text:
Is there any information about the trend of journals preferences regarding Word over LaTeX?
Is there any information about the trend of journals' preferences regarding LaTeX and MS Word?
My main concern is computer engineering and linguistics fields of study.

I have no data to offer.  My observation is that there are a few fields (mathematics, statistics, theoretical physics, theoretical computer science, etc.) where LaTeX is preferred or even required.  For the rest, LaTeX is discouraged or even forbidden (in favor of Microsoft Word).

FWIW, my LaTeX papers were re-written into Word in some economics and statistics journals that they were published in. Proofreading them was a horrible, disheartening experience.

In Computer Engineering, the ACM and the IEEE offer LaTeX templates as well as Word templates for the majority of their journals. I am a great fan of LaTeX as both an author and an editor, however the steeper learning curve tends to put people off using it.

Perhaps the recent question: http://academia.stackexchange.com/questions/21972/journals-not-accepting-tex/21978?noredirect=1#comment46504_21978 is relevant to this one.

Both ACM and IEEE accept LaTeX publication format, which represents computer engineering to a large extent.1
Based on this list which categorizes publications in various fields by their 'friendliness' to LaTeX (primarily linguistics-related), many linguistics publications accept LaTeX (especially those related to computational linguistics / natural language processing).2

1 Cf. http://acm.org/publications/latex_style/ and http://ieee.org/conferences_events/conferences/publishing/templates.html.
2 The list was last updated in January 2010.

I suppose you want to know the general acceptance of LaTeX to decide whether to invest effort in learning LaTeX. I feel LaTeX is the safe choice as, especially in Computer Engineering, LaTeX is widely used - ACM and IEEE have their own LaTeX submission templates. If, in the unlikely case that your publication venue requires Word only, there are LaTeX to Word converters available, e.g. latex2rtf and pandoc. The Tex Users Group (TUG) also maintains a list of converters. This thread and this one discuss conversion from LaTeX to Word.

@ff524 Thanks. I edited the answer to add a clarification. It still does not address the "trend" part of the question (which would be based on historical data of accepted formats). If the answer still seems inappropriate, please let me know if there is a way to simply convert it to a comment.

If you prefer to write a comment on the question instead, you can do so provided you have 50 rep and then delete your own answer.

There are numerous journals and conferences that only accept manuscripts in MS Word format. On the one hand, the journals and conferences that only accept LaTeX are rare.
Indeed, I don't remember any journal or conference that require LaTeX format exclusively.

Although not a journal, arXiv does not accept MS Word documents, and strongly prefers LaTeX submissions.

In CS, no serious journal would accept only Word.

In math, all serious journals require LaTeX.


text:
What can I do to get an admit in a Neuroscience program?
About me:

I work full time often more than 60 hours a week but I want to go to
college to be a neuroscientist.
I live in the US and have bachelors
degree in Chemical Engineering.
My goal is to get a PhD in
neuroscience.
I work in the IT department in a corporate but do
mostly documentation.

My plan is to begin by doing the following -

Preparing for Bio, Psyc and Math GRE subject tests
Subscribe to Scientific Weekly and Scientific Mind to get current research news
Read a college level Biology textbook to get some background on
Biology.

Can you please help me with the following -

Offer some advice if I am headed in the right direction.
What else will help me get into school/neuroscience research.
Any pointers on getting scholarship/aid.
Will I be able to get into a Masters program (with some pre-requisites) or do I need to start from undergrad?

Rather than close, I'd move to academia.SE.

Just to make it clear, you could add your current edu. background. Also you are asking about UG programs, right?

I'm pretty sure if SKA is studying GRE's then they're looking at graduate programs not undergrad.

@Bravo Thank you. I updated the question to add clarity.

@Ryan I am interested in getting into Neuroscience. It would be nice to get into Masters + Phd. But since I don't have any undergrad in Bio/Psyc I may need to take some courses at the undergraduate level.

I am looking for a similar change. I have undergrad in Computer Sci. and am looking to get into Neuroscience research. I guess @SKA wants to what are the best routes possible? Should one need to go back and start from undergrad or can people like us start somewhere in the middle (by taking some Biology pre-requisites etc.). Am I correct?

If you have a background in engineering then taking the biomedical engineering route to neuroscience might be a better option. Also, asking/answer neuroscience questions at cogsci.SE never hurts

I completed my PhD doing almost all my research in neuroscience, so I can give you a few tips from my personal experience.

Neuroscience is by nature a very cross-disciplinary field. I was coming from a psychology background, and my classmates had backgrounds ranging from biology to computer science to mathematics to pre-med. You will be at a disadvantage given your relative weakness in biology, but not a very significant one. Your math skills from the bachelors in engineering will serve you well as you learn about neural and systems dynamics, and the chemistry you learned will be of immeasurable use in understanding the biochemistry of the nervous system.
Given your background, you should definitely be able to apply directly to a MS or PhD program without having to retake (too much) undergraduate coursework. Do note that you may be able to get into the program with the caveat that you will be required to take some undergraduate courses during your first year; this was a common practice in my program. Given how long it takes to complete your PhD anyway, it should not delay you much, if at all.

Coming from an IT/engineering background, you may be interested in computational neuroscience, a subfield which attempts to understand how the brain works—both at a systems-level (i.e., whole brain) and cell-level (i.e., individual neurons)—using computational models. There are entire departments dedicated to such research; it's a fairly large field.

Your action items listed above are all excellent ideas, and should serve you very well. The only suggestion I would add is to simply google the term "neuroscience research labs" and begin browsing around the web to see what types of research is being performed. As you search, google again using narrower terms, to see how broad each subfield is. Consider writing down some of the schools that house labs that sound interesting to you for future reference.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Origin of public defense of thesis
An article on Martin Luther's "Ninety-Five Theses" indicates that he posted the document on the church door according to "university custom". The reference included indicates various books. I recall hearing that this was the source of the public defense of some university degrees, but I cannot recall the source. Is this attribution correct or apocryphal?

That was more a church custom, to publish documents/announcements on the church door. The church near my home has a board on which e.g. church activities, upcoming christenings and so on, are regularly posted to the parishoners. Luther's theses became viral, reproduced by the (then very new) printing press, and what was a minor local complaint became the reformation. This has liitle (if any) relationship to thesis defenses.

Possible duplicate: http://academia.stackexchange.com/q/20542/19607

If it is according to university custom, then the practice must have existed before Luther.

Could you link to the article you read?

It wasn't an article. I recall hearing it somewhere, so that's why I asked the question.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
How to demonstrate mastery of courses not taken during undergraduation
In this answer, Anonymous Mathematician says, "You need to demonstrate that you have mastered the undergraduate material that is less relevant for computer science. For example, mathematical analysis along the lines of Rudin's Principles of Mathematical Analysis"
How can I demonstrate I have mastered materials from Rudin's Principles of Mathematical Analysis or Artin's Algebra for admission in grad school?

I find this a hard question because I regularly have to deal with applicants claiming they have certain skills and because these cases are difficult to deal with. For example, recently an applicant got a bad grade for one module and wrote they really were much better. I decided the applicant's examiners are in a much better position than I to judge the applicant's capabilities.
In your case you want to prove you have knowledge you didn't formally study in your undergraduate school. If so it's impossible to prove your skills unless (1) somebody from your undergraduate school is willing to write a letter of recommendation, or (2) the grad school are willing to ``examine'' you.
In the case of (1) this may work. Unfortunately, (2) means the graduate school have to do more work and I think this is unlikely.
Finally, if the graduate school require the skills, it seems to me they think it is reasonable. In that case, applicants should have taken modules that demonstrate these skills. If they haven't, it seems to me they're not the ideal candidates in the opinion of the graduate school.


text:
Why is it unusual to add a date to scientific papers?

Possible Duplicate:
Why is the date left out of some academic papers?

A scientific paper usually begins with a title, a list of authors with contact information and affiliation, and an abstract. There is usually no date to indicate when the paper was written or first published.
Yet, the first questions that comes to my mind when reading a new paper is often: When was it written? How current is this research? Can I expect that science has moved on since this was written?
However, when I suggested adding a date to the header of one of my own papers, my advisors reacted, surprisingly for me, as if this was a quite outlandish idea. The reason given was that it is "unusual". Is there any rationale behind this?


text:
Will a self-designed major lower my chance of acceptance for graduate school?
I am in the process of designing a major. However, I am worried that using a self-designed major can make an application look bad. As it stands, this potential major is about 70% computer science classes, 30% psychology and neuroscience classes. As such, this leads me to the questions:

Are these self-designed majors seen as "weird" or simply unacceptable?
In general, are self-designed majors unattractive for graduate admissions?
For computer science specifically, do majors matter?

Not trying to deter your goals, but why not just go with a tried and true major (Computer Science?) and do independent studies in your other interests?

As currently written, the question is a bit too specific to your personal situation.

@AustinHenley, thank you for your reply. That is the other option I was considering, and given Amy's answer, it's probably what I'll end up doing.

@geetar how realistic is it for you to pursue a CS degree with a minor in psych or vice versa? Or, how many psych/cogsci classes can you fit in while you pursue a CS major (declaring a minor may help you get into upper divisions courses, and you don't have to finish it!). That will give you some interesting things to talk about in your applications, and I think would cover the bases as far as concerns about CS foundations.

@Amy A CS major with a CogSci minor is definitely feasible, and that's probably what I'll be going with. I asked this question primarily because for the classes that wouldn't be in the self-designed major, but in the CS major, the instructors were terribly bad. "Terribly bad" as in they neglect their students, or they admit they don't fully understand what they're teaching, and compensate for that by making the class stupidly easy. If they're going to do that, I might as well take a summer class elsewhere instead, and study other things in college.

The disadvantage of having a "made it myself" degree is that in situations in which you are being compared with your peers (i.e. graduate admissions), you are comparing apples to oranges, and the admissions committee only know apples. A committee sees two applicants with CS degrees, even if they come from different universities, they can be somewhat certain that both have covered a certain number of bases. In these situations, your degree compared to a CS degree can look like 70% of a degree vs. 100%, even if you have a higher GPA (and this may read as "they have a higher GPA because they took psych classes instead of Operating Systems, Databases, Compilers, Networks, Computer Architecture, and Theory of Computation").
Admissions committees are less concerned with whether you took classes "related to your interests" than whether or not you passed or exceeded the same thresholds as your peers. If you're worried that people wont give your transcript a good look, most won't (especially if you end up entering the workforce). Don't get a degree in anything that will take more than 30 seconds to explain.
Look at all of the people who are doing the work that you some day want to do. Look at all the professors that you might someday want to work with. What did they get their degrees in? (here's a not-so-big secret: most professors hire students who remind them of themselves)
Get in touch with professors at research universities, admission committees, grad students, and get their opinions. Ask "What are you looking for in an incoming student?" People will be pretty forthcoming with you. Ask your professors if they have any contacts at research universities that you could talk with. Also, your professors all got into grad school - ask them how they did it. Find the youngest ones, they'll have the best idea what admissions are like these days.

What did they get their degrees in? — Not so fast.  Just on my hallway, there are computer science professors with undergrad degrees in mathematics, electrical engineering, industrial engineering, and linguistics instead of computer science.  Even my department head does not have a CS degree.

@JeffE - Does anyone in your department have a bachelor's degree in interdisciplinary studies? That was my point.

Honestly, I've never heard of a "bachelor's degree in interdisciplinary studies".  But the ex-linguistics major advises ex-EE majors, and the ex-EE major advises ex-math majors, and so on.... Professors don't just hire students who remind them of themselves.

Are these self-designed majors seen as "weird" or simply unacceptable?
In general, are self-designed majors unattractive for graduate admissions?
For computer science specifically, do majors matter?

Having a self-designed major is definitely not a problem for graduate admissions in computer science.  We don't care what your major is; that's a stupid administrative hurdle.  We only care what you've done.
On the other hand, an undergraduate transcript that does not cover the foundations of a computer science major might be a problem.  My department commonly admits graduate students with non-CS undergraduate degrees, but if they haven't taken at least the core of a computer science degree and a few advanced CS classes, we're more likely to admit them to one of our master's programs instead of to the PhD program directly.
Your transcript will look different to different departments.  The mixed major you describe might actually give you a slight advantage in departments with research programs in HCI and/or some branches of AI, or with interdisciplinary programs in (say) psychophysics or cognitive science.  It might also hurt you at departments without researchers in those areas.
But the real issue, at least for PhD admissions, is whether the admissions committee is convinced that you have strong potential for research in computer science.  At the top CS departments, what classes you've taken really a second-order concern (unless your grades are bad or there are glaring gaps).  Your research potential and experience, as described in your statement and recommendation letters, are much more significant.  If an applicant has a strong research record, and their research interests match our faculty, we may admit them without even looking at their transcript.

If you intend to go into an interdisciplinary grad program, it may actually help your chances of being admitted. For example, my Ph.D. is in Human-Computer Interaction and Computer Engineering. My research had a heavy psychology component. A hint of neuroscience in my background would have certainly benefited me. In HCI, the combination of CS, Psychology, and Neuroscience could make you a quite attractive candidate. Importantly though, it depends if you see yourself applying to one of the truly interdisciplinary programs vs. just applying to a CS program to research HCI. There may be other interdisciplinary programs out there as well that would be interested in such a combination, though HCI seems to be a fairly perfect fit with that background.
The concern I would have is that you are still early in your academic career and your grad school plans may change by the time you are done earning this degree. In this case, a traditional major would probably be a better choice. Keep in mind there are also options for double majors and minors that are well-known degrees as opposed to a build-your-own degree.

If you're at a school where self-designed majors are fairly common, there may be records of what sorts of jobs people with self-designed majors have gotten (and whether/where they went to grad school).

I believe this would hurt your chances. From the point of view of the admissions committee, there's no guarantee that the 70% of CS (or 30% of psych/neuro classes) that you chose to include in your custom major covers everything you'll need in graduate school, and you may have large holes in your fundamentals that would give you a distinct disadvantage.
A much better approach would be to simply choose a standard major and fill all your electives with a concentration of psychology and neuroscience courses. This would still give you multifaceted knowledge while still providing the admissions group a way of measuring you against your peers.

I'm just a grad student with no real insight into admissions processes, but I do believe that this wouldn't hurt you if you wanted to go into cognitive neuroscience. The reason is that neuroscience is such a multidisciplinary field that everyone eventually needs to learn something outside their field. Having that hurdle out of the way before beginning graduate studies would be seen as a plus (in my opinion), but it would be wise describe the  combination of courses a bit in your letter of motivation.
Extrapolating from this, perhaps self-designed majors are less of a problem in multidisciplinary fields.


text:
Are there any academic data sets that force users to release any source code written to analyse them?
I am curious to know whether there exists any data set that forces users to publicly release any source code written to analyse it.

I'm not sure that such a restriction would even be legally enforceable.

@aeismail I am not sure either but I would tend to think that if a contract has to be signed to access the data set then one might add a clause to force users to release the code.

I am wondering if analyzing data to produce aggregate results would count as a "remix" for creative commons licenses.

@aeismail, if the dataset is only available under contract from the owner, then lots of things like this would probably be enforceable (cite the originator, publish the analysis code, etc.). I know of no data set that does this, but there's plenty of academic software whose licenses require citation of the authors.

So the owner of a proprietary data set would demand that software used to analyze it be open-source? Talk about hypocrisy!

@aeismail Can you define proprietary data? (The definition is a bit fuzzy to me)

@aeismail Why would it have to be proprietary data? What's stopping anyone from releasing a dataset under an open license that also enforces you to share code? Maybe in practice it's not feasible, but I don't see why you couldn't.

@FranckDernoncourt: Proprietary just means it's owned by somebody who is controlling access to it.

@RogerFan: Because there's always the possibility that you could use commercial tools to analyze it, and therefore you can't adhere to or enforce such a provision.

@aeismail Sure, but that just means that you can't use commercial tools to analyze it. That's a limitation the license imposes, but it doesn't mean the license is impossible or unenforceable.

@aeismail Thanks. A lot of data sets in the medical field can only be accessed through a contract typically asking researchers to respect patients' privacy, medical researchers are typically fine with it even though it means the data set is proprietary. Otherwise, it may be possible as Roger indicates to add some provision in the data set license without requiring users to sign anything, so as to avoid making the data set proprietary.

@aeismail As for the use of commercial tools to analyze, it might be made possible by defining "source code written to analyse it" as code written specifically to analyze the data set, not general toolkit like Matlab.  I agree that what I am saying is vague, that's why I was looking for such data sets to see how it was handled :)

@aeismail, of course it's hypocritical, but you didn't ask about that, you asked about enforceability. I know of no datasets that do this, but that doesn't mean that someone couldn't try.

Open data licenses apparently do exist, for instance, Open Data Commons maintains the ODbL. I don't think that this has a restriction on code used for analysis, but it does put a share-alike restriction on any derivative datasets.

If you publicly use any adapted version of this database, or works produced from an adapted database, you must also offer that adapted database under the ODbL.

This essentially ensures that the derived database (or steps used to create it) used for analysis must be shared, though not necessarily the analysis itself.
I imagine that you could modify this license to mandate that you share the steps used to create any work produced (i.e. the analysis code) as well under some kind of open license, but I am not a lawyer, and I did not find an existing license that does this in my (short) search. In particular, this could easily be troublesome if you use closed-source third-party software in your analysis (e.g. Stata, Matlab), though people have overcome similar issues with GPL licenses.

The data user agreement for this dataset (MIMIC/eICU) requires users to share their code. https://physionet.org/pnw/a/manage-duas :

If I openly disseminate my results, I will also contribute the code used to produce those results to a defined PhysioNet repository (physionet.org/physiotools/repository/) that is open to the research community.

I don't think that would work in the US, where facts cannot be copyrighted, so -- once you publicly publish data -- there's nothing stopping anybody else from republishing it in a different form. That might be plagiarism, but you can usually get around that by citing the source of your data.

Facts can not be copyrighted but a collection of facts can be, and if they can show that you mined their database they can indeed sue and win. (Common practice is to selectively add a few deliberately erroneous data points in a place where they don't cause trouble, to act as. A "smoking gun" to demonstrate the copyright violation)

US federal law says trap streets are not copyrightable (https://en.wikipedia.org/wiki/Trap_street#Legal_issues) and that facts stolen from other sources don't by themselves create copyright violations (https://en.wikipedia.org/wiki/Trivial_Pursuit#Fred_Worth_lawsuit). However, obtaining facts in certain ways might be illegal, including data mining another database: https://en.wikipedia.org/wiki/Web_scraping#Legal_issues

US law continues to evolve in this area. Understand copyright, and understand that a license agreement is a contract.

@keshlam A collection of facts cannot be copyrighted in the US. The selection and arrangement of those facts can be, but only if there is at least a bare minimum amount of creativity in selecting and arranging those facts.

Also, the dataset does not have to be public. Many datasets are available by application. It could be a contractual condition of being given access to the data is that you have to share the code used to analyse it.


text:
How to assess the chance to get accepted to a master's program in the United States?
Currently I am a student in the Netherlands following a bachelor program in computer science. I am currently considering applying for a master's program in the United States. It is hard to asses my chances, because of the large difference between the systems in the Netherlands and the United States.
There are a few factors which probably affect my chances.

I cannot directly compare my grades with grades used in the United States. In the Netherlands we use a 1-10 absolute grading system. I currently have a grade average of 8.0, only had 7s, 8s and 9s.
One thing I noticed is that in the United States a bachelor program is not naturally followed by a master's program, unlike in the Netherlands where this is the default.
The duration of a bachelor program in the Netherlands is three instead of four years.
Currently I do not plan on applying for a Ph.D position.

Do these factors significantly effect chances to be admitted to a master's program in the United States and how do I asses my chance to get accepted?

I don't think that there's a huge enough discrepancy between the technical content of the European three-year bachelor's and the four-year American bachelor's to make that a big concern.
However, where you may run into problems is that your GPA might not be considered competitive for a top program, if it's only in the 8.0's out of 10. (It might get translated to a 3.3 or so, which would be problematic.) What will make up for this is some statement that you're near the top of your CS cohort, and good letters of recommendation will also help.
Where you'll also need to do some research is on whether the departments you want to apply to offer terminal master's programs; if not, it will make it a little more difficult, as the expectation would be that if you are admitted to the master's program, you will then continue on to the PhD program thereafter. (At such schools, a stipend is typically offered during the master's phase of the program; at schools that offer a terminal master's, the funding sources for the master's degree-only candidates is usually quite distinct, if it is available at all.)

That was my concern because my average is actually high for the program, but is not translatable to a GPA. Most students have around 7.0 on average and 6 is the minimum acceptable grade. Actually according to this article om Wikipedia http://en.wikipedia.org/wiki/Academic_grading_in_the_Netherlands an 8 would be equal to an A, I doubt however that institutions will accept this conversion.

As I said, there are a few ways to get around this: a transcript that shows your relative positioning within the cohort, or statements in your letters of recommendation talking about your performance (showing that you are near the top of your class). As someone who reviews applications, I know that I'm willing to give a pass to low grades if one of the referees tells me that's the standard at the university the applicant attends.

Although OP asked about the US specifically, I thought I'd pitch in a Canadian comment. In Canada it is much more common to have research-based and funded Masters programs in CS and related fields (without the expectation that you will continue on to PhD in the same institution).

In my own department, we compare GPAs with other applicants from the same school.  Over several decades, we've built up a reasonable (but imperfect) mapping from raw GPAs to "normalized" GPAs.  In particular, we recognize 8.0 from the Netherlands as reasonably high.  We also look more carefully at recommendation letters to help us calibrate grades from unfamiliar schools.

@JeffE: I thought that might be the case, but since I didn't have direct knowledge, I didn't want to state something as fact without stronger evidence. But thanks for the confirmation of my expectations! (Over here, we do admissions on a much more localized basis, so the previous school approach doesn't work as well.)


text:
Is it possible to study in China without knowing Chinese?
Is it possible to enroll into and complete a graduate school in China while having only English language skills, without speaking Chinese at all? In particular, I am interested in (theoretical) physics.

I would note that English is the de facto international language of physics, to the point where any practicing Chinese physicist will be proficient in English. Many Chinese graduate students receive at least some of their instruction in English. So you can do physics research in China without knowing Chinese. But living in China without knowing Chinese is a different matter altogether. (I don't recommend it.)

No way. You couldn't even order at McDonald or KFC without knowing Chinese CHARACTERS let alone spoken chinese

@MathNewb Actually... you can. IF you say you want a Hamburger and a Coca Cola in English, they will get it for you. The words for most fast food are bastardized. Even KFC is pronounced Ken Ta2 Ji1 (literally rhymes with Kentucky!).

Why live in China if you don't wish to interact with the locals?

@DavidZ “any practicing Chinese physicist will be proficient in English” — from my experience, I have to disagree with that, for any reasonable value of “proficient”.

@xebtl well, if your experience includes Chinese physicists who are not proficient in English, I will have to defer to that. All the Chinese physicists I've worked with are proficient in English.

@DavidZ So has the only one I have worked with, but I have heard some others speak English such that I could not have worked with them for lack of a common language.  Not to blame them, I am sure learning English coming from Chinese is difficult.

The point is just that the level of English proficiency implied by being a working physicist (even a successful one) is, in my experience, quite modest.  That concerns talks, meetings in person, but also papers in peer-reviewed and copy-edited (?) journals.  (And of course it concerns people from all over, not just the Chinese!)

If you include Hong Kong as part of China, the answer is Yes but limited to Hong Kong. English is an official language of Hong Kong. Universities in Hong Kong all use English as the media of teaching and the common language for research is English. No Physics courses are taught in languages other than English and no faculty members are not proficient in English. See this official website for reference. The best are University of Hong Kong, The Chinese University of Hong Kong and The Hong Kong University of Science and Technology.
Otherwise the choices are limited to those high-ranking universities in China such as Peking University and Tsinghua University. In Tsinghua, most faculty members use English for publication purpose but not at all for communications in research. Most teaching and administration stuff are in Chinese. So you have to learn chinese at least in conversational level to survive a Phd there.

Absolutely. Here is just one example.
There are many trans-national programs all over Asia (China, Hong Kong, Vietnam, Myanmar, etc.). Many of these programs are from partner universities in the UK or the US (and other countries). In these programs, the language of instruction and assessment is English. I teach in one such program (not the one linked above and it is related to business, not physics).
Can you get by without being able to communicate in the local language? That really depends on you. For example, if you are a social person you will really need to be able to communicate in the local language. While everyone (staff, faculty, students) at the university (in your department) will speak English others outside the school often struggle (as you would likely struggle picking up Chinese if you lived in the west).
If you are the kind of person who prefers isolation, then the local language is not so critical. Depending on where your city, you can usually find stores where you can buy most of the food you like (that is, western food) and even a place which will rent to you.
Some schools may well require you to learn the local language. The link above clearly shows it is offered (and you should take advantage of it). If you want to actively avoid learning Chinese, then you need to make sure the school you select does not require it. A quick email should sort that out.

Thanks for the answer. I truly need this info from a Westerner in Asia.

@scaaahu You only need to ask. :-)

As an academic who has traveled to quite a few places where I had no idea (despite some study) of the ambient language, but/and also to quite a few places where I did have an adequate idea of the ambient language...
... and in contrast to the sort of wishful thinking that, for example, leads some tourists to say "oh, everyone speaks English there"... and leads some academics and business people to claim that English is the universal language of ... :
The psychological/cognitive load/burden of disconnectedness from the environment (apart from jokes about starving because one cannot ask for food) is highly non-trivial.
To be in a bubble for a week or so is maybe-tolerable, but for a year or more... I'd not do it. Either find within yourself the incentive to learn the language at least to the level of an 8-year-old, or don't go. The quasi-intellectual, quasi-independent-of-environment pose that has some mythological cachet is not good, in my experience. The people who fare best, in all ways, are those positively interested in the ambient language... and the culture depicted in it, etc.

I don't think so, I am a medical student at China and it is compulsory for us to take Chinese Language. My friends doing their post-graduate degree already know Chinese, so I think it was a requirenment to apply.
Other than that, there are some universities which take Chinese into account but without having it in the actual degree. So just to help you while you're staying at China.

Would you tell us how much Chinese language do you need in order to live in China (such as shopping foods, taking bus transportation, etc)? Would you think one year Chinese language learning class would be enough? or more than 1 year? Thank you for your answer! I have  been waiting for somebody having your background to tell us.

Sure. You only need simple Chinese base, here they teach us the basic life simple things (buying, selling, greetings, communication easily, etc...) and I do study it alone in my spare time. One year of Chinese language is perfect and I don't think you'll need more, plus, you'll get used to it as you live here for couple of years. You're welcomed.

Short answer:
Yes for other majors. Probably not for PhD in physics (you need to search).
Long answer:
Over the past ten years, many university from US and UK launch joint institution, ranging from summer language program to university with PhD program, in China with local universities. You could search for NYU shanghai, Duke kunshan, Michigan shanghai, Nottingham Ningbo, Xi'an Jiaotong-Liverpool University etc (The words you do not recognize are name of cities where the university is located in China, except the last one since I forgot where it is).
The good news is that English is the official communication language in those colleges.
Another good news is that they welcome (truly) international students, since almost all the students are Chinese.
Something you may not be interested in:
I do not know where the OP comes from. If OP comes from Africa, Chinese government provide special program with language program for those who can not speak Chinese.
Comment on comment:
What most Chinese people speak and their English language skills are irrelevant to the question. Most of the time you would communicate with your professors and fellows, other than some random guys on street.

Well... All I'm saying is that if you study in a foreign country then inevitably you will have to talk with the locals at some points. It makes your life considerably harder if you don't speak Chinese. It's not like doing a PhD is not already hard enough...

While the last paragraph of the answer may be technically correct, in that it may be possible to live in China without ever talking to anyone other than your colleagues at the university, it's a lousy way to live. I consider it highly misleading at best to say that it's irrelevant what most Chinese people speak.

That is a minor problem but not a difficulty that actually prevent OP pursuing degree in China. If it is worth mention, I would argue learning how to eat Chinese food everyday is important, since OP is inevitably eat Chinese food (almost) everyday. It makes your life considerably harder if you don't eat Chinese food.

Ok, ok. The language skill of OP would not improved after he come to China, and eventually he dies miserably several days later because he cannot speak Chinese with staff in cafe.

Thanks for your answer. Reading your answer, it is unclear for me why you mention that the physics major needs knowledge of local language in your short answer.

Depending on your home country, you'll probably end up with a scholarship.
Most foreigners coming to an average run of the mill Chinese university would qualify for such. It would be a feather in the cap of XXX Agricultural Normal University to have you as an honored graduate student, so much so they would fork out $$$ for you to come there.
www.csc.edu.cn is an amazing portal for higher education in China and can search by
"English-taught" programs.  I'm sure there's one for you, China is a large place, many cities and many universities.  And there's Hong Kong (and Macau) to go to for English taught programs at a higher price.
Many a student have come to the land of China with zero Chinese but stuck it out and made friends and money.  Inevitably, you'll pick up Chinese along the way I'm sure.

I am a postdoc living in China since almost 2 years. I came here without knowing any one phrase in Chinese.
My answer to the question is: No, it is currently impossible to study in Mainland China for years in a row without learning any form of Chinese.
Apart from the fact that few locals are proficient in English, almost all daily, and probably administrative communication runs in Chinese, and automated digital translators will not provide always a satisfactory solution. Surely local students and deputies will help in the beginning but after a certain time they will become less accessible.
Moreover, Chinese comes as a package: one cannot truly learn the culture without understanding some of the language and vice-versa. Therefore interacting below the surface with locals will depend on learning some of the language even if not at any functional level.
I cannot speak for Macau, Hong Kong, or Taiwan as I have not lived in these areas. I suspect it should be doable in these places, particularly in Hong Kong.

Short answer, possible, but I highly recommend you against it.
Generally, US students are welcome to universities or research institutes in China, especially the top ones (Tsinghua U, Peking U, SJTU, ...) in Beijing and Shanghai. You would get used to everyday life in less than a semester, without learning much Chinese.
However, physics is not a typical major to do so in this case. Top universities have many young professors with their PhD or postdoc done in US, as well as part time professors from top US universities. But there's almost no pure English physics graduate program in main land China.

Maybe you will meet some difficulties at first. You will find difficult to  listen to the class and do homework in Chinese. But at Chinese university, usually you can find Engish text book in the library and your classmates will be willing to teach you Chinese. Teacher's PPT sometimes uses English too. As long as you study hard, you will be accustomed to.

Generally, one can enroll in some graduate programs in China that are taught in English， and in some cases, even if the program is not offered in English, some courses may still be taught in English, so there might be a possibility to still accept you. This will depend on the university and programs. For example, at my university some general undergraduate and master degree courses offered to Chinese students are taught in Chinese while some others are taught in English (it depends on the professor and topic). Besides, I know some Vietnamese Master degree students who did a master in computer science in Changsha without speaking Chinese... and another doing a PhD in computer science in Harbin without speaking Chinese. And there is some post-doc researchers and professors who also do not speak Chinese. I don't know for physics but if you look around, I think you can find. But of course, if you know some basic Chinese, you will better enjoy the life in China. At least, you should try to learn how to buy stuff, ask for the price of something or ask for directions using Chinese, to make your life easier!   There is also some universities in China, where taking some Chinese training is mandatory for graduate studies. For example, in Xi'an Jiatong Univ. some students told me that for PhD they had to take 8 months of Chinese class on the first year. But in the end, they found that it was useful for daily life.  Also if you speak Chinese, I heard that you may more easily get scholarships from the Chinese government perhaps for your studies.


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Why is a tenure defense talk necessary?
Once a tenure-track professor finishes their initial 6 year evaluatory period, I imagine their publication/teaching/grant record should pretty much speak for itself to a tenure committee.  Apparently, as I have recently found out, some departments additionally require a tenure defense talk at the end of this period.  It seems to me that this talk is something akin to a dissertation defense, only on a grander scale of all the research I've done over the initial 6 year period.
But my question is:
Why is it even necessary?
What could be expected from such a talk that wouldn't be readily and easily obtainable from the submitted tenure package?  Is it just a formality or  does it really hold an important weight in the tenure committee's final evaluation to keep me?
Should I just rehash and summarize what is already in my tenure submission package?   Is there something more to it that I should emphasize in my tenure defense talk?

A guess from someone not in Academia--can you synthesize your research and show how it's all related and where it's going to go in the future?

The question is not so much 'Why is it necessary?' but 'Do you want tenure?' If yes, then do your best at it. Joke apart, the point is to see if you are capable of doing an interesting, well-constructed talk that will convince them you're the right choice.

@shane: "Knowing there is a trap is the first step in evading it" - Frank Herbert

I haven't heard of such a thing, which suggests a simple answer: an oral tenure defense is not necessary.  But regardless of whether it's necessary in some abstract sense, it might be a requirement wherever you end up.
It's possible that your tenure defense would be a grueling affair, with the audience trying to poke holes in your research or dispute its significance, but I very much doubt it.  At worst you could expect the same treatment as an outside candidate giving an interview talk.
The tenure defense is presumably intended to give you a chance to explain your research program, specifically what you have done and why it matters.  This is in principle redundant (your tenure file should already do this), but adding an oral presentation could help.  It's often inspiring to see someone present their own work, and it can be valuable to have a chance to ask questions.  In cases where tenure seems likely, the presentation could also play the role of an inaugural lecture, highlighting for the department the work of someone who is about to become a permanent colleague.
This practice seems uncommon enough that I doubt there's a clear standard for exactly what it means.  Anyone considering taking a tenure-track job with a tenure defense presentation at the end should ask how it works at that particular institution.

I imagine their publication/teaching/grant record should pretty much speak for itself to a tenure committee.

Publication records can speak surprisingly unclearly.  A non-expert reading through someone's papers won't necessarily appreciate their novelty or how they contribute to the big picture, and may not even understand clearly how they fit together into a coherent research program.  Keep in mind that most people evaluating a tenure case will be non-experts: even other department members will typically have different specialties, and that's not counting university-wide committees or administrators.
One crucial part of preparing a compelling tenure case is sorting out these issues and framing everything appropriately.  This is done partly by the candidate, partly by whoever is overseeing the case (typically the department head), and partly by the letter writers.
So from this perspective, something more than just a binder full of papers is definitely necessary.  However, the added context is typically supplied through written documents; if there is an oral presentation, then it is just to supplement the written file.

+1.  The time to deal with such a question is when you are interviewing with, or considering a job offer from, an institution that actually has such a rule.  At that time you can find the formal rules, and ask (preferably multiple people) how it works in practice in that department.  Since such institutions seem to be rare (if they exist at all), it's unlikely that you'll interview for a job at one, much less take it, so the question is very likely to be moot.

I've not seen any case (in my U.S. -based experience in mathematics) where the junior faculty person up for tenure had to present a summary of their own work, in effect "defending" it as one "defends" the Ph.D. thesis.
However, I have witnessed many cases where a more senior person with expertise in the tenure candidate's work was asked to describe/explain it, or, really, its significance, to the tenure committee (prior to having the full math faculty vote). But in all the cases I've seen, from both sides, the tone was informational, not confrontational or adversarial. And the candidate was absent.
The necessity of that sort of tenure-defense talk is exactly that the body of work itself is hard to understand, the letters of recommendation are inevitably severely tainted by political gamesmanship and circumlocution and conceivably bias, and, thus, in the end, a local opinion+explanation from someone trusted by the tenure committee is highly desirable... despite all the formal procedures.
I'm inclined to wonder whether the question's premise is partly based on inaccurate gossip.

At my university, it's standard practice for professors who are up for tenure to give a talk. However, it's no more a "defense" than a typical PhD "defense" - there is hardly any offense.

@AndrewMao, in a friendly atmosphere, this could be a good thing! One should be aware of one's colleagues' work... and we should practice communicating in ways intelligible to our immediate colleagues... :)


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Why do national laboratory presentations contain so much info per slide?
I've seen many, many examples of scientific presentations from the National Laboratories in which virtually every slide is oversaturated with information.  If this were an isolated event, I wouldn't have given it any thought.  But I've noticed this pattern in presentations over many years from among presenters hailing from US national laboratories.  Though my field is computational science, I've seen talks from national laboratory scientists in other fields and their presentations also have this same characteristic.
In academia, I've been taught to keep slides as simple as possible, with as little info per slide as necessary.  My understanding is a presentation should be though of as an "advertisement" for the paper to be published.  Thus, presentation slides should be designed to preserve the audience's interest.  One method of keeping the audience interest is to not overwhelm them with too much information all at once (e.g., not too much text and not too many pictures in a single slide).  I presume this is universally true, regardless of discipline.
However, the overwhelming majority of national laboratory presentations that I've seen seem to fill up virtually every available space with as much information as possible.  Why do presentations from national laboratories tend to contain so much information per slide?  How does this meet the needs of their target audience?

Are they in the same field as you?  Or are they working mostly with physicists?  Experimental physics slides are dense.

@noahsnyder:  i'm not in physics at all, but my observation applies generally over all applied national laboratory disciplines.

But many national labs are focused on physics, even if they also have people in other fields.

It really isn't just national labs.  It's commonplace in some fields, in fact sparse, easy to read slides may lead to your talk not being taken seriously unless you're a keynote speaker.  It's made worse by some conferences imposing a limit on the number of slides.

Because no one thinks intentionally about the visual display of information. Old habits die hard.

Does this apply to one specific national laboratory, or have you seen presentations from several? In either case, it would help to clarify that in the question.

It would be nice to see an example or two here. Otherwise it's actually just anecdotal.

Let me try to answer for the tendency in my own discipline (particle physics) where we have this problem across the board (i.e. universities too).
Much like questions and answers on a Stack Exchange site, those slides are expected to form a resource for future investigators. We know there is too much there for anyone to absorb in the meeting, but we also know that more people will dig these slides out of the archive over the next year and study them then actually attended the meeting in the first place.
Yes, in an ideal world there would be a technical report and a deck of slides, but in fact there are only the slides.

Personally I try pretty hard not to do this, and the result is a lot of backup slides and a lot of little URLs hanging around the bottom of the slides.

As an aside, I think that PowerPoint and similar polished slideware makes stuffing them (over-)full way too easy. I use a LaTeX base for mine (just the old slides class with my own library of macros for a long time, but I've started using Beamer) and these tools encourage a better style.
Alas, I know all the tricks to squeeze on just one more thing.

+1 Same thing in our universities for advanced courses. Often, the lecture slides are at the same time a large part of the study material available to students, so they need to contain a bit more than just pictures and keywords, as may be better for the lecture in itself.

On the other hand, LaTeX makes it too easy to overuse equations.  ;-)

My guess is that it's a cousin of the same problem in the armed forces, which has been a problem for two decades. (Note one link is from 2000, the other from 2010.)
On another level, the culture of the national laboratories has been trending in a more corporate direction, and many of the presentations that they need to give have limits on the number of slides to be presented. Managers want the whole "story" told in a handful of slides, which leads to over-compression of information.

From memory, the Rogers Commission Report into the loss of the Space Shuttle Challenger also observed that critical information may have been missed because it was in sub-sub-bullets of very dense presentations. (I can't find it, now, but Chapter V contains an example of such a slide.) So, if my memory is correct, this problem was already being observed in the mid-1980s.

I think it is just presentation style. We have the same in our universities: hey, let's put 3 topics and 5 figures on this slide, so everyone will be impressed! I don't say that everyone should talk like Steve Jobs or the TED presenters, but I believe that presentations should comply some basic rhetoric and design principles.


text:
Web application for managing a library of papers

Possible Duplicate:
Keeping track of bibliography references for an entire research group

Is there a web application which can help the researchers at my group collaboratively manage a collection of scientific papers?
Desired features are:

easily upload pdfs and edit bibliographic info
query the database
export the database (or a subset) as a BibTeX file
define subsets/folders of publications (e.g., all papers related to a project, all papers by members of the group etc.)
should be accessible only for members
should be hosted on our own servers

There are many… In fact, there's a whole Wikipedia page on that topic, which includes many of the criteria you are looking for. You can also check the table in this nice blog post, although it's a bit dated.

In particular, you can investigate: Aigaion, Bebop, refbase, and phpBibliography.

We have a set of PHP scripts which generate output akin to http://www.sat.ltu.se/publications/ . We don't export to bibtex, because bibtex is the input!

Bebop looks nice.

Mendeley, citeulike. Check this question out and the answers.

I'm not looking for a web service like Mendeley or citeulike. It should be self-hosted.


text:
Splitting publication fees among coauthors
What are accepted ways of splitting publication fees among coauthors, when authors are from different research groups and potentially even different institutions? Especially with open access publication, the fees tend to come out at a substantial amount.
In general, the corresponding author seems to be responsible to the journal for the payment of the fee. I wonder what would be commonly acceptable agreements with coauthors to split such fees?
There is already a general question on splitting collaboration costs here, but the current answer does not apply to publication fees, and I am really interested in this specific case.

I think an issue like this should be sorted out early on in the collaboration. Obviously one would expect the first author (team) to cover (most of) the costs, possibly sharing according to input (author order) but in general: whoever has money should use it.

@PeterJansson: Of course the first part doesn't apply to fields (like math) where authors are unordered/alphabetized.

I understand this question is different from collaboration cost. I think you can use the same concept. First, try the institution(s). Their reputation benefits from the publication. They should share some cost. Second, authors with full time salary may be able to (not necessarily willing to) share the cost. If still not enough, divide the cost evenly among the coauthors. I don't have personal experience with this case. Only my two cents.

In a field where there are journals that are very good and do not have a substantial fee, I would hope that the author who is pushing for the open access journal would foot the bill.

I think your question is a little backwards: All ways of splitting the publication fees are acceptable. You might run into some problems with your grant officer about transferring money around, but in the end they will get over it.
The more important question in my opinion is: What behaviour is acceptable from you and your co-authors. I believe the answer is to be nice since these are your co-authors after all. I wouldn't be too put off if a co-author refused to contribute to open access fees or if I was asked to contribute 1/N of the fees for an N author paper where I was a tertiary author and currently under-funded.


text:
How many manuscripts should I agree to handle as an associate editor?
I've been asked by a peer-reviewed journal whether I'd be willing to act as an associate editor for them. The question How to act as an editor? has some useful hints as to the tasks associated with that. But I am still wondering how much time these tasks would typically take.
The form where I accept to be an editor allows me to indicate how many papers per month I'd be willing to handle, and I am not sure what number to give there. My questions is how much time I should expect to take for each paper in the first or second year as editor?

I would start by asking the journal rep how many manuscripts (MS) other have agreed to, or what is typical. I would think that is what the journal reps would consider "normal". You probably have a sense of whether they need you for something very specific, in which case a lower number might be quite acceptable. Once you know what they tyically load on their editors, you should think hard about whether you find the workload acceptable. There is usually no guarantee that the workload is evenly distributed unless all editors are able to handle pretty much all submitted MS.
As editor you will likely need to at least browse the MS when you receive it, chase after persons willing to review, read the reviews and the MS carefully to provide feedback to the author, review the authors revisions, poissibly run the MS around again and then make a suggestion or decision on accept/reject. All this is within some time frame and chasing late reviews and authors who do not return revisions will take some time. I can also add that it will be the problematic papers that will take up most of your time, the good ones usually are not difficult to handle. You thus do not know how much time you will spend on any particular MS. A really good one could take half a day in total; a poor may take at least a day or more. So having slightly scared you with this, I will add that the work also has potentially tremendous rewards (reading brand new research and getting in contact with new persons).
So, in short, how many MS per month is really impossible to answer, it will strongly depend on how you feel about the work and how you think you can accommodate the workload in your own time. I will leave you with this slightly unsatisfactory answer, but urge you to try to get a sense of what the journal expects and what they consider normal. You could also ask to how much time they think the workload corresponds.

This varies wildly. It depends on the journal, how many submissions it receives, whether it has a full-time Chief Editor, whether it has one or more senior Editors below the Chief, whether Associate Editors receive any payment, and whether your subdiscipline is a popular one.
I'm an (unpaid) Associate Editor for two journals. For one, I handle about 6 manuscripts per year, for the second, I have been an Assoc Editor for 6 months so far and have yet to receive any submissions (it's a new journal so it isn't receiving many yet, especially not in my subfield). A colleague is an Assoc. Editor for another journal, for which she receives a substantial honorarium, and she handles 15-20 manuscripts each year.
The only way to find out is to ask the Editor who has invited you to join.


text:
How can my colleague use our joint results in his PhD thesis?
Over the past two years, I've been collaborating with a PhD student. He did experimental work, and I did modeling and data analysis based on his experiments. Now that my colleague is about to write up his PhD thesis, in which way can he ethically include the modeling and data analysis results in his thesis?
I don't need any of these results for a thesis on my own, and we are currently writing a paper on this together, so there are no worries from my side about misuse of these results.
There is the related question Are overlapping dissertations ethically acceptable?, but I am more explicitly asking about how my colleague can present the results which are more based on my work in a good way.

I think this is indeed a duplicate of Are overlapping dissertations ethically acceptable?, because the answers there, do answer your question very well.

@EnergyNumbers I'm not sure: the first answer says “it's okay to do it”, the second one is not exactly helpful, the third one is about division of contributions (which is trivial if A did experimental work and B did modeling). So, I think the question is different here (and silvado is aware of the linked question, and asks for explicit writing advice which is not treated in the linked question).

Don't worry, be happy (and be truthful). There's nothing wrong in including in one's thesis stuff that you didn't do yourself, as long as the delimitation between what the candidate did and what others did is clearly marked. And by that, I mean no lies, but also no half-truths either.
Basically, the presentation will thus depend on the interaction between you two and his part in the analysis (which ranges from “nothing” to “he suggested ideas that I tried” to “he ran my code himself”). In the first case, he could say:

As part of project X, I sent these results to Dr. John Doe at Big U. for him to perform his widely acclaimed topological Bayesian half-filter analysis. This analysis revealed that …

There's nothing wrong with presenting results obtained by others from your work, as long as they shed light into the phenomenon you're studying. I once had a student who published a work, which was built upon by another group during his PhD, and he presented this at some length (and critiqued their extension) in his thesis. That's part of the whole story.
If the collaboration was closer, just make sure the thesis clearly indicates its nature and the contribution of everyone. Then, no fuss!

F'x's answer is good. I would just add that your collaborator should check his institution's thesis guidelines. Mine had specific directions on how joint work should be included in the thesis, such as an extra paragraph explaining who did what part of the work.
Of course, your collaborator's advisor should also be in the loop.

+1 It's always good to be clear. In my field, this is simple: our results are theorems, so you can basically with each of them list, who did what. Well, if it's too complicated, the best idea would be IMHO to include an explanatory section in your thesis, stating which part precisely is your work.


text:
Former professor wants an update to write a recommendation letter, should I include a bad grade?
I studied physics and computer science as an undergrad, got a master's in computer science, and now am applying for a second master's in engineering physics. So, I have emailed one of my old physics professors for a recommendation letter.  He agreed to write one, but has requested more information to do so seeing as though I haven't been in touch since I went to grad school. He didn't specify any particular items, but another letter writer has requested my statement of purpose draft, coursework/research highlights, resume, and unofficial transcripts, so I'm assuming he'd appreciate the same. Because he is from a different school and department and hence unfamiliar with their curriculum, I was planning to send a list of my grad school classes and grades with descriptions included rather than the unofficial transcript which only includes the course number and a brief, generic title.
I'm happy to oblige, except for one thing: I failed a class in grad school.  This is explained by a medical situation at the time; I took the next semester off, it is since resolved, I did well in all my classes afterwards, etc. - it is a non-issue now.
My question is, should I include this black mark when I send him materials? It is not something that affected any of my work in undergrad and will not affect anything in the future, so I'd think it's not really relevant. I'd rather not tell yet another person about how I failed a class, especially someone who I haven't talked to in a while and have asked to write good things about me.

If  you don't include the bad with the good, then you haven't provided a transcript – and you haven't satisfied his request. (Besides, if you "did well in all" your classes afterwards, he should notice that. Plenty of folks have a misstep or two on their transcript.)

True, and I did send the transcript and an explanation to the professor who requested it. This one didn't specifically ask for a transcript - his email only stated that he would be glad to write, and "I look forward to more information." I asked this question because I am embarrassed by the incident and prefer not to discuss it if not necessary. But hopefully the A+'s afterwards will make up for it :)

You are focusing on the little pimple on your nose instead of your nice hair, eyes, etc., and the pleasing effect of the whole.  Just attach an unofficial transcript.  If he has a concern with the little pimple, then give him a brief explanation with a neutral tone.

Why is "old" relevant?

@Michael I suspect he means "Old profressor" as in former/noncurrent professor (not as in elderly). Indicating that it has been as while since he studied under the professor.

@Oxinabox oh obviously. Maybe using "former" would have been more clear :)

"I'd think it's not really relevant" -- if the professor agrees then including it won't affect the letter and you have the benefits described in the answers of truthfully saying "here's my transcript". Whereas if the professor disagrees then maybe you should rethink what you consider relevant, or who you should ask for letters of recommendation, or both...

@Michael Oxinabox is correct (although I am a 'she') :) I updated the title to make that more clear.

Actually, I don't understand the point of the request.  Should not the reference letter reflect the professor's knowledge of the student which should stop at some point in the past.  Why would the professor comment in any way on the student's MS experience? Confused.

I would err on the side of being honest, as you have a legitimate reason for why one specific class was an issue. Whereas that is explainable, it would be a mark against your character if he discovers that you did not give him a complete list of a classes after he requested it.

Thanks for your answer, this is a good point. I don't really expect him to see a complete transcript, but you are right that there is really no reason not to mention it (other than my own embarrassment).

My question is, should I include this black mark when I send him materials?

Yes, you should definitely include it or, at the very least, make it clear to him if you aren't providing a complete list of courses from grad school.  The danger is if he thinks it's complete and makes statements based on that in his letter, for example that you never received a grade less than an A-.  Then he looks clueless (which is bad for him) and the admissions committee assumes he doesn't know what he's talking about and discounts any other good things he says (which is bad for you).
You can just give him the same explanation you're planning to give the admissions committee, and it shouldn't be a problem.

It hadn't occurred to me that he might comment on my grad school performance, since he only knew me in undergrad, but that is a very good point. Thanks for your answer.

You aren't applying to the professor.  You're using a letter from the professor to help where you are applying.  He's writing the letter to help you.  Expect him to have some consideration for what to say about the grade (or even whether to bring it up).
If the people who are going to judge your application are going to see that grade, then it's incredibly useful if someone who is on your side can say something about it.  So yes - of course send it to the professor and give a brief explanation.  What do you think would be worse as someone reviewing applications: seeing that the student had failed a course and reading a letter of recommendation that says: "I know this student is hard working and talented, but struggled during a serious illness that is now resolved", or seeing a letter that says "without exception this student has always performed well."
You should also think about sending a doctor's note along with your application.  Have a quick note saying, "Please disregard my performance in semester X.  I became ill (see attached doctor's note).  I took time off to recover.  The illness has been dealt with.  As you can see from my later grades my performance since then has been much improved."

If your full transcript will be available to the recipients of the letter, you should certainly send it to the author of the letter. At best, "inconsistent messages" in the letter and the transcript might cause delays and/or confusion. At worst, they would be a straightforward and objective reason not to consider your application at all, especially if there are plenty of other well-qualified applicants.
It would be sensible to add a note stating the medical circumstances to both sets of documentation, of course.

Yes.  No professor in the world expects a student to have had stellar grades in every class.  If he asked for your transcripts, he wants to see it all... not just the highlights.
You already know this... or you wouldn't be struggling with it.


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Do spelling changes count as translations for citations when using different English dialects?
Please assume I have a direct quote that contains: "found in the neighborhood".  I wish to use this as a direct quote in my paper.
My spelling checker flagged on "neighbourhood" since I am using Canadian English. If it was part of the citation I would use this answer.  To avoid references to other answers, please assume that I have the best reasons possible to use Canadian English in my paper.  If I change the quote to "found in the neighbourhood" did I translate this answer?  I ask since APA states that translation is considered a paraphrase and has rules to treat it differently.

Generally, if you are using a direct quote, you should not change the content at all, except to add "[sic]" to mark that you are transcribing something exactly as it was found in the source text.

I frequently write papers in (U.S.) English, finding myself needing to cite long passages from others' papers in (U.K.) English. I don't change the spelling. I don't bother with 'sic'. However, in MS Word, I select the paragraph being quoted and tell the spellchecker that the language is English(U.K.) (or occasionally German or Spanish), which stops the spellchecker from flagging them.

Generally don't take spellcheckers' suggestions as anything more than suggestions. They can be useful for avoiding mistakes that really are just typing mistakes or when you had a misconception about a word's spelling, but that doesn't mean everything flagged by a spellchecker is automatically a problem that should be addressed. It can absolutely be appropriate to write things that don't conform to existing spelling rules, like when you're introducing entirely new terminology. This should be the exception, not the rule, but it does happen.

I halve a spell check her, It came with my pee cee. It plane lee marques fore my revue, miss steaks eye can knot sea. Butt now bee cause my spelling, Is checked with such grate flare, There are know faults with in my cite, Of nun eye am a wear.

Firstly, it is far from clear that choosing to use Canadian English in your paper actually commits you to changing non-Canadian spellings in quotations to Canadian spellings. A spell checker merely provides suggestions for you to consider. The idea that because a spell-checker highlighted the word it needs to be changed is false. The rest of the answer addresses the case where you have some other compelling reason to change spellings in quotations beyond the fact that it was suggested to you by a spell-checker.
The situation seems largely analogous to what you would do if the original quotation were, say, "foun in the neighborhood". You would presumably quote that as "foun[d] in the neighborhood", and no sane person would think of this as being a translation. Similarly, what you are in effect saying is that the spelling "neighborhood" is incorrect for the purposes of your paper. So the solution "found in the neighbo[u]rhood" seems to be the appropriate one if you insist on changing the spelling.
The question of why translations are handled differently than direct quotations is considered here:

You may wonder why your translation is considered a paraphrase rather than a direct quotation. That’s because translation is both an art and a science—languages do not have perfect correspondences where every word and phrase matches up with a foreign equivalent, though of course some cases come closer than others. Even in the example passage above I considered how to translate “Les femmes dans des activités masculines”—taken word for word I might have written “Women in masculine activities,” but I thought “Women working in masculine fields” better conveyed the actual meaning, which relates to women working in male-dominated occupations.

Clearly this reasoning does not apply to trivial changes in spelling. Nonetheless, you should make it clear to the reader that you have in fact changed the spelling of the original quote.

If you're going to change the quote, this is the right way to do it. But I imagine the spellchecker will now start complaining that "neighbo" and "rhood" aren't words, which perhaps makes it clear just how silly changing the quote actually is.

Or how one should not be slave to a spellchecker.

"However, it's far from clear that choosing to use Canadian English in your paper actually commits you to changing non-Canadian spellings in quotations to Canadian spellings." <-- this

Isaacg in the comments made an astute observation that I want to repeat here since it's an equally valid answer and comments may be deleted at any time:

Generally, if you are using a direct quote, you should not change the content at all, except to add "[sic]" to mark that you are transcribing something exactly as it was found in the source text.

Put differently: what you can do is write "found in the neighborhood [sic]", with [sic] being the accepted standard in academical quotations to indicate that you are using this quote verbatim, including any spelling mistakes, grammatical errors or regional dialect idiosyncracies from the original author's message.

I don't think this is needed for human readers, they're aware of these common variations. So unless it also appeases the spell checker, it seems worthless.

I think adding [sic] in this particular situation would be arrogant and disrespectful, since the quoted author did not make a mistake, they just used a different (but equally valid) spelling standard.

@Barmar the spell checker doesn't need to be appeased at all (most of them do have some form of "Ignore" burton, though), and the [sic] is useful to ensure that some other human (e.g. an editor) doesn't try to appease the spellchecker and change the spelling.

The only reason the question even came up is because the spell checker complained. And I think a human editor would understand that we don't need [sic] here.

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Is it okay to keep a "Thank you" slide before references?
I am preparing a presentation in LaTeX and got at least seven pages for references only.
In general, as far as I know, a "thank you" slide of a presentation is the termination slide of the presentation, i.e., it comes at the end after references.
Since my presentation part, which demands explanation, ends with a page before starting of references, and I got a long list of references, is it okay to keep my "thank you" slide before references?

I dislike reference slides in talks at the best of times, but 7 of them? Are you sure this is the best format for your presentation? Consider checking this and this.

Also related: What is the best “last slide” in a thesis presentation?

You better be sure your presentation is on point, otherwise a thank you will sound like "thank you for bearing with me"

I like to use a slide saying "Fin."  It usually goes over well.

Please avoid answers in comments. In response to a flag, several answers-in-comments have been removed; please consider writing a proper answer or upvoting an existing answer instead.

Perhaps check out if there are applicable guidelines. For example at my uni, Thank you slides were explicitly not recommended.

It is perfectly fine to have references, sources or deep dive slides behind the thank you slide with no intention to show them (unless asked), this ensures your notes will get published with the slide deck for anybody to study.

There are not references pages in a slide presentation. A presentation should require just few refs and their are better placed where they are relevant. This apply for conference presentation. If you mean presentation in a broader sense, eg kind of review for internal use etc, you just distribute the slides to the interested people. I would never project a slide of references only. At most one containing three/four of them, just to stress the importance to your point(s). What the speaker is supposed to say/do while projecting slides of references?!

Don't even think about going through seven slides of references. Put them in a separate handout or web link. Make the thank you slide the last (or next to last, if you are going to ask for questions).
If you want the references on slides so you have just one document, put them at the end and don't visit them.
Addition: Many commenters note that "thank you"  might not be the best way to end your presentation. Consider verbal thanks and just your conclusions on the final slide, perhaps with a request for questions.

Short citations of key references at the bottom of the slide they occur is not a bad idea, also.

Short references allow listeners to take a photos of the slides if they want to do further reading.

This question was about thank you slides not references. Although we all agree about the referenences, I highly disagree with your recommendation to put in a thank you slide. It only distracts from the content.

On the references As expressed by other posters, seven slides of references sound like an overkill. Though, if the underlying reason to dwell on the references is sound, as it may well be:

I would suggest to choose a graphical format. A graph showing the cross-citations or a timeline could be useful. This gives the backdrop to your own story on why the references are important, other than plainly  numerous.
Another option is to add a textual slide commenting on the references: that they are, say, 200; they date from those periods; they have been published in such and such journals or proceedings; a quick kind of meta analysis, that is. That could actually be intriguing.

On the closing slide I have long since stopped to put the final thank-you-for-your-attention and/or any-questions? slide. Rather:

I say that in spoken words facing the audience, which is a much more open and inviting gesture.
My last slide contains the conclusions, so that the audience can replay in their mind the whole presentation and have handles for questions to ask.
I had acknowledged co-workers and helpful people at the beginning: kind of this work comes into existence thanks to institutions and people.

Perhaps also others see a benefit in doing so.

Yes, I agree with getting rid of "Thank you" slides in the first place. These slides have two benefits: Thanking the audience, and signalling that the talk is over. If you compare this to the benefits of using a conclusion as the last slide (also signalling the talk is over, summarizing the take-home message, providing talking points for the discussion), a "Conclusion" slide beats a "Thank you" slide by far.

@Schmuddi Yes, it felt a bit strange to me that you give a fully-fledged talk to propose certain conclusions, in the end only to hide such conclusions all too quickly.

Por que no los dos?  I agree that a “conclusions” slide is a very useful thing to end on, but I share the OP’s wish to put the thanks-to-the-audience in visual form as well as verbal.  So I often include “Thank you!” on my conclusions slide, set centred below the main summary of conclusions.

Do not include 7 slides of references, that is absolutely no-go. A usual way to show references is at the bottom of the slide they reference (it is easier to find and match with the referenced content anyway).
I personally do not like 'Thank you' slide to the audience, I would thank the audience after I said a few words on the Acknowledgements slide.

Yes, I much prefer having "thank you" appear at the end of the last slide rather than being a slide on its own, particularly if there is something on the last slide which may be relevant to questions.

Presentation is a show. Presentation shall be catchy. Presentations are there to sell the presenter's products. Presentations are fluent, one-way only. From the ouverture to the grand finale.
In academia you are selling your results, your department, your research. The show here is not fancy, full of fireworks and othe ballast, but it is still a show.
Long lists of anything is a show killer, references doubly so. You want the audience's attention and curiosity first, then you can comunicate your results.  You can back your claims thoroughly later; on stage you want to talk about your contribution, not the others'.
If you need to show references and citations, do it at the time you talk about it. No one cares for referencing idea two minutes ago. A footnote is appropriate. You don't mention it in your speech but they who will read your slides later will fing the reference in eyblink; if you would be asked, you can show both your claim and the reference in Q&A minutes.
Another trick is to have couple of uncounted slides with extras. Bigger graphs, detailed images, claims and references - just in case. You can build your presentation in beamer, build your supporting appendix and merge the pdfs. I think you can trick the LaTeX/beamer by using \label{TheLastpage} and \thepage/\pageref{TheLastPage}.

Sidenote: I think this is your first presentation. Try the presentation many times. Try to present it to your friends/colleagues even pets or a rubber duck.
Make yourself comfortable, find the structure, language and pace you are comfortable with (and fit within the time limit).

There's a Latex package for that, in case you prefer to use it rather than doing things manually.

My group tends to work from a set of common templates that have "Thank You/Any Questions?" slides at the end by default.  The same thing ends up happening in almost every presentation: someone asks a question and the presenter rewinds to a previous slide in order to answer it.  The "Thank You" slide is only visible for as long as it takes to ask the first question, then never seen again.  It contains the same amount of relevant information as the black "End of Presentation" screen that PowerPoint displays after the last slide (that is, zero).  For those reasons, it really serves no purpose.
Some of the better presentations I've seen will anticipate the sort of questions that might be asked based on the audience and their background.  The presenter builds a final "Summary" slide that includes some graphs, photos, key statistics, formulas, etc. and is able to use the content of that slide to answer many of the questions.
Another technique is often used for presentations that are being video-recorded and archived.  Instead of a "Thank You" type slide, the video feed simply switches away from the slideshow and cuts back to the video camera that's pointing at the presenter.  This has the added benefit of helping focus the viewer's attention back on the presenter, which is where it typically should be during a question-and-answer session.
To specifically answer your question: yes, it's perfectly OK to keep a "Thank You" slide in the presentation.  It may not be your best option for an ending, however.
Side note: Most slideshow software has the ability to place "extra" slides beyond the end of the slideshow.  They will not be shown when progressing through the presentation normally, but the presenter can manually navigate to these slides and they can be seen when not in presentation mode.  This is usually where presenters add extra content that will be of interest to some of your listeners but is too detailed to go over during the presentation itself.  A "References" section falls into this category.

Early in my career in a talk coaching they told me a very important point against the final "thank you" slide. The last slide should be a conclusions slide, because this slide stays on for the whole duration of questions. That's a lot of time. Hence you'd rather have a summary of your research on that something less meaningful.

While most other comments say including 7 slides of references is a terrible idea, I don't think it's nearly as bad if handled properly. It's a very bad idea to try to discuss these slides in any sort of detail, that much is true. But if you just quickly flip through them - giving the audience enough time to skim but not to read - there is not much of a down-side. Better still would be to not actually go through these slides during the talk, just leave them there for the benefit of anyone who asks you to share the slides, or so that you can more easily answer questions about references during the Q&A.
In any case when I think using the many reference slides is appropriate, I think it's absolutely fine (and even preferred) to include the "Thank You!" slide before them.

Flipping through them at moderate speed might be distracting--I'd probably zone out pretty quickly. Unless it's just a rhetorical flourish ("Look how much work has been done on this topic!"), I'd not do that. OTOH, having them in reserve for questions is a great idea.

I would recommend adding a "Thank you for your attentention. Are there questions?" slide before the references.
Most people will not want to see seven slides of references. But most people would not read one, either.
Keep the references slides, so you can show a reference when somebody asks for a reference that were mentioned in your slides, but do not force the audience to read slides that are too full of text to memorize them or take notes in a short time anyway.
In addition, the references are very useful when you give out the slides as handout or put them online after the talk and they just belong to a scientific talk, even when you only show them when needed.
In addition I would suggest citing important sources on the slides where you mention them like
"As shown by Miller et al. 2016 [7], we can use ..."

This allows the audience to take a note, so they can ask you to show the references slide so they can take a note what paper [7] is, when they are really interested. Otherwise they will at least remember "Miller et al. 2016" and have a chance to find the paper themself.

I am preparing a presentation in LaTeX and got at least seven pages for references only.

I suppose you use beamer and/or advi to show your presentation. You would use bibtex for references.
If it is a formal presentation (think of some PhD defense, or some CS conference) and if you intend to publish that presentation (at least as a PDF file, perhaps as a *.tex one) on some web site, then providing seven pages (with hyperlinks) of references is definitely worthwhile, and is a material for questions.
If you don't intend to publish your presentation (or if that presentation is informal) seven pages of references is really too much.
These slides are a recent example. Many references (but inside the slides, not at end) given as hyperlinks.
Some conferences are requiring a particular and given beamer style.
Most important for an important formal presentation (such as a PhD defense): repeat that presentation several times. Like every movie or theater actor do.
You won't have time to talk about 7 pages of references.
You may keep them to prepare for questions.

When I create a presentation in which I anticipate that there will be a lot of questions, I put a blank slide in at the end (to indicate I'm done).  But, in addition to the slides in the presentation, I create slides that address the questions and discussion that I hope will follow my presentation.
I can remember one presentation where I was told that I was limited to 5 slides and 10-15 minutes (it was not academic, it was a presentation to senior decision makers at a company).  I presented my 5 slides, and the questions started.  I ended up using most (not quite all) of my additional 43 slides, and the questions went on for more than a half hour.  The more you prepare, the more you can impress your audience.
Oh,... Skip the references slides.  You can leave them in the deck (in case someone asks), but don't show them.

I would make a references page with a QR code on it leading to a google docs file / website... with the references on it. Leave this page 30 sec in the presentation and then go on with your thank you page.

If he took this approach, I'd put the QR code (and a full text link) on the thank you slide, rather than having both a thank you slide and a reference slide.

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