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What GPA do I need to have a chance at getting into Harvard's CS PhD program?
By the end of my undergraduate at the University of Utah I will have a year and a half of research and a GPA of about 3.8 overall.

Ask Harvard. Realistically, no one has much of a chance. Too many applicants, too few slots. Tremendous competition. It's more that GPA. Set your sights wider to have a better chance to find a slot.

your GPA is by no means the most qualifying quality, if fact, it doesn't tell Harvard much about you: thousands of people apply to Harvard with an excellent GPA. To differentiate candidates, they'll also look at your work experience (if any), your research experience (if any), your letters of recommendation and letter intent, your extracurricular involvements (were you a part of any relevant clubs ?)

Like 3.2 or so (seriously, because GPA doesn't matter much).

As summarized in the comments, there is absolutely no way of determining what chance you have at any college. I think it's kind of a subjective decision of the college by taking into account several factors besides your GPA, even the amount of scholarship you need to complete your education.
I'll suggest not to tailor yourself depending on the college. Most people whom I read/watch about on how they got into so and so place, I get a feeling that they kind of belong to that place (or more formally what the universities call a good fit). It's the set of values they intrinsically have or have developed that align with what the admission officers envisage for the incoming class. The student might be curious about how nature operates and spends most of their time reading Physics, despite being in CS core course. The admission officers see this and they immediately think about the personal aspects of the student in pursuing something they love. And if other objective things fall into place (test scores, interviews, recommendation letters, other such traits etc.), they offer admission.
Universities always wish for people who can be successful in life. And that cannot be predicted by things like test scores or GPA (although they are important factors in determining the intelligence level or more simply if one can survive the course load at the university). What is better for the university is to observe the response of the student to their environment, the challenges they face, how far do they go pursuing their interests, their creativity, their work ethics, their respect for original work, and in general their interaction with the world outside. Then the university simply considers whether a combination of such a character and their resources would be impactful on the world at large. If they get such a feeling, they simply go after it.
Of course I do not consider other factors here, like if the university has to create its handball team and prefers a handball amateur over you, or if the university has enough funds to finance your education if you can't (don't really know what PhD financing though).
All in all, the point I wish to put across is you can't control such factors, but you can develop a set of values that make you a good fit. The best thing, however, is to try and be the best version of yourself without any end goal of being a good fit for some university, making the best of the opportunities you have and trying to give back to humanity at large. You'll develop values that will help you succeed in any setup and be a better person. And Harvard, though one of the best, is not the end of the world. There would be other colleges where your values fall in line with their vision, and other factors being fine, you would definitely get your chance.


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Research related questions from industrial researchers to academic researchers
If an academic researcher wants to ask research related question or to start a collaboration etc. with another academic researcher, it is usually a matter of a polite and specific email. I have seem such initiatives from academic researchers towards industrial researchers (e.g., a postdoc asking about technicalities of a paper written by a Google researcher directly to the Google researcher).
Is such research correspondence, without any prior research contracts/agreements between the academic institution and industrial researcher's company, also common from the other way around (i.e., an industrial researcher initiating a correspondence to an academic researcher)?
How about research correspondence between researchers in two different companies?
I am thinking of transiting to industrial research from academia and genuinely curious about this.

Any type of contact is possible. However, do remember that if you do not sign a mutual non-disclosure agreement, anything discussed might be used and exploited. Accordingly, it is always best to have one signed beforehand if you wish to discuss something original and important. Anyway, collaboration between academia and industry, if well conducted, is truly beneficial for the advancement of knowledge.

@GiuseppeBiondi-Zoccai, so does the industrial researcher have to ask the academic researcher to sign a form before starting a conversation? From the academic researcher's point of view, wouldn't it be strange to receive an email from an unknown researcher with a research question and also a request to sign a form? Not questioning the system, just curious how it works and how common it is.

Even academic researchers may have confidential projects or may consider filing a patent application. It depends on the risk that your idea is exploited by someone else. In my experience, if people ask me to sign a NDA (non-disclosure agreement) it means they want to talk seriously about something new, so I am actually impressed favorably.

Disclosure: I am a researcher working in industry.
I think that the rule of thumb is: make it as simple as is wise, but not simpler (paraphrasing Einstein).
Always make it clear who you are (name, company, etc), and what your intent is (e.g., better understanding of a paper, creating your own implementation of an algorithm in a scientific publication for research purposes only, developing a new product based on a scientific publication, writing a patent, etc).
Be open and honest (e.g., do not claim that you just want to understand something, when in reality you want to use it in the development of a product).
If you are asking about quite generic technicalities (e.g., something you might also publicly ask to a speaker in a conference), you might just drop an email and ask. As long as you do not disclose any confidential information, and you do not expect so from the researcher, you just can ask the question.
When you do need to disclose confidential information (e.g., specifics about a product your company is developing), you will need to sign an NDA (non-disclosure agreement).
Also be aware that if you are asking the academic researcher to do work for you beyond just answering an email, or provide you with something of value (e.g., working code belonging to a scientific publication) a monetary reimbursement is in place.
For the latter two items it is quite likely that you will need to involve other people within your company (the legal department, a budget holder, your boss, ...) before reaching out.

thanks for the answer. How about industrial researcher to industrial researcher communications/collaborators?! Is it still possible though I am sure legally would be more involved?

@John: it depends about the specifics. Suppose you (as an industrial researcher) want to contact another industrial researcher regarding one of his/her publications. If he/she works for a direct competitor, it becomes difficult. If not, then it is similar to contacting an academic researcher.

FYI (re: paraphrasing Einstein): http://quoteinvestigator.com/2011/05/13/einstein-simple/

I don't think there is that much difference between academia and industry except that in industry you probably have to clear it with your boss and/or IP lawyers before you mail ideas out of the company.  I have received "cold" contact emails from industry, sure, not that many I've been able to act on though.  I think the problems are pretty much the same: how much time does someone have, do they even read their email or not, etc.  You will get lots of variation both inside and outside of academia on this.  If you have enough money to pay for a PhD student for at least a year, then you will probably have not too much trouble getting someone's attention in academia wherever you are coming from, if you've done enough work to be sure you're approaching the right person / someone actively researching the area you need.
The other easy way to get an academic to collaborate with industry is to hire them as a consultant.  But again, it has to really be their area, and they have to have time available, so you need to do research.  But if you get the wrong person, they may be able to suggest someone else or at least something to read (if the problem's already solved so no longer of academic interest.)

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When listing refereed papers in a CV, should I highlight my name in authors lists?
I am experimental physics grad student updating my CV / publications/talks list in preparation for applying to postdoctoral positions.
In my refereed publications list, while a few of the most recent papers have me as the first author, the majority do not. So my question is as follows: Should I highlight my name in the lists somehow? If so, italics, boldface, or something else?

I do not generally see people highlighting their name in a CV in this way, and I do not think that it is necessary (though perhaps the culture in experimental physics is different).  In a CV, you are by definition an author of every listed paper, and papers where you are first author leap out pretty easily to the eye already---unless you've got lots of papers, in which case, why worry about it?  If you highlight your name, on the other hand, I think that it could come across as insecure, since it is not normally done.

very field specific. In my field they do. If there are 4 or less authors on all your publications, it is probably not necessary. It is only necessary if your position will not be noticed in a cursory look, such as a 10 author paper (and in some fields, yes a 10 author paper does have meaning, shockingly).

@WetLabStudent By your handle, I'm guessing that you are in biomedical sciences?  In the work that I've done in that area, I've had my share of high-number papers (the largest at the moment is 32), and I've not seen this sort of highlighting amongst my collaborators or their students...

nope not in the bio-medical sciences, wetlabs exist in all of the natural sciences. I don't doubt your personal experience, this may just be field specific in a cultural (rather than rational) way.

@WetLabStudent I'm not doubting your experience either: I am, however, wondering what your field is?

Actually my user name is meant to be somewhat ironic, I'm an mathematical biologist who does 'some' limited experiments. And as a Theoretician I do them rather poorly, hence wetlabstudent is my nickname, despite basically every component of the name being incorrect. BTW I will delete this comment eventually to avoid this answer from turning into a conversation

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Public data repositories: Multiple figures as one reference
my current manuscript is combining work in multiple research fields, so naturally it's difficult to find good journals to submit it to.
At the moment I'm down to one journal where I would really like to submit it, however, the author's instructions of the journal make it difficult to wrap all my data into it.
I'm only allowed 2 tables and 3 figures and all supplemental material needs to be uploaded to public data repositories like FigShare. There is another table and 3 more figures that I would like to include that way.
BUT
The journal also only allows 30 references. At the moment I'm at 29 references. I have never used FigShare before but as far as I understand it, I need a new reference for every figure or table I cite that way?! So that would leave me at 33 references and I really can't afford to cut my text. I also don't have any redundant references.
So as I said. I would really love to still be able to submit it to that journal somehow. Is there any way that I can upload all my 3 figures and 1 table in a public repository and cite it as one single reference in the manuscript?
I hope my question makes sense so far.
Many thanks

When I hear public repository, I always think github. Might not be originally intended for figures, but maybe it works for you?

@Dirk I would avoid github for something like this. With a journal article, permanence is important, and github is not ideal for that. Changed user names, changed repo names, deleted repos, a hostile takeover of github, etc, could all break his article. It also makes manipulating figures and other content post publication easy. There's no guarantee that other options like FigShare are 100% permanent, but they probably are a safer bet, and have systems in place to ensure users can see the original figures.

I routinely use OSF (Open Science Framework) and have a single reference to Supplementary Materials that links to a compressed file on OSF. You can "register" (fixed snapshot) the set of materials you want and have a single reference (including doi). I don't do it quite like that, I simply refer to Supplementary Figure 3 or whatever in the paper, and provide the link in whatever way the journal requests supplementary materials be linked.
But it doesn't have to be a single compressed file. The way OSF archives work is that the single link is to something more akin to a webpage and you can have multiple files able to be downloaded as well as a wiki style information page. It would be annoying for your readers to have to download multiple files though.

Just in case other people will have similar questions:
I found OSF really better for the specific issue that I had. I put all files in a "supplementary" PDF file and referenced that. Then I created a folder for the raw picture files in high resolution.
I feel like I got the best of two worlds. The reader can just download one supplementary file and use it along my manuscript and in case he is really interested in the data he can just click on the high resolution file. Let's hope my editor will see it the same way.
Also liked the usage of OSF much better than Figshare. Thanks for that.

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Publishing Consumer Fraud
I'm in the awkward position where I have been giving a data set from a company strongly indicating that consumer fraud occurs in a certain business sector (insurance). The data permits me to identify the corporations conducting the fraud.
I come from a completely different scientific background than consumer law. Therefore, my questions regarding this matter:

Is an academic peer-reviewed journal even a suitable channel for this kind uncovering?
If published in an academic journal, will I be able to name the companies conducting the fraud?
What journals might be suitable for this?
Do any similar cases come to mind which I could study?

Thanks

If you are in the US you should (and really must) speak with your local IRB before going any further.

Your university (assuming you work at one) surely has a legal office. I would suggest to pay them a visit.

Isn't engaging in fraud practically part of being an insurance company?

I'm voting to close this question as off-topic because it's a legal question rather than an academic one, and A) a lawyer reading your question won't answer it because they won't want the answer to be construed as legal advice and B) a non-lawyer is likely to give you bad legal advice.

I think you could potentially keep this question on-topic if you rephrase it to be able how to address these issues as an academic, in which case you would get answers like the ones in the comments (i.e., directing you to legal resources that likely exist at your institution that could help you with this). Any other type of answer you get here I'd strongly suggest you ignore.

There are two aspects to this, one in your domain and the other outside it.
If you have a data set, assuming it is valid and accurate, you can analyze it an publish your findings. That is just science. Like any other study, your methodology is important and your conclusions must follow from the data.
But alleging fraud is a legal matter that should only be left to lawyers, courts, etc. It is not your proper role, even though your findings may be interpreted to imply fraud.
If you name companies at all, stick to facts, not allegations. Don't use legal terms, especially legally loaded terms that might lead to a charge of slander, whether justified or not. The company lawyers are better than any you could afford.
Facts, however, are facts, and can be reported and analyzed. Do that, but leave the legal implications to those better placed to follow up on them.

Let me try to be more clear. First, analyzing data seems to me to have no legal issues.
However, I warn the OP not to make statements that can be interpreted as allegations of misbehavior on the part of others. They may have an "action at law" against you if you do that and it will be expensive to defend your actions even if you are correct.
Let others form the conclusions from your research rather than making or implying accusations.
If legal authorities have some evidence of fraud they can act on it. That can bring the courts to bear, but the regulatory authorities have to act first. That would, perhaps, be a criminal matter and it would be out of your hands altogether. (Note that some improper actions handled by authorities are also civil, resulting in fines, rather than criminal. But still it is up to them to make the allegations and follow it up.)
If you make allegations and are sued, on the other hand, it is a civil matter and the courts are only involved in the adjudication of the dispute between the parties. But being sued is not without cost, even if, again, you are correct. If you allege publicly that a large company has committed fraud you may well be sued and the company probably has a highly qualified legal team that will do what it can to shut you up. If you are Jeff Bezos you can fight such claims since you can afford the best lawyers yourself. Otherwise it is a financial life wrecker.

Careful!!  Truth is (at least in principle) an absolute defense against libel claims in the United States, but the same is not true in all countries. Speak to a lawyer first.

@JeffE, but it doesn't stop you from being sued and you have to defend, requiring your own lawyer. The civil law is often used for intimidation rather than justice. So, "in principle but not necessarily in practice".

You're right, of course. But the conclusion is the same: "Merely" reporting and analyzing facts can still lead to serious legal difficulty. So even in the US, your advice "Do that" is a bit careless.

@JeffE, that depends of course on what you say.

"A person is considered innocent until proven broke"... Does truth & justice or the most expensive lawyer prevail?

Can courts in the US really "allege fraud"? Your answer reads like "Hope some lawyer-scientist will stumble upon your publication and decide to take things to court." Is this actually what you're trying to say?

@sgf, I don't understand. Courts aren't involved except to adjudicate disputes between individuals. If I say you have committed fraud, you can sue me. I have to respond to that suit to avoid summary judgement against me. I dare not do that without a competent attorney. But if you are a rich company or individual you can afford the best representation and I cannot. A "stumbler" has no "standing" to sue. It has to be you, the person accused, not a random person. (US perspective).

@Buffy "[A]lleging fraud is a legal matter that should only be left to lawyers, courts, etc" - This read to me as if courts could allege fraud.

@Buffy But the more important point is that you seem to be considering two alternatives: Publicly denouncing company X as fraudulent, or just publishing the facts. There seems to me to be an obvious third alternative: Very carefully taking the necessary legal steps to stop the fraud. This will of course also involve a lawyer, but it seems to me that this is OP's proper role as a citizen (if, indeed, they are.)

@sgf. I don't mention "courts". This is civil, not criminal law. You aren't "arrested" by authorities. But you can be ordered to appear in court where the civil dispute is handled. Courts don't initiate anything. Only the "aggrieved" party can do that.

The OP could inform the "police" or other authorities that fraud has occurred. They might open an investigation, but the OP wouldn't be part of it. The OP can't sue the "perpetrators" unless the OP has been defrauded personally. This is called standing. I can only sue on for damages done to me not to others. As you say, there may be other alternatives than the ones I suggest. My intent was only to warn the OP away from anything that makes any allegations whatever because of the personal risk it entails.

@Buffy The so-called police?

@sgf. not every authority is necessarily called "police". There are regulatory authorities and such. But you can only make a complaint. Then it is up to them to follow up or not.

Fraud can be criminal or civil. One can easily run afoul of criminal laws and end up in prison by lying to customers. Libel can be civil or criminal too, though criminal libel is far more rare.

@ASimpleAlgorithm, I'm speaking about "alleging" fraud, potentially slander/libel. Not the fraud itself.

@ASimpleAlgorithm, and others. According to the UN charter, defamation (slander, libel) should never be a criminal matter. Some countries have been called on this. https://en.wikipedia.org/wiki/Defamation.

@Buffy not strictly true.  you can allege fraud against the government and sue on the government's behalf.

@emory, please be more precise here. The crime would be fraud, not slander. Alleging a fraud isn't what is being called a "crime" anywhere here. Things are being conflated that are not the same. Using "fraud" and "allegation" in the same sentence has become too confusing in this comment sequence. Again, defamation is  properly  a civil matter. Your comment doesn't speak to that at all.

@Buffy I mean if your data suggests that a 3rd party is defrauding the government (but not you personally) then in the US (and many other countries) you can file a 'qui tam' lawsuit and if you prevail be entitled to a fraction of damages.  1. You do not have to be personally damaged to have standing (though it helps).  2. There can be an upside as well as a downside to making the allegations.

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Rapid publishing experiment
In 2015 or 2016, there was an experiment by a group of post-docs and graduate students to ideate, research, and publish a scientific article (on a pre-print site like arxiv.org) in 24 hours. The topic was something to do with social networks, but the speed of writing the paper was the main point. Can anyone point me to that paper? A group I'm in is going to attempt a similar experiment. Thanks!

There is a well-known paper in my field that is 1 page long and was written in 1 day. (Including the research.) OK, the currently available version is 2 pages long.

I believe you might be thinking of the "72 Hours of Science" experiment, which resulted in this preprint. This was done at the Santa Fe Institute, and you can find the news release describing the project here. As they say, finalizing the topic and organizing tasks took up pretty much the first 24 hours, so also fitting the research and write-up into a mere 24 hours sounds rather difficult.
There was a second 72 Hours of Science in 2017, resulting in this preprint. The project has also inspired the Complexity72h workshop, and possibly other follow-ups.


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How to know if one is suitable for pursuing academia or Research work their entire life?
I am a PhD student in engineering in an university in Canada. I am close to completion of my thesis but I am not very proud of my work. I have couple of publications from my work, all in decent journals. I feel that I have not utilized the opportunities available to me and wasted time in personal activities that did nothing to my CV.
Owing to my inadequate performance during PhD. I am constantly regretting my decision of pursuing higher studies. I was never a star student. My undergrad was from a very low ranking school where I had received very average grades. However, I somehow got into the top graduate school where too I struggled in getting average grades. My research there was very unimpressive and not a single professor urged me to pursue PhD. My master's advisor even expressed shock when I had asked for his recommendation for applying to PhD school.
However, luck struck again, and I got into a reputed PhD program. My advisor has had a lot of patience with me. She is a hands off kind of person, but she has never complained about my performance till date. Now as I am completing my thesis, I am confused about my future career trajectory.
I feel like I do not belong to academia or research industry as I don't possess the necessary skills (sound technical skills, exceptional analytical skills and focus). I feel like a failure who is in a wrong profession. I really don't know what to do now.
My only reason for pursuing PhD in my current field of study was that I loved the process of researching. I loved finding reason behind why a physical phenomenon occurs. But, I now feel that just love for research is not an adequate reason for doing PhD or master's degree.
In short; I have realized that I am not not suitable for academia or research industry as I don't possess the necessary skills for pursuing research. I should have taken the engineering job after my undergrad as I was never built for a life in research.

I have couple of publications from my work, all in decent journals. That's something to be proud of. More than I had after completing my PhD.

Possible duplicate of How should I deal with discouragement as a graduate student? See also https://academia.stackexchange.com/questions/87668/how-do-you-come-to-terms-with-the-fact-that-you-might-never-be-among-the-best-in

Whether or not a career in academia is suitable for you is hard to say for us who don't know you. Be aware though that impostor syndrome is common among researchers, so you may not necessarily be the best judge of your own capacities. Why not ask your advisor what she thinks?

You can still take a engineering job with a PhD the only disadvantage now is that you have to live with the higher income compared to a engineer with "only" a bachelor degree.

Here is an easy way to find out: would you still do research if you have 1 million dollar ? Yes - remain in academia, No - you are suitable for industry.

"My research there was unimpressive and not a single professor urged me to pursue PhD" - When you first started speaking, your ability to form words was unimpressive, but now you can speak. When you first started walking, your inability to stand up was unimpressive, but now you can run. Society's first phones were unimpressive when we look back at them, now we have supercomputers in our pockets. The point is that just because you might be 'unimpressive' now, does not mean that you will continue to be unimpressive in the future. Keep developing yourself if it's what you want to do.

So you are going to finish your PhD soon and you are thinking about what to do?
I understand your regrets, but they don't help you (as you probably know yourself).
The question remains: What are your options now?
First of all, you do not make a decision for your entire life. You can start a research position and leave it after three years, it is not really helpful to try to plan for 30 years of more. You can either try to get a research position after your PhD, and if you get one, decide again after two to three years. Or you can look for challenging positions in the industry. Both approaches are entirely sensible.
Just don't consider leaving academia as a failure. Most people leave academia sooner or earlier and many find an interesting, good job.

This is a great answer for anything related to one's career.  You don't have to figure out what you want to do for the rest of your life; figure out what you want to do now, and if that changes down the road then adjust accordingly.  That's been the story of my career (I'm 10 years in now after 6 years of grad school), and its worked well for me.

I don't want this to sound wrong, but those "star" researchers / inventors need support and there are many places where competent people are needed.
The other thing you don't touch on is teaching - do you enjoy seeing others benefit when you explain something? If that gives you a buzz, then check out that direction.
Best wishes anyway.

You say

My only reason for pursuing PhD in my current field of study was that I loved the process of researching.

There. That's the core. Do what you love. If you won't, you'll regret it for the rest of your life.


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When writing an email asking for PhD positions/projects
I've recently finished in Masters in Neuroscience in Germany ( & bachelors in pharmacy), and I'm trying to find a PhD position in European countries like Belgium, Sweden, Switzerland, etc. In most of them, I have to contact the professor I'm interested in working with myself. I've already emailed a lot of them ( app. 20, with 6 replying no positions available).
-The problem is, I'm afraid if my emails are too generic. Here's the part from my emails where I have some concerns:
"As you will see in my resume, I have steadily oriented my education and experience towards becoming an accomplished researcher of regenerative medicine/technologies for the nervous system. Being a pharmacy & neuroscience graduate gives me a unique perspective that is useful when exploring the regenerative capacity of the nervous system, whether through manipulating neurons directly, manipulating surrounding glia, or the use of stem cells."
For the rest, I clearly stated that I'm looking for a possible position in their group, what my previous accomplishments are, as well as who I am in a brief description.
Naturally, I only emailed professors whose research I like and is linked to what I want & mentioned in this paragraph. So, is it inferred that I like their research/field, or is it still to generic?
Of course I read their about their projects on their group pages, but I'm not sure if I can go as far as reading their articles, since it would take too long, they may have no positions, and I don't know how many should I contact. So I wrote it in a more general manner, and if a professor/group leader expressed interest, then I would read in a lot more detail about their work (their articles & reviews). But is this truly the only way for them to consider someone?
-Another point is how many emails. One acquaintance mentioned that he had to send upwards of 300 emails to find a position. I simply can't believe he can send that many emails, without them being a single copy, but with each professor's name. I think it would be in the range of 20-50 emails, but that's pure conjecture on my part. I need to know from your experience, since if they're not so many, then I can read more about the professor's work in detail.

Quite simply, if your email to me does not explain why you want to do a PhD in my group, I am probably not going to respond to your "cold" email, unless your CV is so outstanding (several papers, good grades, working with people I already know, etc.) that I can't help but take a closer look.
So you need to make sure that your email not only expresses your research interests, but also explains why your profile makes a good fit for the group to which you're applying.
Also note that if you're sending a "cold" email and the professor isn't in the process of advertising a position, you still may not get a response.

The volume of emails requesting a lab position received by most professors in my field is large and unceasing. This means that you have at most a few moments of attention from the prof who is skim reading your email.
By far the majority of emails read along the lines of "my name is X and I would like to do a PhD in your lab", usually followed by "I have graduated from [insert foreign institution] and would value the opportunity to perform my PhD in your lab". There is usually no information that describes why the work your lab undertakes is an important part of the decision process that lead the applicant to email the prof. Nor is there a description of what the applicant brings in the way of unique ideas/approaches that will forward the work the prof performs.
Cold emails from excellent candidates will always have to compete with those from less exceptional candidates, and are out numbered by the latter by at least 20:1.
Spend the time to personalise the email. Suggest approaches/experimental plans that will address areas of interest to the prof. If possible,  go to scientific meetings and initiate a face to face contact that will notify the prof for your intent. Maybe try writing a traditional "snail mail"  letter (you know, written on paper and sent by post) - this at least will force the recipient to spend a moment or two longer on the correspondence and may provide a novelty factor that aids in distinguishing you from the rest.

Stepping from a masters to a PhD program is a huge undertaking. While times are tough, research dollars are scarce, and busy under-funded professors may be unlikely to respond, consider consulting your advisor:

Take a printed copy of your application letter and ask for constructive criticism.
After sharing potential research groups you have targeted, ask him to recommend some others. Perhaps s/he might write a letter of recommendations to a colleague.
Read How to Win Friends and Influence People.  It will accelerate  your career.
Finally, keep your chin up. Changing institutions is hard work. Spend a little time every day doing something you enjoy, for a positive mindset will give you that extra edge.

I agree fully with the previous answers, but there are a few things that I would like to add to them.
Note that this can be very cultural and what works in one area may not be appropriate for another, but this is my take on things.
Firstly I would always show some passion for the subject and demonstrate your background knowledge of the area. For example, in your case, why are you interested in researching the regenerative capacity of the nervous system? This may be obvious to you, but don't be afraid to spell it out. You can talk about benefits to society or possible applicability to other research or whatever you feel is appropriate. You mention many techniques, but why are they relevant / important? How is it related to the work in the specific research group? Always ask yourself why (and personally, I start by writing the why because it is the most interesting and compelling part).
Secondly, and related, people are (on the whole) vain - show genuine interest in the person and their work. Don't over-compliment, but certainly show that you know what they do and why it is important. Then you can talk about why you are the right person etc. etc.
On the issue of how many emails to send, I would say quality over quantity. Take the time to tailor each one to the specific professor / research group and really appeal to them rather than just sending out hundreds of emails (I would certainly not be proud of having to send over 300 emails to find a PhD!) Also, don't be afraid to send a follow up email if you don't get a reply. You really have nothing to loose from this - showing that you have the passion by sending a follow-up will certainly not harm your chances.
Finally, there is a lot of material around to help you with this. A particularly good (and classic) book is How to Win Friends and Influence People by Dale Carnegie - old but very very good (more about management, but the psychology is the same). There is also a lot of overlap with careers advice on how to write a good cover letter and how to send speculative job search emails so search online for these. Also, your previous University probably has a careers department so they can really be very helpful in providing honest feedback on your emails / letters.
TL;DR: Always show your passion for the area and talk about the recipient (and their work). This is the best way to capture someone's interest. Talk about yourself last.
Good luck with your search.


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Should I be worried about low undergraduate grades during the COVID-19 crisis affecting grad school admission chances?
I'm currently in my undergraduate junior year studying Mechanical Engineering at the University of Waterloo in Canada. I'm hoping to apply for Top 10 US grad schools in mechanical engineering in about 18 months. In response to the worldwide COVID-19 health crisis, our institution has (as have most academic institutions) switched to online teaching and made many changes to the structure of our courses to accommodate the situation.
As part of these changes, the university has offered students the option to selectively change the grade reporting on their transcripts to CR/NCR (Credit/No Credit) at the end of this semester. Normally, my grades would be pretty good (hovering around ~3.9 GPA) and I wouldn't bother to report my grades as a CR instead of as a percentage, but this crisis has completely disoriented me and made it difficult to focus on my studies.
Furthermore, the university has allowed instructors to retroactively adjust the course breakdown/weighting away from the original syllabus--this means that tests/projects that were originally worth 15% of the grade might have been increased to upwards of 40% weighting. This has had a negative impact on my course grades as well, as I was hoping to make up for poor showings on some of these lower-weight deliverables with strong final exam performances. Instead, these final exams are going to be worth much less now.
In the aftermath of these changes, I'm contemplating using the CR/NCR option on some of my course grades, particular with any grade that ends up lower than my current GPA. However, I'm worried about how this will be interpreted in my grad school admissions in a couple years. In normal circumstances, I think changing a percentage grade into a CR/Pass grade would be a red flag that a student's performance in the class was less-than-stellar.
Given the COVID-19 crisis and its effects on academia as a whole, are admissions committees two years down the road likely to be understanding if I decide to take advantage of the CR option now? Should I make use of it and explain that this was "the coronavirus semester" in my application package, or am I dooming myself by converting my grades from percentage into CRs?

For what its worth, my own institution is offering a similar option for students to be graded Pass/Fail, but they will explicitly be noted on the transcript as being pass/fail because of the COVID-19 crisis. Yours may be similar.

In 18 months, no one will have forgotten that Spring 2020 was the coronavirus crisis.

The situation is chaotic and it is difficult to make a prediction or give firm advice. Either path could be better than the other, depending on the judgments of others.
However, one prediction that I can make with confidence is that universities sending out grades will also be sending out explanations that extraordinary measures were taken in extraordinary times. Furthermore those receiving grades and such will understand that the situation was chaotic and that the ordinary procedures need to be modified.
If it were me, I'd probably opt for the grades rather than pass/fail. If necessary, I'd just explain that the general chaos affected my performance somewhat and the grades may not accurately reflect my potential. I'd suspect that letter writers would back that up. But that is partly because I'd have a history of excellent performance generally and not one that would be questioned in the absence of the current situation. (This is the hypothetical me speaking, not the real me.)
But the pass fail option can also be explained fairly easily that the risks were higher due to general disruption and you considered it the safer option as the rules were changing, making earlier assumptions invalid.
I expect that there will be more emphasis put on interviews and on letters of recommendation for a while until things settle down again. But that is just a guess.

Worth noting that some testing or exams are often part of the interview process.

Should I make use of it and explain that this was "the coronavirus semester" in my application package, or am I dooming myself by converting my grades from percentage into CRs?

You shouldn't have to explain that it was "the coronavirus semester" (though it probably doesn't hurt to mention it, I guess), but more importantly, you also aren't dooming yourself with your grade conversion. For God's sake, this is a global pandemic. Everyone is aware of it.
To add on to Buffy's answer: I can tell you that at my school, a large US research university to which you're probably applying, I received a university-wide email affirming that admissions to our graduate and professional schools would be evaluated holistically and take into account the highly unusual situation in Spring 2020, and that departments would not be penalizing students for taking classes Pass / Fail. That's the right decision. If a school was going to dock you for it, that's probably not the ideal place for graduate school.


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Work life balance and managing the effect on mood in mathematical physics research
For the last year, I have been working on my thesis in the area of mathematical physics. It's been a long project with many challenges and hurdles and progress has been slow. At the same time, I have managed to be in a stable long term romantic relationship with whom I cohabit, and spend a significant chunk of my time. In the light of that, I have kept my work time and personal time separate. I try, as much, not to think about work off work hours, and I am decently successful at it.
Now, the issue I have is with my mood. When I have a great day at work, and problems get solved- I am ecstatic and fun to be with. But on days when things don't work, I am not a great person to hang around. I am silent, and worry too much. Almost always, the problem solves itself in the next few days, or even sometimes after a good sleep. I know this; I know that I will manage, yet I somehow can't make myself feel good on days like these, and in research- I have a lot of such days. I wonder if anyone else has experienced the same, and if so, how do you deal with it? I feel like this is in general very important for my well-being if I remain in research.

See this related question.

What is your exact question?

The question is explicitly written: I wonder if anyone else has experienced the same, and if so, how do you deal with it?

Probably a pep talk isn't going to be a big change in your life, but it sounds like you have good work life balance only when work is going good. Maybe your balance isn't related to time considerations.
But maybe you just need a more realistic set of expectations about research. If it is real research then it can't really be scheduled - results can't anyway, only effort. Some problems are hard. Some will require years of work for resolution. Some will require armies of researcher working for years to obtain key results. In mathematics some questions have stayed open for hundreds of years. In physics, it is decades, at least. There is no real reason to be overly frustrated by the difficulty of intellectual work. If it were easy and could be done on schedule people would hire unemployed coal miners to do it.
So....
Well, you have already had the insight that some things just come to you when you aren't trying. Too many people don't understand that and think that longer days and shorter nights makes them more productive, not just more tired.
So, find a way to put down the responsibility for work when you call it a day. Close your notebook and say - enough. Life is good.
That is my mantra, actually. Whenever I'm feeling a bit "off" I just say it: Life is Good. Deep sigh. Relax. The work will still be there when I return.
Is this just a psychological trick? Yes, of course it is. But you can also make it a hook to take control of your own psychological state. You don't have to be driven by those moods.

However, if you also have the experience that you have stray insights when not working, then you may need another trick. Especially if you sometimes lose those thoughts since you aren't focusing on them. I developed the habit of always carrying a few index cards and a pen, no matter where I was. Some of the cards had a few notes on things I needed to review and some were blank. If I found myself with a few moments, I could review my notes. If I had an interesting thought, I could write down a few words so as not to forget. I discuss the Hipster PDA in some detail in the linked post on another site.

Really like the index cards idea.


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Does posting paper online anonymously prevent me from publishing it in journal?
I am a high school student and I am trying to publish my first research paper in mathematics.
However, I have already had my full paper posted without author information on the website of another organization. Now this paper (in pdf) can be found by Google. Does this prevent me from publishing the paper in a journal because of plagiarism-check issues?
I can prove that I am the author in the following way: that organization where I posted the paper can provide proof that I uploaded it and that the paper contained no significant plagiarism because it was checked by Turnitin.com's software before upload. The plagiarism-check report and the paper were posted online at the same time. How can I provide a proof like this to a journal? (I have not submitted the paper yet.)
(For lack of experience, I did not know that I should not have done this.)

Journals also differ in preprint policies. Check here: http://sherpa.ac.uk/romeo/index.php

Assuming you didn't actually publish it - you only posted a preprint - then the answer is no, it does not. However you will need to prove that paper is written by you and therefore not plagiarized. Submit the proof together with the paper, or you are likely to receive a desk rejection. You could for example upload the proof as a source file, and add an explanation in the cover letter.
If you did actually publish it then the answer is yes. Journals generally do not republish already-published papers.

There are two complicating factors involved here. It may or may not be possible, but it depends on these issues at least. Even if it is possible, there may be some "risk".
When the "organization" published your paper, did you assign your copyrights to them? It is possible that you did, and also possible that you retained all rights and just gave them a limited license to publish. The outcome is very different for these two situations. What did you sign or implicitly transmit to them to make it possible for them to publish. If they hold copyright or an exclusive license then there are things you cannot do yourself. Copyright law varies widely from place to place but is generally becoming more restrictive.
The second issue is that many places won't publish anything that has already been published. Many of them actually want you to sign over the copyrights and don't want to be limited by some prior license that you gave to another organization. This is very strict with some of them. But it is a limitation imposed only by their now policies and these vary. It would be a mistake to try to publish with such a journal without informing them of the situation.
But even if neither of the above considerations apply, you might have difficult claiming that a work is yours. If the original publisher makes the claim then it will be believed (most likely), but if only you make the claim it might be open to dispute unless you are backed up. In an ideal world (not this world, unfortunately) this would be a simple matter.
Therefore, the place to start is with the original publishing organization. You don't describe its nature. I worry about reputable organizations publishing the work of students anonymously as you have stated unless the is very controversial and you need some form of anonymity for personal protection. But you don't describe the circumstances.
But is that organization that holds the key. If you ask and they say no, without a legal reason, then you proceed with some repetitional risk.
An additional complication is that if you simply reuse what you previously published, without citing it properly, you can still be accused of self plagiarism. Normally one cites and quotes ones earlier work, rather than just reusing it.

By the way, turnitin isn't a sufficient check to prove the absence of plagiarism. Plagiarism is much more complex and subtle than what can be judged by an algorithm.

I don't think journals actually use TurnItIn to check for this, the methods they use may be more or less effective, but if they do find out you published somewhere else, the TurnItIn saying it's not plagiarized won't help your case.
Journals tend to not publish articles published elsewhere. However, their concerns here is being second fiddle to a competing journal. They don't actually care that much about you keeping your research a secret until the moment you submit. You can go to the journal's website and read their publication guidelines and policies to learn exactly what they allow and don't. For example, many journals are okay with research being published in arxiv.org or as a thesis. If in doubt you can always email the journal, say where you published and how much the text changed since then, and if they say no that settles it. I wouldn't try to lie about it, because not only could you get caught while in review, but if you are found out after being published the paper could get retracted, which could look even worse than not being published at all.
The real problem is that it was published anonymously, so from their point of view you might be trying to steal someone else's work. But you say you can get the other organization to confirm your authorship, so it shouldn't be an issue. I would proceed like so:

Submit the paper normally
If the submission form asks whether the paper was published before, link to the article and explain what sort of organization published it and point out important ways in which your manuscript is different from the version published there (if it doesn't ask, you should probably mention it in the "other comments" box)
If they ask about proving that you published the other one, then provide your proof from the other organization


text:
Standard protocol for withdrawing published paper that has wrong (or erroneous) data (published without wrong intentions)
Suppose a research group publishes an article after thorough data analysis, statistics based on repeatability and reproducibility of experimental data. Now I consider three cases:
a). Published article had erroneous uncertainties associated with measured data
b). Published article had erroneous measured data notwithstanding repeated experiments
c). Published article had wrong interpretation of measured data
Now, in such cases, what is the standard protocol for withdrawal of published paper, and whether it is really necessary? If the same research group publishes another article giving more accurate experimental data with revised uncertainties with more reliable and logical interpretation, does this in any way puts a question mark on the credibility of the research group?
What according to the strictest ethical rules of publishing should be done in order to accept mistake and provide justification on why the earlier interpretation was wrong and what makes the research group change its view on the same experimental data (in this case, revised data)?

Retraction is usually only used when there was misconduct. If you made an honest mistake, it's sufficient to contact the publisher and ask to publish a corrigendum to the paper (different publishers have different procedures for doing this). If you just no longer believe the conclusions you made are correct, that doesn't even need a corrigendum, it's just part of the normal scientific process; next time you write a paper on that topic you can spell out your criticism of the previous work and why you don't agree with the conclusions. This is part of why science is supposedly "self-correcting".
I certainly don't think publishing a corrigendum or a new paper criticizing your previous work would cast doubt on your credibility. To the contrary; being able to criticize one's own work and recognize problems in it is an important part of doing science, so doing this would not reflect poorly on you, it would reflect well on you.

Not every published paper is right.  Publications are a snapshot of authors' understanding at a given time.  If they don't stand up to history, the literature corrects itself.    Descartes's publications on the pineal gland as the generator of motor actions have never been retracted!
If a paper is wrong because new data or new understanding has changed the authors' outlook, perhaps the best course of action is to publish a new paper, specifically discussing the previous paper.
If there is a real MISTAKE or MISREPRESENTATION in the original paper, the editor should probably be contacted about the possibility of publishing an ERRATUM.  Retraction should be reserved for the most severe of cases.

Some papers can't be "retracted" if they have been printed and widely distributed. Corrections can be issued in some journals.
But, another way to correct the record is to attempt at least to publish another paper updating and citing the old paper. Spell out the errors in the original. You may or may not want to say why this happened.
However, such a paper is only likely to be accepted (I think) if you provide a correct interpretation. I think this is your situation here.
Whether it puts a negative slant on the group or not, leaving it uncorrected will probably do more harm.
You might want to try to work this out with the editor of the original journal if possible. But, as Scott Seidman implies, people make mistakes. It goes along with being human.


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International Code of Ethics for order of co-authors in research papers
In many cases it so happens that multiple workers are involved in a research problem under the supervision of group leader. We will assume that group leader is the corresponding author of a manuscript. Now, I have the following queries:

Who will decide who the first author will be? I am talking about a scenario when all the co-authors are PhD holders. If there is a dispute, who has to resolve and how?
Who decides the sequence of co-authors in the manuscript, first author or corresponding author? Is there any international code of ethics in this regard?
Again, we have to assume that it is practically impossible to quantify the contributions of respective co-authors in a well-funded, well-qualified research group. And qualification sometimes comes along with ego. How can the corresponding author decide that the second co-author has contributed more than the third co-author, and the ordering will not change (whosoever had decided based on point 2)?

Welcome tot the Academia Stack Exchange You should note that in many fields & locations the basic assumptions you've made here aren't often true. For example it's fairly common for the corresponding author to be the person who writes the actual words, or the member of staff closest to that.

Welcome. Mentioning your research field would help a lot, as the order of authors varies.

The meaning of author order varies across fields. In some fields, authors are listed alphabetically. In others, the order reflects some sort of perceived contribution. Some people prefer to be the last author.
The only unified code, and it is unwritten at that, regarding author order, is to talk to your authors and be considerate to their feelings. It is academic misconduct to leave someone out as an author. Similarly, it is wrong to list someone who should not be an author. This means that it is up to everyone to decide. If your research group is so disfunctional that this is hard, have those conversations at the start. In fact, I advise everyone to have those conversations at the start and during the process just to keep hard feelings from developing.

As far as I know, the only "international code of ethics" in this regard is that all authors must agree on the author ordering, or the paper cannot be published.

Who will decide who the first author will be? I am talking about a scenario when all the co-authors are PhD holders. If there is a dispute, who has to resolve and how?

If there is a dispute, they have to negotiate until they find an ordering that everyone agrees with.  Nobody has the right to put your name in a certain position without the consent of you and all the other authors.  (It is irrelevant here who holds a PhD or not; the authors have the same rights no matter what kind of degrees they have or don't have.)
If the authors can't reach agreement, they can't publish the paper.  A subset of the authors could decide instead to publish a new paper with the remaining authors' contributions removed or recreated from scratch.
Of course, the authors could agree that they are going to let a certain person decide (the corresponding author or whoever), and that they will follow that person's decision.
Commonly, the journal will require every author to sign a statement (or click a check box) that they approve all aspects of the submitted paper, including the author ordering.  So if anyone disagrees with the ordering, they withhold consent and the paper doesn't proceed until agreement is reached.  Or, in some cases, the corresponding author is asked to certify that all authors consent.  It would be extremely unethical for them to certify this if the authors do not all agree to the author ordering.

Who decides the sequence of co-authors in the manuscript, first author or corresponding author? Is there any international code of ethics in this regard?

Same answer.

Again, we have to assume that it is practically impossible to quantify the contributions of respective co-authors in a well-funded, well-qualified research group. And qualification sometimes comes along with ego. How can the corresponding author decide that the second co-author has contributed more than the third co-author, and the ordering will not change (whosoever had decided based on point 2)?

As above, the corresponding author can't make any such decision unilaterally.

"As far as I know, the only "international code of ethics" in this regard is that all authors must agree on the author ordering, or the paper cannot be published." I'm guessing that holding a paper ransom to improve your name's position on the authors list is what would be best described as a "career limiting move", right? ;)

Since you don't specify the field, I'm not sure how helpful this will be to you, but recently there has been a movement in economics to encourage the publication of papers under a system of certified random author ordering. You can read more about this trend at https://www.aeaweb.org/journals/policies/random-author-order.


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Changing level of difficulty of assignments for a course based on average class performance

As a teaching faculty in mathematics, do I need to change the difficulty level of assignments after assessing the average class performance in the first couple of lectures? I am not sure if this is done across universities in graduate level courses.
Or do I continue to maintain the rigour irrespective of whether students are following(enjoying) the lectures. Should the teaching faculty worry about the faculty grades from students at the end of the semester course?

In the most common scenario, there will be students from weaker background, and we need to be responsible for them as well.

I would suggest that you step back and ask yourself why you are giving these assignments. Some people give out assignments purely so that they can grade students and then they think about fairness of grading, etc.
But, if you consider that it is through reinforcement and feedback that students actually learn then the solution becomes clearer. If you consider that the human brain works by actual physical rewiring - connecting synapses - then you see that students need these exercises to make the material clearer in their minds and so that they can move the ideas from short to long term memory. This is discussed in the book The Art of Changing the Brain by James E Zull. It is pretty fundamental to learning theory in general.
Thus, the exercises should be there to enhance learning, primarily.
So ask yourself whether the exercises you use are enhancing learning or not. Or are they just a stumbling block that some students can't get over? If it is the latter, then you should use different exercises that better enable learning.
My goal was always to teach every student. If I had a reasonable number in a class and if they were willing to do what it takes to learn, then I could be successful. But for many students it takes a lot of practice to come up to speed, as well as a lot of feedback.
But my goal was never to just deliver information and use what you want of it. Wikipedia does that job pretty well.

However, for your weaker students - those who are willing to do the work, anyway, there are other options. If your current exercises are good in some ways and you don't want to drop them, you can provide additional exercises for those who want to try them. These might be chosen to better enable good performance on the current set. But you should also provide some mechanism for the students to get some feedback on these new exercises. From you is probably best, but sometimes peer-review might be sufficient. Or even set up study groups among the strugglers.

No and yes.  The time to assess the class performance is not after a few lectures but after a term.  Students will naturally adapt and the quality of their work will rise or fall with the expectations (to within reasons) of the instructor.
Changing the marking scheme mid-stream is not generally a good idea.  If really the remaining students do poorly overall, the instructor can always discretely rescale the assignments to help the class before final submission.
In case of immediate doubt, ask the previous instructor (or another faculty member) for example assignments or comments on assignments to make sure your expectations are completely out of line with previous years.  It could just be this is a habitually “hard” course where historical averages are low.

Just change the marking scheme.
Instead of all points for final correct answer, which is what some do, (and I found it brutal - a 20 point question graded as 0 as final answer had the decimal point in the wrong place).
Try doing partial marking based on relevant parts of the solution. I do do this, X points for this, Y points for that and you can make the final answer worth 30% or 50% whatever is appropriate.
This helps the weaker students who may not complete the question in the allotted time as they get points for the progress they made.
That way you don't have to re-write the assessment questions, just a marking scheme.


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Does the usage of mathematical symbols work differently in books than in theses?
From what I know, one cannot use a mathematical symbol for two different notations in a thesis. Is this right? The thing is that I am trying to cite a book in my thesis, but this book uses (tau) for both viscous stresses and reynolds stresses. Can I do the same in my thesis or do I have to choose another notation?
Bear in mind that I am new to academic writing, thanks!

Are they just using tau to represent any stress?

So why not just define a tau with a subscript v and a tau with a subscript r - make it clear in your nomenclature and you're sorted.
See:

The subscript might be confused as an index

@user2768 So seems to work fine for things like Cp and Cv... And if you have properly defined it in the nomenclature then there should be no confusion - perhaps for those who don't read it properly...

In principle labeling subscripts are typeset in an upright font (\mathrm or \text if you're a LeTeX user) and indexes in italics. But few readers actually pay enough attention for that to be reliable.

@dmckee are you assuming Latex or Word? All I wanted was to show an example. It may be better to make sure subscripts follow the standards set by the particular institution where the thesis is being submitted.

@Solar That convention comes from a standards document. I think. But I can't recall which one just now, so I could be fooling myself. In any case, I don't usually both to follow it. Too much trouble and as I say, readers don't notice. But I'd never attempt serious mathematical typesetting in Word, even though the tooling has improved a bit.

I tried your suggestion and since I am writing about these tensors' components, it seemed not eloquent having so many subscripts/indices with different meanings.

@MazenDraw You are responsible for your writing, clarity and notation. Check with your advisor and your institutions standards.

@dmckee It's an ISO standard that can be found also in the SI brochure and the IUPAC Green Book.

@MazenDraw You have many other possibilities. You could, for example, keep the tensor component indices as subscripts and put v/r as a superscript, use another typesetting trick like primes or tildes to tell different taus apart, or another letter altogether.

@SolarMike I have decided to use a comma between the subscript and indices. I will discuss this with my mentor as most of you suggested. Thank you all for your insight and for taking the time to answer quesions that might be trivial to you!

@dmckee The subscripts shall be upright if they are abbreviations of a word (like here). If they are just another variables, they should keep their own formatting.

@MazenDraw Do you mean something like τ_{v,i} and τ_{r,j}, where i and j are integers? (If so, don't, it becomes really hard to read.)

@user2768 Well, in theory they could be integers but I am using x,y,z notation for 3D second order tensors. I wanted to use something like this for example \tau_{\mathrm{r},xx}. Would this also be confusing?

@MazenDraw Personally, I find any label in a subscript annoying.

From what I know, one cannot use a mathematical symbol for two different notations in a thesis. Is this right?

That's certainly good advice, since it avoids unnecessary confusion.

The thing is that I am trying to cite a book in my thesis, but this
  book uses (tau) for both viscous stresses and reynolds stresses. Can I
  do the same in my thesis or do I have to choose another notation?

Presumably you don't intended to use τ to mean viscous stresses and reynolds stresses in the same context, because usage of τ would then be ambigious. So, I presume you'll be using τ to mean viscous stress in one context, perhaps an entire chapter, and to mean reynolds stress in another context, perhaps a different chapter. This seems reasonable. However, you needn't use the book's notation, especially if there is a risk of ambiguity.

Using the same symbol with two different meanings in two different chapters does seem to increase the possibilities of confusion...

"This seems reasonable."  No, it's not, and academics, and indeed any one hoping to get an idea across, need to stick with a consistent method for describing different phenomena, constants and variables.  It is not reasonable to basically require you to keep looking back a the beginning of a chapter in a book to determine the symbology, even given you understand what each symbol should represent normally.   The book made a mistake in overloading symbols like that.

@opa : In my opinion, there's nothing wrong with using the same symbol to mean different things in different contexts, especially if they are analogous. When a student has 15 equations to solve on a test, all involving the variable x, do you think the student is confused because x appears several times in different contexts? Of course not. And if the author actually simply mentions that the symbol means this or that when it is about to be used, what's the problem?

@opa In this case it is quite common to use tau for any kind of stress. I would certainly be confused if the stress wasn't denoted by a tau. Look into Pope's Turbulent flows what kind of symbols they had to employ to stay unique in the whole book but still I expect he uses some kind of tau for these two stresses. The book uses the same letters with many different typefaces for various variables, because the number of symbols is limited.

@opa You've quoted me out of context, the very next sentence starts "However, ..." Anyhow, I appreciate your concerns, but I'm inclined to agree with MPW and Vladimir, especially "it is quite common to use tau for any kind of stress." Of course, it really is case dependent, that is, in some cases it may be okay (because the discipline does it that way, for instance), whereas in others it might not.

From what I know, one cannot use a mathematical symbol for two different notations in a thesis. Is this right?

Such things are not governed by hard-and-fast rules.  Your institution might have specific style guidelines for a thesis, but notational choices are usually at the discretion of the author.  Of course, it's ultimately your advisor and/or committee who decides whether your thesis is acceptable, though it's unlikely that notation alone would be the cause for rejection.

The thing is that I am trying to cite a book in my thesis, but this book uses (tau) for both viscous stresses and reynolds stresses. Can I do the same in my thesis or do I have to choose another notation?

It's up to you.  Make your own decision as to which way will be the most clear.  You can ask your advisor if you are unsure.

Depending on field there may also being standards which are strongly adhered to, in which case it is best to follow the standard. Good luck if the thesis guidelines and the standard are in disagreement.

I agree with this, but since OP is asking us for advice, it seems reasonable to be a bit more definitive. For my part: I would advise against overloading one symbol, and would be unconcerned about citing a book without adopting the book's notation.

@cag51: Feel free to write such an answer.  It seemed to me like the question was mainly about what is required, not just what is best, so I addressed that.  I don't know enough about the situation at hand to be able to give suggestions on what to write in this case.

Perhaps for some perspective: the scope of a "name" can be limited, that is, "local", or it can be "global". Even fairly basic programming principles nowadays (with virtually unlimited namespace, as opposed to 1960's Fortran) recommend keeping namespaces as local as possible...
... and this advice applies to most mathematical notation, as well. That is, there are really very few symbols/notations that are understood globally and unambiguously. That's fine. I think one should be reconciled to (re-) setting the "names" in a given "scope", and not at all depend on document-dependent notation/names as though they'd be something the reader would have assimilated. (Excepting perhaps a very small number...)
Even then, if "tau" has two different and conflicting senses in the literature, there is no genuine intellectual/scientific purpose served in being mute on the point, and trying to find a way to dodge the operational ambiguity. That is, in each of your sections or subsections, tell what "tau" is. Done.
That is, do try to find a viewpoint from which this is a non-issue.

Using the wrong "tau" in a calculation for a real engineering problem will never be a "non-issue"...

@SolarMike, presumably symbols refer to things which have a larger existence/sense/context than that single symbol. One of the points I try to make with my grad students (in math, in the U.S.) is to not get hung up in symbols, to use context to make sense of things, and so on. If someone's writing something to be checkable/readable, I'd want to also be able to check what the symbols referred to, etc. Seems like it'd be good practice.

so you’re saying an answer is better than the correct answer or "some understanding" is better than a thorough grasp - bridges fall down for less...

@SolarMike, I don't see how you are interpreting my comment as "some understanding is better than thorough grasp". In any case, I meant to say, again, that I want my students to be able to explain (to me, for example) the context sufficiently to justify (to me, for example) a supposed parsing of symbols. I am intending that this be a better understanding rather than a too-glib, superficial one (that may also be "brittle" or non-robust under context-shifts).

authors: Vladimir F Героям слава


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Changing citation reference systems
I am writing a research paper for the first time and I submitted my paper to a journal, in which the references in my paper were addressed in parentheses, as follows:
".....be preferentially located in the nuclear interior (Saccone et al. 2002; Cremer et al. 2015), consistent with a less compact organization and an enrichment of long-range chromosomal contacts with other active TADs and potentially multi-TAD hubs (Yaffe and Tanay, 2011; Olivares-Chauvet et al. 2016)."
The journal rejected it, and I submitted it to another journal which wants the references as follows:
".....be preferentially located in the nuclear interior [1-2], consistent with a less compact organization and an enrichment of long-range chromosomal contacts with other active TADs and potentially multi-TAD hubs [3-4]."

Saccone et al. 2002
Cremer et al. 2015
Yaffe and Tanay, 2011
Olivares-Chauvet et al. 2016

In the current format I have, all my references have the name and year in the parentheses and the full references at the end of the manuscript. The new journal wants it as numbers in order of occurrence in the manuscript.
Does anyone know any easy way to change the formats, without buying any software? If this question is out of scope of this forum, is there an appropriate one where I should ask?
Any help would be hugely appreciated, thank you so much!
Cheers,

Oh, nobody told you to not do these things by hand? References are so much easier to manage with computer programs...

Hi Wolfgang, thanks for your reply! Do you have any solution to this? Which software program can I use that can convert it automatically? Thanks!

EndNote, bibtex, and basically every one that's out there allows you to use a "style file". Changing the style is as easy as loading a different style file.

The easiest way to switch from one reference style to another is to manage the references using softwares. You may use Mendeley or Zotero, which are free reference management softwares. EndNote is another option but you need to purchase it. A free version of EndNote with basic functionality is also available.

If you use LaTeX, use bibtex as your reference manager.

Can it automatically do it for me by processing my the references in between parentheses and convert them into this format in word?

@rishi: Yes,  but first you have to create a library containing all the references used in your  manuscript and cite the references using the software. Then,  changing from one style to another is automatic.

Thank you so much! Do you recommend Zotero?

@rishi: It depends on your preference and which one you find more user-friendly.


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how to include editorial work in list of publications
Is there an acceptable way to include editorial work on journal articles in my list of publications?

What kind of editorial work do you mean?

Contributions such as editorial work must go under "Scientific and Academic Activities" in a CV and not under "Publications", because for it to be posted under "Publications" one must be an author on that publication (which editors are not).

Or it could be called "Service"


text:
Should I leave my undergraduate research project?
I’ve been working on a project for about 4 months simulating optics in a beamline for ANL. I’m the only person on the project developing the simulation. The software being used is brand new, open source and clunky. The documentation is poor (at best) with no real tutorial or users manual. There are consistent occurrences of bugs.
Anyway, I’ve been putting in 10-15 hr weeks and most of it has been spent learning the software and building summary PowerPoints (that have ultimately been deemed useless) based on examples in tutorial. That was the first 3 months. The pay period has since ended but I’ve elected to assist because I was led to believe the project would end shortly after and I’d be able to co-author a paper.
Now, it seems I have about 30(optimistic)-70(pessimistic) hours until I’m done based on what’s left. My advisor is bad and typically rejects any questions I have and says I simply have not been putting in effort. There’s little to no guidance in the project and my advisor always says how he could just do it himself much faster.
I have another project starting in a few days that will require 40+ hours a week that’s paid.
The combination of lack of respect for my advisor, other time commitments, and overall distaste for the project leads me to believe I should respectfully tell him I can’t continue working on the project.
Should I end it? If so, how should I go about it?

What are your goals?  Why are you doing research?  Anyway, I see no reason to continue with a disrespectful advisor.

First, ask your advisor for the level of commitments to have a co-authorship on a publication. Do so in writing (e.g. via email).

Dear Dr. ...:
I am making plans for how best to complete the project. Since I am no longer being paid, I need to schedule my time properly. I am especially interested to contribute sufficiently for a co-authorship on a publication. Looking ahead, I cannot however make an unlimited and open-ended investment. In this regard, I have two questions that I hope you can address.

What remaining objectives do you need me to complete in my work toward a co-authorship?
How long do you anticipate that I should need to spend on the remaining work?

I look forward to a prompt response.
Regards,
J P Bear

Second, prepare to leave.

Make photocopies of all notebooks that you kept.
Collect the electronic work that you have done to date. All of it. Every scrape. Organize it as best possible by themes (e.g. Reports, Presentations, Code, Raw Data, ...).
Burn it all on two copies of a CD or DVD. These are the immutable copies of the documents. You might need to find them again some time later. You can also store files in the cloud or on magnetic media. But, gosh what will you do when that cloud is sold to some third party who trashes your files or your magnetic USB stick happens to land in an NMR lab by accident, what then? Or, what will you do when you would be called to a court dispute about the co-authorship on a publication and you have a USB stick that ... well ... they will NOT accept as evidence in your case because it was not an immutable copy?

Third, generate a thank you letter ...

Dear Dr. ...:
Thank you for the opportunity to work under your supervision. I have appreciated the chance to learn how to program simulations for optics for the beam line at Argonne National Laboratories.
I am providing you with a CD that contains all of the electronic files that I generated over my project period. I am also submitting to you all of the notebooks that I kept with records of my work.
--> The wording in the next paragraph depends on what you did and did not discuss. It also depends on what you do and do not wish to continue doing.
[We discussed the possibility that my work will contribute to be a co-author on a publication. I am ready to assist in editing this publication when this decision is made. I am also willing to provide email or phone support to transition my work to the next team member.]
I can be contacted at the address below for questions.
Sincerely,
J P Bear

Fourth, hand the letter, one CD, and all of the notebooks that you kept to your advisor.
Fifth, say goodbye and start the other project.

"Burn it all on two copies of a CD." .... it's not 2006 haha

@AzorAhai I am glad to hear your recommendations for better alternatives to create immutable archives of relatively small segments of electronic data.

Pretty much any other way there is of transferring data: email it, put in on the cloud (Dropbox, OneDrive, Box ...), or if you really like being able to lose your data, put it on a USB.

I said immutable. Your methods are not. They are also subject to third party tampering. So, they are not certifiable. So, they are to be ignored. Try again perhaps?

I see no reason to go this overboard for undergraduate presentations ... code and data should already be on shared, protected resources or third-party archives where the advisor has them. If you are transferring those on CDs, something has gone seriously wrong a long time ago.

If there is a need to be "certifiable," then there should be instructions for how to do that. Every university I've heard of has secure cloud solutions for that, I've seen OneDrive and Box used. I'm not sure why there is a concern about third-party tampering, but a secure cloud server with revision history will certainly resolve that.

My long experience has trained me to store electronic files in an immutable format away from the cloud even today.. Paraphrasing a colleague of mine from other cases ... While the upside advantages to doing this seem to be minimal or even non-existent, the downside risks to not doing this are too high to avoid that you do not do it as a matter of some formal routine. I also do not say that files cannot also be stored in the cloud (or on other media). Finally, I can agree on the value of some of your suggestions. Perhaps you might stop implicating that mine are of lesser value (haha).


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Do researchers do their own statistics?
I'm writing a small paper on statistics in science and I was wondering whether in most fields researchers do their own statistics, or do they usually have a statistician in the department to do it for them?
For example, say I am a researcher in psychology at a university and I designed and performed an experiment. I now have the data I wanted and it needs to be analysed. Will I do this myself or will I ask a statistician to do it for me? What is usual in science?

There are so many factors going into this that it's going to be impossible to answer.

"Do researchers do their own statistics?" - Yes. And no. And also sometimes. "Will I do this myself or will I ask a statistician to do it for me?" - This one is easier to answer: Yes.

This is not my field, but I am surprised at the combination of "designed an experiment" and "do not know how to analyze the data". I naively expect that the integral part of the experiment's design is to decide on how the data will be analyzed before it is collected.

A researcher in such a field that can't do their own statistics isn't going to get very far. Of course, consultations with experts is generally useful and specialization is also useful. But you'd better understand it or you don't know what you are doing.

We may be able to answer this question, if you tell us the field. I can tell you that most psychologists and social scientists do their own statistics.

@Buffy I suppose it should be this way, but in fact it is isn't. Anecdotally, many researchers in the social sciences plug their numbers into SPSS and it gives them an R and hopefully "some stars". I wouldn't be surprised if practices in other disciplines were similar.

Both scenarios are quite common, and commonality varies by discipline - but I can tell you for certain both happen enough that you should not be surprised by either case. There is also somewhat of a hybrid approach, where many researchers do their own statistics (or have a favorite collaborator who does it for them as part of their contribution) but they may consult with a statistician for some additional guidance or advice, formally or informally. If I were forced to guess, I'd say that in most social science fields I'm familiar with (many with connections to Psychology) I'd be somewhat surprised if less than 75% of statistical analysis was handled by non-statisticians.
In practice, it tends to vary by individual study as well, and will change over time with any given researcher or team. Some people do certain kinds of stats only (ANOVA for everything, yay!), and if they can't do that they won't do any - or they just do an ANOVA anyway. Some people do no stats of any kind, ever. Some people develop a quantitative focus and start doing their own stats, and then become known as "the stats person" and end up becoming involved as a collaborator for others with a focus on research design and analysis, even as they continue with non-stats tasks (coming up with their own research ideas, running their own studies, etc.). Some people end up running into problems they realize don't fit the stats they are comfortable with, and work together with an outside person (consultant, statistician, etc.) to guide them or handle the analysis, but only for that problem (ex: they realized they needed a survival analysis but hadn't done that before, so they wanted to be sure they were going about it reasonably but then did the actual analysis mostly themselves).
So, in a nutshell: researchers of all kinds do stats always, sometimes, and never, and the mix varies heavily by discipline, problem type, and weather.


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Combine multiple major fellowships?
I have received both the NSF and another major fellowship (non-federal). Both stipends cover more than my departmental funding; do I get the sum of the stipends?

Probably not. You need to check the fine print on the fellowships and/or discuss with the contacts at each sponsor. Getting paid by two places for one position is generally frowned upon.

I don't know the answer to that, but I'd really want to have this question.

First of all - congratulations!
To answer the question, the NSF provides specific advice on this question:

May I accept or be paid from a private Foundation Fellowship?
Supplementation to a Fellowship while on Tenure is at the discretion
  of the GRFP Institution. Fellows should check with their COs.

In practice, I've found that you can at times get funding to combine with the NSF, but it is often intentionally limited by your local institution/department. For instance sometimes you can get summer funding or a 0.25 FTE assignment even while receiving the NSF, but you may get administrative pushback, and they are loath (or simply will not) allow more than that.
You will generally have a higher likelihood of getting them to agree if you can take the funding at different times. The NSF GRFP for instance is for 5 years, but only 3 years includes funding. If you have a fellowship that provides 1-2 years of funding, you can take that first and then stay "on reserve" with the NSF - and most institutions will be somewhat unlikely to object to that. One institution I talked to offered a 1 year fellowship, and on asking them they replied that I could take the 1 year and then take the NSF funding in other years, but that I would not be permitted to take them both in the first year.
But ultimately, the NSF says that is up to your local institution, so you'll have to check with your department to see what they say.
For completeness, note that the NSF explicitly cannot be combined with other fellowships provided by the US government (they mention "DOE, EPA, NIH, NOAA, USDA, DHS, DOT, NASA, etc."), but as the OP mentioned non-Federal this should not apply to them.

First, congratulations! Second, first check the scheme notes for the fellowships. Usually they want you to have the money in some form, so it is useful to talk to them after you figure out what the scheme notes technically say and weave your proposal to them around those notes.
I held an NSF and an EPSRC fellowship at the same time. Instead of balancing it .5 FTE on one and .5 FTE on the other (which would count as a year on both of them), I alternated years on each one of them, which meant my fellowship lasted longer than it would have.
Talk to your university too to see what their preference is, but mainly find what is close to the scheme notes and propose something that works for you to everyone that seems fair. I doubt you'll be able to get "double paid," but potentially having a longer period of funding seems very plausible.


text:
Master's Thesis Validity
After completing my Master's Thesis, I continued to learn about the topic and unfortunately what I found is unsettling.
I found that the whole hypothesis is wrong. The basic assumption on which we could do some useful work is wrong. My supervisor and his supervisor both are working in the same field for years.
The topic was offered by my supervisor from the University, who is a PhD student and the topic was also verified by his supervisor. Still, its frustrating to find how they could have missed such a basic assumption and expected[Maybe] a student to figure that out.
Now my Questions are:

Isn't it the supervisor's responsibility to verify these things before?
What should I do morally, should I inform my University/supervisor? If yes. what happens to my Thesis grade.
Since I entered the Master's curriculum to continue into a PhD program, and since I want to continue in the same field as my Master's Thesis, how does this whole wrong hypothesis scenario affect my chances of getting a good PhD program.

As I can think, why would some professor hire a student for PhD, when if he/she reads my Master's Thesis can understand the whole idea/hypothesis amounts to nothing.

While applying for any PhD program, I need to provide at least 2 academic references. After figuring out regarding my Thesis, I can't even think of asking my supervisor of his recommendation. What do you think, how should I go about finding right references.

Honestly, I am really stressed and am thinking of enrolling into another Master's program, but I wish there is a way to find a right PhD program.
I am sorry for not providing details of my Thesis/Uni etc. for obvious reasons and for a long post with many questions.
Please help, as this whole scenario is really freaking me out.

What field at least? The answer for math might be different from others for example.

Why is it that you can't think to ask your supervisor for a recommendation?

@Buffy Computational Neuroscience.

@BryanKrause I think it does not make sense to ask for recommendation as morally if the person did not put enough effort to verify things for a master's thesis, how much he/she would think while writing a recommendation.

@matharug It's more of a problem that your supervisor didn't teach you that research is often about failure and finding out what doesn't work than not "verifying things" - what were they supposed to verify? Why bother doing anything if you already know how it's going to turn out?

Is this a correct interpretation? You were given assumptions by advisors as a starting point. Taking those as true you came to come conclusions that turn out to be consistent with the assumptions, but invalid in the real world. The (possibly) correct methodology applied to incorrect assumptions led to incorrect conclusions. Now you know better about those assumptions. Does that capture it?

And to follow up, are those assumptions actually wrong, or just the result of some fundamental disagreements within the field between different groups of researchers? I don't know enough about your field to know, but suspect such things exist in some fields. In that case, perhaps your further study has just taken you across a boundary into another set of thought patterns.

Buffy BryanKrause Please see my comment to Allure's answer.

One of the most revolutionary physics results of the last century is the Michelson-Morley experiment. The experimenters set out to measure something, but measured zero instead. It turned out that the basic assumption (Aether theory) was incorrect. That didn't jinx the experimenters in any way; instead their names have since become immortalized in undergraduate textbooks and one of them even went on to win a Nobel Prize.
Is it the supervisor's responsibility to verify these things before engaging a student? Maybe, but without knowing the details it's hard to say. In the case of aether theory for example, it's the experiment itself that's supposed to verify the assumption; in other cases, there's still a good chance there's something subtle that you're missing (or why would they engage you to study it?). This means the solution is to talk to your supervisor. See if you can convince him/her that the hypothesis is indeed incorrect, because a basic assumption is incorrect. If that's true, that's quite a result: it means both your supervisor and your supervisor's supervisor assumed something that seemed reasonable enough to engage a student to work on, and then later turned out to be incorrect. If the field at large also made the same assumption then even better.
As for getting into a PhD program, don't worry about it. Showing that a basic assumption is wrong is quite an achievement, and this should be reflected in your recommendation letters. It's possible the admissions committee will read your thesis and find out that you didn't discover anything revolutionary, but that's not a big deal: as illustrated above, proving that something doesn't work / doesn't exist is still a result.

Allure :- I understand and I already know what you are saying.  I will try to say something which might be close. The whole wrong assumption thing, I am talking about is like assuming Pythagoras theorem is wrong and based on that we prove a set of theorems. My argument is anyone working in Math's will know Pythagoras Theorem is not wrong, so new theorems are wrong. Thus the validity of whole theorem proving work. Hope you can relate, else I will think of a more closer example.

@matharug again I can't say for sure because I don't know the details, but even this example doesn't seem that bad to me. There's plenty of work that go something like, "if we assume the Riemann hypothesis is false then ...". If the Riemann hypothesis is later proven to be true then all these results are bogus of course, but a priori you don't know if the Riemann hypothesis is true. If you've now done the equivalent of discovering that the Riemann hypothesis is not true, then you've really discovered something important. Again, talk to your supervisor.

@mathg - I know at least one person who published a successful paper after making an elementary maths error, realising that others in biology might have made the same one, and then using that to prove a bunch of established papers wrong. With a little savvyness, issues can be turned into strengths


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Dr. rer. med Title
The doctorate title "Dr. rer. med" is awarded to non-medical postgraduate researchers from University Hospitals.
Is it equivalent to a PhD, or Dr. Eng. etc.?
Is it recognisable in other countries abroad, besides Germany?
Is it acceptable for both academia positions and private sector?

This answer seems to have some of the information you're looking for.


text:
Remote PhD Using My MSc University's Lab
I am currently pursuing my MSc in Applied Engineering, concentrating in Mechatronics and conducting research in cloud-based heterogeneous robotics. My current university does not have a PhD program for engineering.
Are there universities that would allow me to remotely enroll in their PhD program and conduct my research using my current university's equipment?

Why would your current university destine equipment an space to someone working for another university? And what if the university you apply for has actually better equipment?

My university would be happy to allow me to use the equipment to conduct PhD research. I've already expressed this interest to my research advisor, and he was looking into it but is buried in committee and paperwork stuff for awhile.
Better equipment would certainly be fun to work with, but my MSc is only scratching the surface of what can be done in my current lab, and I'm really eager to continue work here.

You could look into doing a jointly supervised project. Your MSc supervisor and someone else from another institution could both supervise the project. You might be able to spend some time at the other institution and use their lab facilities too.

It depends on the country and the PhD program.
In the UK, you could look for a relevant supervisor in nearby universities (e.g. a couple of hours drive away) who might be interested in your proposed project and might be able to fund it (even if you don't need lab space, you'd pay fees etc). You would probably need to meet with them (and other academic supervisors / trainers) every quarter, with more frequent email / phone / video contact - depending on the particular universities rules & regulations. I've seen lots of people do these sort of multi-site projects.