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In literature review, ok to comment about reproducibility?
A high-cited paper in a field of Computer Science (that I'm working with) about an important algorithm does not tell readers about its implementation details. Since the authors were from a company, this is understandable.
In my investigation, I found that some implementation details were very important to get right, in order for my implementation to work. The overall process of getting it right took a little less than 2 months. This means that the paper could be, in general, hard for people to reproduce. There is also no open source implementation available.
My question is, is it fair to comment in a literature review that this paper "does not include some implementation details, which we have found to be highly important"? Also, does offering the implementation details in our paper count as a (maybe small) contribution?
Thanks in advance :)

The literature review is part of a "Related Work" section of the paper.

Yes, you can comment on the difficulty of producing an implementation and hence, on the difficulty of reproducing the results. That is pretty natural.
But, "algorithms" as properly understood in CS don't actually depend on implementations, having a high level definition that can be implemented in several ways. That assumes, of course, that the description is correct and complete.
I can't comment on whether two months is a reasonable time to build an implementation from its abstract definition or not. It might be, of course, since implementations are often imperfect.
To turn it around, an implementation (specific code) is often the worst way to define/describe an algorithm since it may depend on language/machine specifics that are not inherent in the algorithm itself. The code may not give the same insight that a higher level description could provide. That may well be the reasoning of the originators, not an attempt to protect trade secrets or related things.


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What are "fake", "shady", and/or "predatory" journals?
This question is in response to this very interesting question. The original post mentioned that they wish to retract their paper from a "fake" journal. I don't know what a fake journal is but better safe than sorry so I want to make sure what defines a fake journal. In the comments, other people also mentioned "shady" journals and "predatory" journals. This is the first time I encounter these descriptions so I would like to know more about what they entail. I would be interested in hearing about your experience with such journals as well, if any.

They are the Yahoo! Answers of the academic publication world... with a paywall.

Related: "How do you judge the quality of a journal?" http://academia.stackexchange.com/questions/101/how-do-you-judge-the-quality-of-a-journal

A "fake" or "shady" journal is a low-quality journal that does little or no quality control.
They are often called "predatory" because they prey on people who are under a lot of pressure to publish, charging high author fees for promises of quick publication. (Since they do little, if any, peer review, the time from submission of a paper to publication is often very quick in these journals).
They often engage in deceptive practices to make themselves appear legitimate, such as:

Pretending to be affiliated with a reputable professional society
Claiming an "impact factor" when they do not have one, or when they have an "impact factor" from some entity other than Thomson Reuters ISI
Listing important academics on their editorial board, when these people never agreed to serve in this capacity.

Publishing in one of these journals can be very damaging to your academic career. At best, it shows that you don't know what journals are considered reputable in your field; at worst, it makes you look like you are trying to "get" publications without doing the work required to publish in a reputable, high-quality journal.
An academic librarian named Jeffrey Beall kept a list of open-access journals and publishers that he considered to be "predatory." (The links are to archived versions of the pages).  His lists were quite well-known - you may hear people refer to "Beall's List" when talking about predatory journals.
Between the growth of open-access and the Internet making it possible for literally anyone to start a "journal," these "journals" have been popping up at an alarming rate. The NY Times even ran a story about it recently.

So "fake"=="shady"!?
I think each of these defines 2 different types of unethical activities with fake been non-existent (as in no ISSN, no editors at all etc) and shady being less transparent, poor or no review etc.

Yes, I was kind of wondering as well if "fake", "shady", and "predatory" can refer to three separate categories or not. I guess they may in some specific cases, but best to avoid all of them. :)

@Armand I think "fake" refers to a journal "faking" its status as a reputable journal (which is also "shady" behavior). I don't consider a journal more "real" if it has an ISSN.

@Armand I do not think that there is an agreed-upon distinction between shady, fake, and predatory.

In the previous post linked to in the OP's question I suggested in a comment the term "shady" in response to the proposed "fake".  First let me say that "shady" is not a technical term; I used it on the fly to mean what it usually does in contemporary non-academic usage.  I think the term "predatory" is more precise (while still being colorful) and should be preferred.  I do think the term "fake" should be avoided because there are a smaller number of scams in which there is actually no publication involved at all!

So journals like this are analogous to how vanity presses used to be viewed?

@neilfein Yes, good point. They're basically the low-rent version of the good old vanity presses (some of these "journals" operate out of their founders' living rooms) with even more blatantly deceptive practices.

I would lump all three into the 'Avoid when at all possible' category.

Isn't it against the law to write a journal's name into a list of "predatory journals"? How come this guy does not get sued?

@cagirici - What exactly would he be sued for? In what venue? By which entity?  If he put forward "truth" as his defense (since "truth" is considered a defense against libel in many US states), how would they disprove it?   Even though there's a knee-jerk belief that anyone can be successfully sued for anything, that's a rather lazy belief.

Emphasis on Beal's list being ones that he thinks are predatory. He lists absolutely zero objective requirements for making the list and he has included journals that many academics disagree with him on.

Jeffrey Beall, who works for the University of Colorado, Denver, maintained a list of predatory journals. He also publishes his criteria for determining which journals/publishers are predatory. (both links are to archived version of the pages) The criteria are numerous (and I find many of them amusing). The main thrust of the criteria are such things as:

Lack of transparency (in both business model and editorial process)
Disregard for intellectual property
Promise to publish anything in exchange for money
Dishonesty (in business model and editorial process)
Poor (or no) peer review

-1: without mentioning that this list is solely based on the subjective opinion of Jeffery Beall, with zero transparency (and zero explanation) for why specific journals make the list, this answer, in my opinion, misrepresents the list. In my field, there are journals on Beal's that conduct extensive peer review. For example Frontiers [which is considered as reputable as PlosOne]. They regularly reject applications to become an associate editor. They regularly reject papers. It seems like they were listed because they sent out too many emails when they first started.

From Beall himself "Frontiers does not meet the criteria for inclusion as a predatory publisher ... [But I am including them anyway because] there is value in sharing others’ experiences with this publisher". This shows just how scientific this list is. It does appear that Frontiers engages in some sketchy behavior, but so do many reputable for-profit journals.

... and a very good question indeed. The present answers do a good job, but it's worth emphasizing that there is a whole continuum between legitimate journals and what amount to conning schemes.
"Predatory" is used to describe a journal that hinges its business model on getting article processing charges from authors, whilst providing a very low quality journal. "Fake" is less defined, but it carries the connotation of a journal that pretends to carry out rigorous peer review but in fact doesn't (which is what makes it damaging on a CV: it looks like you too want to skip formal peer review but pretend you still did it).
"Shady" is a much more informal term, and denotes a journal anywhere in that continuum. I intentionally used this term in my answer to keep it broadly applicable, in terms of any journal of possibly not-so-good standing which is, after publication, thought to have a negative impact on one's CV.

There is a special class of 'fake journal'. Some long-standing real (but minor) journals, which are listed on the Web of Science, but only have print editions and haven't moved online, are having fake websites created by criminals, which are purporting to be the official website of the journal. In essence, the identity of a real journal has been 'hijacked'. Obviously, the websites charge 'article processing charges', which is why these scams exist, but the articles 'published' are NOT listed as part of the output of the journal on the Web of Science. Most of these journals have been forced to very quickly enter the internet age to try and fight this! This is surprisingly common - see the (archived) list of hijacked journals here: https://web.archive.org/web/20170111172313/https://scholarlyoa.com/other-pages/hijacked-journals/

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changing the field of specialisation in PhD
I have a masters in management studies with a specialisation in Marketing. Can I now do a PhD in Psychology? What would be required to become eligible in India? Esp. Mumbai? What are my options?

You should ask the universities where you want to do phd. If there is a good interdisciplinary topic/project, this mitht be possible.

I have a masters in management studies with a specialisation in Marketing. Can I now do a PhD in Psychology?

It sounds unlikely without taking at least some more relevant courses, but I would recommend to check the websites of Mumbai Universities' Psychology institutes, pick out fields of research that sound interesting to you, and send a brief, concise e-mail to the respective group leaders where you state your education and interest.

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What should I do if I'm trying to go into academic from a mostly non-academic background?
I have finished an undergraduate programme in Biology, and went on to do a Masters in Global Health.
The problem is that I don't really have any articles of thesis to show. My undergraduate programme didn't have the option to do a thesis (I assumed all undergrad programmes did, so I didn't look into it before joining). I did a thesis for the Masters, but it wasn't that great. My supervisor at the time took on too many students and couldn't give us proper directions. I guess he assumed we knew what we were doing, but I hadn't had previous experience so I had no clue (he was also banned from being a supervisor for my course afterwards as a lot of students under him were failing due to lack of guidance). I actually finished it, passed and managed to graduate, but it is not good and I wouldn't submit it to a new study.
Needless it is to say, I also don't have any letters of recommendations. I'm quite introverted and, although there were a few tutors and lecturers who knew me, none did any major works with me and I didn't ask for letters of recommendation.
I'm currently working at a non-academic field, to do with Health Policies, but I want to go back to an academic field. I'm at a loss of what to do though.
I was wondering if it would be possible at all to do a PhD or research position (mostly because there are more paid positions or grants for these), or if it would be best for me to do another masters (only reason why I hesitate is that they are very costly). Or maybe I should approach some old teachers and ask for recommendation letters? I could ask some from my current manager at work, but then he would take it as me wanting to quit my job, not a good move until I do have something lined up.
Anybody has advice? I'm based in Europe, btw.
TLDR: have an undergrad and masters, but no (quality) thesis, and no letters of recommendation. Working a job, want to go to academia. Which routes could I take?

Why do you want to go to academia? What do you hope you hope to accomplish?

@KevinMiller It's a complicated answer. I've always enjoyed reading, and learning, and thinking, and becoming specialised in a topic. At the same time, academia provides an opportunity to provide some input or insights into issues which could be helpful. In my current job we have to "specialise" in what the client wants, in a short period time, and it is often not scientifically-based, and very biased. Academia was the area that drew me in for being the opposite of that. I hope that clarifies some of my reasonings.

Have you talked with some of the tutors you worked with? Is there a reason why you do not want to ask them for letters of recommendation?

@KevinMiller at the time I wasn't considering I would need it, and thought I would be able to ask my supervisor later (at the time I didn't know who would be my supervisor). Now I'm not sure they would remember me.

Do you want to change fields? To what?

@Buffy it's not really changing fields necessarily (it's still health-focused). However, during my undergraduate I was more lab-focused, now I work in policy. I'm not 100% sure which side of health I would like to focus on if I switch to academia, but as I don't know how to go about it, it's difficult to search for opportunities. For example, if it would be best for me to do another masters first, then maybe I would need to approach it from a different perspective than if I try straight for a PhD.

First you need to decide what you want to do with your life. I suggest you spend some time and effort on that part. Then the rest will become clearer. Conferences are a good way to see a lot of options (about academia) in one place, though they are mostly virtual now.

@Buffy Thanks you, that does sound like it could help give me direction, I'll give that a try.

Generally, I do not believe that it will be problem that you do not have an extensive Master thesis. Most universities are likely to pay more attention to your grades and other documents such as letters of recommendation, motivation letters, etc.
So, the letters of recommendation could be a problem. I would advise reaching out to your old professors and tutors. Focus on those from whom you received good grades, briefly explain your reasons for reaching out now (in 1 or 2 sentences), and mention that you got a good grade in their course. At least in my experience, most professors/tutors will be willing to help. If it puts you in an uneasy position in your current job, then you should not ask your manager a letter of recommendation. This can easily backfire. However, it does not have to be your manager writing the letter. If possible try a more senior colleague whom you can trust.
If you apply for a Ph.D. position that is associated with a specific project, then make sure that you do your homework on the topic and show it in any application letter or motivation letter. The same holds for any position that associated a specific advisor from the beginning. In this make sure you know the advisor's work and research agenda.
If you feel not ready for a Ph.D. you could also consider programs that include coursework in the first year. Overall, do not overthink it, and do not forget that a Ph.D. program is there to teach you how to do research. In your application focus on conveying that you are able and willing to learn how to do that. Your professional experience could be a plus and more important than the perceived quality of your Master Thesis.

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Considering reapplying to a PhD program due to family emergency
During last year's CS PhD application season, several elderly family members of mine were hospitalized due to COVID-19. I was greatly impacted by this event as they looked after me during my teenage years. As a result, I was not able to focus on school work for two months and ended up only submitting 3 applications. Fortunately, all of my family members recovered.
I end up getting admitted into one of the 3 programs I applied to, and it's a decent program. However, I'm considering reapplying next year because there are a few programs that I didn't apply to (I wanted to, but wasn't capable emotionally) but could likely offer a better fit in terms of research interest.
In particular, I will be reapplying to the program I got in. Would this be viewed negatively by the committee for that school? Or, would it be possible to defer my admission until next year? How should I communicate this to the admission committee at that school?
(Background: In general, the program allows for deferral.)
Any advice would help. Thanks.

why would you be reapplying to the program you got into, is there soem scolarship/fudning aspect here?

As I (perhaps) hinted in the prompt, there are other schools that could offer a better research fit (e.g., more potential advisors in area of interest). It would not be a terrible choice to attend the current program, but I'm simply asking for more choices as I'm planning on taking a gap year anyway in my home country after years abroad.

I don't see any downside to applying anywhere you think would be a good fit. Universities certainly understand COVID disruptions.
I assume you turned down an invitation. You will need to decide whether to refer to that in a new application, but a few words should be enough in any written materials ("Family responsibility due to COVID..."). You might be asked in an interview and you can expand it there.

If you've been rejected by a place, though, it probably isn't worth the effort to reapply unless there has been a change in your CV and visible accomplishments.

Thanks for the answer. I haven’t turned down the offer yet. Can I defer the offer, apply to other schools, but make sure to accept/reject the deferral before next year’s decision deadline?

That is up to the school in question. You would need to ask them. But you might just phrase it as a delay in acceptance for family/medical reasons and see if they are happy with that.

Do you mean it’s better to keep it he excuse “general” as opposed to going into full detail (ie, I’m reapplying because I only applied for 3 schools last time due to family/medical emergency)?

I wouldn't talk to one school about applications elsewhere. That doesn't seem productive.

I see. I’m just concerned that the school could ask: “why don’t you just defer as opposed to delaying acceptance?” It would be hard for me to provide a reasonable answer without mentioning other schools.


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For an undergrad, which is more important? LoR or publication
I'm an undergrad studying math and CS at a US college. My plan is to go for a PhD in machine learning afterwards. Currently, I have two research experiences under my belt. The first experience has finished, and I have a strong LoR and a first-author publication at a small conference (along with two second-author workshops). The second experience is on-going.
My dilemma is that my second experience has very low probability of me publishing anything. In this experience, I work closely with a professor at my college, along with several lab mates, but she is an undergrad professor so her focus is on teaching. In other words, although she can write me a strong LoR (we know each other quite well), I basically have no hope for publishing (at least she hasn't brought this up by herself).
So, my question is, should I give up this opportunity to pursue one elsewhere that might result in a publication? Or should I stay with this opportunity and keep working hard and impressing this professor?
*Context: machine learning PhD application is quite fierce nowadays and more publications should help, but LoR also helps, so I'm confused.

In the US, good letters of recommendation are a must. Research experience, especially resulting in publication is definitely a plus, but since it is still a bit rare, you are probably already ahead of the curve there.
The "problem" with undergrad research is that, given the time (and maybe money) constraints it is hard to reach a conclusion on anything that is very significant. In research, you don't know the answers when you start and you are looking at the unknown. There is no schedule that you can apply to actually reach finality unless the problems are rather straightforward. The time between writing the paper and publishing it can also be long and indeterminate if the journal is reputable. Conference publication is a bit more time predictable, since the conference will be held on a certain date, but if you miss a deadline, the next opportunity might be a year away.
If you are doing something hard, then my recommendation would be to keep at it. People will, I think, reward you for that even if you don't reach a conclusion, provided that the advisor can praise your efforts and predict your future success.
I think you are already in a good position on this point, though doctoral admission is dependent on many things beyond the two you mention. But, in the US, letters are essential.

Of out curiosity, what are other things that you think are very important?

GPA, especially in major courses. Maybe the GRE for some places. What you say about yourself and how articulate you are.

As you said, I might be "ahead of the curve", but I don't feel this way. In the following blog (https://timdettmers.com/2018/11/26/phd-applications/) on machine learning PhD application (pay attention to the section "Can I get admitted to a top school?" and the Q & A at the bottom), it seems like it's extremely competitive to get into top schools. Maybe I'm confused between a "good" school and a "top" school. Anyway, there seems to be a lot of noise out there, which makes me very hard to evaluate my own progress.

There are varying definitions of "top schools". But, yes, it is essentially impossible to get in to the "top 10" because there are so many fewer slots than applicants. Make your search broad, looking at the whole range of R1 schools. The 50th or 60th ranked is still very good and they probably have several top faculty in any case. The advisor is probably more important than the "reputation" of the school. If your search is too narrow (on any scale) you lessen your chances. Exploit connections of your advisors if possible.

Where "impossible" means low probability. The main thing is that an admissions committee can make a comfortable prediction of your success - in the program and beyond.

Thank you for the great advice. If you don't mind me asking something irrelevant to this post: how does student-advisor matching work after I get admitted to a program? As you pointed out, lower ranked schools still have top faculty - how do I get matched to them?

You may be assigned an advisor at entry with little choice. But they are mostly just for course selection advice to help you get through the qualifying exams. But you should be allowed to pick your own dissertation advisor. Insist on it. But look around at several faculty before you do. Their fields. Their reputation generally. Their reputation for how they treat students. My biggest mistake in grad school was failing to change advisors since I was too introverted to speak up for myself. Talk to some other, more advanced, students as you go along. Pick a mentor or two.

My main mentor was actually in a different subfield, but he was very helpful generally. My relationship with my eventual advisor was good but he was standoffish. You can normally wait a year or two (at least) before you need to ask to work with some individual.


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Translate the laws abbreviation of non-english speaking country in English written paper?
I'm working on paper discussing protection of National Park in Tatra Mts., splitted between Slovak republic and Poland: TANAP (Slovakia) and TPN (Poland).
I want to include the indication of laws declaring protected sites - however, those are the abbreviations in Slovak or Polish, respectivelly. Thus, for to say that TANAP has been declared by law SNR č. `11/1948 Zb . (in Slovak)
meaning is:

S - Slovenska = Slovak
N - Narodna = National
R - Rada = Council
c.- number
Zb. - Zbierky Zakonov = Collection of laws

thus SNR č. `11/1948 Zb  == SNC n 11/1948 Cl ?
If I will not translate law abbreviation, everyone can easily find a specific law. If I translate it, it would be (maybe) more comprehensible to reader, but really hard to find a law if needed.
Thus, in english written paper, should I translate law abbreviations/annotations in origin in non-english or not? What is the common practice?
Thank you a lot, I really appreciate your help.

I seriously doubt the translated version you've shown would make any more sense to the reader and so would just leave them as is.
If the distinctions in the various abbreviations are important, you may want to explain them by including them in a spelled out fashion and mentioning that the abbreviation used comes from the original language. But the reality is, it sounds like the people reading your paper will be familiar with the laws of both countries, and so such information may be entirely superfluous.

ok @guifa, I am going to leave it as it is (in original language) and I'll see what reviewers would say as well .. :)

The reference you are providing has a two-fold goal. First, it allows a curious reader to find the full text of the law. For that, you should provide a searchable identifier in the original language. Secondly, it should tell a lazy reader what the reference is about. For that, also provide an expanded translation to English.
In your case, I'd go with

SNR č. `11/1948 Zb = Slovak National Council law no. 11 / 1948 Collection of Laws.

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Have I given my PhD supervisor enough time to react to serious issues before raising it above their head?
I've been having doubts about the progress I've been making during the start of my PhD. About 2 weeks before I was due to go abroad for a placement at another lab I raised these concerns with my supervisor and they traveled the length of the country a week later to meet me in person to help with how I was feeling.
Now two months have passed (I'm still overseas), and my project is well overdue for a third party progress review within my department. This shook me again when it was brought to my attention, and I started to worry about the progress I've been making again. Adding to this, discussions with the experts at the overseas lab have made me question the value of my research as a whole, and whether or not anything I've done so far or will do for the next 8 months or so is actually worth anything - regardless of whether or not I'd made any real progress with it. (Which I haven't, but that's a whole topic in and of itself).
This has left me feeling terrible and I'm having thoughts of quitting my PhD. I told my supervisor how I was feeling again two weeks ago and they promised a phone call to talk about it, but they don't seem to have found the time. I'm so concerned that I want to raise the issues over their head, but I don't know whether I've given them enough time to respond. Part of this is because I'm out here to do an independent piece of work and not my PhD, so I wouldn't have noticed any changes that we could have implemented in my PhD project. I also haven't actively bugged them about how I'm feeling, as sending constant email reminders makes me feel even worse.
I could raise these issues with my third party project reviewer, as that's largely what they're there for, but I don't know if I've done enough myself to rectify the situation before raising the issue higher up in the 'chain of command'. Should I?

I'm not familiar with a "third party progress reviewer" in a PhD program: is that another professor in the department, or what?  Is such a person really "over the head" of your advisor or just someone else to have eyes on the case?  Anyway, if the thing you want to report is that you are unhappy in the program and considering dropping out, what do you hope this reviewer will tell you that your advisor has not or cannot?

It's another professor in the department, who is (in my case, at least) junior to my supervisor, but does serve as a second pair of eyes on the project. In principle what would happen if I were to this third person is that they'd let the department administration know that there's a problem, and what I would want from this is that my supervisor would spend more of their time on my issues. In my home country I work in a lab away from my university, so I can't just visit him any time I want, which I think makes it easy for my (exceedingly busy) supervisor to forget to find time for me

A peripheral comment: your description of the situation is already not so easy to parse... so if you present what you perceive as problems to someone else, you might want to refine the language... Specifically, much of your description and the implied context are very "in your own head", and this does not reliably translate to anything else.

and what I would want from this is that my supervisor would spend more of their time on my issues — What are your issues, though? You are unhappy and want to quit your PhD studies? What do you want your advisor to do about that? It's no wonder (to me, at least) that your advisor isn't spending more time on your "issues": if you have some technical (or whatever your field is) matters to talk to your advisor about, then do that. Sure, advisors sometimes help their advisees through difficult times, but it seems like you are creating a lot of drama where there isn't any need for it.

Ask again. Professors are busy and things (however important) can slip the mind

The straightforward answer to your question 'have I given my supervisor enough time?' is no.
You are having doubts. Having doubts is common. Doing you PhD may or may not be the best thing for you. You work may or may not be important. Your supervisor may or may not be supervising you well. You may or may not be making good progress (although working on a completely different project is not really part of your PhD). But your case is almost certainly not exceptional. You say that your supervisor already traveled a significant distance to talk to you before. That's a lot of effort to go to.
Your doubts are not really issues that your supervisor needs to fix; they are your thoughts and feelings that you need to work through, with some input from your supervisor. You don't want to 'take it over their head', but you can ask for advice from others who might be willing to give it. I would not expect the 'third party review' to be the right place for that, although you might consider afterwards asking that person if they would meet up with you over coffee one time to give you some perspective on your worries. They might legitimately be able to put some context on the relevance of your work (depending a bit how friendly/competitive your field is).
Being overdue the review without realising it almost certainly should not worry you so much. If it's overdue because your supervisor doesn't think you are ready, you should probably already be aware of that. It being overdue because they think its a pointless piece of bureaucracy, or at least that the deadline is stupid, would be perfectly normal, particularly when you are overseas working on a different project.
I would suggest emailing your supervisor again, saying that your feelings are really bothering you, and that it would help if you can fix a definite time to skype, even if it has to be some weeks away. They could well be very very busy.
Also, do not make hasty decisions. Unless something specific comes up (eg. a high-paying job offer you are really interested in), I would think there is no need to come to a conclusion in less than a couple of months, and it may well not be sensible to do so. You probably didn't decide to do a PhD on a whim, so don't let sudden feelings now override that. If over a sustained period of time you decide that your PhD really isn't right for you then feel free to quit. But don't throw it away until you are sure.

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

I agree with 'Jessica B' points but also consider these.
As a recent PhD graduate and a student Union representative for the duration I came across a lot of issues and as a rule of thumb (at least in the UK) I recommend complaining (but make sure this is not detrimental to your progress). A lot of academics treat their job as a cushy position for life and operate as slave drivers (AKA PhD student supervisors) with no regard for you. Don't quite, but feel free to use it as a threat to get the job done (loosing a PhD student after a few months has a terrible effect on an academics career as the decision is not taken likely). Note this does not apply to the supervisor that does their job or better still goes above and beyond.
All in all it's your PhD and you are paying to get it (even if you have a scholarship), so you expect to gain something out of it with receiving the support you are paying for. University's treat everything as a business except their 'customer care' because most people don't demand the quality they deserve.
Another important note, if you are a lazy person who hasn't done anything and do the things above they will throw you out, but if you have achieved the basic things expected of PhD students and not receiving the due service you will win.
Again use the above as a fluid guidance in your decision making process.

"A lot of academics treat their job as a cushy position for life and operate as slave drivers (AKA PhD student supervisors) with no regard for you" -- I appreciate that you will have seen cases as part of your union work, but this level of generalization does not seem helpful to me, unless you add some context about the institutions and the disciplines

Some qualifiers on "University's [sic] treat everything as a business" would also be welcome


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Should I include the country when citing government agencies in APA?
I use APA citation style. When I cite a government agency as the author or publisher of a work, should I include "United States", "U.S.", or omit the country entirely? Is it ever appropriate to include a country in brackets or parentheses when it isn't part of the agency name?
Some agencies have United States as part of their formal name, even if they don't often use it, eg. United States Drug Enforcement Administration. Other agencies don't have "United States" as part of their formal name, eg. the Federal Bureau of Investigation. If there is potential for confusion with the agency of another country with a similar name, can I put the country name in parentheses or brackets, eg "Federal Bureau of Investigations [U.S.]. (2019). ..."?
I'm in the United States in a context where documents from the executive agencies of other countries are unlikely to be cited, so I tend to omit the country. However, if I do cite, say the Department of Education of South Africa, do I need to add U.S. to my references to disambiguate them? This is not a minor change, as it effects alphabetization.
What I found online:
The Pen and the Pad uses examples which omit U.S.
Washington & Lee University library guide uses this example:
United States. Department of Justice.  Office of
     Justice Programs. National Institute of Justice.
     (1998). High school youths, weapons, and violence:
     A national survey by J.F. Sheley and J.D. Wright.
     Washington DC: National Institute of Justice.
     (Research in brief)   (J 28.24:Y 8)

All those periods in an author sure seems clumsy to me. I probably would have done "National Institute of Justice [U.S.]. (1998)." or "United States Department of Justice. (1998)."

My preference would be to just use "U.S." inline versus omission, spelling it out, or using parentheses.  Think this is adequate to give the information but is tight and doesn't look awkward.
I would use this both in text (for example funding acknowledgements) or citations.  Also spell out agencies.  Not CIA or BUPERS but whole name. Note, it is fine in normal conversation, emails, etc. to use the acronyms if context and audience make it clear [for example in a question here about U.S. specific funding agencies I could say "NSF" in an answer].  But not in peer reviewed literature heading out to the world.
P.s.  There is some fussiness about U.S. versus US.  I would stick with U.S. as the more traditional and common spelling. (But let copy editors do what they want--this is minutia.)  US is preferred in the context of the military and in some newer style guides.  U.S. is still more traditional in grammar texts, newspaper style guides, and civilian parts of U.S. government.


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Masters in physics, wanting to pursue PhD in mathematics -- how "best" to proceed?
I am currently about two semesters away from receiving a Master's of Science in physics. Originally, I planned on pursuing a PhD in physics, but during my studies, I have learned that there is just something about mathematics that fascinates me. I find that more and more of my imagination and time is spent directed towards numerous fields/topics in mathematics. I have procured texts on model theory, topology, meta-mathematics, philosophy of mathematics, &c. &c., and find it hard to peel myself away from them even when my academic duties in physics demand it. I have been doing a lot of introspection and reflection regarding this over the past few years, and I have seen myself happiest when learning about and doing math. So, I am taking it upon myself to start researching the opportunities and challenges that I may face in considering going to school for a PhD in mathematics after receiving my master's.
Assuming that I were to follow this path, what sort of things should I begin doing to give myself every advantage possible moving forward? I know this is a very open-ended question, so I will provide some additional context.
I assume that, going into a PhD program in mathematics, I should expect things like diagnostic exams and qualifying exams. I would want to go into these doing as well as possible, naturally; in general, what sort of topics fall on these exams? Do they differ widely from program to program? I have yet to start looking into the math programs available at my current institution (and, honestly, I believe that I would prefer looking at programs elsewhere), but I plan to touch base with professors in the math department for their own particular insights regarding this.
Furthermore, as someone with formal training in most of the salient mathematical prerequisites for physics, I realize there are likely many topics I should get much more familiar with, likely on my own. Most of my training is in differential equations, linear algebra (of course, only so much of it has been prevalent in my physics career), and calculus (I, II, III). As someone with a bachelor's in philosophy and religion (and applied physics), I have some training in very rudimentary symbolic (and Aristotelian) logic. Highly salient topics like discrete mathematics and real analysis I have not received formal training in. Furthermore, I have no formal training in abstract algebra. Should I absolutely seek to attend some of these courses at my current institution before I receive my Master's? I have always been somewhat of a fruitful autodidact and would have no issue learning these on my own, but I assume that it would be much more attractive to math programs should I have taken these courses, or have at least audited them.
Apparently a lot of my concerns are with exposure to certain topics, but I do realize there are likely numerous other things that I should begin considering as soon as possible, as well. I welcome and would greatly appreciate any insight that you all may have regarding this. I'm certainly not averse to future research in fields with interfaces between physics and math; formal theory and the mathematical structure of physical theories such as quantum mechanics are both intriguing to me, too. So I haven't resigned myself to "wash my hands" of physics by any means!
Thanks in advance, and if you have any questions for me that will help me help you, let me know. I look forward to your replies!

I'm not sure which country you are in, but in EU a lot of PhD admissions are interview based and do not require prior knowledge in the topic, just a "relevant" background. For quite a lot of math topics, physics fits well inside the "relevant" tag.  I had absolutely zero knowledge of the field I got into my PhD, including the mathematics of it. Got in, and got the PhD thingie in the end too..

Have any of the math courses you took been proof-based? Before you make the decision to do a PhD in math, you should make sure you love proof-based mathematics, not just computation and application.

I would say yes, definitely take upper-level undergraduate math courses like real analysis and abstract algebra before applying to grad school.  Both to prepare you with the necessary background and also to make sure this is the kind of thing you enjoy.

And, also because this coursework may be required in the admissions process.

You’re going to want to study as much math as you can this year and possibly get a second Master’s, in math.

Also, I would urge a little caution because I’ve seen a similar pattern several times: somebody encounters graduate physics work, feels uncomfortable with the ambiguity and uncertainty involved in physical reasoning, and tries to fall back to the safest, most “rigorous” thing they can find, which often is something like philosophy of foundations of mathematics. They view this mathematics as just an improvement on physics, where everything is magically clear cut and nothing is uncertain.

But actually, math is nothing like physics. If you were motivated to study physics by a desire to understand our universe, you will not find the answers in set theory and logic. (On the other hand, if you only did physics because you were good at symbol manipulation as a kid and physics has symbols, and you genuinely liked only the symbol manipulation part, then I suppose the switch would not be hard.) You have to understand that the motivation of a mathematician is completely different, and come to terms with that before proceeding.

Thanks to everyone for the helpful replies. To address Ander Biguri's question, I am in the US.

(I meant to put this all in one comment -- sorry. Couldn't edit after 5 minutes)
I have not taken a highly proof-based course, other than my linear algebra course. And, I suppose, my logic course, to a degree. I do enjoy doing proofs, and have done so on my own outside coursework, but only formally done them for linear algebra. I'm going to see about taking one of the suggested courses, and see if my preference for proofs extends to those as well. ;)
Thank you knzhou for the detailed responses. In my case, the symbolic manipulation preference seems to apply.


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How can I structure my undergraduate thesis to include two slightly different projects?
I did a research internship/ co-op in my final semester (our uni gives the option to choose between that and staying on campus for project work under professors). There, I was a part of two slightly different projects, one completed and another ongoing. I am finding it really hard to come up with a direction on how to include both of them in my thesis.
A bit of brief into the work done: The main problem was to design a Content-Based Image Retrieval System. It mainly consists of three parts- User Interface(web development), Feature extraction and Similar Image Retrieval (Deep Learning). For the first project, we designed and developed such a system after reviewing established papers. I was responsible for the literature survey and designing the user interface. For the second project, we are designing a system based on Ontology and Deep Learning both.
Although the problem statement is similar, both the parts have vast and different literature surveys. The proposed method, as well as conclusions, also differ.  While I was responsible for survey and website development in the first project(ie.software-based work), for the second one I am responsible for all research, design and development of the project (ie. research-based work).
What could be a possible coherent structure that includes both the projects in a single thesis?
Any help is appreciated!

What does your supervisor say?

My supervisor has not been able to detail the structure as he is down with Coronavirus but he did emphasize that there needs to be a single thesis. I was thinking of putting in a part 1 and part 2 after the abstract so that I could freely add different chapters (literature surveys/ methodology etc). for both. But he strongly advised against it. It is not likely that I will hear from him soon and the submission is due 30th May. I have written down all content. I just need a direction on how to merge them.

Your thesis can be outlined 4 chapters as follows:
Chapter 1: General introduction and review of literature~ you can divide or combine in background, approach and hypothesis,statement of the problem, justification of the research, and objectives of the research. but both projects only have the same problem statement. so you can separate 2 big parts in this chapter and each part has various sections.
Chapter 2: Your first project~ Exposing what you did in a logical way. This chapter is concise as you mentioned.
Chapter 3:Your second project~
3.1 Introduction
3.2 Materials and methods
3.3 Results and discussion
3.4 Conclusion
Chapter 4: General conclusions and recommendations for both projects conducted~ general conclusion, key innovation, recommendation and future prospects.
The best way to make sure that it had better get consultancy from your supervisor or a mentor who is an assistant of your supervisor.

Hey, thanks a lot for this! I have a small doubt though. The literature review for both is extensive and quite dissimilar. How do I include them into the structure? Just label them as literature survey 1 and 2 or what?

If it is broad and dissimilar, just divide 2 parts. for example: 1.1 your first project ( one by one of detailed sections 1.1.1; 1.1.2; 1.1.3,...). 1.2 your second project ( similarity..). I'm not very confident with my suggestion because if i look through your thesis. i would give you better advice. It is my pleasure. May I know which university you are studying?


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What does an NSF-sponsored conference mean?
Do the sponsors of a conference have anything to do with the quality of that conference? In particular, can someone conclude something of a conference's quality by an NSF sponsorship? I searched around looking for NSF funding criteria but could find very little.

I'd suggest that prestigious organizations, including companies, will sponsor a conference only if they have high confidence in the organization and in its organizational committee. Associating themselves with less than fully reputable conferences has negative value for their reputation.
To get NSF (or IBM...) sponsorship, someone has to ask for it. The reputation of those who ask is, I assume, one element in any decision, along with an analysis of the likelihood of positive contributions of conference presenters, papers, etc.
However, I doubt that very many people use the list of sponsors to decide whether to submit to a conference or not. But, they probably use a similar quality index to that used by potential sponsors.
And, a collection of weird sponsors, might, on the other hand, indicate something negative about the conference.

I see, so it certainly isn't particularly important but is also a positive sign. Do most reputable conferences have such corporate or government sponsors?

Depends on the size probably. Big conferences are expensive to run.

This is probably field dependent. For example in computer science, conferences are typically selective and there is a hierarchy of prestige. This answer will cover mathematics, where journal publications are what similarly "counts" on your CV.
As Buffy said, funding from NSF (or any other agency) is a sign of confidence in the organizers and their plans. In practice, it also means that you might be able to have your travel to the conference funded.
But keep in mind that "quality" may mean different things. I am an organizer of an NSF-sponsored series of regional conferences, and a major stated aim of the conference is to give local researchers an opportunity to speak and interact with the community. This includes early-career graduate students, as well as faculty at teaching-oriented schools who may not have many other opportunities to present their work. We aren't selective; we give an opportunity to speak to more or less anyone who requests one.
We indeed take pride in running quality conferences -- but it's worth keeping in mind that "quality" is not necessarily the same thing as prestige.

"In practice, it also means that you might be able to have your travel to the conference funded." By whom? NSF? In your field, do grants not pay for travel to conferences unless they're sponsored by certain groups? Confused by this statement

I some fields, many good researchers have no grant and the grants that exist have only minimal funding for travel.  A large part of NSF funding of a conference is often to pay for participant travel.

@AzorAhai-him- I'm writing a conference grant right now.  One of the selling points of this conference as far as the NSF is concerned is that it (and the area it is in) engages professors at teaching-oriented universities in research.  Almost all of the grant will be spent on travel support for attendees who do not have their own grants (and that's almost all of the US-based attendees).

@AzorAhai-him- Our situation is the same as what Terry Loring and Alexander Woo described. Travel is funded by the NSF (which, in practice, means by the conference organizers). In math, faculty at teaching-oriented schools are unlikely to have grants, and even at research oriented schools funding can be hit or miss.

Interesting, I hadn't heard of such an arrangement. I work in an expensive field where travel costs are relatively small compared to the science.

Being "NSF-sponsored" just means that the NSF contributed some funds towards the conference.
The NSF has a limited budget and wants to give money only to conferences that are worthwhile for some purpose.  (Note that sometimes the purpose is related to "broader impacts" rather than "intellectual merit".  For example, one of the selling points of the conference I'm writing a grant for is that it (and the area it covers) engages professors at universities where research is not a priority.)  However, a small conference grant of say $10K is a very small amount for the NSF and they're not going to expend too much effort vetting the conference.

I can think of two mechanisms by which a conference might be considered to be "NSF sponsored".
One would be an NSF conference grant, where somebody organizes a conference and specifically applies for money to support that conference.
A second mechanism is if there is some larger NSF grant, and part of that grant has been specified to support a conference.  For example, if somebody writes a grant to develop educational techniques, and part of their plan is to disseminate the findings, and in the grant they propose the best way to do that is to hold a conference, and funds are requested to support that conference.
I wouldn't think that NSF sponsorship would influence a person's decision to attend a conference, unless of course that sponsorship pays the attendees' way!  It's possible that the speakers may be a little bit better than those in an unfunded conference, but not necessarily.  Also, means of funding has zip to do with whether the conference is appropriate for a given individual to attend.


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Funding for new faculty
looking for advice on what factors do granting agencies such as NIH takes into account while funding new researchers.
I am set to start as a new faculty soon. My Post-doc was short because of the faculty position offer. I could not generate preliminary data for the research area that I am interested in for a million reasons nevermind. Please, can anyone advise me on how to navigate the grants? I am reading books on the subjects but they assume the ideal PI, the Ideal Postdoc with the ideal supervisor, and unfortunately, my situation is tight with limited publications and high aspirations.  Any advice will be highly appreciated.

Reaching out to senior faculty in your dept. will be of great help. Many schools have a proposal development office who conducts seminars + talks for new faculty and new hires.

@Buffy thanks! noted!

Reaching out to senior faculty in your dept. will be of great help. Many schools have a proposal (or grant) development office that conducts seminars + talks for new faculty and new hires.


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Recommendation from foreign professor for defense/intelligence research internship
I'm looking into applying into research/academic internships in defense and intelligence agencies in the U.S. given my previous work experience and my research interest for the next year. All of them unsurprisingly requires letters of recommendations.
I know one professor who could give me a strong recommendation...only that he's native Chinese. Would his background be an issue, raise suspicion, or be a big red flag?
I apologize if this sounds offending. I feel like I'm opening up a hornet's nest. I'm not familiar too much on the academic side of these things. I know if I applied for work with these agencies, the background of this professor would've raised some concerns over any recommendation he could've written.

I assume your location is U.S. and you're a U.S. citizen.  Do you know if that Chinese professor is a U.S. citizen?

Writers of your letters of recommendation do not have to be US citizens. If that were a requirement I'm not sure I could hire anybody at all these days.

@JonCuster No, of course U.S. citizenship is not a requirement for writing a recommendation letter. The OP is asking if recommendation letter from a  foreign professor would be an issue for defense and intelligence agencies  research/academic internships.

@scaaahu - I guess I should have been more explicit. I hire into sensitive positions. Many professors who write letters of recommendation are not US citizens, and that does not impact things at all. Some good percentage of folks I work with are naturalized citizens. There is no need to worry.

@JonCuster Naturalized U.S. citizens are U.S. citizens by definition. Many professors who write letters of recommendation are not US citizens, and that does not impact things at all sounds like the answer to OP's question.

Thanks for the feedback to both of you. I would upvote if I could :)

For the most part, as long as the recommendation is strong this will not be an issue. Your reliability as an intellectual in the Intelligence Community is a function of your personal characteristics not the nationality of the people writing your Letters of Recommendation. While it is true that substantial affiliation with foreign nationals can raise questions, they are not necessarily obstacles to clearances, so long as your other bona fides are in order (e.g. finances, drug use).
Depending on the area of intelligence, an Letter of Recommendation from a Chinese national may actually help you. If you are an expert on China, or are hoping to work on China as a thematic interest, showing that you have ties to China is no bad thing. Even in the security clearance process, you will need to reveal this association, and doing so up front is only to your benefit.
Far more important is the content of the Letter of Recommendation, and the nature of the relationship. While not a part of your question, these kinds of Letters of Recommendation should be very similar in character to other academic letters. If this recommender would not be your Letter of Recommendation writer for other jobs, I would not make him the writer for this job, either. You want people who know you and your work well, because they will be able to write the best Letters of Recommendation, regardless of national background.
On a side note, while it won't hurt you if your Letter of Recommendation writer is Chinese, if s/he is an American citizen it cannot hurt for them to say so in the letter. It changes the dynamic of the background investigation, just a little.

Appreciate the detailed response about this.


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What should a work supervisor put in a recommendation letter for someone applying to statistics PhD programs?
This fall, I'll be applying to PhD programs in statistics in the U.S. I'm currently a full-time student in an applied math master's program in the U.S.; until this fall, I was a part-time student and a full-time data analyst at a financial services company. It looks like I'll only be able to get two good recommendation letters from professors, so I'm considering asking my former work supervisor to write one for me. She was my supervisor for two and a half years, during which time we worked together closely on many projects. She doesn't have a PhD in statistics or any other field, but she was a data analyst before becoming a manager. What sorts of things should I ask her to write about in her letter? The professors I'm going to get letters from taught statistics classes that I took and are supervising statistical research that I'm doing; I'm guessing that I should ask my former supervisor to write about things that my professors might not touch on, but I'm not sure what those things should be.

What sorts of things should I ask her to write about in her letter? Why not let her decide?

@user2768 Since she isn't an academic, she probably has little or no experience writing recommendation letters for people applying to graduate programs. If I don't give her any suggestions, she might write about things that an admissions committee probably wouldn't care about, like my Tableau skills, rather than things they might care about, like my ability to manage projects, work with clients, etc.

Often, PhD applicants come along with transcripts showing solid grades in their undergraduate courses. However, this does not always translate into an ability to apply the material in real-world settings, or to find and successfully pursue interesting/important questions. These are naturally important skills for success at research, and may be areas where your supervisor's reference can be very helpful. Some specific questions that I would value seeing addressed in such a reference (which obviously may need some refinement depending on exactly what your current job involves):

Can you work effectively without close day-to-day supervision?
Can you come up with useful ideas/questions/tasks for yourself? Are you an effective problem-solver?
Are you able to weigh up the pros and cons of different strategies and arrive at a sensible recommendation for what to do next?
How do you respond when someone disagrees with you about the correct approach to something?
Are your solutions realistic, effective and properly-tested?
Are you able to adapt your thinking/approach as circumstances and requirements evolve?
How do you respond if it turns out you're wrong about something or have made a mistake?
What do you do if you're stuck on something?
Can you explain your work clearly and concisely? To non-specialists? To experts? In conversation? In a formal presentation? In writing?
How do you deal with colleagues? Are you collaborative? Are you good at teaching someone something new?
Are your technical skills up to scratch?
How do you respond when under pressure (e.g. deadlines)?

Finally, remember that examples are worth far more than unsubstantiated statements.

The readers of such letters will normally be looking for predictions of success in the academic program and thereafter. The past is less important (what you have already done) unless it supports that prediction of success.
If the letter writer understands that, and they are supportive, then you should be fine. But a "bald" statement that "I predict the success of this person." is too easy to discount. It needs to be a bit more subtle than that.

So she should explain why she thinks I'll be successful as a PhD student and as a statistician using what I did under her supervision. Are there certain categories of things that would convince an admissions committee more than others, like time management, communicating results, etc.? My former supervisor doesn't have a PhD, so I feel like I'll need to give her guidance more specific than "explain why you think I'll succeed". I'm not completely sure how to make it more specific.

There are a lot of possibilities. Dedication to task. Creativity. Questioning attitude.

Having written letters for students outside my discipline, here are some things she might be able to write about that your professors might not.

Ability to work collaboratively in a team.
Ability to explain statistical concepts to non-statistician clients/team members.
Flexibility.
Ability to take on new challenges, such as with a particularly difficult set of data or complicated sample.
Ability to communicate results effectively in writing and presentations.
Organization and reproducibility of your work.
Work with diverse groups.
Desire and willingness to learn new things.

These are all things that a faculty member looking to bring someone into their work group might want to know and would value.  If the letter writer can provide examples of this that would be very good.


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Is it discouraged to use a sans-serif font for a scientific thesis?
I'm currently working on my bachelor's thesis in Computer Science at a European university. I've been fiddling around with the layout a lot recently, and specifically tried out using fonts other than the default one that comes with LaTeX (Computer Modern). I found some sans-serif fonts, e.g. Fira Code or Karmilla, to be very easy to read and pleasing to the eye. I haven't checked with my advisors yet, but I'm almost certain they won't mind -- of course, I will still double check with them before handing in my final draft. There are no specific design guidelines set by my university in regards to fonts either.
Are there any other reasons to avoid using custom fonts, specifically sans-serif ones, when writing a thesis or dissertation?

Especially the comments on this.

@GoodDeeds thank you, this makes me even more confident that it's okay to use fonts other than Computer Modern, especially considering that there is no template my university provides for theses. However I'm still wondering if it might be considered unprofessional to choose a different font.

I'll note that this site uses a san-serif font. Readers frequently complain that long posts without frequent paragraph breaks (wall of text) are very difficult to read and understand. A serif font might partly correct for that having more "redundant" visible signals about the text. (That isn't the only reason of course.)

Will your sans-serif font adequately distinguish III from Ill? And rn from m? If so, you have my blessing to use it.


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How to create reference list with maths in title on Mendeley for Latex
I have been using Mendeley for a while to create my bibtex files and use them in Latex. However, recently I came accross some papers such as this one, which have math symbols in their titles and when I try to create an entry in Mendeley and use it in my Latex document the title gets messed up. How can I create a Bibtex file containing papers with math symbols in their titles via Mendeley?
I've tried to type the code on the title section on Mendeley but it doesn't seem to work. Thanks!

Mendeley defaults seem to be to automatically escape LaTeX special characters, which can mean math mode text gets mangled. In my version (1.19.4), this can be changed by going: Mendeley Desktop -> Preferences -> BibTeX and unchecking Escape LaTeX special characters (#{}%& etc.)
Edit: once you've done that you can include math mode markup in your titles, as suggested by @Federico Poloni, e.g. {$2^2$}, and it will not be mangled by Mendeley.
This will mean that all special characters will not be escaped, so you'll have to do it by hand otherwise your compile will likely throw errors. For instance titles including & will need to escaped manually (e.g. \&) in Mendeley.

Does this mean one needs to manually adjust titles for every paper with math symbols? Is there no way to automate this? Mendeley's doi-based lookup feature seems to write down titles in non-LaTeX form. Not only it's time consuming to make these adjustments, but if you accidentaly press lookup on a paper you had already adjusted you need to adjust it again...

I am not a Mendeley user, but have you tried putting the math formulas inside braces, e.g., title = "A new proof of {$a^2+b^2=c^2$}"? This is the proper Bibtex syntax to include math in paper titles.


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Applying to PhD Programmes with novel undergraduate degrees
I'm applying for undergraduate studies and there is one question that keeps returning to my mind. Lots of novel degree programmes started to emerge within universities (at least where I live). For instance, one started offering a course in "Quantum Engineering", another one in "Nanostructure Engineering". Undoubtedly, a major cause for that is marketing (they sound nice), but when I looked into them, most are just interdisciplinary, specialized degrees in physics with chemistry.
Now, assuming I'm willing to pursue a PhD in an area related to those previously mentioned degrees, how would having one of those degrees affect an application as opposed to having a standard degree in physics?
On one side, I find such degrees more commensurate with my interests and intentions for further study, which would allow me to specialize earlier. Thus, I should be able to find and perform relevant research or internships more easily. But I'm also worried that such novel degrees would spark cynism and distrust that could be disadvantageous to a potential application for a PhD.
Thanks in advance for any response.

I would be wary of specialising too early- your interests may have changed three or four years down the line. An alternative course of action might be to start on an ordinary physics degree and choose to take optional courses in quantum and nanotechnology if possible.

Note that I'm answering this from the perspective of an applicant rather than someone on a PhD admissions committee.

"(...) how would having one of those degrees affect an application as opposed to having a standard degree in physics?"

I don't think that the name of the degree itself would affect your application. However, I think it would be a good idea to make sure that you carefully explain the content of your degree (for instance, in your research statement/ statement of interest/ personal statement, or get one of your referees to do this in their letter), so that the admissions committee understands what courses you have taken and how these relate to a more "standard" degree scheme.
From the degree titles that you mention, I'm guessing that these will involve a large amount of normal undergraduate physics and maths, the names of which will also be on your transcript for the admissions people to see.

"I'm also worried that such novel degrees would spark cynicism and
  distrust that could be disadvantageous to a potential application for a PhD."

The most important component of a successful PhD application is your demonstrated aptitude or ability to perform research. If you can do this, and do it well, then I think the name of your degree will matter less.
I speak from personal experience on this; my undergraduate degree is in Astrophysics, with a lot of specialised astro modules, but for my PhD I'm moving into theoretical cosmology, an area which is more commonly populated by applied mathematicians and theoretical physicists. I just had to make sure I "sold" my degree to the admissions committees by explaining that my degree was sufficiently theoretical. Getting some research experience by writing a dissertation during my fourth (Master's) year undoubtedly helped this.
If you're still worried about people distrusting the value of your degree, I would recommend trying to find out if the degree scheme is accredited in any way; for example, here in the UK, all reputable physics degrees are standardised and accredited by the Institute of Physics. I don't know what country you are in, but something similar may exist there.
Finally, as I mentioned in a comment, it might be best not to specialise too early (although you sound as though you have a pretty good idea of what you want to do). The option in this case would be to enroll on a straight physics degree scheme and specialise later on by taking any optional modules that are available (modules which would probably be mandatory if you were on the Quantum Engineering scheme, for example). The best person to advise you about the possibility of doing this would be the admissions tutor at the university offering these courses. They will be able to tell you what combinations of modules lead to which degree.

I have never heard that graduate schools worry whether an applicant has completed an accredited program or not. Some employers do care, but the OP probably doesn't care about this. If it's a new degree program in the U.S., it quite possibly isn't accredited, because the accreditation bureaucracy can take an inordinate amount of time.

@Peter The graduate schools might not care, but it may give the OP some peace of mind that the degree is legitimate and follows a standard physics curriculum.

Caveat: I'm a mathematician, and I don't really know how physics (or other disciplines) graduate admissions committees think (although I expect it differs substantially from committee to committee).
If you take nearly all the courses that a standard physics major is expected to take, I don't think a novel name on your undergraduate degree is going to keep you from getting accepted into graduate school in physics. It certainly wouldn't in the math graduate admission processes I've been involved with.
If you don't take all the courses that a standard physics major is expected to take, then this could pose a barrier to being accepted at a physics graduate school, as you wouldn't be able to start taking the standard physics curriculum in graduate school. (But with great recommendations, you should be able to overcome this disadvantage.) Many departments use the GRE as a filter, so it would really help to have enough background to get a reasonably good score on the Physics Subject GRE.

"how would having one of those degrees affect an application as opposed to having a standard degree in physics?"
It would make no difference.  In your PhD application, make sure you state what kind of research you are interested in performing.  If the things you studied in your Bachelor's are relevant to the research you want to perform, everything is fine.  If you only studied quantum engineering and you want to get a PhD in gravitation, then there would be a problem.  The problem is not in the name of the degree, but rather in the mismatch of content.
It is good that your university realises that Quantum Engineering and Nano Engineering are becoming their own disciplines (though the latter is still ill-defined).

In many physics departments, graduate students are not only expected to do research; they are also expected to take a standard introductory graduate physics curriculum and to be teaching assistants for large undergraduate classes. If you're not qualified for these, you may have difficulty getting admitted, And (this may be related to the above considerations) if you don't know enough to get a good score on the Physics Subject GRE, for many departments in the U.S. you will have a very small chance of admission.

@PeterShor In my experience (quite out of date now) the Physics Subject GRE was a test of how fast you can answer freshman-level questions.  A nonmajor should be able to get a good score.
I doubt admissions committees care much about how students will do in graduate courses or as TAs.  They just want students who produce quality publications.  The exception would be low-ranked programs; they accept students just to get a source of TAs, then kick them out after qualifying exams.

GRE Physics Subject Content: Classical Mechanics, E&M, Waves, Thermodynamics, Quantum Mechanics, Stat. Mech., and a little bit of special relativity and laboratory methods. That sounds to me exactly like the first five semesters of undergraduate physics. If you knew all this as a freshman, kudos to you. And if the OP has the first four or five semesters or so of undergrad physics, physics departments will probably be willing to take him.

Princeton Physics PhD Departments Admissions: your coursework must include the core of an undergrad physics program: mechanics, electricity & magnetism, thermal and statistical physics, quantum mechanics, and experimental (lab) work. Slightly less background than required for the GREs, but still a lot more than freshman physics.

@PeterShor in my experience the GRE subjects you listed are included in freshman physics textbooks.  In second and third year physics the topics are taught again, but at a higher level than in most GRE questions.


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Failed undergraduate research project: does it belong in my CV?
I'm an undergraduate who is going to apply for scholarships and to graduate school in physics in the coming months. At the start of last semester in August, I tried to join a group of a respected professor, where I was assigned a theoretical project. I've met with him maybe three times during the few coming weeks, before we mutually agreed that the assigned problem is pretty much a dead end. The professor had no idea for another suitable project, so I decided to join a different group, with which I stayed until very recently, when an analogous issue occured (but in this case I have actually done some work until that happened).
I was debating whether this "project" deserves being mentioned in my resume, at least for the sake of continuity, and so far have received contrary pieces of advice. Currently, that project is listed on my resume as follows:

Worked with […] at […] on a project attempting to reformulate the
  definition of quantum-mechanical work for autonomous Hamiltonians.

I am certainly not going to ask for a letter of recommendation from that professor since there are others who know me much better. I only want to know whether the inclusion of the above description in my resume would have a positive or negative influence on my application.

I think for an undergraduate student, it is quite valuable to show that they have experience working on a diverse range of problems with different people, even if some of such projects do not lead to anything substantial.
Usually for grad school application and other fellowships there is an essay component. It may also be useful to mention such projects (briefly), and how such experience clarified your research interest/taught you how to do research/provided cross-disciplinary/cultural experience, etc. The exact messaging of course depends on what you think the program is looking for from the applicants.

There is, or should be, no shame in not completing an undergraduate research project assuming that it was real research, not just an exploration into a relatively known space. Real research = exploring the unknown. Real research results can't be scheduled to meet with academic scheduling. It is, in its very nature, open ended, both in time and in results. This is why, in fact, it is impossible to even give a firm deadline in graduate studies. It also explains why some academics produce few papers with a long interval in between.
So, yes, list them. Given the constraints, it is a good thing that you worked on tough problems, rather than a bad thing that you didn't complete them.
And, when you say failed, I hope you just meant "didn't complete" rather than received a failing grade. Note that your professor also "failed" in some sense by suggesting a project that had a very uncertain probability of success.
It may well be that this professor would be a good reference, though a face to face conversation would help you know whether such a letter would be supportive. I wouldn't dismiss the possibility out of hand.
As a doctoral student, I worked on three problems in succession. It was a "three bears" situation. The first was too easy, and I produced theorems every day. It was fun, but my advisor and I agreed there was no real substance. The second was too hard and nothing I could think of (nor my advisor) could but the slightest dent in the shell of it. Again, abandonment was the right path. The third problem was just right and I was able to complete the research with good results in about a year or so. But, it wasn't over until it was over.


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Do you have any paper academic calendars or planners to recommend?
I wanted to ask if you have any specific paper calendars or planners which cover an academic year (October - September) and which you can recommend for PhD students? Thanks a lot!

Easy, go buy a filofax and the calendar inserts for the year in question. Separate the months as necessary - job done.

This may not seem relevant, but it is something I've found very useful/indispensible over the years, both for studying and for teaching. I actually required some of my students to use them.
It is called a Hipster PDA, which is nothing more than a few index cards and a spring clip to hold them together. I discussed it in answer to another question at CSEducators here. See that link for a fuller description and a further link to pictures, etc.
The reason it is so valuable is that it is both simple and flexible. It is easy to carry everywhere and can be rearranged as needed. Cards can be added and discarded. Valuable cards can be saved in a card box. You can use it for class notes as well as planning. You can use it to take quick notes in meetings or to jot down email or phone numbers, etc.
One advantage of it as a note taking device is that it forces you to condense what you hear in lecture rather than to try to capture everything. This makes your brain work harder, which aids learning.
At the end of a class, for example, you can make a card listing the two or three most important ideas from that class. Review that card at the beginning of the next.
Another advantage is that you are writing the notes, not typing them. This sounds backwards until you realize that writing by hand engages the brain in a different way (and more deeply) than typing.
You can develop your own "header" system for labeling the cards (dates, classes, ...). You can use different colors of cards for different things. You can carry the most currently relevant cards with you. You can spend a few minutes of otherwise "dead" time reviewing notes.

Welcome to Academia @Stack Exchange!
From your question it is unclear, whether you are having any specific (academia-related) requirements in addition to the shifted year cycle.
If this is your only issue, you can use any planner which allows you to remove and exchange the calendar sheets. Since the new ones are coming out quite early, it's easy to build the calendar you need...

This does not provide an answer to the question. To critique or request clarification from an author, leave a comment below their post. - From Review

@Scientist it does answer the question: Any planner will do (if this is the only requirement).


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How to get an up to date PhD title in Cloud Computing Security?
I have got a PhD scholarship in Cloud Computing Security, and its about one year am doing research and literature review in that field. However, I haven't reached any point to start with, I'm a little depressed with that. The problem is my supervisor cannot guide me and he doesn't has a very good background in that field and I can't ask for alternative or second supervisor, because the university rule doesn't allows that.
Any advice on how to choose a topic, as I required to publish two papers in high impact factor (Thomson Reuters) journals before submitting my dissertation?

If you supervisor cannot supervise you, then you need to change supervisor. The university rule must be broken. (Actually, the rules probably define ways to change supervisors, because the university will surely have made such a change previously.)

@user2768 thanks for your reply, I have tried that several times. Now I'm trying to depend on myself..

Is there a more senior researcher at your university who does know the field? If so, even if you can't have a second supervisor (and note that rules like this can often be bent for good reason), might they be willing to help you unofficially?

What does "up to date PhD title" mean?

@Flyto thanks for your reply, there were two researchers, unfortunately currently they are not available at the university.

@AzorAhai, I mean current hot research topics

@JavaCrawler By "PhD" title did you mean something like "dissertation title"?

Dear @AzorAhai, I'm planning to work on Cloud Computing Security, and I'm planning to work on a much detailed area.

I'm still a bit confused by what  you mean by "up-to-date PhD title"

@AzorAhai, I mean which area of cloud computing security is better to do research on.

You have a couple of options, I hope. One is choosing a new topic that your supervisor is more familiar with. He or she is the one to help you with that, so you need to have a discussion about it.
However, while your supervisor isn't familiar with the topic you have, he should be familiar with how to do research and to get quickly to the edge of the known world in any given (similar) field. So he may be able to help you find the resources you need and even respond intelligently to your questions and concerns. The only thing that he can't help you with is specific topical questions (facts and techniques). But he can help you find the places in which you can learn that.
Even if he were more up to date in the field, you would still need to read a lot of papers and work to understand them and the remaining work to be done.
At some point every doctoral student needs to surpass the understanding of their professor. That doesn't mean the professor is of no use anymore, it is just the specific topic that you are then able to teach them, rather than the other way round.

many thanks for your recommendation, I may think about that way.


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How do I track down articles referenced in the article I'm reading?
In General Terms
I am majoring in piano performance (classical), which is not considered academic where I live (the Netherlands), although the dutch Bachelor/Master of Music degrees are internationally recognised anyway. As such my subject knowledge of music is easily sufficient to read journal articles about classical music, but I was never taught how to navigate journals. I am looking for certain information, which I know a certain author has published about. So far I have found two articles that mention the information I am looking for, but both defer to different articles, neither of which I have been able to access.
I was hoping the community here could explain to me how to look for these articles. Although I would be helped by someone pointing out where to find the specific articles I want to read, a more general answer about the approach I could take will probably be of more use to future readers; I personally would be happy with either style of answer.
I am not sure whether this question is on-topic (but I hope it is). On the one hand, I suppose the skills necessary to read and find journal articles (in other words, the skills I'm missing) are an important part of academia, making this question on-topic. On the other hand, I am neither an academic, nor an active member of this community, so I am in no position to judge what is and is not on-topic here.
In Specific Terms
I am looking for publications about improvising cadenzas in Mozart piano concertos, by Robert (D.) Levin. I know he has published about this, since he mentioned his work in this area during a lecture I attended.
I started by searching JSTOR for articles written by Levin and found one article related to what I am looking for: "Improvised Embellishments in Mozart's Keyboard Music" by Robert Levin.
This article (although very interesting) doesn't contain much about cadenzas, except for one sentence on the last page:

I have chosen not to treat the construction and rhetoric of cadenzas here, as I have done this elsewhere.

Ironically, this is exactly what I'm looking for. Fortunately, the "elsewhere" has a footnote, reading

See n. 1 and Levin 'Improvisation and Embellishment in Mozart Piano Concertos', Musical Newsletter V/2 (Spring 1975), pp. 3-14.

I assume "n. 1" is referencing footnote 1, which reads as follows:

For discussion of these sources see R. D. Levin, 'Instrumental Ornamentation, Improvisation and Cadenzas', Performance Practice

and unfortunately the rest of the reference is obscured by a misprint, courtesy of Oxford University Press (I even contacted JSTOR support to check), but here the second article I found comes in handy. I found it through Google on scribd.com and it's called 'Improvising Cadenzas in Mozart'. It was written by Leslie Hart in the series 'The Creative Hornist', with series editor Jeffrey Agrell. This article contains a bit more information about cadenzas but I'm concerned about the quality. Fortunately, it has a footnote very similar to n. 1 from the Levin article:

Robert D. Levin, 'Instrumental Ornamentation, Improvisation and Cadenzas', in Norton/Grove Handbooks in Music: Performance Practice: Music after 1600. ed. Howard Mayer Brown and Stanley Sadie (Norton, New York, 1990), 283.

I assume this has to be the source, just in a different citation style. I think this citation means that Robert Levin wrote an article that was then somehow incorporated in this handbook. (Is that correct?) This handbook I could find on amazon but it is prohibitively expensive; I would gladly pay to read this article, but I'm not going to buy a $550 book for one chapter - would it be possible to somehow buy (access to) only the article separately?
This leaves me with the other source mentioned, "Improvisation and Embellishment in Mozart Piano Concertos". Unfortunately I have no clue how to find this article. Searching the full JSTOR catalogue instead of just the part my school has a license for turns up a few more articles by Levin but not this one. JSTOR doesn't even list "Musical Newsletter" as a music journal. While searching for this 'musical newsletter' with Google, the only reference to the 1975 issue I could find was in the catalogue of the San Francisco public library – not a big help. Is there any way I could read this article? Does this Musical Newsletter still exist?
How should I proceed?

The best way is probably to ask a librarian.  If you have access to an academic library, or maybe a music school library (or maybe even a large public library), those librarians should know (or be able to find out) about this.  And after you do it a few times, you will also know how to do it.

@GEdgar I just checked the website of the closest academic library and apparently you can just call them if you have trouble finding information – even if you're not a student at that institute. I had no idea librarians did this, thanks!

@GEdgar you should write your comment as an answer- I agree that asking a librarian is the right approach.

Have you tried google scholar?

@HEITZ No, what is it and how do I best use it?

@11684 just go to scholar.google.com and search away. The advantage is it seems to index widely. For instance, I can search for medical publications even if I don't know that pubmed is better.

@HEITZ Thanks, Google Scholar looks like it could be really useful in the future. For these two articles, though, it unfortunately doesn't turn up any more information; it just finds what I already have: the title, author and containing journal or book.

libgen has all of worlds articles

Google Scholar is great for journal articles, not so much for books.

@11684 oh it's not gonna get you around a pay wall. You might have to pay for the article unless you have access to an academic library. If you do, make a list and present it to your librarian...or pay for it

@HEITZ I understand this, and as stated in the question I am more than happy to pay for these articles, but Google Scholar doesn't provide a link, just the mentioned details in unclickable text.

@11684 right, but the journal it's published in will be noted. Go to the journal's direct website. Most have figured out a way to take your money.

And as also stated in the question, one article is published in a very expensive book and I'm looking for a way to pay just for the article instead of $550 for the book, the other one is published in a journal that I can't find at all ("musical newsletter"). @HEITZ

Then you have to locate the book at a library, then make a copy. Your academic librarian will help. Sometimes you have to dig around.

The best way is probably to ask a librarian. If you have access to an academic library, or maybe a music school library (or maybe even a large public library), those librarians should know (or be able to find out) about this. And after you do it a few times, you will also know how to do it.

Maybe you should follow the references of the articles you did find. And also look on Google Scholar, but I'm not sure if they have articles on music. Combine key words and the name of the author you want.

Following the references of the articles I did find is all I want to do. In fact, my question is how to do that. I have looked on Google Scholar which turned up nothing.

Google Scholar is not useful or reliable for many things... Unfortunately, well, ok, but it's not magic.


text:
Why don't papers have their titles as a filename?
Often(basically always but I'm not 100% sure) when I download papers from any journal they have random letters and numbers as their title, this is quite annoying and I have to rename the document to have a descriptive name. Why do this files have these random filenames instead of the titles of the papers?

There is no requirement that published paper titles be unique. There is a requirement that the filenames be unique.

I mean the title was just a suggestion, adding the authors in the end might solve it or something else like adding a numbering.

When combining with bibliography management software this need perhaps no longer exists. Also, individual's naming preferences are not at all the same, maybe it's easier just to keep the random chain of characters. Yet, if you're interested to rename them, so programming at the user end may like this may work?

The filename is some sort of encoding that is compatible with the database in which they keep the papers, it might have a real world meaning or not. It is optimized for their own processing. I seriously doubt that they use a flat file system to store the documents.
But in general, trying to use a paper's title as a file name won't work anyway, since some characters that might occur in a title aren't accepted in filenames on every operating system. Colon and slash, for example, are problematic. There is also the problem that a paper might need to go into the database during the acceptance/review process in which the title of the paper isn't finalized.
In addition, while we like the titles of papers to be unique, that isn't always the case. So, some disambiguation needs to be done.
What you have, actually, is a reference to the paper that represents its "identity". This is similar to a pointer or reference in a programming language. The thing referenced can change arbitrarily, but its identity doesn't. This help guarantee that they don't lose it.

Last point besides, this sounds like it is practical reasons why it is not done, but many other platforms and services allow for smart filenames. This answer makes it sound like all digital files could only have bizarre names, which is obviously not true.

@Hakaishin but when I put a file on my system, I know pretty much what works and what won't. I don't know what will work on yours, nor certainly everyone's. True that systems are getting smarter, of course.

@Hakaishin Yeah, but many platforms don't allow for that. There are probably academics out there running 10 year old OSes.