertise to make a direct judgement; they have to rely on the trappings of success instead.  At my university, it is a de facto requirement that all promotion references must be full professors (preferably with chaired positions) at top departments, in top colleges, in top universities.  Professional society fellows and major award winners are even better.
Referees must be obviously impartial.  Thesis and postdoc advisors are right out.  At my university, any faculty member from the candidate's PhD department is barred, but this is not universal.  Frequent and/or recent coauthors/coPIs are out.  It's okay to have a few letters from former collaborators, as long as the coauthored work is far enough in the past and represents a small fraction of both the candidate's and the referee's research record.
Referees must be familiar with the promotion standards of the candidate's institution. At my university, this means that almost all letters must come from faculty at top American universities.  I was explicitly warned not to ask for letters from European researchers, because they tend to write blunter ("more honest") evaluations than Americans, and in any case, European promotion systems are different.  This is another reason for needing letters from top institutions; a supportive letter from a significantly lower-ranked school will likely be viewed with suspicion, because the writer "doesn't understand our standards".

Multidisciplinary research makes this much more difficult.  The strategy I would recommend (and have applied myself) is to find referees that cover most of the different disciplines of the candidate's research.  To pick a random example, a candidate studying molecular simulations might request letters from other molecular simulators, from other computational scientists, and from polymer chemists.  This may require a higher than usual number of letters.

An additional complication at most US universities is that a majority of the referees must be chosen by the candidate's department, without the candidate's knowledge or direct input.


Where would you publish a serious research proposal/idea that you don't have time to work on yourself, but would still like to get credit for?

Does a solid, well substantiated research proposal count as a legitimate contribution?

No, it does not.  A plan for achieving something, where none of the steps have been completed, is not a significant achievement.

Sometimes it is necessary to do experiments or calculations in order to form a plan.  That could be an achievement.


What to do with PhD advisor who does not revise journal manuscript

You may have tried the following approach already. If not, here it goes:
You could approach your advisor by asking whether he thought the draft was missing any results or needed additional work. If he says no, then, ask whether you could set a target date for submission and to have weekly meetings to discuss various parts of your paper. Also, express your concerns and explain how important it is for your career to get credit/recognition for your work. All of this can be done politely and face-to-face.

This approach worked for me when I was a graduate student.


Is the evaluation section of a paper a "contribution," if it only describes the performance of the proposed system with no novel ideas?

There are no official standards for what constitutes a valid use of the term "contribution".  It's intrinsically a vague word, and authors can use it in many ways.  It would be inappropriate to list something as a research contribution if there's absolutely nothing at all original about it, but a small amount of originality could be enough (and opinions can differ as to where the threshold is).  Of course it would be foolish to highlight the less original parts of a paper as contributions when this might distract readers from the more original parts, but that's a different issue.

You haven't given enough details to say much about your particular case, but making small modifications to an evaluation framework could be considered a small contribution.


Yes, you can. There is absolutely no difference in the citing a digital material of the same printed book as a reference. You may cite the e-book just the way you would do with the printed book. This applies not only to your bachelor thesis but to all publishable content. Just make sure you get the edition and the page references, pp, right (if any).


Appropriate response to fellowship award notice via email

There is no reason why you can't just reply-all to such an email, letting everyone know of your decision at the same time. Those who don't need the information can just ignore the mail. And include a thank-you with the acceptance.
If you decline it, then the same would apply, with "thank you, but ..." for the award.


Is there a way to find review articles by the keyword?

To me, using academic citation databases (such as Scopus or Web of Knowledge) is the obvious choice for these types of searches, since they have option for filtering on article type (which Google Scholar doesn't have). You haven't explained why you "... feel some limitations.." when using ScienceDirect, so it is hard to know exactly what you feel is lacking. If your issue is that it is a closed subscription platform, you can also use PubMed, which can also filter search results on article type (as review[Publication Type] in advanced search or by clicking on "Review" in the left panel when viewing search results). The main issue with PubMed is that it has a smaller coverage than the other databases, at least in some fields of science.


Can (and should) an editor referee a paper he's in charge of?

That editors occasionally act as reviewers is not uncommon. This does not mean it should be the norm, quite the contrary. As an editor (in Chief), I have on occasion stepped in and performed a second review when I have felt that it has been needed to speed up the process for a paper, most often because of a lack of response from reviewers that have once agreed to review. In addition, I would only take on paper where I have the specific expertise.

Stepping in do perform reviews as an editor requires attention to the roles of reviewers and editors and I feel it is important to let the authors know that I have stepped in to do the review and also why. Since, I as an editor have the final say in advising the authors on how they should revise their manuscript, for example by valuing the reviewers recommendations into a reject/major revision/minor revision/accept decision, adding own opinion to the mix is not as far reaching as might be thought. It is not unheard of that editors may look away from reject or accept recommendations based on information not observed by reviewers, but as rare as such instances are, should the intervention of an editor in the review process be. So in conclusion, yes, editors can add reviews but should do so with extreme caution and rarity.


Appeal process for PhD dismissal due to health issues

If this is in the US, the precise nature of your health issues is protected by HIPAA and is none of your department's business. Documentation affirming only that those health issues have substantially interfered with your academic performance should be issued by your disability services office, who have experience with such things. Medical disabilities are disabilities and as such are legally entitled to reasonable accommodation.


Should I let my former undergraduate advisor know that my PhD advisor was abusive?

I'm sorry to hear about your experience, that sounds very distressing.

From what you've posted, it looks as if your undergrad advisor is sympathetic and thinks well of you. That being the case, you probably don't have much to lose by discussing it with her, especially if she asks about it.

It's also unlikely that you'll get much personal benefit from discussing it, other than a sympathetic ear (which is sometimes well worth having!) But it's quite possible that you'll be helping other students. If she is aware of this behaviour, then she's in a much better position to look out for other students who might run into the same problems with this guy.


What does "principled approach" mean in papers?

(I am in mathematics, but similar language is used roughly similarly, I believe.) As a place-holder answer: a "principled" approach in science is at least opposite to a quick-and-dirty, or ad _hoc_, or "kludge-y" approach, the latter three synonymous expressions meaning that the priority is getting some result out, perhaps even finding some rationalization for the conclusion one wants. Obviously a non-principled approach more lends itself to corrupted (but also quick, desired, easy) results.

The "principled" approach "takes the high road", does not bias conclusions, does not rationalize-away weaknesses or flaws in methodology or information.

That is, one could hope that a "principled" approach involves no conflict of interest for the parties involved, and could be trusted. At its worst, "unprincipled" approaches (which no one would ever admit to, except perhaps as a mildly perverse claim to fresh unorthodoxy) produce completely untrustworthy outcomes, because those outcomes are chosen in advance, and whatever results are obtained are "interpreted" to support the original premise.

A hilarious example I witnessed was a computer science M.S. (details elided to protect privacy), on which I was an "outside examiner", in which "the goal" was to prove that two bunches of events were correlated, thus proving that the people who were promoting the one as "cause" of the other were right, and people should invest in their product. (Nevermind that correlation is not causality.) The guy failed to find any correlation in any of the first twenty or so statistical tests he applied... but he kept at it, until he found a statistical test that did seem to assert a slight correlation.

Of course, what he had really proven was that there was apparently no correlation... but, taking an "unprincipled" approach, claimed the opposite of what his own evidence showed, etc.


Accidently gave essay notes to a classmate

You have taken appropriate action already. If you meet up with the person warn them against using the notes. But, if you want some additional security, print out your notes and get someone you trust to sign and date them. Now you have a clear marker. I doubt that this is necessary, but if you are paranoid,...

But any infraction of rules would be by the other student, not yourself. Notes are just notes. Relax.


Is there any general consensus that either Elsevier or Springer is viewed as more prestigious for publishing in engineering?

You need to understand that the quality of journals is not bijectively related to the company that publishes it. Elsevier and Springer are publishers, they have a portfolio of journals and are sometimes hired by professional or academic societies to provide publishing services.

The quality of the journal depends on other factors, mostly the editorial strategy which is the job of the editorial board, who are independent from the publisher. As a result, even though both the company that you listed are reputable publishers, there are large variations of quality within their respective portfolios.

The best way to know which are the good journals in your field is to ask your colleagues in particular your adviser. You can also ask the scientific librarian(s) of your institution. This is a typical task that they do. Another clue is which journals publish the good papers you read and intend to cite. If you are in the biomedical sciences, the impact factor is a useful metric, although like everything, it's not perfect.

There are also limiting factors to consider, it might be that your institution or your funding agency have requirements regarding the public archival of preprints. One example is the NIH Public Access Policy, which requires that:

"all investigators funded by NIH submit an electronic copy of their final peer-reviewed manuscripts of articles that have been accepted for publication. Submission is to take place “upon acceptance,” and the article must be made available in the PubMed Central database within one year of publication."

(All the medicine-related Elsevier journals I know about comply with this requirements, but it's best to check).


Where to publish helpful, but informal papers?

If you don't know where to publish something, but nonetheless it is of an appropriate standard and you consider it worth sharing, why not posting it to arXiv? You won't get prestige just for submitting, but:

people can find it,
you can easily point to it,
it is timestamped.


How to find grant opportunities for academic position?

Since you are in Europe, EURAXESS (which belongs to the European Commission) may be a suitable platform to you. National funders from the EU (and beyond) regularly list their calls there.
There may also be national databases of research grants (provided by official bodies). For instance, as regards Germany, the DAAD offers this Scholarship Database, while Austria offers a comprehensive and always up-to-date list at grants.at.
The analogy for the U.S. seems to be grants.gov.


Viability: Physics undergrad to Neuroscience/Psychology PhD?

According to this UC Berkley site physics is an appropriate background as long as you meet some additional requirements.
http://neuroscience.berkeley.edu/ph-d-program/how-to-apply/


Is there any disadvantage to having open-access publications?

No. The important point is whether the journals are good (= publish good papers) rather whether the access is open or restricted. This being said, in many fields AFAIK the better journals are access-restricted.


Is a pre-doctoral licentiate degree worth anything?

Here is some experience from Sweden:

First of all, the licentiate isn't really a degree that you can study towards per se, at least not in our institution. Much more, it is an optional, but highly recommended, midterm step in doing a PhD. I guess there has to be some theoretical way of formally studying only towards a licentiate, but I do not know any such case and I would not really see a reason why you would want to do it.

  Is it accepted as proof of any kind of practical research experience in larger institutions outside of Finland and Sweden?

Presumably not. Even in Sweden the concept isn't well-known at all outside of academic circles. In practice there are more advantages to having a licentiate within academia than outside - for instance, post-lic PhD students in my department get a little higher salary and some small additional rights, such as being able to act as official primary supervisors for master students. However, mainly the licentiate is considered to be a semi-formal "half-time" exam for the PhD, and used as a test drive for the actual thesis defense.

One small additional thing:

  being awarded a licentiate degree entails having a postgraduate degree anyway (a Master's degree, which very much could have entailed doing research itself)?

In Sweden, and more generally in most of Europe, a master's degree isn't generally considered a "postgraduate" degree in the same sense as it is in the US. Our master programmes are primarily by-coursework with a one-semester thesis project at the end, and while the master programme should get students in touch with research, I don't think most people would consider the average master graduate to be a researcher in any definition of the word. Also, many (most?) of our bachelor graduates continue on into one of our master programmes. This is very different to the licentiate / PhD track, that only a small minority of students chooses.


Will a recommendation letter such as that written for John F. Nash be convincing?

Even though the event that inspired this questions may or may not have actually happened, the question is still a valid one.

I suspect it greatly depends on who wrote the recommendation. If the person writing that recommendation is a great authority in this field and is known for not giving praise easily, then such a recommendation letter might help. On the other hand, if I were to write such a letter...


How important is number of publications and prestige of the publication outlets for getting a tenure-track job?

This anecdote suggests that number of publications and prestige of corresponding journals/conferences is not as important as people usually think:

  Summary data of the short list from a past search for an assistant professor in Psychology at the University of Virginia. For this particular search, more than 100 applications were received. The Table presents the 11 applicants that made it to the short-list. All short-list candidates had at least 4 publications and at least 1 first- authored publication. Based on publication numbers, there are clear stand-outs from this group such as the postdoc with 35 publications, an assistant professor with 21 publications, and a graduate student with 10 publications. Further, these candidates published in prestigious outlets. However, none of these three were selected as a finalist. In fact, two of the three interviewed candidates were among the least productive on the short-list.
  This anecdote suggests that some degree of publishing productivity is essential to get into the pool of competitive candidates but, after that, other factors are more important for getting the job. http://arxiv.org/abs/1205.4251

The cynical interpretation of this anecdote is that the only thing that matters is whether A) you know someone and B) the committee happens to like your research topic. However in my experience what's more important is C) how high-quality the committee judges your research, together with it being on a promising topic. "Promising" is of course very subjective, and usually has something to do both with the topic being good science and its ability to get grants and yield interdisciplinary collaborations with others, including others in the department.

Unfortunately, people do get really downweighted for being in an area that doesn't mesh with the department or meet its needs. And those needs often aren't clear from the job ad.


Submission procedure for letters of recommendation

Consult the application page of the school you are applying to. Most institutions make it pretty clear how letters of recommendation are to be submitted. From an ethical standpoint, the letters should never pass through your hands, just as your transcript should be mailed directly from your undergraduate institution without going through you.

If the application process is completed online, as most are these days, you will have to provide email contacts for your references. They will receive emails from the application system on how to proceed. Their access to the system should be generated automatically. Neither you nor they should have to create accounts for them.

If the institution is insistent on using snail mail as the means of submitting information, then provide each of your letter writers with an envelope that is already addresses and has proper postage. That way your letter writers can seal the envelope themselves and drop the letter in the mail.

It is possible to submit the same letter to another institution. I have read some letters that were clearly done that way (e.g., addressed to a different institution, describing the candidate's aptitude for an unrelated position, photocopied, or dated five years ago). I would not do this. Submitting identical letters to multiple institutions (and it is usually obvious, because a good letter is tailored to that institution), implies three bad things about you:

You are too lazy to ask for new letters of recommendation.
Your letter writes did not know about the second application, so their comments are not relevant.
You didn't trust your letter writers to write you a good letter for that position.

Just ask your letter writers to write new letters to each institution. This second letter will not be written from scratch, so it won't be as much work for them. Likely, they will edit a letter they wrote about you previously to create a new letter specific to the new institution or position.


Research promotions in the middle of post-doc contract

When I recruit postdoc it’s under the assumption that they are taking on a transitional role. In some sense I believe it’s in both our interests to have them leave sooner if possible. It’s good for them (pay bump, tenure career starts etc), and for me it helps since it signals to future postdocs that I’m able to get them on the right track to a faculty position.

In some cases it’s the opposite: a person has secured a faculty position straight out of PhD, and then postponed their start date to take up a one year postdoc (in MSR/Facebook research etc, or with another research group). This is usually done to build up one’s professional network before committing to a department.


Why are some research groups not so ethnically diverse?

I'm a PhD student based in Sweden, working in a group where everybody except the PhD students are German. Another group in the same building has several Russians, and a recent Russian PhD student had a Russian supervisor. So the tendency to mono-culturalism is not unique.

Probably, many institutes have statements  promoting diversity. In practice, these don't mean much, because recruitment depends on academic networks, skills of applicants, etc. There can be different reasons for a group to tend to mono-culturalism. Some reasons I can think of:

A professor heading a research group in a foreign country probably has an extensive academic network from his/her originating country. Academic networks are powerful sources of recruitment of new staff, either senior staff or PhD students (e.g. via a Master thesis supervisor recommending them). So applicants might simply be more likely to be from the same country as the head of the group, even if the head of the group is 100% honest in his/her selections.
PhD students may appreciate if they can work with a supervisor that speaks their language, particularly if they are not so comfortable speaking English.
It's culturally easier to work in a group with several people from ones own country.

All these factors can contribute to groups in country X with group members primarily from country Y != X.

Probably there are other reasons that I didn't think of.


Should academic papers necessarily carry a sober tone?

Are jokes or anecdotes fine as long as they do not appear forced?

To me, there is a single measure for this: does a sentence X contribute to the paper, or not. If the answer is no, it shouldn't be there at all.

To apply the principle to the joke: if the joke illustrates a common problem which needs a solution, or illustrates a common (perhaps insufficient) solution to a well stated problem, then it certainly has a place in a research paper.

I understand scientific writing as a form of literature. I do not see any reason for literature (including scientific discourse) not to be entertaining as well, when appropriate. But everything has its time and place. However, it shouldn't be forced and has to fit the main contribution of the paper, hence the filter rule above.


"Dear Editor,
Thank you for accepting my booknote for publication. I'd be happy to be considered as a potential reviewer for your publication in the future.
Best wishes,
user82138"

Perhaps this is facetious, but as far as I know there's no special code that needs to be invoked when communicating with journal editors. Concise, plain English will certainly suffice.


Do TAs in the US usually grade student responses?

Yes, this is common in the United States.
With the assumption that "Evaluate the answer sheets" means "Grades assignments/projects/exams"
In both my undergrad and graduate studies and personal experience as a TA, assignments/projects/exams were often graded by a TA.
In my experience I've found that a Professor will generally only participate in the grading process when:

The subject is very specialized. i.e. a semester project, or something that aligns with a professors specialty

The amount of student in the class is very low (< 50). Many of my smaller undergraduate classes were graded by professors either exclusively or in conjunction with TAs.

If we look at something like Penn State's School of Science TA Info Page they specifically list grading a a responsibility of a TA. This responsibility along with the prerequisite that the TA either took that class and did well previously or has extensive knowledge of the subject is very common across Universities in the United States.
You also mention that a TA would "prepare presentations, frame questions, do a textbook reading, take small lectures" This can also be true, but varies more between professors than the position as a whole.


How to respond to a reviewer's comment when he is asking for experimental data but your paper is based on theoretical calculations?

Essentially, the reviewer is saying, you cannot/should not propose a new theory in a vacuum. One of two approaches apply:

Do you have a new theoretical approach that will explain observations that existing theoretical approaches cannot yet explain? Demonstrate this categorically by taking the experimental results modeled with the existing theories to model with your new theory. It seems that you argue that this is not the case for your theory. So ...

Do you have a new theoretical approach that points to new insights not yet measured by any existing experiments? State concisely what experimental measurements will be needed to validate your theory. You infer that this is your case.

Being somewhat aware of DFT and its applications as well as being experimentally inclined, I must say tangentially that I cannot trust that absolutely no experimental results (e.g. from spectroscopy) exist anywhere that can in some way validate your new theory, even in part. Alternatively, I cannot trust that your theory has absolutely no relevance to direct new experimental approaches in order to validate it (e.g. again spectroscopy).
In summary ... Einstein's Nobel prize was for a new theory that explained oddities in experimental observations (the photoelectric effect). Einstein's theories otherwise were put forward with proposals for experiments that might test their validity. You are being asked to do one or the other as well.


You can lookup the names of the authors in a patents search engine such as Google Patents or PATENTSCOPE. Each patent application has three dates: filing date, publication date, and the issuing date. Once a patent has been filed, it becomes in a state called patent pending. In the US, a patent application is published after 18 months of the filing date and so people can loop it up using search engines. However, in the US, before that, there is no way to tell if the authors submitted a patent application other than asking them. However, that does not constitute a legal issue for you because the authors' work, in the US, is not protected until the patent is issued. So if you cannot find a patent using one of the search engines, it means that the work is not protected and it would still take several/many months for a patent to be issued. Note that in other countries, published patent applications may be protected even if a patent has not yet been granted.


Is it possible to start a PhD at 36 without taking a huge hit financially?

I did my PhD in computer science in the Boston area. Through an RA and a bit of TA, I had my tuition, health insurance, and conference travel expenses covered, plus a stipend which has since risen to $36,800 before tax per year. (With a bit of googling you can look up what financial support various PhD programs offer, as well as health insurance costs for dependents -- for a large family, this might be $10,000.) That was enough for a modest but comfortable single person's lifestyle in expensive Boston, but I would struggle to support a child or mortgage with that. PhD stipends will vary by field (i.e., how much funding professors have) and by university (i.e., local cost of living).

You will know your financial situation and it's up to you to judge whether you can cut your expenses and/or dip into your savings to make that work. PhDs are getting longer, so keep in mind that you probably need to do this for about six years.

There are a few other options to make it better financially:

Ideally you can work something out with an employer where they will pay you while you do your PhD, probably in exchange for some part time work or a promise that you will continue working for them afterwards. Such an arrangement is more common for shorter programs like an MBA.

It's also possible to spend some time during the PhD working in a company that is somehow related to your studies. For example, a lot of computer science PhD students will do internships at companies like Google or Microsoft. A 10-week summer internship could give your annual income a >$10k boost.

If it all gets too much financially, you can take a year or two off your PhD to work and then come back to finish. That's not ideal, because it interrupts your work. However, it's better than needing to drop out entirely.

Overall, however, I think it's unavoidable that a PhD will entail a financial hit. A PhD is almost never a good financial decision, but if you are passionate about research it's definitely worth it.


Go see him. Failing that, go see the department office. They can intercede for you if he isn't responding. Actually four days isn't so much time in a busy season. And he may not realize your urgency.

Email is not your friend here. Especially if your advisor is a generation or two older than you.


Is it common to claim co-authorship by helping writing a paper without doing any research

people who help write papers may help fulfill one of the pillars of scientific discovery... communication of the science.

There is an appropriate place to credit people who read your paper and offer useful comments on it: the acknowledgement section. It is very common to see acknowledgements "for providing valuable feedback", "for suggesting a cleaner presentation", "for pointing out important related work" and so on. Even "for providing a simpler proof of Lemma X.y".

None of this rises to the level of co-authorship.

What's worse in this case is that

  At the end, he will claim the co-authorship of the paper.

While I'd find the idea of co-authorship for such contributions odd, I would not think too much about it if it were negotiated in advance (as is the theme of many of the answers on this site). But to offer what appears to be unconditional help first and then (when the student really has no choice in the matter)  to demand co-authorship is plain wrong.

To answer your last question on what to do, the answer, as is always the answer, is to negotiate things up front. It's a little awkward, but a little pre-collaboration awkwardness is MUCH better than a lot of post-collaboration recrimination and hostility.


That depends on the requirements / prerequisites of the specific program you are applying to, but Masters classes assume you already understand the topic at a Bachelors level and unless you have at least a strong minor in that area you are unlikely to succeeded and thus unlikely to be admitted.

A better approach might be to ask schools if they would let you use any part of you existing degree as "transfer credits" toward a faster Bachelors degree,  then continue from there to the Masters.  You might be able to complete the new B in three years, or even two, if you have good enough grades in material that overlaps their program.


Is an algorithm that stitches together various algorithms "good enough" material for IEEE Trans?

"Stitching together" some existing algorithms is not necessarily bad, if the combination is both valuable and non-trivial. It can be argued that a lot of today's research in computer science is mostly stitching together ideas that have existed for a long time. Further, I am a huge opponent of the notion that it is somehow better / scientifically more valuable to come up with your own (almost always inferior) algorithms for well-known standard problems just so that one can claim to have a higher "novelty".

That being said, it is of course hard to answer your question without knowing the concrete work. As a rule of thumb, read through a number of back issues of your selected journal. If all of them seem to have a much broader contribution than what you have in mind, your idea may be too small (but don't let the impostor effect get you, either).


Techniques to remain focused while marking examinations

There is two issues in your question.

How to be fair to each student when it comes to this boring task of evaluating them

My own policy is the "mark-one-question-and-shuffle" : I correct the first question/problem for all the students, then I shuffle the whole stack and go for another question that I also pick at random. This way if I am tired or in a bad mood, it will impact everybody, so it will be fair.

How to stay focus for a long marking session

I cannot answer to that and I guess it depends of many personal factors. Personally, I find marking tasks boring but easy to do and easy to focus on. It's like driving, some people can drive for hours, others can't. To tell the truth, marking is somehow relaxing for me.


The first paragraph of any paper or proposal is always the hardest for me to write, and the first sentence is the hardest part of that paragraph.  In my experience, no matter what I write, it sounds hackneyed; fortunately, the same is true of everybody else's first sentences, including all of the sentences you and other other answers have suggested.  I used to spend days agonizing over the precise choice of words in each opening sentence.

So a few years ago, I adopted the following strategy, which works surprisingly well:

Typeset the phrase INSERT FIRST GRAF HERE in bold red 18-point text at the top of the first page of your proposal.  Promise yourself that you will write this paragraph only at the very end, after you've written and polished everything else.
Start writing the second paragraph, which explains in broad strokes the substance of your proposed research.  Assume that the first paragraph has already explained how novel/important/cool the research area is.
Make sure your introduction includes a few paragraphs describing specific prior work and its impact, as well as the specific work you are proposing and its potential impact.  Keep it high-level; this is just the elevator pitch.  You'll include a more detailed description of both of these points later.
When you are completely finished writing and polishing the rest of the proposal, delete the phrase INSERT FIRST GRAF HERE from the top of the first page and submit the proposal.

Yes, I really have done this, multiple times; and yes, the resulting proposals were funded.

To put it more bluntly: Just get to the point.


Don't stress too much for your proposal. In all likelihood your PhD will evolve as you progress. As you said you've been reading a lot. Don't be surprised if there is little material to reference. After all, that is the point of doing Ph.D. research: you will be adding to an area of knowledge which at present is little understood.

My Prof once told me that in year 1 the student should be guided, in year 2 the student finds their feet and in year 3 the student leads their supervisors

And yes, speak with your supervisor. This will answer your doubts and display you are really commited to being rigourous.


How to improve my Analytical Writing skills for the GRE?

I don't have any specific sites or resources but I have some advice,

Write, write, write, and write some more

Get a notebook and set aside 40 minutes every day to write a sample essay. A list of topics can be found on the ETS.org website (so I guess I have one resource :) ).

Then analyze and grade your own essay. Compare to the template, to any available sample essays you find, etc.

The best way to improve writing is to write.


Does translating an academic work in the humanities or social sciences improve your CV?

Been there, done that. Didn't even get a print out of the translated chapter, nor a hard copy of the edited volume.

Make sure the article is at least of some interest to you personally, otherwise the whole process quickly becomes taxing.

The assumption is also that you will translate into a language that is your mother language, or that will be even harder, and actually you would be badly advised to even consider completing the task.

Translating does not improve an academic CV because translating an article is either a skill people assume you have to be able to carry your usual research, or translations are given to language professionals who can value the experience on their CV.

Unless you're able to bargain some sort of deal that is of interest to you with the people who ask for the translation, or the author of the article to translate, it will only be a "service", for glory.


What are the pros and cons of publishing a new unpublished idea in a poster session in a leading conference?

In my field (in computer science), posters are usually a "low cost, low benefit" activity.
Pro:

A small amount of visibility
A small but nice CV entry
A small opportunity for feedback and input

Cons:

A small time investment for actually developing the poster and, sometimes, writing up an accompanying paper
A small cost for registering at the conference (I assume that the conference will be online due to COVID19, otherwise the costs could actually be larger)

In the end, it probably won't make much of a difference, unless lightning strikes and you happen to get amazing input/feedback/collaboration opportunities (not impossible to happen but unlikely).


Incorporating results of supervised student theses in own thesis

Be explicit.

Write very carefully what ideas were yours, which experiments were yours and which were not.

So for exapmle:

  I observed the results of the experiment, from which I hypothesised that X might be true. Fooing that bars would reveal if this was true. Ms Jane Undergrad fooed 8 bars, revealing an expessed of buzzed widgets in some conditions (Figure Y). In a parrallel approach, 8 nature wotisits were collected and the nozzle lengths measured (experiment conducted by Mr. Bob PGT Masters). I analysed this data using the SuperWiz alogrithm and concluded that the hypothesis was true.


Group members want to work using virtual meeting (google hangouts) but we already have bad group dynamics

I know this answer comes too late for you.

But I agree with your assessment. This group project is only going to sink from here. To which, I would build on one existing comment already offered to you.

  Raise your concerns to them, and then listen to what they have to say
  with an open mind?

That being said, do not raise your concern to them as a group, raise your concerns and listen to each what has to say with an open mind, but do it individually first. If you bring this concern to them as a group, most members of your group will probably just make the most expedient decision that takes the least amount of commitment on their part, a vote will be quickly called, and then that will be the end of it.

Also, I agree that the Professor wouldn't want to be bothered with such a problem. Learning to work with unmotivated colleagues is a fact of life. This is your problem to solve, not his.


How to ask a postdoc professor for experimental work when my PhD experience is computational?

Your age isn't material. You have skills. Tell a potential advisor that you are looking to expand your skill set into experimental work. Perhaps your computational work can complement the experimental, looking at problems from two aspects.
Even if you are still doing mostly computational stuff in a new post-doc you will get connected with the experimentalist's outlook and start to absorb those skills. Joint papers would be a good way to get recognized.
But just ask for what you want and say why. It is perfectly reasonable. A post-doc should be a learning experience, not just a repetition of you doctoral studies.


Will the university reprint the diploma with its original signatures or generate a new diploma with signatures of current university officials?

The policy depends on the university.  For example, replacement diplomas from Harvard include the names of the officials who were in office at the time the original diploma was issued, but without signatures, while those from Stanford include the names and signatures of the current officials.  Some casual web searching suggests that Stanford's policy is more common, but it's certainly not universal.

  However, a diploma does not have issuance date (only the date awarded).

Reissued diplomas are typically marked as such.  For example, this is part of both Harvard and Stanford's policies, and web searching suggests it's very widespread.


Relevant experience but I did a mediocre job.. should I include it in the cover letter?

This may depend somewhat on your country and your discipline, but in general a PhD is a research degree.  Research experience is the absolute most important and relevant experience.  Any research experience at all is better than none. You should mention it.