How do you cite articles from a "database?"

The first two sources of information about such questions are

The publisher of the database may have specified how they want to be cited.
In fact, The Cochrane Collaboration has such guidelines:

Cochrane Policy Manual: How to cite our products
Cochrane Reviews: How to cite Cochrane Collaboration products

The APA style guide may have said something already about this data base.
This is also the case:

How to Cite Cochrane Reviews in APA Style
They explain how a journal article style should be used with year as volume and monthly issue:

  Singh, J., Kour, K., & Jayaram Mahesh, B. (2012). Acetylcholinesterase
  inhibitors for schizophrenia. Cochrane Database of Systematic
  Reviews, 2012(1), 1–101. doi:10.1002/14651858.CD007967.pub2

If these would not have lead to the required information, a more general idea is:
Following the DOI of your example, I end up at a page of the Cochrane library that also has a tab "Cited by". You could have a look there how other people actually cite the report.
If all this had failed, I'd propably have gone for a technical report style citation.


Tips for transition to online classrooms given university shutdowns in response to COVID-19

This is marked for community ownership so constructive edits will be welcomed. It is, however, more directed at those who can design a course, rather than a TA who has limited control.
Background
Many of the teaching techniques we use are not optimal for learning. They have been designed for economic efficiency since they scale. Some of them have been a bit obsolete since the creation of the internet. But face to face classes in real time are no longer necessary. Lecture is efficient (one teacher, many students, synchronous), but again, not optimal. Testing is a poor way to guarantee competence. This current emergency can be considered to be an opportunity to rethink everything we do toward finding better ways to educate people. We are forced to act and the old ways don't work in a new environment. We should be looking for new ways.
The essentials of teaching are Delivery, Practice, Feedback, Assessment. All of these require Two Way Communication. They don't require synchronicity or exams. The first job is to teach people, not to grade them. If you get that part backwards then you are only "teaching" people who don't need to be taught.
Every student is different. Nearly every student learns differently from the way their instructor does. The instructor has been proven to stand out in a particular system in which others have failed. As an instructor you have an obligation to every student willing to put in the effort, not just to the ones naturally predisposed to "win" in some system. Not every student starts at the same place with the same understandings. The same words don't necessarily have the same meanings to different people.
Some people have handicaps that prevent certain kinds of interactions. Hearing impairment and vision impairment are obvious ones, but there are others.
Learning is individual, but the process need not require isolation. It can be a communal process with learners helping each other. Denying students the option of working together is sub-optimal. A course can be a communal activity, not a hierarchical one.
Some students will succeed no matter the system. They don't really need you for anything more than pointing to important sources/ideas. But most actually require your assistance since insight into a topic can be hard to come by. Many students actually need to be taught how to learn. If you change the system of learning they may need to be retaught how to internalize ideas and turn them into competencies. It isn't automatic or obvious.
Learning isn't "consuming" material. It requires active participation. It requires a change in the brain (The Art of Changing the Brain by James E Zull)
All of these things have long been taken into account in designing educational systems, but the current practice is a compromise that values economic (scale) values over educational ones. Not everywhere, of course, but the exceptions seem few to me.
Let's assume that everything is on the table, except that students and instructors can no longer meet face to face in groups. Meetings of any kind need to be small and optional with alternatives provided. Computer communication of some kind is needed, but costs are an issue as is the privacy of all participants.
What to do, what to do.
Ideas for Delivery
There are a lot of ways for students to have access to the material of a course. Books are traditional. Lecture has replaced most other methods. But lectures are longer than they need to be. Some research I read suggests that lectures of 10 to 15 minutes are more efficient than hour or longer lectures (https://spokenimpact.com/what-is-the-ideal-length-for-a-presentation/). Those contemplating video should take note of that. Video also needs to be accompanied with a transcript to aid those with impairments.
Moreover, students need to be able to review material. Video is difficult in this regard since it is hard to quickly return to a small part that needs review without watching longer sections, which leads to boredom. Transcripts can mark the time that important ideas are introduced.
There is a fine line between having good and poor production values in video. If they are too good, a video talk becomes just entertainment with poor learning, unless other means are used to encourage/enforce engagement. If they are too bad, then students will get lost and frustrated. Video professionals are good at this sort of thing, but it is hard to bootstrap immediately at scale.
Delivery alone is just media. Students need to incorporate what they see in a lecture, long or short, into their long term memory and into their effective competencies. More is involved than the eyes and ears. Students often think that the will automatically "learn" what is presented to them in a lecture, talk, demonstration, etc. but it is anything but automatic.
Caveats: Any "solution" that requires real-time synchronous presence on the internet will probably fail. And it will fail invisibly for some. Connections are dropped, servers overload, etc. It is hard enough to keep students off their phone when in a class. It is probably impossible to do in a real-time internet lecture. Other distractions will intrude. Moreover, unless you have an exceptional communication system, students won't be able to interrupt you when you make a mistake, as you will. No questions are likely to be asked in real time. It is also difficult for a presenter to give a lively talk with no audience feedback at all. Especially if you are trying to do this under emergency conditions without training and experience.
But if you absolutely must use synchronous delivery you need to do two additional things. The first is that you need to record and post your lectures so that those who must miss the original don't lose access.
The second, just as vital, is that you provide a real time feedback to yourself (or to an assistant sitting by your side) so that questions can be asked as you lecture and so that students have a way to mention/note errors you make.
And make sure that students know what to do in the case that you lose the server and the ability to broadcast. Avoid chaos and uncertainty as much as possible.
Ideas for Practice
Student practice exercises and tasks may not need to change much. Students, depending on the field, need to write, solve problems, and other things as appropriate. For the most part this can probably proceed largely unchanged. Instructors have access to many such student exercises. If the students have a text book they probably have a bank of suitable exercises and questions.
And note that practice and reinforcement is probably the most important element in a delivered education. The "content" that a student needs is, for the most part, available to them. There are exceptions for very advanced work, but the world's knowledge is pretty much available. Instructors help students choose the important things and avoid the garbage, of course, but it is up to the students themselves to learn by reinforcement (combined with feedback). Whatever the topic, competence comes from repetition and reinforcement. The only thing I teach nowadays is Tai Chi. We have a saying that you need to repeat a movement ten thousand times to learn it. Somewhere in those ten thousand tries, insight will start to develop. The same is true in things like mathematics and writing poetry.
So, remember that the things that you make the students do to learn are much more important than the things you say. Good course design focuses on the student tasks, not the lectures.
I caution, however, that copyright considerations may apply if an instructor tries to utilize exercises from copyrighted material. They are, in a sense, publishing things they send to students in an online course. Caution and legal advice is useful.
Ideas for Feedback
Feedback is two way. You need feedback from the students on your presentations and assignments. Students need feedback on their own work. A number or letter grade on a paper isn't feedback. It gives no basis for understanding how to improve.
If the materials presented are well vetted, such as textbooks, the need for feedback to the instructor is a bit lessened. But videos, especially those prepared in the moment are likely to contain errors. Shorter videos are easier to fix than longer ones. But, unlike face to face classes, the instructor isn't likely to be interrupted when there is a misstatement or an omission. Moreover, you need some indication that the students have actually understood what you have been saying and presenting. Again, in fact to face classes you can look at expressions on their faces for some important feedback.
Lets assume for the moment that you have already taught your students the importance of taking notes during presentations. At the end of a lecture you can ask individual students, perhaps volunteers, to tell you an important idea from the talk. You can do this two or three times and give them feedback on their replies. This can be transferred to online learning. If readings or video presentations are short (and, I assume asynchronous) you can ask students to send you a summary of the lesson. Restrict them to one or two sentences. Another possible request is to ask them to send you a possible exam question on that material. At some point, all student replies, perhaps anonymized, can be made available to everyone. By glancing through the replies you learn whether they are getting the main points and they are also getting the reinforcement they need.
Giving feedback to students on their work is critical to learning. This involves answering questions that they have, but also showing them where they are making mistakes, and why, in their own work. The previous section talked about repetition and reinforcement. It is possible for students to learn and reinforce the wrong message. If you get an incorrect idea deeply ingrained in your mind it can be difficult to dislodge. All student work needs to be commented on, not just graded. Publishing solutions to exercises after the fact can help, but it isn't the same thing.
This idea of individual feedback is one of the most difficult things to arrange in the modern educational system, simply because of scale. My university teaching (and student life) mostly involved classes of fewer than 30 students. At that scale, I could easily give good individual feedback on weekly assignments. At 40 students I found I needed help. Massive courses have a problem here that requires tools - probably better tools than are now available. I'll note that Harvard's CS50 course is delivered to about 800 students at a time. But the staff for the course is about 40 individuals, so the ratio is about 20:1. Some of the staff are graders who comment on student work. Others are TAs who hold individual "recitation" sections of 20-30 students so that questions can be answered and misconceptions dispelled. I worry that moving such recitation online might not work as well at scale unless there are communication tools that let people learn from the questions of others. Many students are reluctant to ask questions. The brave students willing to do so actually contribute to the education of their peers. But, answering a question for a single student, say in an office, is much less productive than answering it in public, so that all can share the response. Tools are needed for this, though they can be pretty simple. University managed email lists subscribed to by students and staff are pretty effective.
But if students produce "papers" of any kind, those need to be annotated and returned. More than a numeric or letter grade is needed. Something as simple as pointing a student to a place they need to review is helpful. But the goal is to foster insight. PDF files can be annotated and returned, but the process is awkward at best. And, again, there is the scale problem. It takes time to review and time to annotate. Then, the student will likely have questions that need to be addressed based on the annotations. The increase in awkwardness using current tools may require more staffing to make things work effectively. Even a simple email to a student takes more time than jotting a comment on a paper and then returning it at the next face session.
Ideas for Assessment
In my view, evaluation and assessment are the most difficult issues we face in moving to an internet model. However, they also, again in my view, have the most potential for long term improvements in student learning, provided that we take the opportunity to learn how to do a better job of it.
The first principle of assessment ought to be that any sort of evaluation have an actual educational purpose, not just a "sorting" purpose. I think that many of us aren't doing a stellar job of this, having opted for easy solutions that scale, rather than solutions that aid student learning. Multiple choice tests are overused and while it is possible to design good ones, it is devilishly difficult. Things that rely on machine grading in general are too likely to also rely on only shallow learning and memorization, rather than deep learning and mastery. If the students can be held in a room and closely monitored this sort of thing tells you something about them, but it can likely be better. Move them outside your purview and it becomes nearly impossible. And it even fails at scale.
While you can do some technological things to lock up a student's personal computer they are intrusive but also ineffective. You can enlist a vast army of TAs to monitor student webcams (intrusive, again) but even there, what happens slightly off screen is invisible. Without such intrusive measures students have access to helpers both human and electronic. Closed-book, closed notes exams are probably a mistake in any case, but online they are difficult to impossible to monitor. There are too many inducements for students to break the rules to really assure validity. Honor codes, such as those of Dartmouth College do have a positive effect, but part of that effect is that the codes have been in place for half a century.
I have some personal suggestions about alternatives to examinations and, especially, high stakes examinations such as finals that account for a large fraction of a students grade. I don't claim these are the only solutions, but am more interested in sparking thoughts about how we can do a better - more learning focused - job of evaluation and assessment. I implemented these more and more as my career progressed and I learned more about students and about learning.
The first idea is to reduce the overall effect of any given exam or test. If you have forty small items you can get at least as good a picture of a student's progress as if you have only one or two large ones. Moreover, high stakes testing too often leads to poor student studying habits, such as cramming for exams and cheating.
One technique I used toward the end was "cumulative grading". A course had 1000 points assigned to it and different student activities were "worth" a certain amount of points. A project might be 100 points. The result was evaluated (and commented on) and a certain number of points was awarded, perhaps 80. I also published the minimum number of points necessary for each letter grade, say 800 for a B. When a student accumulates enough points to "earn" the grade they desire they no longer need to do more. There was no risk. Another feature of it was that if the student wasn't satisfied with the points earned they could re-do the work and possibly earn additional points. Some limits were put in place, but they were generous. The philosophy behind it is "You aren't in this course to prove to me that you don't need to be here." But note that I could do this since the ratio of staff to students was good. This is hard to scale without help.
The second main technique I used and can recommend is to make almost all assessment and evaluation based on student writings and projects, not examinations. And, if the nature of the course permits, use group projects primarily. For my courses the group size was usually between two and five. These groups can meet in cyberspace or, if location and other factors permit, they can meet face to face. The projects might be large or small. They can be graded once or often. Points can accumulate. It is the project that is graded, not the individuals, so everyone earns the same grade unless that is impossible. Peer evaluation is used to award bonus points or to solve issues of non-participation, etc.
If there are a number of group projects students can move between groups if needed. But students also need to be taught how to run an effective group project. In the courses I taught, dividing up the work "equally" was always discouraged and if done, usually leads to poor outcomes. Students need to form teams, not just amalgamations of individuals. In CS this skill will be valued later in their careers.
Also, peer evaluation has to be properly managed. Students don't "grade" one another. They comment on the contributions of a few or all of their team mates. "Who was the most helpful team member? (or three top members) Why? What did they contribute? What was your own chief contribution?"
At a certain scale or with sufficient help you can easily determine who falls into which important grading groups. Who is excellent in all respects? Who shows promise? Who is getting by? Who is deficient? Who has failed? Elaborate point systems in which an 85 is somehow significantly different from an 87 have little real meaning in my opinion.
To emphasize a point above. In many fields, even very technical ones, writing is an important skill. Writing essays on a given topic is good professional preparation for a budding mathematician. Exams can be replaced with such essays, lessening the needs for security and such. They seem to me to be much more value long term than skill at exams. But you can probably expect that students will hate it initially.
The above, of course, are just ideas. But I found them to be more aligned with the teaching mission than the more traditional lecture and test.
Ideas for Communication
To handle all of the above with online courses the main need is for effective communication between faculty and students and, I found, between students themselves. One goal is that what any student sees can be seen by any other student.
Communication tools need not be complex or comprehensive. But they should permit asynchronous communication and should permit many-way communication. Threaded email lists are very useful and don't require extensive facilities. They can be private lists, managed by the university alleviating some privacy issues, open to only class members and staff. Documents can be distributed. Questions can be asked. Questions can be answered at any time of the day or night - even by other students. Someone needs to monitor these to make sure that misinformation is quickly corrected and that any rules about posting or not posting certain content are maintained.
If project groups are long lived, then each group can have its own mailing list and can also use other tools they find for communication.
Another useful tool is a group chatroom. Group chats can be held periodically, though the email lists were more useful for discussing course material. These are necessarily synchronous and so not every student might be able to "attend". But it is easy to capture the complete conversation as a text file and send it to everyone or post it on a course web site.

My own expertise in this comes from helping to design and deliver a graduate program in which students met face to face only once a month for half a day per course. All work was done in groups (of about 5). Face time was only used for things that could not be done on line. We used simple tools for communication. All student-professor communication (other than personal things) was open to all students. Students could ask questions at any time and other students were encouraged to answer from their own expertise. The course was always live, every hour, every day. Questions got answered quickly, if not always perfectly. Students didn't get stuck. The goal was to build a learning community. That community has persisted past graduation.

Minor updates only anticipated.

An interesting alternative view can be found here:  https://anygoodthing.com/2020/03/12/please-do-a-bad-job-of-putting-your-courses-online/. Thanks to user curious for pointing this out.


When writing multiple papers from the same dataset, how do you handle the methods section?

There is a divide in how to approach this question based on the type of methods section, as there are two almost entirely distinct forms of methods sections in scientific publications.

"Prose" methods: This type of methods description is part of the main flow of text, and presents the methods in an explanatory fashion.  Such a methods description is expected to be either unique or else credited as being reproduced/adapted from another publication.  An example of such a paper (in particular Section VI A, B).
"Cookbook" methods: This type of methods section comes at the end of a paper, after its discussion and conclusions, and is effectively a compressed "appendix" with no narrative exposition, just an extremely terse summation of particulars.  Such a methods section is not generally subject to concerns regarding self-plagiarism (and arguable not even copyrightable!) because they are essentially just recipes: there are only so many ways to say "Cells were cultured in LB medium at 37C." An example paper with such a methods section.

For your particular case, then, if you expect both papers to be under review at the same time, then you should already be making sure that the reviewers know this is the case. The papers should likely be referencing one another as "under review", the cover letter should make the existence of the other paper clear, and you should likely submit it as review-only supplementary information.  If you are creating "cookbook" methods, that's enough to deal with self-plagiarism.  If you are creating "prose" methods, then you should explicitly note at the beginning of the section that it is shared between the two papers, thereby making an explicit declaration of shared/adapted text and defusing concerns of self-plagiarism.

Finally, if one paper ends up significantly preceding the other, such that they are not effectively co-published, then you can simply remove its references to the other publication and change the references in the second to refer to prior rather than simultaneous publication.


What are "executive members" of a conference or journal?

These conferences typically have an Executive Committee, consisting of the Chairs of the various threads in the conference. Some typical examples are the Conference Chair, Program Chair, Tutorials Chair, Posters Chair, Educator's Symposium Chair, etc. It will normally be around ten people and they are responsible for the overall running of the conference with each having primary responsibility for one aspect (other than the conference chair who has overall responsibility).

This Executive Committee will meet several times in preparation for the conference, usually face to face and usually at the Conference Venue at least twice. The meetings are where problems are addressed and, hopefully, solved.

An "area chair" may also have a co-chair to aid with their area. They might attend meetings or not, but are ready to serve if there is some issue with the chair. There may also be a few others with somewhat lesser responsibilities. They are arguably part of the Executive Committee. Doctoral Symposium Chair might fall into this category.

The Program Chair is a special case and there is usually a Program Committee with several members. They may meet separately from the Executive Committee and are responsible for the overall program. They see that the right papers are accepted and that everything in the main program fits together by assigning papers to sessions. Again, they are arguably part of the Executive Committee.


Is there a place for publishing ideas (no tangible results)?

While you might struggle to publish something like this in a journal, in Computer Science there are other venues to look out for, such as conferences and workshops. These are smaller (and sometimes less prestigious) than journals, but usually with a tighter focus: you can often publish work-in-progress or position papers.

Edit: Some conferences are large, prestigious events, and will expect a substantial contribution to the field, so before you decide where to submit, take a look at past papers, and the sort of thing they tend to publish.


How to deal with the wealth of "help" available for programming assignments?

Most people should require nothing more than the textbook and my lectures.

Probably most professional programmers today could do their jobs armed with nothing but the lectures from their programming coursework and the complete official reference material for the programming languages and libraries they are using. But why would they, when there are much more useful resources available online that allow them to do a better job, more quickly?

Your students (understandably) approach this the same way. Why would they do their homework with just the textbook and lecture notes, when this isn't the most efficient way (with respect to time, getting a good grade, and actually learning)? (Yes, the Internet can be a tremendously useful aid for learning and not just copying.)

In my experience, the best way to deal with students using online resources is:

Encourage students to use online resources. Recommend specific online resources to them that you consider most helpful and reliable.
Require students to cite all the online resources that they used. (And depending on the assignment, to also explain how they used it.)
Educate students who use online resources that are flawed about how to better evaluate the online resources they choose to use. ("This website seems useful at first glance, but it actually doesn't apply to the problem in the homework assignment. Here is how you could have known that...") If you do this successfully, this will probably be the most valuable thing they learn in your class.
Assign a mix of problems, including some that can't be answered immediately with a simple Google search.

If you want them to have some practice solving programming problems without the assistance of the Internet, you can occasionally give them a small (< 10 minute) problem to complete in class.


Variation in drop dates, and effect on student outcomes

I'm not personally aware of formal studies on the subject, but at my undergraduate institution there was a carefully thought policy that seemed to work fairly well.  They had not one, but two different drop dates for classes, with different intentions:

The first drop date, ~5 weeks in, left no record at all, and was intended to allow "class shopping" and academic risk taking. This made registration a low-stakes decision. A student unsure whether they could handle a hard class or undecided between two classes could simply sign up, try things out, and then make a decision after a couple of weeks, before investing too much.
The second drop date, ~12 weeks in, left a record on the internal transcript, and was intended to allow a failing student to triage and focus on their remaining classes.  It still didn't show up on external transcripts (except as a light-load semester).

With these two dates as long-standing and well-accepted policies, professors tended to include them in their planning.  Most of the early "shopping" drops happened in the first week, so professors tended to wait until the second week before doing things like arranging tutorial sections or setting presentation schedules.

Similarly, grading policies mostly tended to assume that D, F, and late drops were synonymous.  Thus, many classes set their first quiz before the first drop date, to let students have their first serious assessment of their progress before that decision deadline.  Likewise, curves were often set to assume the worst grades would have gone to the students who dropped, meaning that students who stuck out the class were not unfairly penalized (though they could still fail if they did that badly).

These policies I'm sure do create some statistical GPA inflation, but I doubt it has much significance because 1) it would not generally affect the stronger students, and 2) significant failures are still visible as gaps on a transcript.


Etiquette for discussing authorships, expectations, etc. with potential advisors

Think of your first meeting as a mutual interview. The adviser wants to know if you are worth spending time and money on. You need to ask questions to determine if the adviser is worth spending years of your life on.

Good topics for the first meeting are:

The adviser's expectations of you (including hours worked per week, number of papers to publish before graduating, etc.)
Your expectations of your adviser (Do you get vacation time? How long does it take your students to graduate? How much grant funding do you have? What earns me authorship on papers? etc.)
Your potential project (What are the long-term goals? What are the short-term objectives? Have other students worked on this project before?)
What preparations do you need to make? (Should you take a particular course? Should you read certain papers or books?)

You should also try to get candid answers to these questions from the students who already work for your potential adviser.


PhD in Machine Learning from CS Department or from EE Department?

It's not about the department.  Choose an adviser that is good in machine learning (ML).  He/she might be in CS or EE.  In my university, there are staff members in both departments who can supervise ML projects.   Choose someone who fits your interest and work style; see recent question regarding selecting an adviser.


Does this ProQuest "docview" URL include a DOI?

It's not a DOI. It's probably a ProQuest-specific identifier.

First, it's not in the correct form: DOIs look like "10.1000/xyz123".

And as a rule, to check if something is a DOI, you can enter it into the resolver on http://doi.org

Here you get a "not found" error i.e. it's not a DOI:


Are professors generally straight forward about admission decisions?

I take "I cannot make any promises" to mean ... I cannot [i.e., I won't] make any promises.  Behind that door could be anything.

In other words, it added no information to your decision about whether to respond in advance to School B's offer.

I wouldn't recommend asking the same professor again, but a more informative question for you to have asked would be when (with specific reference to the April 15th deadline that most graduate programs operate under) you would hear back.

Your best bet is to wait.


Help picking an appropriate citing style

Though I'm not a fan of it in general, in your case the IEEE style could work very well.  In the body of the paper, references are numbered in square brackets, like this: [1] and [2,3].  In the bibliography, you'd just have one entry per web page, with the URL.  If you use LaTex, it's easy to make these all active hyper links, so that your professor can click on the "[1]" to go to the bibliography entry, and then click on the URL to go to the StackExchange web page.  It's also possible to make the references hyperlinked in MS Word, but it might take some manual formatting steps to link each reference to each bibliography entry.


Second revision, one of the reviewers said I should completely rewrite paper with new ideas and methods, because it is not innovative

Based on your comment, I understand that the reviewer doubts the novelty of your work, without specifying details (previous works achieving the same or something very similar as your work).

This kind of feedback is essentially worthless, and should not influence the decision on your paper (if it's a sane editor).

I recommend the following strategy: Systematically address all other reviewer feedback and, based on your revisions, write a strong author response letter. Regarding the criticism of novelty, include a response among the following lines in your response letter:

  To our knowledge, our work is the first to achieve X. We discuss the novelty of our work in comparison to related work in section Y of the paper. We would appreciate any pointers to additional works which should be considered in our discussion.


When should some research be censored/blocked due to social implication concerns?

In general, research should not be censored.

It is, of course, generally accepted that research methods should be subject to ethical limitations.  Likewise, at some point there is a distinction between scientific investigation and the engineering of dangerous things like nuclear weapons and zero-day code exploits where society generally agrees that it's better to not put these capabilities into the hands of every random individual.

That's not really what you're asking about, though. What you're asking about are studies that look into the differences between groups of people that society already treats differently.  Whenever somebody goes to publish a paper on the differences between men vs. women or blacks vs. whites or homosexuals vs. heterosexuals or any similar category, this is a paper that should rightly be treated with great suspicion.

The reason, however, is not that there is some politically correct conspiracy or societal engineering agreement in academia.

Rather, it is the exact opposite: due confirmation bias and similar effects, there is an unfortunately long history of scientific investigations that purported to prove that horrible injustices were actually appropriate.  Over and over, people search for justifications for societal structure or pre-existing beliefs, often mixing up cause and effect (e.g., having characteristic X is bad for your health vs. being treated badly is bad for your health, and your society treats people badly if they have characteristic X). Moreover, such studies have often been embraced by larger society---even despite countervailing evidence---and this pattern has caused (and continues to cause) massive amounts of harm to massive numbers of people.

Thus, any honest investigators with an understanding of the history of their field should look at studies like the one you reference in your question with great suspicion.  No censorship need be involved---but it's entirely reasonable for peer reviewers and other gatekeepers to be exceedingly careful and stringent about what they choose to endorse as being scientifically valid.


What happens when I can no longer find authors of a paper that I am submitting?

This is a tricky one!  Since some venues may require each author to sign over copyright, it complicates matters above and beyond the ethical question of what is right.

If you feel they deserve authorship, you should IMHO make a good faith effort to find them (web search, ask the university for contact info, etc).  But in the end, if you can't find someone and they contributed data but not writing the paper, I see no way you can include them as an author.  An acknowledgment would be appropriate.


Does in review mean an external reviewer is assigned ?

'Under Review/In Review' can mean that your manuscript is currently assessed or 'under review' by the assigned editor. This could be very likely, since you mentioned the status changed straight from 'waiting for assignment' to 'in review'. During this time your manuscript could be checked for formatting guidelines, the editor might judge the article himself or he might be in the process of trying to find suitable reviewers. For details on the different status messages of journal's workflows, here's a great answer.

Especially around holidays it might additionally be hard to find reviewers, and get back their scores within a certain time period. Also, even if a journal claims to normally take one month until the first decision, I suspect these times can have a big variance.

I suggest to wait until the holiday season has passed, and then follow up if the status has not changed yet.


How can a PhD student enlarge his academic collaboration network?

Of course, you’ll get there by engaging in a lot of activities where you will meet new people and work with people who will learn to know you. I recommend choosing them according to a few criteria:

Activities of a seemingly technical (or practical) nature. As a PhD student, you probably don't want to be on boring committees, board-style meetings, interdepartmental seminars. You will meet people, but not in a way that fosters collaboration. (However, you may want to attend these events for other purposes. Meeting key people involved in hiring decisions at a given institution is one such purpose that comes to mind.)
Informal settings. This favors meeting new people and getting to know them much better. Favor small meetings over big ones. Aim for a few persons you want to meet. Identify people you would like to approach (at a big event), then check what events they attend.
Manage to invite people for talks at your institution. Okay, this one might be a bit difficult for a PhD student in some places, but if you can manage to get someone invited for a day or two, get him to give a talk and discuss your research and his, it will be worth it.
Do not shy away from “learning” events: tutorials, “hands-on with XXX library” type of things.

All in all, I think the kind of events you want to engage in are:

Open source projects: you listed that one already
Workshops close to your research topic: these typically involve few people and long discussions. Many of my strongest collaborations (and a few friendships) grew out of workshops.
Tutorials organized on topics related, but not too close, to your research: you will learn stuff, meet people in a relaxed setting. Don't be shy of going to workshops where you already know some of the stuff, if only to put it in practice and discuss with the best experts. Also, be ready to present your own work and identify convergences with lecturers and other participants.


Do universities prioritize research experience over industrial experience for master?

Based on my experience (for thesis based MSc): a big yes. Because universities are mainly interested in research and publishing papers. Although industrial experience might be relevant but research experience is key.

However, for course based master degree usually students are not required to publish. Thus, it might not be an extra point to have research experience.


If you're black, how do you answer "Oh you're a professor? So you teach African Studies?"

What's wrong with a sensible answer:  "No, I teach Chemistry."


Where do all the research paper annotations go?

I was recently introduced to this site: hypothes.is (I have no affiliation). In essence, any PDF with a URL when opened with their layer allows you to see comments and highlights from anyone else who has chosen to use it, or sub-groups you can join or arrange.
I have not seen anyone in academia use it, but perhaps you could start. It does seem like it could be useful for a small group of people who want to understand a paper.


How do I reference the Python programming language in a thesis or a paper?

In order to cite a programming language, a possible way is to cite the reference manual, including the version of the language you use (your approach might no longer work with the version of Python available in 20 years ...).

For instance, you can have a citation like:

  Python Software Foundation. Python Language Reference, version 2.7. Available at http://www.python.org

According to this thread, you can also cite the original CWI TR:

  "G. van Rossum, Python tutorial, Technical Report CS-R9526,
  Centrum voor Wiskunde en Informatica (CWI), Amsterdam, May
  1995."


How much damage would I be incurring if I turn down an informal postdoc offer?

Since you haven't  agreed to take the job, there's no damage being done at all.  Being offered a job does not put you under any obligation to take it, in academia or otherwise.  You shouldn't feel embarrassed or awkward.  If you're sure about your decision, then it's helpful to tell the professor now.


NSF IIS status date changed, status still pending

That almost certainly means that proposal has gone through a review panel, and does not indicate what the recommendation from the panel is. There are several internal stages the proposal goes through after panel review.


Does uploading a paper to arxiv with the same title but different author list affect citations?

Search results on Google Scholar usually club together citations on different versions of the same article (see screenshot below). Moreover, since Google Scholar works with preprints, and preprint servers like arXiv have options to add or replace author names, in my opinion, this will not affect your citation count. However, make sure that when your paper gets published, the author list is updated in arXiv as well.


To choose which Masters program to attend, should I favor institution or specialization?

If your interest is in "industry," I'd choose a school based on the institution. Most employers look at that as the "headline," and often "gloss over" the actual content of the degree.

If your interest was in research, I'd go the other way and emphasize "specialization." Because that is what research is basically about.


Should I put an ongoing research position that I recently started on my resume?

It's up to you, but the guiding principle is "Anything on my resume is fair game for the interviewer". If you've worked long enough to be able to talk for a couple minutes about what you do there and what you've learned so far, then go ahead and put it down. If you wouldn't feel comfortable talking about it, leave it out.

Resumes do not need to have a complete breakdown of every job position you ever had; you're highlighting your strengths to get the recruiter/manager/professor to notice you, and ask you questions on the interview. The resume is mostly only good to get you to the interview, so again, only include it if it something you can talk about comfortably. Good luck!


Email affiliation for an undergraduate student with a complex university address

Use your university address, even if it is weird and complicated.  Nobody will hold an official bureaucratic policy of your university against you.

You may, however, wish to see if your university supports email aliases.  Many universities have an official "full" email address, but also a shorter and easier version.  Others allow you to activate your alumni account even while still a student, and you might then use that alternate (and persistent!) address.

Separately: do not hide your paper from your professor.  Assuming your professor is basically ethical, then either a) your professor should be an author and will explain why you should add them, or b) your professor should not be an author, in which case they'll celebrate you without asking to be added.


Associate Editor is our faculty member, so he/she will not handle our paper, right?

Yes. An editor from the same institution as the authors has a clear conflict of interest, which is to be avoided.


Is it a good idea to get involved with journals as an associate editor prior to getting tenure?

I think my first recommendation would be, do not see editorship primarily as a career move/booster (if it ever is). Become an editor if you enjoy that side of the publishing and you think you have something to contribute. I had some opportunities with editing conference proceedings and thematic issues which gave me the insight that I really enjoyed working on that side of publishing (along with my research, admin, students etc,).

Signing up to be an editor is a longer term commitment. You need to check with the journal if they have a "from now on" or fixed periods for editors. You should probably expect to be involved for, say, three years under most circumstances. You should also check the expected work load in terms of, say, papers per year (but expect the workload to vary significantly over shorter time periods).

Being an editor can be very fruitful since it may give you new impulses on scientific writing and thinking and other similar aspects that can help your own development. As an editor, you will perhaps also gain some reputation, your name will be seen in amongst hopefully respectable peers (the other editors). Not that this may be of direct importance in terms of tenure or so but it may develop your network of contacts. There are many positives that follow from serving as editor, in my opinion, and it will be up to you to take the opportunity to serve as a fair and sound editor. There are no doubt tricky issues concerning ethics that will pass your desk but solving such issues together with other editors is a good and useful learning experience.

So in the end, become an editor because you want to, the chore will take time from your other duties and you need to be prepared to provide that time on top of everything else over a longer period. As you become seasoned, the time you need to spend on each paper diminishes somewhat so initially, you may find the time consumption larger than expected.

EDIT: I guess my point is that the editorial work takes time and effort but is also rewarding on a personal level (how, is personal). How this spills over into your situation in terms of meriting is for you to assess. Does your workplace appreciate such efforts? If you really want to do it, will the opportunity arise again any time soon? Are you willing you sacrifice some spare time if need be, and over some longer term? Clearly it should not reduce your other activities that are meriting for your career (research, publishing, teaching supervising etc.) so you need to balance between your own interest and what you need to do. That is why assessing how much time will be required(on average) is a good starting point.

My personal view throughout my early career was to jump at opportunities that I felt strongly about and where I could see something good coming out at the other end. By good I mean both for myself or for my career. I figured, the only thing I had to invest was my time and I needed to invest it wisely to help me get a permanent position but also to do things I really liked. So on the whole, quite egotistical, but then I have not been much for spending much effort on stuff I did not like or saw a point in. Of course one cannot jump at everything without the risk of hitting the wall. So, in the end, I think it is your interest and time keeping that decides. What you engage in can be either directly rewarding or indirectly so, and as long as it provides a positive, I think it is worth considering.


I would not worry about your verbal and AWA scores at all. They are quite decent and frankly, most math departments do not care too much about them, as long as they show that you are sufficiently proficient (which your scores do). Indeed, given how tightly constrained your schedule will be in the next couple months, I think it would be a waste of time to attempt studying more for these sections.

Getting a 170 in Quant is the only reason I would retake the GRE. However, even then I do not really think it's worth it in your case. Since you expect to get the GRE-math subject test with such a high percentile, this will clearly demonstrate your quantitative abilities. In other words, because of your subject test score (plus your transcripts/letters of recommendation), it will be obvious that the 5 points you missed were due to a lack of concentration or because of anxiety during the GRE, rather than lack of quantitative understanding.

Also note that for many departments, GRE scores simply serve as pre-filters; i.e. some universities might not consider your application if your scores are below some threshold, but otherwise the scores won't make too much of a difference.

In summary: There are more important parts to your application, and I think it would be a waste of time and money to retake the GRE.


How to cite regularly published editorials that have no specific titles?

Citing editorials, using APA Style, is actually not that difficult. You just have to specify the relevant type of material ("Editorial" or "Letter to the editor") in square brackets and provide the full date of publication. The latter, in combination with the title of the editorial, naturally serves as a unique identifier for the piece (so, no subtitle is needed). For example, for the first source that you have mentioned in your question, I think that the appropriate citation would be the following (support):

  Last Word. [Editorial]. (2005, June 24). New Hampshire Business
  Review, p. A1.

In regard to the second source that you have mentioned, I think that you incorrectly refer to the entry as summary. IMHO it is simply a bibliographic entry, referring to the corresponding regular published article. In that case, I would cite the original article and not the EBSCO entry.


asking professor to fund Master's student

You might be mistaken about your professor having funding in abundance. Even if he has managed to bring in a lot of funding, he might be spending it all on research and researchers.

One possible way to address this might be to approach your professor at an appropriate time and gently bring up the possibility of receiving funding for your work. I would even leave it up to him how many hours per week should be paid.

As a matter of fact, you might mention immediately that you also keep working if there is no pay. It might seem that you will not receive anything when you mention this, but your professor might feel that it is morally right to provide some funding, and it will make the conversation less awkward.


Is it socially acceptable to directly contact renowned academics as a student?

Yes, it's perfectly fine to do so. To maximise the chances of a response, make sure your email is clear, concise and polite.


Published and unpublished dissertation; DOI assignment

You should avoid citing it twice, because it's the same work (think of it as a book published by two different publishers - you wouldn't cite both versions). Whether you prefer to cite it with a ProQuest DOI or with a link to the university repository is up to you, though possibly a given journal may have an opinion on which they prefer. Depending on how formal the citation style is, you could do something like:

Bleckh, A (2015). ProQuest citation; DOI. Copy available from [repository]

which would let you use both access methods.

For DOIs, it's unlikely that your repository will assign a DOI to their version - most repositories aren't set up to issue DOIs. The repository is intended as an alternative way to access it rather than a different publication, and so material hosted by a repository tends to give the bibliographic details of the "real version" rather than provide their own.

(Also, I'm not sure what you mean by "maintaining" - are you envisaging updating it over time? This would be quite unusual for a doctoral thesis...)


Academic tassel at convocation: left or right for dual undergraduate/post graduate students?

At my institution (in the United States), students always wear the tassel on the right, even if they've earned a prior degree.  At Commencement, the President tells the students when to switch.  (In our case, that's everyone at once, after diplomas (really, diploma covers) have been presented.)


I'm unhappy with my Master's. Should I drop out?

I think to really enjoy academic life, your motivations should be academic, and I now realize that my motivations certainly aren't.

No human being can -- or should -- have only academic motivations.  In this statement I find a kernel of truth: "An academic career is not a good one for those who are not motivated by a love for and a desire to work in their academic subject."  But also I find a kernel of falsity: "The only worthwhile reason to have degree X in subject Y is a love for and a desire to work in subject Y."  That's really not true: in modern life, degrees -- and increasingly, "advanced" degrees like master's and doctorates -- are necessary credentials in order to attain any of a variety of non-academic jobs.

If I understand your current situation, then:
(i) With one more year and with full financial support, you can complete a master's degree.
(ii) If you drop out now, then not only do you not get the degree but you will have to pay a financial penalty.  (So you say, anyway.  In the US, students who drop out of a degree program do not have to pay back their stipends.  It sounds like you are outside of the US.  It might be worth exploring -- carefully -- whether this is actually true in your program.)

In other words, looked at in non-academic terms you would be paying a nontrivial amount of money for the privilege of extricating yourself from a master's degree program and sparing yourself one year of doing something that you do not enjoy (but are doing well in; you seem not to doubt that you could get the degree with one more year of work).  Okay, if you drop out of the program right now, you will do....what??  If the answer is that you have a lucrative and long-term job lined up now, it would make sense to drop out (and try to put your degree on hold, if possible).  If you do not have something specifically positive lined up but are just looking to release yourself from the drudgery: I don't think that's a rational decision.  Ten or twenty years from now you may well look back and wish you had finished the degree.

I am not going to pick apart your entire message, but at several points your reasoning seems predicated on faulty assumptions.  Just a couple examples:

  I had previously worked in industry and didn't have much of a pleasant experience, so I believed I would fit right in to academic life.

That makes no sense to me.  For many values of X and Y, liking X is positively correlated with liking Y.  I have never heard anyone say, "If you don't like this, then I know you'll like..."  I have a friend who made the same mistake in the other direction: as an academic he found himself weighed down by his colleagues' and superiors' expectations of how he should spend his time and conduct himself: he found these expectations both too numerous and too nebulous.  So he switched to an industry job to correct it.  Suffice it to say, he didn't stay in that job for terribly long.  There are (at least) two problems with this reasoning: (i) There are more than two walks of life...many more.  The majority of human beings are not working in either academia or industry.  (ii) Not all forms of unhappiness can be cured by any change of location.  Some of them are more internal.

  The upside in dropping out now is that I would gain a whole year to actually focus on my life,

Not being a graduate student is neither a necessary or sufficient condition to actually focus on your life.  Try focusing on your life while completing your master's degree.  Yes, it's challenging...but worthwhile.

  I've also been told that every grad student thinks about quitting at least once, and I know many others like that, but that doesn't make the situation better. Actually, it makes it worse for me, because it seems that nobody has any confidence in their work, and nobody is expected to have that confidence whatsoever. I find that extremely unhealthy and demotivating.

Then I have good news for you: in five years of graduate school, I never thought about quitting -- not once.  I had my better and worse moments, and yes -- at times my confidence lagged -- but I was at all times completely confident that I was doing what I wanted to be doing with my life.  My graduate school cohort consisted of people who were amazingly (indeed, intimidatingly) competent, enthusiastic and successful: the vast majority of people around me reinforced my interest and inspired me to work harder.  You don't sound like you're in a very positive cohort.  If you did decide to stay in academia past your master's degree (which I am not recommending if you continue to feel the way you do now, but it is possible that you could have a change of heart), you should make it a priority to place yourself in a positive academic environment.  It makes a world of difference.

Good luck.


Should you cite somebody's Transfer Report? (Confirmation Report)

If it is published somewhere, then you should feel free to cite it. However, if it's not, then you have a challenge. You might cite it as, more or less, "Author. Title. Transfer Report, University, Year. (unpublished personal communication)" Which indicates that you friend or colleague gave you a copy in which you first found the information you are referencing.

I think such an approach gives your colleague credit and gives readers at least some hope of being able to track down a copy if they want to verify your claims about what it says.


Applying to graduate school after the deadline

You will probably be rejected, but if it costs nothing but effort, then you may as well. I doubt there would be any lasting effect if you want to re-apply in the next cycle.


I would imagine most institutions would consider it discriminatory to judge on age, and in some places it would just be illegal. The real consideration is always whether the prospective candidate has a reasonable chance of success. Having appropriate education, or a reasonable substitute is of course the main criterion, though demonstrating research-level ability always helps (research publications etc.).

Personally I have seen PhD candidates of all ages. There's some skew to the distribution across disciplines (business and history for example often have higher proportions of older doctoral candidates than, say, mathematics), but this seems to be more a socio-cultural thing than any institutional influence.


Grad school admission after bad grade in research class for different discipline

Welcome! The gap year is a good idea. A lot of research in graduate school (and beyond) is (in my experience) similar to that linguistics class: confusing, unstructured, little guidance, figuring methods and new things out on your own, shaping your own experience. So the best way to set yourself up for success is to figure out what you could do differently in a similar situation to succeed. Where else could you find resources? How could you figure out direct questions your professor could answer? (Or that a different professor could answer for you?)

There are similar questions about recovering from a bad grade, such as this one: How does the admissions process work for Ph.D. programs in the US, particularly for weak or borderline students? and this one: Does a bad grade in one course (with otherwise OK record) affect graduate admissions?

You may or may not need to explain what went wrong in that linguistics class as part of the graduate admissions process. But you should get it straight in your mind so that you have clearly learned from it, and so that you can deal with this better when you encounter similar situations in the future. That is, you can take charge of this story and it becomes less about that professor and more about a mistake or a problem that you've learned from and figured out how to overcome.  Good luck!


Can I present a conference paper if I am not a researcher?

Of course you can submit any paper you want. There are a lot of people, for example in the industry field, that submit papers to conferences.

But as they have stated in one comment, as soon as you start preparing a paper, that per se converts you into a researcher.

Good luck!


While there is no real harm in citing it, it is unlikely to be necessary. Common knowledge is one of the exceptions to the requirement for citation. Many things that you first see in a course fall under this cover, even if they are new to you.

But you seem to be more speaking of copying the notes, rather than citing them. That may be a different issue if they can be considered to be copyrighted. In that case you want permission from him.

Do a little research in a textbook or two. Do those definitions, or something essentially similar to them appear there? I suspect they do. If so, there is no need to be concerned. And also note that one of the exceptions in copyright law (most places) is that for some things there is only one effective way to state something, so it's expression can't be copyrighted.

And it wasn't your professor who originated these ideas.

But an acknowledgement to your professor for introducing you to these ideas would be a courteous thing to do.


Synonym for the job title of assistant professor

I think you should just introduce yourself as

  I work as a professor at the University of X.

omitting the assistant rank that can cause misunderstandings.

The following conversation line feels also very safe:

  – Where do you work?

  – I do research and teach at the University of X.

which might be a better fit since it explains your job in a short sentence. However, nothing wrong with the first line that does not require a question to feel natural.

The actual rank (assistant/associate/full) might matter in a formal (mostly, written and official) context and rarely means a lot outside of the academic system. And that seems to be exactly the situation you happen to encounter issues.

Related questions:

How an assistant professor is called in North America?
Can I call an assistant professor Professor?

Cultural and linguistic differences can play a role, so it might not be as appropriate in certain countries; though, I doubt that would matter at all in a circle that is not familiar with academic ranks at all. Moreover, it is likely that there is no confusion because the rank in the other language is very different.

You might also dig in the direction of "Head of XXX lab" (in case it applies) or "research group supervisor", but I don't think there is a good reason. An assistant professor is a professor and no elaboration is needed in a laid-back unofficial atmosphere.


Can non-reviewers influence the decision about a paper in a program committee?

In theoretical computer science conferences (which often use EasyChair), I have seen the following practices:

Once all reviews are in, PC chairs often encourage all PC members to comment on all papers on which they have something useful to say.
Sometimes the comments are just discussion that may influence the final decision in borderline cases.
Sometimes the assigned reviewers modify their reviews based on the comments (e.g., they realised that they overlooked some important point).
Sometimes the PC chairs ask some of the assigned reviewers to incorporate the comments in their reviews.
Sometimes the PC chairs ask non-reviewers to convert their comments to (short) reviews.


Is it prudent for new faculty to abstain from voting in a job search if the rest of department faculty is highly divided?

It could be. It could also be a disastrous move. There is no way an outsider can judge just how messy your department is. Your best bet is to find someone in your department that you trust and ask them. I personally think jut abstaining for a hiring vote is a little weird. If you go down the abstain route, you may be best off abstaining from all votes.

The STFU strategy can work, but in really divided departments, at some point before tenure review you are going to have to take sides.


Is it acceptable to cite an article from a corporate website? Can Wikipedia be used to prove credibility?

I agree with the answers posted here so far, but I want to add a few points.

You can realistically use any source in your paper, but it depends on how you use it. If you want to write about what X company says about a particular topic, then using that particular web article seems appropriate. If you want to write something informative about a particular product that X company happens to use, then citing that article (written by X company) is a less than ideal choice. As @Buffy mentioned, the company has a vested interest in portraying the product in a certain way, but as @Richard Erickson mentioned, this article (or Wikipedia) can be a good initial stepping stone.

Articles that you use for information need to be peer reviewed in order to have a high level of credibility. Not having access to books is not a valid excuse; universities have a plethora of resources for this exact circumstance. I recommend Inter Library Loan (ILL) for hard to get books and journal articles. Your professor may have suggestions on where to start.

tl;dr:

you can use anything as a source (even Wikipedia), but it depends on how it’s used
peer reviewed sources are best for research credibility
you can find obscure resources using your university’s library privileges
consult with your professor


Reusing figures from other articles in one's thesis

In the US, you are legally in the clear if you have permission from the copyright holder, which is likely the journal. That being said, it would be polite to ask the authors, too.

Both of those being said, you probably have a fair use right in the US to reproduce the images verbatim in your thesis for the purposes of commentary, critique, criticism, or the like. However, fair use is a defense to copyright infringement, so if you don't want to run the risk of getting sued and having to defend yourself, getting written (including email) permission to use the image from the copyright holder is the best strategy.


I have chemistry as my majors but I recently failed my phd qualifying exam

First, this is a good time to review all of your options. Try to find a few that you haven't yet considered and figure out the pros and cons.

But if you really still want to pursue a doctorate, I don't think the door is closed. There are quite a few people in the same position as yourself, though I don't know about how it is in your field.

But, the way to figure out your prospects, really, is to put together all of your qualifications, even including non-obvious ones, and apply to a few programs.

There are a lot of reasons for failing comprehensives/qualifiers. Many of them are incidental to your actual suitability for a degree. But it would be good if you figure out why you failed yours and see if there is some remediation that needs to be done.

One reason is over-confidence. Another, at the other end of the scale, is lack of faith in yourself. There are also technical reasons, of course. Figure it out.

Personal note. I've been in the same situation. The faith of one professor in my ability helped me move to a much better situation with a much better advisor. Then: success.


Literature Review versus Literature Survey. What is the difference?

Reviewing the literature relevant to a given field is a standard part of doing research, as this serves to put your work into the context of the larger discipline in which you are working.

If there is an actual difference between the "literature survey" and the "literature review," it's that the latter can serve as a paper in and of itself, and is much more extensive than a literature survey, which is typically a major part of the introduction of a research paper.

The literature review as a standalone article could be compared to a "curated" overview of the literature in the field—who has done what, how do papers relate to one another, and what are the most important present and (possibly) future directions of work in such a field. Such papers can also be considerably longer than a traditional research paper, and some reviews might cite as many as a thousand references!

In comparison, the literature survey of a standard research article is usually much shorter (1-2 journal pages), and will not cite nearly as many papers (anywhere from 10 to 100, depending on the topic and the amount of relevant literature available).


Are concerns about studying in Russia reasonable?

I try not to think of myself as a person influenced by the US propaganda (I am more acquainted with Soviet and late Russian propaganda, more likely). However, I can not really advise you to go for degrees in Russia.

First of all, the STEM subjects were traditionally strong in the Soviet time due to the nuclear project. Unfortunately, the professorial level degraded significantly in the post-Soviet 90s, and did not fully recover yet.

Second, you are probably aware that most of the universities in Russia teach courses in Russian. Unless your Russian is already fluent (or at least basic), be ready to spend a year or so mastering it before you will really address your subjects. Unless you plan to work in Russia afterwards, the knowledge of Russian (as opposed to English) is not something that increase your career progress dramatically.

Lastly, having summa cum laude BS and MS degrees, as well as a PhD (or Cand Sci as we call it) from strong Moscow Universities myself, I probably can confirm that many HR departments prefer to see something easily recognizable on your CV, e.g. the University of Oxford as a trademark impacts your progress much better than the Moscow Institute of Physics and Technology that sounds almost like Inshallah Salam Alaikum University for someone who never heard of it.

On the bright side, studying in Russia you most definitely will experience interesting adventures, befriend the best guys and hang around the most gorgeous young ladies. Also, if you can solve problems you face in Russia, you arguably are ready to solve them in any other place.


How do I best position myself to get an NIH R01 grant?

For the NIH NIDCD (and likely other institutes, but I don't have the data), a great way to position yourself for an a new-investigator R01 is to first get an F32 post-doctoral fellowship since 70% of those with an F32 post-doctoral fellowship who applied for a subsequent RPG (predominately R01 and R03 awards) were successful. There might be better predictors, but 70% is pretty good when it comes to funding pay lines.

You should also be aware that the R01 club is not as closed as your question makes it sound. Historically, 25% of R01-equivalent awards are made to new investigators.


How to avoid letters while searching pubmed portal?

You are really asking two questions, a technical and a principal. As for the technical, let us assume your search is #1, then you can exclude letters by searching:

#1 NOT (letter[PT] OR comment*[PT])

Note the asterisk to also include the commentary publication type.

As to the other question; "Can these be considered valid articles?" - yes, they can! And in some cases, the information provided in comments can be as important or perhaps even more important than what is provided in the article commented on. So whether you should include them in your search highly depends on what the purpose of your search is. Are you getting a rough idea of the available literature? Then fine, exclude them. Are you doing a systematic literature review? Include them! There might be crucial information regarding data or conflicting findings. It should be possible to quickly (manually) exclude irrelevant letters.


Author qualifications to list in medical journal

If there are guidelines they’ll be in the instructions to authors in the journal you’re targeting.

If there aren’t guidelines, just list the degrees you have.

Definitely don’t substitute PhD for your DPhil. It won’t be as confusing as some, and lets the reader take a view on equivalence.

(The far more common confusion in medical journals would be the MD.  In US system medial education that’s a basic medical qualification that almost everyone has (unless they have a DO). In the British system it’s a higher degree equivalent to a PhD, and if someone lists their qualifications as eg MPH MD there’s no quick way to tell which they’ve got).


How much percentage royalty do I get from Springer (as the paper's author) and how I can apply for royalty payment?

You get nothing: Welcome to academic publishing.


Book chapters and theses in literature review: to include or not?

(Almost) everything is based on previously published work! But I think maybe you are referring to what we call the "secondary literature", which is review articles, books etc that don't present novel research (the "primary literature") but rather summarise or package up other research articles.

Yes, secondary literature can certainly be included in a literature review, especially if it gives ideas/opinions that have not been prominent elsewhere. However, if you refer to particular results then these should always refer back to the primary literature, even if you also give a mention to how those results have been described or discussed in the secondary literature.

(Note that dissertations/theses very often fall under the category of primary literature, in fact in some areas it is a requirement that they include novel research)


How cite sources of 100-years-old analytical technique in a theory section?

The real question is whether you need to cite anything at all.  In your field, if this information is considered undergraduate-level material that every practitioner should be familiar with, then you can simply assume that all readers will be able to reference their favorite textbook if they care, and launch right into the relevant review.

If you are speaking to an audience that may not be so familiar, however, you definitely do need to cite.  You don't need to put in lots of citations, however: you can simply say that this is well-established information and give one citation to a good textbook:

  The principles of X-ray diffraction are well-known (see, e.g., [textbook]).

For example, when I am writing to a computer science audience and need to say something about the NP-completeness of constraint satisfaction, I would probably not include a citation, since this is such a foundational concept to the field at this point.  When I write to a biology audience about the same problem, however, I explicitly note that these are long-established facts and include citations to basic textbooks.


How to stop being obsessed with manuscripts status

Start on a new paper.

Fall in love.

See a therapist.

Take up a new hobby or sport.

Get a dog.

Talk to your mom/kids.

Re-read Lord of the Rings.

Design a new course.

Go for a walk/run/swim/ski.

Repeat as necessary.

Not joking here. You are probably just bored. Do something that makes you less bored.


How should I phrase a question about an *ordinary academic matter* to a Professor?

Your confusion on this matter is understandable, but despite your misgivings, it might surprise you to learn that --unlike a divinely-sanctioned emperor-- there are no special protocols required when communicating with a professor, especially in relation to a standard academic matter.  All that is required is basic courtesy and clarity, as would be standard in any professional communication.

Whether you are communicating by email or directly in person, it is important to remember that there are no special magic words that you need to say when dealing with basic academic matters with a professor.  Be as clear and polite as you can, and get to the point about what you want.  Basic courtesy with pleases and thank-yous will be sufficient to ensure your communication goes well, and being clear and succinct will help your professor to deal with your matter without having to waste a lot of time.  Many administrative matters (e.g., reviewing a mark, applying for a program, etc.) involve the application of university policies, and it will be helpful if you have already read the relevant policies prior to communicating with your professor.

Emails: Many of these matters can be dealt with by email.  Composing an email to a professor is no different to composing any email in a professional context.  You should be clear and courteous, and get to the point of what you want to ask them.  Ideally you should use a level of formality that would not be out-of-place in an office context.  It is good practice to use the person's academic title (Prof, Assoc Prof, Dr, etc.) and spell their name correctly; this is easy to do, since academics almost always have a university web-page with this information, and a quick web-search will find their information.  If you are not familiar with how to write an email in a professional context, there are many, many, many, many websites that give tips on how to do this.  Some general tips are:

Write your email in a professional manner;
Have a clear subject line that tells them the topic;
Remind them who you are (unless they know you well);
State your request clearly, and give relevant context;
Make your request consistent with administrative procedures at your university; and
Ask your professor if he/she requires any further information.

Professors are generally quite informal in their email communications (with some exceptions), and they are also used to dealing with young students who have not been in a professional environment before.  This means that the bar for communication is low; if you fall short of the ideal standard of professional communication, your professor is not going to be angry at you.  Just try to be clear and polite, and you will be fine.  It is good practice to get into the habit of professional writing while at university, and these situations offer you a good opportunity to practice your communication skills.  If you would like special help with this, go to the academic-skills center at your university and ask them to teach you how to write a professional email.

Direct meetings: Emails are generally the best method of communication when dealing with simple administrative matters.  This is because they give both parties a record of communication and they allow the academic to deal with the matter at leisure.  Nevertheless, for some academic inquiries where a back-and-forth is required, it might be quicker and easier to talk directly to your professor in-person.  Depending on how important the professor is, it might not be easy to get much time with them.  You might require an appointment, or it might be possible to just knock on their door and ask to speak to them, or see them after class.  (If you are in a course with this professor, they probably have set consulting hours for the course when you can come and see them.)

Dealing with academic matters in a direct meeting is similar to email.  Be clear and polite, and get to the point about what you want.  Remember that you are talking to a busy person with lots of things to do, so you want to help them to understand what you want and deal with the matter quickly.  There are generally no special formalities required, but it is good practice to communicate in a professional tone.


Should I introduce myself to my supervisor via e-Mail or set up an appointment to introduce myself?

I would send mail suggesting you think it might be helpful to meet, just to get to know each other, and ask if your supervisor might suggest a time that's convenient.


Is completing two years of your PhD sufficient to satisfy journal reviewing requirement of having a PhD?

"Having a PhD" means that you completed the entire degree program—including writing, defending, and depositing a dissertation—and were formally awarded a degree by the host university.  Current PhD students would not qualify as reviewers for the journal you describe.


Does a few years work in-between study hurt Physics PhD application to a top 20 US school?

I'll offer several opinions.

Work experience does not help you get in to physics PhD programs.  It probably does not hurt either, but you should explain in your application why you did it and how it made you a better student.  Use a better explanation than the one you gave in the comments.
I actually view an MS as a black mark.  In the US, if you have an MS in Physics it implies you either
a.  Could not get in to a real PhD program.
b.  Failed out of the PhD program.
c.  Dropped out of the PhD program.
An MS in physics will cost money and essentially duplicate the first part of the physics PhD.  A PhD makes more financial sense than an MS.  This is not true in other countries or disciplines.
Publishing more will definitely help your application.  If you have lots of publications the rest of your background will be ignored.

Though you did not ask, I would like to point out that delaying the start of your PhD will delay the end of it, and the benefits that come from having completed it.  On the whole I recommend you start your PhD now, assuming you really want to get one.


How can I assess the quality of a paper outside my field?

This question concerns assessing the quality of papers outside one's field.

The question seems to be more leaning towards the quality of journals outside of one's field. Here's a brief list of pointers (some of which also appear in this question):

check if the journal has an impact factor (some good journal's don't and vice versa, so beware of false positives and false negatives)
find out the most prominent literature indexes in the area and see if it's in there (e.g., DBLP for Comp. Sci., PubMed for life sciences, etc.)
check the Australian ranking tables (don't take them too seriously: there is no such thing as a total ordering of journals)
check for journal citations in Scholar/Academic Search/Scopus
otherwise check paper citations in Scholar/Academic Search/Scopus
find out if the publisher is reputable (Elsevier, Springer, a good university press, etc.)
check Beall's list to make sure the publisher is not "predatory"
find out if the editors-in-chief are established academics (e.g., high h-indexes in Scholar)
talk to experts in the area
apply common sense.

The last point is particularly important. Though it is easy to discover if a journal is excellent or terrible, in between those extremes, there's a lot of grey. For example, new journals may be much-needed and drawing quality work from quality people, but they won't have a high h-index or an impact factor, etc.

For those grey areas, talking to an expert who knows the field is important.

  AllPsych Journal

This doesn't seem to be a formal journal, but rather an informal way for authors to publish educational articles online. All papers are published on the web-site, there's no mention of an editorial board, a publisher, a means of submission, etc.

Of course, this says nothing of the quality/utility of the papers published there: just that it would probably not count in academic circles as a "traditional journal".

For the quality of a paper itself independent of the venue, check how many citations it has in Scholar versus it's age, check the nature of those citations, check the h-index and background of the authors, etc. (Of course these methods are only an approximation for reading it and making up your own mind as to its quality, but since it is outside your area ...)


How to review a manuscript where the software is difficult to install?

You should ask your editor for advice on this. I doubt, however, that you should reach out to the authors in any way. But the editor can, on your behalf, ask the authors for specific instructions for installing the software on your OS. The editor can make this a condition of getting a review.

Moreover, the editor can communicate your concerns about missing files or whatever else is important to complete a review.


When referring to study at Oxford why is the word "read" used?

This is just a peculiarity of British English that read can have this particular meaning. The New Oxford American Dictionary says:

  read
  3. chiefly Brit. study (an academic subject) at a university: I'm reading English at Cambridge
    [ no obj. ]: he went to Manchester to read for a BA in Economics.

So, it's more about language itself than the official title of the diploma or an academic custom.

— Hey, wait, but where does this idea come up to associate “read” with “learn, understand”? Surely there is a reason? And why is it English only?

Well, as it turns out, the meaning of “learn, understand, think, explain” is actually the original meaning of the Old English word from which we inherited read! The Old English word is rædan (“explain”, amongst its meanings), from Proto-Germanic raedanan, from Proto-Indo-European root re(i)- (“to reason, count”).

Now, in many languages, the words derived from this root kept their original meaning. In German, raten means “to advise, counsel”; in Icelandic, ráða means “advise, decide, solve”.

Now, at some point something in Old English went sideways. Wiktionary states very clearly:

  The development from “advise, interpret” to “interpret letters, read” is unique to English

Etymonline is more specific:

  Transference to “understand the meaning of written symbols” is unique to Old English and (perhaps under English influence) Old Norse raða. Most languages use a word rooted in the idea of "gather up" as their word for "read" (cf. French lire, from Latin legere).

Now, the original meaning of the word read is retained in some contexts in British English, but was lost in other forms of the English language, such as American English.

As a summary, the hard question is not really “why can read mean study”, but instead: why did read come to mean “read”?

(source for the above: my memory, which is backed by the most excellent Etymonline)


Engineering degree structure in the United States

Most ABET-accredited programs in the US offer a 4-year Bachelors of Science in XYZ Engineering (sounds like the equivalent of a BE from your home country).  Most science programs (i.e., Physics, Chemistry, Biology, Sociology, really any type of science, hard or soft) are 4-year programs as well.
Many programs have an optional honors thesis that students can pursue if they are interested - it's rarely, to my knowledge, required.
US engineering programs don't typically emphasize research - though this depends on the school - but most emphasize a capstone project during one's third or fourth year.  This can range from working with an actual client (like my undergrad did) to working on a project that the professors running the project determine.
Generally speaking - all students complete the capstone, research/honors is optional.
Practical experience is what's most important - that comes from the capstone project, laboratory exercises, and above all internships/co-ops/REUs.


You should cite it as a book and include additional information if it is electronically available.

  Author Surname Author Initial. Title. City: Publisher; Year Published:Pages Used. [Available at: http://Website URL. Accessed Month DD, YYYY.]

Example:

  Lenga RE and Votoupal KL. The Sigma-Aldrich library of regulatory and safety data. Milwaukee: Aldrich Chemical Company; 1993:23-34


Does the journal Physical Review require an institution in the affiliation field?

To my knowledge, there is nothing preventing someone from submitting a paper to a journal without a formal institution as part of the reader's address. You might have to write something in a web form such as "self-employed" or something similar if institution is a required field for submitting the form.

However, it is fair to say that under most circumstances, if you are submitting a paper without institutional affiliation, it will probably be subjected to heightened scrutiny relative to a paper with more "traceable" affiliations. Unaffiliated authors are usually treated with some skepticism in the academic community, and papers by such authors tend to to be viewed as "crackpot" papers. (Granted, having an affiliation does not preclude the possibility of submitting such papers, but the likelihood is somewhat lower.)


Do US REU programs sponsor the student visas (J1 or F1) for international candidates?

All official participants in NSF REU programs must be US citizens or permanent residents per the NSF REU homepage:

  Undergraduate students supported with NSF funds must be citizens or permanent residents of the United States or its possessions.

A self-funded student or non-NSF REU funded student would simply be an intern or student at the host institution.


Professor for a performance class is scheduling class time different than the class time listed in the catalog

Performance groups, even when taken for credit, operate outside the "norms" of scheduling. It is unlikely that your concert will take place at the same time as your scheduled rehearsals, so you will need to make an "exception" to the rules just to participate in the performance—which is kind of the point of the class in the first place!

That said, the faculty member overseeing a performance class does need to be respectful of the schedule to the greatest extent possible. It is not fair to ask students to completely rearrange their schedules when alternatives are possible. If the faculty member does not believe there are enough scheduled hours to get things done, then there needs to be an adjustment in the course.

However, he will "get away" with this unless people make an issue of this. It sounds like there are a large number of people impacted. If so, then there is enough ground support that you can challenge it collectively without reprisal. (You can also "take it up the food chain" if the professor is unwilling to make changes.)


Coming from a "No Name" University outside the US, what are my chances for admission

At least in my department/school in the U.S., we have several individuals from African countries studying for doctoral degrees. I'm a little concerned that there seems to be a disconnect between what you say about your performance (above average) and what your professors are saying (no one would want someone like you, possibly because of where you studied).

As far as I can tell, most schools in the U.S. encourage individuals from diverse backgrounds to apply for their programs, including graduate school. So, I would not make a blanket statement that your country of origin and/or background is an immediate disqualification.

Regarding your academic background, even U.S. colleges differ in terms of academic programs and rigor. That is why the graduate school admissions process involves many different parts, including standardized test scores, interviews, and/or letters of recommendation, that help the admissions committee get a more complete picture of you and how you may fit within the program.


Advice for writing Lab Manuals for undergraduate students

Having written up a few such sets of course lab notes, the best advice I can give is to offer an "idiot-proof" introduction so that anyone can get the first lab started. From there, I tend to curve the difficulty of the tasks, such that the first task should be trivial, yet the last task of the session is more challenging. I then tend to suggest a couple of improvements or suggestions for the curious to consider or try out.

For subsequent labs, I presume knowledge from previous sessions is retained, and consider it a prerequisite. I give progressively less guidance on using tools or techniques for repetitive tasks through the different sessions.

To give an example, if it was a programming exercise, the first set of notes will be thorough and tested on an unfamiliar colleague, to ensure they can run the software needed, and get a "hello world" to run. This includes showing which buttons to press, and how to save and load work. While experienced students may skip this part, that's their choice... I find it worthwhile to write this, even if just to give the TA something to point students towards if they have problems.

As a student works through a given session in the notes, I make the tasks gradually reduce the direction given. So the first exercise could be to ask the user for their name and echo it back - I'd tell them to use the input command, then the print command. By the end of that session, the recap exercise night be to write a program to ask for 2 numbers and multiple them, returning the result. There wouldn't be any more guidance than that. For "optional extra ideas", I might suggest to keep asking for input until the user provides none, or something similar as a little teaser requiring some reading ahead and independent research.

The next session would not go into the same detail on getting set up, and would begin from a higher difficulty level (wouldn't step the student through which function to use, in the case of my trivial example above).

By the final session, there would be limited guidance and much more explanation of concepts or suggestion of references to look at. I favour leading people to good sources and suggesting they read it, rather than trying to reinvent the wheel, but this might not work in all cases.

In particular, physical laboratory activities with chemicals or equipment may not work with this model, as you may have obligations to detail all procedures for health and safety purposes. In that case, I would leave the analysis and explanation to the students, giving progressively less help in finding the right places to read about the expected results etc.

Ultimately this depends on the discipline and the expectations of the principal academic teaching the class. I do find students like the rising difficulty, as there's both sufficient help to get started, bus also a good sense of accomplishment to finish the exercises and have worked it all out.


Community colleges are organized differently between the states, but here's where you can find the current job listings in California, the biggest state:

https://www.cccregistry.org/jobs/searchForm.aspx

You'll have to do some reading (I got five pages of results for "mathematics"), but some of these positions are clearly tenure-track, and some are clearly not. In my district, the SFCCD, all the full-time faculty positions are inherently tenure-track.


How important are classifications (ACM, AMS, PACS...)?

From the ACM page "How to use the Computing Classification System":

  An important aspect of preparing your paper for publication by ACM
  Press is to provide the proper indexing and retrieval information from
  the ACM Computing Classification System (CCS). This is beneficial to
  you because accurate categorization provides the reader with quick
  content reference, facilitating the search for related literature, as
  well as searches for your work in ACM’s Digital Library and on other
  online resources. It also ensures correct placement when a review
  appears in Computing Reviews.

There's similar verbiage for the AMS MSC.

In other words, the institution needs it for their own databases and search mechanisms. The AMS probably needs it for something similar. So your use for the classification system depends on how much you expect people to search for your work using the classification structure provided by the institution. For math, I'd expect it to be used a lot: for CS, not so much.


How to format the name of an R package in thesis?

You can do this by adding the following to your preamble. Something like this:

\newcommand{\pkg}[1]{{\normalfont\fontseries{b}\selectfont #1}}
\let\proglang=\textsf \let\code=\texttt
\begin{document}
Then you can refer to R as \proglang{R}, to a package
\pkg{packagename}, and to a function as \code{functionname}.
\end{document}


The time frame you mention is within what can be encountered. The time frames also differ wide between disciplines but also from journal to journal so one way to check how reasonable it is will be to check the journal for how long it has taken other papers to go through to acceptance. Many journals state this for each article and hopefully your journal does so as well. If no such information is stated you can try and ask a senior colleague who may have a perspective on the journals and their turn-over times.


Copyright and Plagairism Policy for Reviewers of a Rejected Paper

I'm pretty sure that you won't be told who had access to your submission absent a lawsuit, which I don't advise. However, you might be able to instigate an investigation by contacting the conference chair (or program chair,...) of the conference you submitted to.

You could send both your own work and a reference to the other work you found to the chair and ask for an investigation. The chair knows who saw your paper and might be able to establish an improper connection if such exists. I wouldn't express it as a complaint or an accusation, but simply a request that the committee investigate.

However, even if such an investigation is undertaken, and it might not be, you might never hear the results. This could be true even if sanctions were applied to another researcher.

On the other hand, there is plenty of evidence in the history of the world of parallel research and independent researchers coming to the same conclusions nearly simultaneously. Newton and Leibniz parallel investigations that led to the Calculus is a classic example.

While we like to think that our thoughts are our own, it is usually true that we build on the shoulders of others. The giants that you had access to are also accessible to others. Your insights might be shared, especially in any field that is especially active.

I'll note that while copyright law varies around the world, your claim of copyright might be weak if your paper hasn't been published anywhere. This might be mitigated if you put an explicit copyright claim in the paper itself, but local laws will determine that.


How should a student defend his 1st authorship in front of his advisor politely and effectively?

In addition to Peter's answer, one should also keep in mind the accepted practices in one's field of study. For instance, in some fields, such as economics and parts of mathematics, alphabetical order is the default; in other areas, such as organic chemistry, the principal investigator of the lab—not the primary author of the paper—has traditionally been given the first spot in the list.

If you are in a field where the order is somewhat preordained, it's going to be very difficult to change that tradition, for many reasons. In such cases, you should optimize your placement within the "available" options.