journals - What do publishers provide to authors in different disciplines?

Discussions about academic publication (for example, the recent Elsevier boycott, the actual cost of publication, open-access initiatives by universities and funding agencies, citation cartels, or post-publication review) are often muddled by the fact that publication practices and culture vary significantly from one discipline to the next. I would like to see some of these differences explicitly teased apart.

I'm particularly interested in exactly how publishers in different disciplines help move authors' ideas to formally published papers. Publishing in any discipline requires the combined effort of authors, publishers, editors, and reviewers, but the distribution of these efforts (and their associated costs) seems to vary from one discipline to the next.

What specific services do publishers provide to authors in your discipline? Please only one answer per discipline. (If necessary, define "discipline" as "set of researchers with the same publication practices".)

(At a deeper level, I am curious why so many people seem to associate the value, authority, and prestige of various publication venues with their publishers instead of their authors, editors, and readers. But that's not a good question for StackExchange; let's stick to the narrower factual question.)

I'll provide an answer for my own discipline.

Deferring Admission to reapply for some PhD programs next year

This question is related to one of my previous questions:

Changing University in First year of Phd

I just completed my senior year. I have been accepted to a grad school (say University X).

I want to reapply for some PhD programs next year (fall). But, at the same time, I don't want to lose the only PhD seat I've got.

So, I was thinking about deferring the admission to University X in order to apply to few other universities for next fall.

I have 2 questions regarding this:

1. 
   

   Should I mention about my deferred admission to Uni X in the Phd applications for next fall ? If I don't, Would it be treated as academic cheating ?

   
   


2. 
   

   How much deferring should be enough ? (Next Spring, Next Summer or Next Fall)

   
   

cv - Is it a good or bad idea to list declined fellowships (for a PhD program) on one's curriculum vitae?

E.g. as shown in the example here.

• 2011—Centennial Fellowship, Princeton University Department of Atmospheric and Oceanic Sciences (accepted)


• 2011—Top Student Award, University of Washington (declined)


• 2011—Program in Climate Change Fellowship, University of Washington (declined)


• 2011—Faculty Fellowship, Columbia University (declined)


• 2011—Charney Prize, Massachusetts Institute of Technology (declined)


• 2011—Regents Fellowship, Scripps Institution of Oceanography (declined)



• 2011—Chair’s Award, Stanford University Department of Earth and Environmental System Science (declined)

Answer

Aeismail makes an important point about location: what's standard in Germany differs from what's standard in the US.

In a US context, I would strongly recommend against listing things like declined graduate fellowships. It will look strange, and even beyond that it can work to your disadvantage: everybody will already assume you declined several attractive offers, so giving an explicit list will do nothing but focus attention on what isn't on the list. (If the list of declined offers is short, readers will be disappointed, and if it's long, they'll spend more time speculating about what's missing than being impressed.)

The only time I'd recommend highlighting this sort of information is if for some reason you had to turn down a vastly more prestigious offer than the one you accepted. For example, maybe you were offered a tenure-track job at a top department, but ended up working as an adjunct in the middle of nowhere so you could take care of a relative. You should then make sure everybody knows this the next time you are able to apply for jobs. However, you should be very careful when doing this, because if the prestige difference isn't absolutely universally acknowledged, then you run the risk of offending people who feel you are unfairly denigrating a perfectly fine career path.

research process - How should a social scientist deal with envy of disciplines that are more quantitatively rigorous?

I am a student in social science who got into quantitative research at the start of my graduate school. Since then, I have had the valuable opportunity to take many Statistics classes and become aware of this world I had not known before. However, with it comes the curse of envy, as I cannot help but feel that my discipline, albeit using quantitative methods, is not as sophisticated (i.e. using a method without understanding the assumption and the derivation, basically relying on canned statistical package that others recommend). Outside of academia, the industry job market has also spoken that these quant researchers are more valuable than I am.

With this attitude of mine, I've become increasingly cynical about my discipline. I don't feel that the work that we do is "scientific" and "accumulating knowledge." I don't think that my industry job market can be competitive. This obviously has harmful effect on both my mental health and my research. I just want to learn more stats, write more code, instead of doing the research of my field.

On rare moments of clarity, I suppose this envious feeling is turtle all the way down perhaps. I'm envious of the statisticians, but maybe the statisticians are envious of the mathematicians, etc. This is why I decide to ask Academia Stackexchange for perspective.

From my occasional conversations, I get a sense that some of my fellow students may have the same feelings. However, given the toxic nature of my thoughts, I can't really discuss them widely with friends, not to mention with my professors.

How to deal with these thoughts?

PS: The relevant xkcd that will inevitable show up in the comments :-)

PPS: Given the gravity and scope of this question, I don't feel entitled to picking a "correct" answer. Thus I will just let the community upvotes decide the visibility of the answers. I hope that the answerers don't mind -- thank you for your insights.

phd - What steps could universities take to reduce Ph.D. drop-outs?

One of the major issues in universities with respect to PhD is the high dropout factor. Demotivated students cause a big loss to the university - a lot is spent on assistantships, but in the end, the students quit without making any meaningful contribution.

What steps do/should universities and faculty members take to reduce alarming drop-out rates? One step is obviously to choose the right women for the job, which we expect the admissions committee to do anyway. PhD involves years of wading through uncertainty and possibly it is in these years that students get distracted and unfocused. How should universities ensure the students remain unwavering in their efforts during these uncertain years?

Answer

One difficulty is that it's far from clear what the ideal dropout rate should be. Probably not zero, for two reasons:

1. 
   

   Even the best students sometimes find that their interests change over time, in ways nobody could have predicted. Dropping out may become a quite sensible choice, in which case it's harmful for the university to discourage it.

   
   
   


2. 
   

   It's reasonable for a university to give someone a chance even if it's not certain that they will succeed. The only way to get a really low drop-out rate is to admit just the applicants that are obviously destined for success. The top few schools can get away with this, but if everyone tried it, then many talented candidates would be shut out from graduate school.

   
   

So some attrition is OK, and some is bad but may be a necessary consequence of policies that are on the whole good. The question then becomes how you distinguish these kinds from needless and damaging attrition, and then how you minimize that kind.

Advisors play a key role here, because some are much better than others at being supportive or motivational. However, at least in mathematics, most advisors don't supervise very many students, so the numbers often aren't large enough to see patterns clearly.

I'm sure people have studied this problem, and perhaps identified best practices for addressing it. However, in my experience any studies or solutions are not especially influential (at least in the few math departments I've been in). Most discussions are at the stage of trying to figure out whether there is a real problem and if so why, rather than what to do about it.

Is it bad for one's future career prospects if the PhD thesis topic is broad?

As a graduate student in the PhD program (I will be graduating in about 2 months), my research has covered a wide range of topics rather than nailing down one specific topic (super-specialized). In fact, my thesis is broad enough that my current working title is something along the lines of "Toward the Application of Electronic Structure Theory to Solve Relevant Chemical Problems." (Can it get any more general?) There is nothing informative from that title as it completely leaves out details. The problem is, each paper I've published is its own research focus without any connection to the next outside of the fact that computational chemistry was used for each.

I've read in other places that a thesis topic is critical because it is the basis on which you launch your career. Is it bad to look like a 'jack-of-all-trades' person? There must be a better way to handle this.

Answer

short answer: I think the title is not suitable as it is, and thus may harm your career: currently it doesn't look like a jack-of-all-trades, but the title looks like jack-of-no-trade. However, it may not be a problem if you are already comparably well known for your work (i.e. people know jack has his trade(s)).

But I think it would be good to put in some effort to make it more precise about your contribution to the field.

---

long answer:

Disclaimer: I'm chemist. Not theoretical chemist, but chemometrician which means that I also do calculations (though of a different kind) in order to solve application problems.
I believe my situation is similar to the OPs in that we both work at problems where in order to solve application questions some method needs to be developed further. I call these 2 aspects of my work the "theory" and "application parts of the work.

In my experience you can easily end up with the title of all or most papers emphasizing the application, and thus looking very diverse while the common topic (the theory) is de-emphasized. Several reasons can cause/contribute to this:

• the application problem may be understandable and important to a much wider audience than the small field of experts on the theory you use and advance to solve the application question.



• therefore, the pubications are targeted to journals the application audience reads


• and you do not want to frighten them away by heavy theory terms in the title.


• Also, in my field it is much easier to get funding for working towards the solution of some medical application (and doing the necessary data analysis theory development under that hood) than to get funding for developing data analysis theory (and demonstrating this with the medical application).
  And this of course may bleed through to the paper and thesis titles.

In the end, the theory development - thus the common topic of the papers - is mainly to be seen inside the papers. Of course in this situation it would be good to have also a theory paper out that brings together the theory developments and just touches the applications as examples. However, this may look like one more disjoint topic on the first glance.

For example, my publication list has a whole lot of medical application (though I always try to sneak in the theory developments also into the title of the application papers), and a few papers which focus on data analysis methodology - while the common points of all these papers exists: chemometric data analysis and vibrational spectroscopy.

Two more points to consider:

• 
  
  

  The very general title you give sounds like a typical working title to be put into the forms at the beginning of the PhD before the specific line of the thesis is known. I don't see anything unusual in a situation where at the end of the work this working title is updated by a specific title.
  To me, this seems to be the underlying question here.

  
  


• 
  

  If you are in a theory group or are the one in your group who does theory development, the fact that you actually do theory development may be so obvious that you didn't think of stating it. But the fact and preferrably also the specific type of theory development should be in the title.

  
  

So my questions to the OP are:

• 
  
  

  Does this description of application vs. theory aspects reflect your publication situation?

  
  


• 
  

  In particular: by unrelated topics, do you mean something like the application question/chemical problems you solve are unrelated? Or do you mean that neither the chemical problems nor the methods you used to solve them are related?

  
  

My recommendation without knowing more specifics is:

• 
  

  Explain to your non-chemist grandma what you've been doing. Make a list of the points.

  
  
  


• 
  

  Fill in the sentence: My papers tackle application problems about ...., but what I've really been doing is ....

  
  


• 
  

  Don't be afraid of a long title. My guess is that the working title you posted is shortened too much: as you say it is not informative any more as the specifics have been cut out. Put them in.

  
  

bioinformatics - Confusion related to a term probe-by-background interaction

I was reading a paper related to bioinformatics where it uses the drug response on the cancer cells and the gene expression of the individual cells are studied to find any useful insights. Specially, using the gene expression of the cells a predictor of the drug response is created.

They have stated that just using the correlation between the gene expression and the drug response might not be a good predictor. But the genes interact through signaling pathways to drive a particular drug response.

What these guys have done is like used PCA on the gene expressions of the cancer cells to use the components which preserve the greatest variance.

Actually, I didn't get what they mean by probe-by-background interaction and how it is calculated.

Can anyone please explain. I googled for a while but didn't get it.

Here are some quotes from the paper where the term is used

Towards this end, we have compared how well drug response can be predicted by simple statistical models, which either directly relate probe and background networks to drug response or consider probe-by-background network interactions.

To generalize this approach, the term ‘probe’ could be replaced by individual transcript expression levels measured through other gene expression methods. Similarly, ‘background networks’ and principal components are used interchangeably. Generally, ‘background networks’ could be represented by any data reduction method that summarizes the expression of a gene network. We demonstrate that probe-by-background network interactions significantly enhance drug response predictions, over and above the predictive power garnered through utilizing individual probes and background networks alone.

professors - Who pays travel & per diem costs for invited lecturers?

When an academic is invited to give a talk at another university, are their food and travel expenses usually fully reimbursed by the university that invited the professor?

Answer

In my experience (as a visiting guest lecturer while a grad student elsewhere) the travel expense and accommodation were covered not by the university that hosted me, but by grant money from the professor that invited me. That being said, these visits were for a few days and included both the guest lecture, and some research/discussion on ongoing projects.

I did not claim a per diem for food, but I am sure that if I had it would have been covered, too.

evolution - Why is green fur not a thing?

In most biomes on earth, and certainly in the most densely-populated, the best camouflage color or pattern for an animal would be a variant of green, so as to blend in with the leaves and grasses of the surrounding environment. Whether predator or prey, the art of not being seen is hugely important in the natural world, and yet to the best of my knowledge there isn't a single mammal on the planet with fur that is even partially green.

Is there a reason for that? It seems like animals have evolved some pretty crazy color patterns to break up their silhouette or blend into the background, but why haven't any mammals taken the obvious route of "look like leaves"?

Is it really THAT not-easy being green?

Answer

The technical answer is: Because the coloration of skin and hair is done by the two forms of melanin: Eumelanin, which is dark brown to black and Pheomelanin which is yellow to red. This enables colors from white (not pigmentation) to black (dense eumelanin pigmentation) and also colors in between by different ratios of the two pigments.

The evolutionary answer is that it obviously made no evolutionary advantage to have other colors. If you look closer at this, you will see that most habitats are not green or only for a part of the year. If you think about african plains, these are mostly brown, something like artic landscapes are only green for a very short timeframe in the summer, for the rest of the year these are white to brown. And even tropical rainforests are mostly dark to brown on the ground. They would clearly stick out of the environment with green colored hair.

For all these different habitats the animals living there have adapted their hair color. It is not uncommon for artic animals to change their hair color with the course of the year, dark to brown in the summer and white in the winter (artic foxes and snow hare) for example. Animals which live in deserts will have a paler color than those which live in dark colored mountain areas.

See this article for more information: "The Adaptive Significance of Coloration in Mammals"

Also interesting in this context is this article which looks at the reason for zebra stripes: "The function of zebra stripes"

What percent of assistant professors generally receive tenure, and how does this percent vary depending on both school and field?

Are new assistant professors more likely to receive tenure in an expanding field, like biology? And are they less likely (percentage-wise) to receive tenure at elite schools?

Answer

This is actually quite a difficult question to answer specifically. Here is a brief paper reviewing some of the reasons why good data is unavailable on even very basic questions, together with some references to what is available. In the U.S. case, everyone agrees that, in general, the higher-ranked one's university, the more difficult it is to get tenure. Departments at some elite schools are notorious for their unwillingness or inability to grant tenure to their junior faculty over a very long period—in some cases, decades. (Just last year in my own field, for example, one of the leading departments tenured one of its junior faculty for the first time in more than twenty years. This is an extreme example, but you get the point.)

Beyond the well-known general patterns and the (sometimes widely-reported) particular horror stories, though, many very interesting questions remain difficult to address systematically—including your one about expanding versus stable fields. The question is complicated by the fact that the institution of tenure itself is changing, as is its role within the university. As Wikipedia notes, in the United States "The period since 1972 has seen a steady decline in the percentage of college and university teaching positions in the US that are either tenured or tenure-track. United States Department of Education statistics put the combined tenured/tenure-track rate at 56% for 1975, 46.8% for 1989, and 31.9% for 2005. That is to say, by the year 2005, 68.1% of US college teachers were neither tenured nor eligible for tenure; a full 48% of teachers that year were part-time employees.

Should I add references to conference presentations?

I am preparing a CS conference presentation and wondering how can I handle the references. I am thinking about three different possibilities:

1. Ignore them!



2. Just list them at the end of the presentation


3. List them and cite them within the presentation.

I chose the first option since anyone interested can go and check the whole set of references in the actual paper.

Does this mean not crediting the others for their work? How this is usually handled in CS conferences?

Answer

If the slides you're using are going to have "independent life,"—in other words, if you're going to make them available separately from the conference paper (on your website, for instance), then the citations should be included as part of the presentation. I would follow posdef's example and place the citations on the same slide as where it's needed; this will save the reader from having to flip back and forth between different parts of the presentation or between the presentation and the paper.

Not including the citations is a bad idea, because it means you are potentially failing to give people the credit they deserve for ideas that were originally theirs. Even though it's "just" a conference presentation doesn't mean that the rules of crediting people for their work should be ignored. (Citing the work of others is also the right thing to do from the perspective of "playing nice with others." Taking credit for other people's work can make them leerier of working with you.)

phd - Applying to Ph.D. with 5 years in Bachelors

I will finish my 4 year bachelors program next year, in a total of 5 years.

I had failed many many courses in 2nd year and my cgpa was around 2.4

Then I had that enlightenment and decided to become an academic. Since then, I have increased my cgpa to over 3.5 and turned all F's to A's. For last 3 semesters I get averagely 3.9 gpa each semester

I still have some C's in few courses from 2nd year and instead of graduating this year, I will graduate next year.

I have managed to boost my cgpa amazingly after such things but I want to know if this extra year will cause me any trouble during Ph.D. applications.

Answer

This sort of thing should be explained in the cover letter. This trend is pretty common; freshmen enter college ready to party, realize halfway through that their grades are actually important, and then buckle down and do good work for the rest. You simply need to state that, despite your initial behavior, you are fully committed to your education. Given a 3.5 GPA at the end, I don't imagine you would have too much trouble.

Do note that this will vary as a function of the universities to which you apply; some may take a harsher view than others. Still, you have a good explanation for the one bad year, so it shouldn't post too much of a problem for you.

graduate admissions - Can a masters student apply for a second masters in the same field at another university?

Are students with masters degree allowed to enter a masters program in the same area at a good university?

Is second masters a good option for a better research experience and improving your CV before applying to a PhD in top programs? I am specifically interested in US universities and computer science.

eyes - Why can I see a light flicker when it's in my peripheral vision?

When I'm looking at an old CRT monitor or a worn fluorescent lamp, but not directly in the center of my gaze, the light from it seems to flicker. When I focus my gaze onto the monitor or lamp, the flickering stops.

Why can I see a light flicker only when it's in my peripheral vision?

Answer

Your retina contains both rods and cones. Cones are color sensitive, slow, and concentrated near the center of your field of vision. Rods are "light" sensitive, fast, and concentrated near the periphery. You want to be able to respond quickly to a threat "in the corner of your eye" without needing to see the color of the threat.

This is nicely explained by this diagram (source: http://hyperphysics.phy-astr.gsu.edu/hbase/vision/imgvis/retina.gif)

So when you see a CRT in the corner of your eye, your rods respond quickly enough that you can tell the light of the CRT is flickering. As you turn your gaze towards it, you get the higher resolution, color rendition of the cones - and lose the temporal resolution.

immunology - IgA-s in an immune system vaccined intramuscularly against Hepatisis A

As IgA are immunoglobulins associated with secretion and mucosis membranes, I am interested whether after intramuscular vaccination with Hepatitis A vaccine IgA antibodies will be produced by the immune system before an actual infection?

Also, would they be secreted into breast milk, intestine lumen etc. before the infection coming in a traditional (gestational) way?

Or does it take to have the antigen presented at the mucosis mambrane to start IgA production or secretion?

university - What are the repercussions of a "vote of no confidence" made by faculty?

As an example of a vote of no confidence, recently, the academic world has been shocked by the Salaita case at the University of Illinois. I happen to be a UIUC alumnus, so I guess I'm more concerned about the current state of affairs in my Alma Mater. So I just read an article on the web about the case: More Votes of No Confidence, a Weird Ad, and a Declaration of a Non-Emergency. The article states that

Tonight, the major news out of the University of Illinois is that two more departments have taken votes of no confidence in the leadership of the UIUC: the department of history (nearly unanimous, I’m told) and the department of Latino and Latina Studies. The latter’s announcement reads:

The faculty of the Department of Latina/Latino Studies (LLS) at the University of Illinois at Urbana-Champaign met on Wednesday, September 3, 2014 to discuss the University’s revocation of an offer of employment to Dr. Steven Salaita. We concluded that this revocation and the subsequent public statements by Chancellor Phyllis Wise, President Robert Easter, and the Board of Trustees about Dr. Salaita’s appointment demonstrate a clear disregard for the principles of academic freedom, free speech, and shared governance, as well as for established protocols for hiring, tenure, and promotion. The faculty of LLS therefore declares that we have no confidence in the leadership of the current Chancellor, President, and Board of Trustees.

That means that six departments have now voted no confidence, two of them fairly large departments, representing a significant number of faculty in the humanities. Word is that we should be expecting at least four more votes of no confidence by the end of the week, for a total of ten.

I know the best thing that can happen in the current state of affairs is that UIUC's own faculty boycott the Board of Trustees and Chancellor Phyllis Wise.

So my general question is, what are the implications of such a vote? What does a "vote of no confidence" really mean?

EDIT

As suggested by @MadJack, here's the New York Times article on the case of Salaita.

phd - What is a European Doctorate Programme?

I am currently a PhD student in a EU country and recently I was advised to pursue a European Doctorate Programme.

I thought that, being "European", it was some kind of regulated, inter-country program with specific rules, but I cannot find any "official" documentation from any European institution. The only things I can find by searching on google are doctorate programs from various universities that claim to be "European".

I am aware that some EU students are encouraged to do 3-6 months of their PhD (or more) abroad, but I don't know if by doing this their PhD qualifies to be a European Doctorate.

So, what is a European Doctorate Program? Is there any regulation for it by a European institution? How does it relate with doctorate programs where students decide to spend some months abroad?

Answer

I am curious to understand if there is a tangible difference between a national degree (of an EU country) and the European degree.

As for the rules for qualifying for the European degree, I found these rules to apply:

1. The doctorate must, in part, have been prepared during a research internship period of at least three months in another European country.


2. Oral thesis presentation authorisation is granted on the basis of reports submitted by at least three professors comprising at least two from higher education institutions from two European countries other than the country in which the oral thesis presentation is to be held. The host laboratory representative cannot submit this report.


3. At least one member of the jury should belong to a European higher education institution from a different country to that in which the oral thesis presentation is held.


4. Part of the oral thesis presentation should be conducted in an official language of the European Community which is not the language of the country in which the presentation is held.

Edit (because I still cannot leave comments):

• 
  

  Some universities might require a 4 month stay abroad for acquiring this title.

  
  


• 
  

  As for the difference in the value between the two degrees, there seems to be none. The European Doctorate seems to be a label added to the normal doctoral degree of an EU academic institution as a proof that the abovementioned requirements are accomplished. This seems to be a way to promote cooperation among EU universities from different countries, PhD student mobility and the writing of the dissertations in English, as in many EU countries they can still be written in the official language of the country.

  
  

citations - Do you need to read a whole article before citing it?

During writing my academic paper, I need to cite a definition in a scientific paper. The other part of the paper, is irrelevant to my work.

I have been advised that if you will cite a paper, you need to read that paper entirely. But in this case, it seems useless to do so.

It also happened a few times when I wanted to cite from some books.

Answer

No, you don't have to read the whole paper. If you think you do, ask yourself this:

do you also have to read all papers cited in the paper?

For example, I recently needed to know a certain function of n. Some computer experimentation suggested that it might be 3*2^n, let's say. Then I found a paper published in a reputable journal that claimed to prove exactly that. As the reasons why it was 3*2^n were probably rather unrelated to what I was trying to do, I cited them but did not check their proof.

On balance, I think that making every author read every paper they ever cite would slow down the progress of science.

Caveat: this may be field-dependent. For instance, if the paper can be thought of as consisting of just one long definition, then yes, one should read the whole thing.

eyes - Why can cats interpret things on a monitor/tv, but dogs cannot?

E.g. you can see a lot of videos where cats are smashing some mouse or spider on an ipad, but I have never seen it with a dog. I have a dog myself and I know that he sometimes responds to the sounds from the TV, but not to the images.

Why is that?

Answer

Cats and dogs can both view tv screens & monitors ... though their viewing experience is a little different to ours thanks to differences in cone structure leaving them color blind and giving low acuity.

Both species have lower levels of color vision than humans. Cats see slightly more color (in the blue green and yellow end of the spectrum) than dogs do so they may get more of an immersive experience from watching TV.

Further, cats and dogs need a higher frame rate than humans to make it appear as a smooth film, a phenomenon known as flicker fusion, in humans we require 15-20 frames per second, dogs require 70fps and cats about 100. Before the frame rate of televisions increased in recent years it would appeared to them to be flashing images, similar to when you point a digital camera at a screen which may explain why the dog is not interested in the TV, it'd be like staring at a strobe for hours on end. Here is a paper which discusses flicker rates and color vision in dogs.

To summarize there are several factors which influence the "enjoyment" an animal can take from watching a TV - their response to TV imagery will depend on the frames per second, colors, contrast, clarity, movement, subject matter, and (perhaps most importantly in my opinion) the temperament of the animal, for all of which there are difference between the species.

From sciencenordic.com:

"We humans need about 16 to 20 images a second to perceive what we see as continuous film, whereas dogs need about 70 images per second.

So a few years ago, Fido was probably confounded by his master's behaviour of sitting for hours staring at a flashing succession of images. With modern resolution and quicker imaging, dogs have become potential television viewers.

This has not gone unrecognised in the USA, for example, where hopeful TV producers have started special TV channels for dogs.

If you have other pets, however, you need to think twice before placing them in front of the TV.

Birds need at least 100 frames per second to see TV images as a moving picture. Having a bird in the same room as a TV with a lower frame rate than that will be very stressful for the creature."

publications - How do I overcome fear of rejection when writing academic papers?

I don't know how to put it. I have never published before. Previously my one paper was rejected, that was because the experiments were not ready and my advisor asked me to still submit it just to have practice.

Now, 6 months later, I am writing another paper (on a similar topic). I have done some experiments, some are still going on. My advisor had advised me that "even if your experiments are not complete you should still start writing the paper".

But I'm doing a lot of procrastination and I think I am scared of writing and possible rejection. I have done a lot of writing in other forms before, like blogging etc. But the thought of writing an academic paper with all the stringent rules (everything has to be clearly written, cited, nice flow of thoughts) is scary.

Please let me know how should one's mindset be while in the process of writing a paper.

Answer

There are two points in your question: writing a good paper and the fear of being rejected. For the first point, there is no miracle recipe, although there are some clear guidelines of what is expected to be in a paper. You can find many useful resources on the Internet on "how to write an academic paper", and you will have to select what suits you the best. In general, a good way is to understand what you like in your favorite papers, and reproduce the same scheme.

As for the fear of rejection, well, it's a bit cliché, but you just have to get over it. People get papers rejected all the time, even the top professors, sometimes it is fair, sometimes it is not. If you plan to pursue in the academic world, you should expect to get papers rejected until you retire. It's normal not to like it, but somehow, you have to deal with it.

Most of the time, when a piece of work reaches a good level of maturity, I build a quick "submission tree", that is, I look at which conferences I could submit the work, and the overlap between the notification dates and the submission dates. At the end, I have something like: I could submit to Conf1, and if it's rejected, I have one week to make it better and to submit to Conf2, and if it's rejected, ..., or I could submit to Conf3, and if it's rejected, I have two weeks to work more and submit to Conf4, etc. So, basically, the possibility of rejection is directly included in the submission strategy.

university - Academic salaries at European universities

Is there a good source to compare academic salaries at European universities? For example, what are the salaries of full professors in different countries?

I would particularly welcome a possible source, a link pointing to a page where this information is available.

Answer

I think this page has what you are looking for. As far as I can tell (e.g. for France) the numbers are fine.

However, we should keep in mind that the comparison can be made difficult. For instance, "full professor" is not an actual rank in french academia. You are either a "maitre de conférences" (roughly equivalent to assistant prof. position to "junior" associate prof.), then "professeur des universités" (roughly from more senior associate prof. to full prof.).

graduate school - How undergraduate research area affects Ph.D. admission chances?

I would like to do a Ph.D. in CS and I will start doing research as an undergraduate student soon, and I will be applying next year (December 2014) at good (say top 15) US universities. My problem is that I have interest in many areas and I don't know which one to choose. At first, I thought that would like to do research in Machine Learning, but then I realized that there are many undergraduate students doing research in that area so it will be more difficult for me to get in a good school by having research experience at that area, as I am not coming from a highly ranked program.

In addition I am an international student, currently studying Computer Engineering and not Computer Science and this may affect my application as well. So I am thinking about doing research in another area that may be a little less competitive and choose my field of interest (it may be the same) after I got into graduate school.

So my question is:

• Will it be better to choose something that is less competitive (that still interests me) as a research area for my undergraduate thesis?

stem cells - Could fingerprints potentially be changed using a gene gun?

Not to confuse with your "DNA fingerprint" I've read surgery is readily used to not just remove but even to change people's prints through employing very small grafts between opposing hands.

About 5 years ago a Chinese group identified SMARCAD1 as a key player in the development of fingerprints. this was discovered by generating gene expression profiles of people with a very rare condition called adermatoglyphia. These people have no finger prints.

A gene gun, which uses micropartical bombardment is a technique that propels microscopic particles of heavy metals, coated with the gene of interest, "deep" into tissues.

If you were to alter the genetics of the epidermal stem cells, you could potentially permanently change the tissue that arises from those stem cells. Could this in principle work if over expression of SMARCAD1 resulted in remodeling of the prints or has other more important genes been shown since to be involved?

Do any model organisms have fingerprints, or a version thereof?

I know I'm fishing here, lots of questions. I thought it was an interesting topic and wanted to see what people here had to say.

graduate admissions - Doing MS in CS from low ranked university versus applying again next year?

I have done my undergrad in electronics from India and want to do a masters in computer science. My initial goal was to do it from a good university but I got rejected from all the ones that I applied to, even though I have very good GRE scores but an average GPA (68% approx = 3.1) with no industry experience. I got acceptance from a university in TX that has no rank published on usnews rankings.

Should I accept going to low/no rank university now or should I try again next year?

Secondly, is it okay to request the university to defer the admission for a year so that I can apply for better universities next year? I think it's highly unlikely that the university will hold the spot for me for an year but still asking to get some advice. Thanks in advance for helping me on this.

Answer

Please don't rely only on a ranking to figure out if a particular university is the right place for you. Here is what you can look at instead:

• 
  
  

  course offerings at the candidate university

  
  


• 
  

  schedule of classes for next fall and spring -- this is important, because some institutions list mouth-watering courses which are almost never offered in practice

  
  


• 
  

  faculty profiles

  
  


• 
  

  faculty publications

  
  
  


• 
  

  opportunities for student research projects and collaboration with industry

  
  


• 
  

  the institution's commitment to assisting students with their job search

  
  


• 
  

  their calendar of events to see what sort of seminar talks and cultural events take place there

  
  



• 
  

  their list of student clubs, to see if you will find like-minded souls there

  
  

citations - Does anyone still care about the name and address of a publisher?

As a follow up question to my previous one, under which circumstances is it reasonable to include the name and/or the address of a publisher in a citation?

In my opinion the most important characteristic of a citation is that it uniquely identifies a given publication and makes it as easy as possible to access it. This, however, is usually already given by title, authors and, if applicable, the title of the collection (proceedings, journal...). If available, a DOI alone would be sufficient for that.

As secondary feature, further details provide more information about the properties of a publication without the need to look them up explicitly. For example, the year is usually very interesting to assess the timeliness of the related work.

Neither the name nor the address of the publisher seems to fall in one of these categories, even though it might be reasonable for example for some exotic books that are otherwise hard to find*. For this reason I usually omit the publisher's name and address in citations, partly to keep them brief, partly since I am not aware who the publisher actually is, partly because others in my area of research (CS) do the same, partly because I am too lazy to put work into something that seems superfluous to me. Sometimes, however, the publishers and their addresses are added during copy editing, so there seem to be at least some people with a different opinion than me.

• Is it considered bad academic practice to omit the publisher and the address?


• What are other advantages or disadvantages?


• Does it depend on the type of the cited publication? Books might be different from articles in journals or conference proceedings.


• Does it depend on the type of the publication I write? In a short paper, brevity might be more important than in a PhD thesis where accuracy is essential. What about a publication list in a CV?


• Does it depend on the area of research? Maybe we computer scientists are just lazy?

_{*Maybe someone wants to drive to Heidelberg to ring the bell at the Springer office just to be told that it a given publication was actually published by SpringerOpen in London...}

Answer

It's always important to know the venue for a scientific publication, not just in case you have to track it down, but also in order to understand what sort of review or other vetting process (if any) the publication will have gone through.

For a conference or a journal article, that's the name of the conference or the journal. Thus, I wouldn't typically bother including the publisher---although many such effectively include the publisher in their title (e.g., IEEE Signal Processing, ACS Nano, Nature Methods).

For a book, however, the publisher is the venue, as they decide what merits publication and how to try to ensure validity. Knowing that a book is published by the Oxford University Press means something, just like knowing that a conference is sponsored by the IEEE. It's not a guarantee of correctness any more than journal peer review, but it does imply some basic degree of quality control.

As for address: while it might theoretically be useful for disambiguation, these days most large publishing organizations have multiple sites and are really anchored by their online location rather than their physical location. Thus, I find address completely useless in a citation of recent work and will omit it unless forced by a publisher.

Finally, note that all of this does change if you're talking about works that are not accessible electronically (e.g., much of the literature before the 1970s or so), for which as many hints as possible are useful if one must track it down.

career path - How long before PhD graduation should I start applying for post-doc positions?

My earliest PhD graduation date is 10 months away. Funding permits me to stay 1–3 months longer, so the final date is still uncertain.

It is never too early to make contacts for possible post-docs. But how long in advance is too early to formally apply to post-doc job openings or funding opportunities? Depending on the bureaucracy, the path from applying to starting can probably be anything from a week up to a year — someone I know is applying with ESA which had the opening advertised in August, application deadline in October, will have interviews in December/January, and the commencement of work only in September, 13 months after the initial job advertisement. My personal guess is that the long time between interviews and starting is to create a level playing field between those who do and those who don't need to go through a visa application procedure.

If I'm too early in applying for a post-doc, a hosting institution might prefer someone who can start earlier and where the graduation date is more certain. For example, in my case the graduation date is still uncertain, so there is a risk in accepting even if they are willing to wait. Project funding might also require the money to be spent rather soon.

If I wait too long, there might be a considerable period where I'm between jobs. Having a long (>6 months) period between jobs is a disadvantage for me. Maybe it's also a disadvantage for a hosting institution (I'm not sure).

How do I find the balance? For example, considering the duration of funding and visa applications, does it make sense to apply e.g. 8 months in advance? Or is it in any case virtually inevitable to have at least several months before my PhD graduation and the start of a post-doc?

Answer

It depends on the type of funding associated with the postdoc position:

1) If the funding is already there and has a limited duration (for instance a one-year funding within a one-year research project), then indeed, the recruiter might not want to wait 10 months for you, since it would mean that an important part of the funding might be "wasted".

2) If the funding is already there, but can be used later on (for instance a one-year funding within a five-year research project), then it could be possible to start only in 10 months.

3) If there is no funding yet, and you need to get it yourself, then you have to start as early as possible, since it can take a long time for the whole process to finish.

Note that case 3 is usually a process you started with a potential advisor, rather than answer to a particular announcement. In any case, it's always a good thing to informally contact potential advisors directly to see about the specificity of a particular position.

copyright - Chapter in printed thesis vs. journal article

My computer science PhD thesis contains a chapter which is heavily based on an already published conference paper. I have published my thesis online, and fulfilled the requirements for my degree this way.

Nevertheless it is customary in my group to also publish the thesis as a proper book, to get shiny printed copies and to make it available to libraries etc.

Now I was invited to submit an extended version of my conference article to a journal, and since the thesis chapter was already an extended version of the conference article, I used material from there and the journal paper turned out to be very similar to the thesis chapter.

Will the journal publisher (Elsevier) likely accept a paper that has significant overlap with a chapter in a book that is not peer-reviewed, but (by then) is commercially published?

(This question is about copyright and publishing, not about citations and giving proper attribution to the other work.)

Answer

(Note: This answer doesn't apply to hard-copy theses provided to your university library as part of your degree requirements. These count as theses for the paragraph on exceptions.)

You're dealing with two separate issues here. The scholarly ethics of duplicate publication and the copyright issues. Let's tackle them one by one.

Scholarly Ethics

Most academic journals will not consider for publication work that his previously been published elsewhere (or is being considered for publication elsewhere); furthermore, the submitting author will usually be required to explicitly confirm that the work is not published (nor being considered for publication) during submission. This is known as the Ingelfinger rule. Subject to a few exceptions, discussed momentarily, the mode of publication doesn't matter: peer-reviewed paper, conference proceeding, book/book chapter, newspaper article, blog post, vanity publisher or predatory journal, it's been published. This doesn't simply apply to the manuscript, it applies to the work (So you can't rewrite the same analysis of the same data and claim the rule doesn't apply). You can read the reasons for (and against) this on Wikipedia.

Now, as I mentioned, there are some widespread exceptions, principally for things that happen in the normal course of academia. So inclusion in a thesis, even one that is made available online, is not usually considered publishing; similarly for conference presentations where no proceedings paper has been published. Expansion of communications into full papers is typically allowed. Increasingly, the use of pre-print servers is becoming permitted. Some journals/fields will permit submission of journal articles that heavily expand a conference proceeding, but in other fields this is a no-no.

Specific policies are set by individual journals/publishers. For example, Nature, Science and Elsevier.*

This means, when publishing, you should publish the peer-reviewed academic version first, then, subject to copyright, you can publish your book.

Minor consideration: (self) plagiarism. You should always reference the first publication of your work in any later re-publication, to avoid accusations of plagiarism (with a possible exception for publications derived from PhD theses). So even if a publisher allowed you to submit a journal article after you published your book, you would still have to cite your book.

*Interestingly, I did once inform Elsevier that a paper in one of their journals seemed to have been previously published elsewhere, and got ignored.

Copyright

Your options for republishing the paper as a book will vary depending on the copyright status of your publication. Here are some possible scenarios (not all will be available with all journals):

• 
  
  

  Open access publication that leaves copyright with the authors

  
  
  
  
  • You can do what you want to republish the article, including republishing it as-is, since you hold the copyright
  
  
  • You probably can't reuse the publisher PDFs for republication, as they will probably have trademarked logos on them
  
  
  • You will need to appropriately reference your original paper to avoid self-plagiarism
  
  
  
  


• 
  

  Open access publication that leaves copyright with the journal

  
  
  
  
  
  • You may be able to republish the paper under the open access license. This will depend on the license chosen by you/the journal.
  
  
  • You will need to consider whether there are clauses restricting things such as commercial use and the preparation of derivative works
  
  
  • You may find the license too restrictive, in which case proceed as for a non-open-access publication
  
  
  
  


• 
  

  Publication is not open access, copyright is with the journal

  
  
  
  
  • You cannot reuse the article without permission from the journal
  
  
  • You could try contacting the publisher, or using the Copyright Clearance Center to obtain permission
  
  
  
  • Otherwise, you will need to ensure that your book is different enough from the publication that it is not an infringement of copyright
  
  
  • Typically, this would require completely rewriting it from scratch (not merely paraphrasing), ideally restructuring it and re-drawing all the figures (trying to make them as different as reasonably possible from the journal version)
  
  
  • You may be able to obtain permission for specific components of the paper (e.g. figures) individually via the Copyright Clearance Center. In that case, you could use them as is, with appropriate acknowledgements
  
  
  • Academic ethics still dictates that you cite that your source is your original paper
  
  
  
  

Summary

Publish the paper first, then the book. You state that the book is merely "customary" - it can wait. Consider the copyright issues before publishing the book - this may mean you have to either seek permission from your publisher or modify your thesis chapter, if it is too close to the published paper. Protect yourself against allegations of self-plagiarism - ensure that your paper is very clearly listed as a source in your book.

postdocs - Criteria of experience recognition for "TV-L 13" position

I know that the topic of stufe for "TV-L 13" contracts in German universities has been discussed several times, but I was not able to find the answer to my question. I am offered a post-doc position with salary level "TV-L 13". I have a 3 year PhD and 3.5 year research experience. However, the administration wants to put me on stufe 1. They argue that although my experience is relevant for the current position, the type of contracts that I had are not suitable. Is TVL experience really dependent on the type of contract rather than the actual tasks performed? Also if you managed to successfully argue for inclusion of you PhD as experience, how did you argue for that?

I understand that they base it on the following document (I used google translator so only roughly understand that point):

Liegen die im Weiteren erläuterten Merkmale vor, findet zwingend eine Anrechnung statt: Berufliche Erfahrungen setzen das Bestehen eines Arbeitsverhältnisses voraus (im Umfang von mind. 25 v.H. einer Vollbeschäftigung). Ausbildungszeiten, Volontariate, Praktika (mit Ausnahme eines Anerkennungspraktikums i.S. des Tarifvertrages), Stipendien, Werkverträge, freie Dienstvertrags- oder sonstige Vertragsverhältnisse können nicht als berufliche Erfahrungen angerechnet werden. Eine einschlägige Berufserfahrung liegt nur vor, wenn die frühere, prägende Tätigkeit im Wesentlichen unverändert fortgesetzt wird. Ausreichend kann auch eine gleiche oder gleichartige Tätigkeit sein, sofern sie in der Wertigkeit der jetzigen Eingruppierung entspricht. Maßgeblich ist das für die frühere Tätigkeit nötige Wissen und Können und die dort erworbenen Kenntnisse und Erfahrungen als prägende Elemente auch für die neue Tätigkeit. Beide Tätigkeiten (konkrete Aufgabenstellung) müssen nach Aufgabenzuschnitt und Niveau gleichartig sein. Liegen die vorgenannten Voraussetzungen vor, ist des Weiteren nach der "Herkunft" der beruflichen Vorerfahrung zu differenzieren - Zeiten bei anderen Arbeitgebern dürfen auf dieser Ebene grds. nur bis zur Stufe 3 (!) angerechnet werden. Die nicht zwingend anzurechnenden Zeiten können aber als förderliche Zeiten anerkannt werden, dazu s. u.. Zu den vorgenannten Tatbestandsmerkmalen ist die Sonderregelung im Hochschulbereich zu beachten: Zeiten mit einschlägiger Berufserfahrung an Hochschulen oder außeruniversitären Forschungseinrichtungen werden bei Beschäftigten der Entgeltgruppen 13 bis 15 grundsätzlich anerkannt; bei Beschäftigten der Entgeltgruppen 9 bis 12 dann, wenn sie im Rahmen der Planung, Vorbereitung, Durchführung, Aus- und / oder Bewertung von wissenschaftlichen Vorhaben einen wesentlichen Beitrag leisten.

ethics - Attributing Second-order Citations

Imagine that a paper by [Author A] has pulled together some literature on the misuse of a technology in context X. I now want to talk about misuse of the same technology but in context Y. When creating a different narrative and putting together different arguments, much of what I say uses the references of [Author A] with a similar or the same opinion.

Take the following made-up quote from (Author A):

Technologies have values embedded in their design (Author B).

I think it would be wrong to only directly cite [Author B] and make a similar statement without acknowledging [Author A] since the idea really comes from the way that the latter uses the former. Also, it would just feel wrong since someone else has done a lot of the work in finding the references.

This occurs many times and so it would also be obvious how I found the sources (of course, I will state in the background section that I did a backward search to find sources). At the same time, my analysis is different and hence I cannot just say "read [Author A] for a literature review]" - I need to connect it all to my topic (and also other areas not covered by [Author A].

What is the correct and, if allowed, most elegant way to handle second-order citations? Particularly when I need to do it many times. Is there an alternative to using second-order citations?

N.b., this isn't a meta-survey like you would find in medical science or similar.

Answer

There are two simple ways to deal with this, and you can choose the one you prefer.

1. 
   

   Describe in the introduction how you found the two papers and cite them both. Choose the one you prefer and mention that you will be citing this paper only. Which one you prefer is up to you: maybe you choose one because of its better writing style, because it is the first one, or because it is the second one and it refers to the first one, allowing readers to find both. Then cite the single paper.

   
   


2. 
   

   Describe in the introduction how you found the two papers and cite them both. Cite both papers every time (why not?). For example: "Technologies have values embedded in their design [1, 2]."

   
   

There are no rules about what is the best way, but you should always consider the point of view of the reader of your paper: what would you like to see when you read the paper? Personally, I have a slight preference for (2) because it will allow me to quickly find both papers, even if I decide to read, say, only the results section of your paper.

Finally, you can avoid citing the paper "many times" by re-structuring the text in your article: it should normally not be necessary to cite the same paper more than once in the same section, so you will have to cite them only 3-4 times (introduction, methods, discussion).

phd - How can I find out if someone really holds a doctoral degree?

We're currently interviewing candidates at my company and I'd like to verify if some of them really have the academic degrees they claim. One in particular claims a doctoral degree from a German university.

I've contacted the university, and the dean wrote back saying that they could not provide this information without the written consent of the individual.

I found this policy rather odd; I would have thought that the granting of a doctoral degree was public information. Is this normal? Is there anything else I can do to find out?

I obtained from the library a copy of the thesis in question but it was in German. I also found through Google a spreadsheet which appears to be a list of dissertations published by that university, but it is unclear whether these are doctoral dissertations or not. The person in question and his dissertation are in that list.

Answer

When you get an academic degree from a German university, you usually get two official certificates. One (labeled Urkunde) is official proof that you hold the degree but does not include a grade. The other (labeled Zeugnis) is official proof of your grade but (according to some bureaucrats, though I suspect they just like to make life difficult) not of the degree. I think for doctoral degrees it is common that these two documents are combined into one, which is then also labeled Urkunde, or in this case Promotionsurkunde, but includes the grade. The grade for doctoral degrees is still often in Latin, in which case the best grade is typically summa cum laude, followed by magna cum laude.

A normal practice to make sure applicants actually hold the degrees they claim to hold is to ask for photocopies of their degree certificates along with the application. This timing makes it less awkward to ask for proof. Also, faking a certificate, even if it's only a fake photocopy, is a more serious offence than just lying about a degree, and at that point the reward of this more serious fraud isn't even certain yet. It is also possible to ask for a certified photocopy. I am not sure why this is done; maybe it repels a few more liars.

German universities are in fact not allowed to hand out any data about their faculty and (former) students. I would consider the spreadsheet linked above a weak form of corroboration. Weak because it looks more like someone's personal effort than an official list. (Even two dissertation titles are missing.)

Of course, technically even an authentic doctoral certificate is not proof that the holder of the certificate really holds the degree. There might have been a subsequent revocation for plagiarism.

One factor that may lead to even competent people committing fraud is the requirement of thesis publication. Once all other requirements have been satisfied, people usually get a warning that they are not allowed to use their degree before publication of the dissertation. As far as I know this is done quite consistently because even with the warning it does happen occasionally. Of course this is less of an issue nowadays, as the publication is often done electronically.

(I earlier wrote that standard practice was to hand out the certificate before publication. Some people protested, and I must agree that what I wrote was obviously wrong. It doesn't make sense for universities to hand out proof of something that is not true yet, and they don't do it. Sorry.)

population dynamics - What is the percentage of people living in England in 1500 AD whose lineage is still alive?

This sounds a bit random, but it stems from a lecture in statistical genetics which I attended a while ago. We were shown a population lineage graph from which it was clear that most lineages eventually go extinct. The further you go in to the past, the smaller the percentage of the individuals living at that time whose lineage is still alive today. This probably makes sense in the context of evolution.

So I am curious about the speed of that process in human populations. I am aware that this speed, quite possibly, varies over time and geographically. Are there any estimates about that speed in European populations? To be more specific, I would take England at 1500 AD as a starting point. What is the percentage of the people living in England at that time whose lineage still exists?

EDIT

I am very grateful to @Richard Erickson for the reference to the Galton-Watson process. It is really fascinating that +70% of all known Chinese family names have become extinct. It would be really interesting to know more about the speed of the process of extinction - in particular in European populations.

publications - Access to scientific articles that cite mine after leaving academia

I used to work in academia. I was lucky enough to publish important papers in peer reviewed journals that now regularly get cited by other papers in peer reviewed journals. I have left academia to work in the private sector, so every time I get a notification that my work has been cited elsewhere in a non open access journal, I can't even see how it was used. I should be able to ensure my work isn't mis-quoted or wrongly interpreted, but I can't without paying extensive fees for each and every article...

Is sci-hub my only non-option because I refuse to use illegal means?

Requesting a copy of the PhD thesis from an author?

I think that many unpublished theses are available in libraries etc and reading relevant theses is a normal part of research and does not involve asking the author's permission. But suppose a humanities PhD student has seen a thesis title (2008, so presumably in electronic format), that is relevant to their PhD subject and they want to read the thesis but unlike most theses it is not available in the student's libraries or online etc, probably due to the author's geographical location. The author is now a lecturer with a page on the university website. Should the student just email the author and say "Hello I am a PhD student in your field, can I please see your thesis?" Is this a big deal? Are there any do's or don'ts in making this request?

Thank you...

What systems are most effective for monitoring student attendance?

I work in the Computing and Mathematics School at my university (UK). This year the School has adopted a fairly aggressive policy regarding student attendance. If a student has a poor – or zero – attendance rate, the student is contacted and a dialogue opened. This has many benefits including identifying those students who have possible undiscovered or undeclared learning difficulties.

If a student’s attendance rate remains poor following a first intervention, a process of issuing formal warnings commences, culminating with the withdrawal of the student if the student does not start to engage with their course.

Attendance is presently monitored at all laboratory and tutorial sessions. Attendance is not presently monitored for lectures.

Our current system comprises a series of shared Google spreadsheets which contains the details of all students for all classes. Staff members enter attendance manually into the spreadsheet for their class.

The difficulty with this system is that there is presently no automatic link between the existing official university student record database and the attendance register spreadsheets. This means if students change groups, enrol late, withdraw, change course or units, all this information must be dealt with in a robust manner. Currently, such changes are implemented manually. This means errors are likely to be introduced into the attendance register.

I notice that there are a number of commercial attendance monitoring solutions available which are based on hardware, e.g. Telepen. I would be interested in anyone’s experience with such systems, however I don’t forsee these to be ultimately workable in my case owing to the large cost.

I am interested in software solutions. If your institution monitors student attendance, do you use any specialist software? If so, what do you use?

Another option – a preferable one – is to work within the existing university data systems. All the necessary information regarding student details and activities is available. The problem arises when we try to ensure our ad hoc attendance register contains up to date student information. Ideally we’d use our Virtual Learning Environment to enter attendance data. Our VLE is Moodle. Are there any Moodle users out there who use Moodle to record attendance?

Answer

Following eykanal's comment to the question, I have researched the possibilities via Moodle. For the record I have found that Moodle has an attendance module. I haven't learnt yet whether this module has the complete functionality that we require, but it's a start.

Moodle attendance module

research process - How to deal with my results being stolen?

I have experienced a couple of times the following problem: I have asked another researcher to cooperate and provided mathematical results (as a basis for an algorithm). The cooperation has not proceeded as fast as expected and the other party has taken my results and integrated them into a work that he has published with other people. There are two questions:

1. 
   

   How to initiate cooperation with new people and still avoid this problem? The mathematical properties are central in our research. New algorithms cannot be created, unless we first invent some clever properties that prune the search space (so, the properties are the heart of the algorithm, the rest is usually straight-forward). So, they have to be invented first and this inventing happens to be my speciality. Unfortunately, it is easy to proceed without me, when I have done this difficult part. So, I don't know whom and when I could give the results. They should be shared pretty soon, since we should all be able to ponder together how to integrate the new properties in the algorithm. Sometimes we may also find that they are not useful or strong enough and new results are needed, so ideally this invention-brainstorming process would be iterative.

   
   


2. 
   

   How should I refer to my own results, if others have published them first? Should I still give a reference to their publication, when I use them for something new? This is now an important question since I have invented a new use for one of my previous results. (Naturally, I don't like the idea I should refer to somebody else for my own invention.)

   
   
   

I would also like to understand the behaviour of those other researchers. I have a few hypotheses:

• It's possible they underestimate the invention work, because I usually present only the final results as nice compact proofs + explanation what the result means in practice. In reality, deriving the results may easily take 100 hours or more - proving by trial and error, guided by intuition and earlier results.


• I have been only a post-doc, when this happened, so I had no authority. They may think it is easier to get a paper published if it is written with some better known researchers.


• These people have been from other countries and had a different mother tongue than me, while they have published the results with people who were either geographically close (even the same research group) or spoke the same language they did. So maybe the question is about easy communication and cooperation?


• The original research had suffered from delays, like rejected project application. It would have continued but not in the original schedule (from my part). So maybe they wanted to get things published faster or even assumed I won't get any funding for future research.

What do you think is the explanation? Understanding the reasons would help to avoid the problem in future.

career path - Sign of researcher's professional maturity

When one applies for an academic position (especially for a permanent one) or for a significant funding, (s)he is often asked to show his/her professional maturity in research in the motivation letter/research proposal (or sometimes one is asked to indicate how (s)he would reach this maturity).

The questions is: what are the signs of professional maturity in research that might be mentioned?

My background is theoretical mathematics but the question has little to do with a particular field as usually the positions and funding in question are for researchers from a broad range of scientific areas.

Answer

Signs of professional maturity in a researcher:

• Having written and administered a grant proposal


• Having been invited to sit on a review panel


• Having been an invited speaker


• Having guided or mentored students


• Having organized a conference session



• Having published a review paper

phd - What types of questions should I ask in a cold-email to a professor?

I'm applying to a PhD program in computer science. My friends and advisors all recommend that I cold-email the professors I'm most interested in working with and have a conversation with them about their research. However, I feel like just asking something like "What type of research do you do?" would just come off as lazy since most professors already have information on their website.

So that leads me to wonder, what are some productive questions that I could actually ask professors in the context of a cold-email or scheduled phone call?

Answer

However, I feel like just asking something like "What type of research do you do?" would just come off as lazy since most professors already have information on their website.

Yes, don't ask anything you could reasonably learn from their web site, their publications, textbooks in this area, web searches, or Q&A sites. It's incredibly annoying when people write to ask me to put work into explaining something to them, when they show no sign of having put any work into this themselves first. (The worst question of all is "how can I apply to your department?", since that one can be answered in a few minutes by anyone with internet access.)

Also, don't volunteer your services for the professor's projects or propose a collaboration in a cold e-mail. This might be appropriate later, after you have established a serious research connection, but until that point it's awkward. Nobody is going to say yes based on very limited information, and the choice of no vs. maybe puts people in a difficult position: if they say no based on very limited information, it may come across as insulting, while if they say maybe it can come across as overly encouraging.

So that leads me to wonder, what are some productive questions that I could actually ask professors in the context of a cold-email or scheduled phone call?

From my perspective, the only really productive approach is to engage seriously with the professor's research area. If you can propose new ideas or questions and start a conversation with genuine intellectual content, then that's great. It will be a worthwhile discussion for both of you, regardless of whether it helps you get admitted, and you may end up impressing the professor. But this is a high bar, and you shouldn't expect to be able to send substantive messages to many people. If you can't think of anything genuinely interesting to say, then it's better not to say anything at this stage (you can think a little more about this area before e-mailing the professor).

The focus should be on the subject matter. When random strangers write to me, I'm not particularly interested in telling them about myself (to the extent I want to tell the world about myself, it's far more efficient to do so publicly, rather than telling one person at a time). I'm even less interested in hearing an infinite series of random people tell me about themselves. Most of them want to be admitted to grad school in my department but aren't going to be, and it's just not a good use of time to read a lot of e-mails in which applicants tell me more or less the same things they are going to say in their actual applications. On the other hand, I'm always pleased when I get an e-mail that starts a genuinely interesting research discussion.

publications - What are pre-print repositories for math and physics alternative to ArXiv?

Are there other widely used academic pre-print repositories other than ArXiv? My interest is especially towards mathematics and physics.

If possible, one characteristic that I'd like to find in other pre-print repositories is the possibility to update the paper without leaving the older versions online and a better organized "author page" (and, as a note, I personally don't like Research Gate or Academia.edu, which also, as far as I understand, shouldn't be considered pre-print repositories).

Answer

In mathematics and physics arXiv is by far the most used and reputable.

Of course, there are thousands other ways to self-archive your paper using not dedicated solutions (like personal website, GitHub, etc) and some general (like FigShare).

Yet, when it comes to pre-print services, they only one I am aware of is http://vixra.org/. It has policy of accepting everything; however, it has reputation of crackpotism (as arXiv is popular and editors rarely reject from it, so for the majority if researchers there is no reason to choose viXra (unless as a protest or something)).

conference - What do I need to ensure my presentation will go smoothly?

From a technical stand point, what do I need to show up to a conference with (in general) to ensure that my presentation will go smoothly?

Two things I can think of:

• Presentation remote


• Equipment to connect my laptop to the projector

The remote is simple enough, it just needs to work with my computer and be reliable. Connecting my computer to the projector is not trivial since a lot of laptops don't come with DVI or VGA output any more (mine doesn't!). What kind of output do I usually need, DVI or VGA? Do I need something like this which supports all output methods (seems like over kill but might be a good investment)?

Is there anything else to make sure I am prepared to deal with the technical aspects of a presentation?

Answer

From less esoteric to more (I've seen all these things happen):

1. Make sure you know how to "send the image to a projector". Not all laptops do this automatically, and I'm surprised at how many people don't know how to do it. I've also seen people be confused by the mirroring feature on Macs.


2. Verify that there's a power outlet or some place to plug in your laptop. Driving a projector eats power, and you don't want to drain your battery during the presentation


3. Turn off screen savers. at the very least it's annoying, and sometimes the screen saver does wonky things to the projector display.


4. Turn off your notifications (mail, facebook, twitter, skype...). It's amusing for an audience (but not for you) if during a job talk they all get to see a subject header of the form "Interview at University X" where X is not where you're at :)


5. Make sure you have the right display converters. Usually something that converts your laptop to a VGA is standard. Macs are particularly difficult in this regard.



6. Watch out for resolution issues. Most laptops are smart enough to drop resolution to deal with a projector, but sometimes they're not.


7. Keep a backup copy of the slides in a portable format (PDF or PPT) on a usb stick. In the worst-case you can always borrow a laptop (from the previous speaker even) and load up the slides. Dropbox/a web page is ok but not great because it requires an internet connection.

And above all, as David M. R. says, check the setup beforehand if you can. Even that doesn't guarantee a smooth presentation, but it eliminates a lot of the potential problems listed above.

funding - Is there a financial benefit for PhD student to join a funded research project

I'm a first year PhD in Computer Science at a UK university. Recently, my supervisor has asked me to join a funded research project consisting of other post-docs and lecturers, i.e. I'll be the only PhD student in that project. My supervisor believes that it will be helpful for me to join since my research topic and a project's theme have many similarities, which I also agree. However, he doesn't mention anything about if I get paid to work in that project. So, I wonder if it is normal for a PhD student to work in a funded research project without getting paid.

Answer

I'm not in the U.K., but in my part of the world, it's common (one might say usual) for computer science PhD students to be paid. Is the determination of whether a PhD student is paid related to whether the project is funded? Not necessarily.

When is it appropriate to ask about payment?

Should you talk to your supervisor about this? Instead of asking

Is it normal to not be paid?

ask yourself

Is it unusual to be paid?

In any scenario in which is is not unusual to be paid, it is neither inappropriate nor offensive to (politely) ask whether you can be paid for work you are doing.* In your case, it is definitely appropriate. So, go ahead and talk to your supervisor about this.

_{* Here is an example of a scenario where it is not usual to be paid, and it was therefore inappropriate to ask for payment. As you can see, it's an extreme example :)}

biochemistry - enzymes that stabilize DNA loops

As a follow-up of a previous question, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops.

I have read that cohesin is one of such enzymes, but works as a transcription factor by binding specific DNA motifs.

My interest is in knowing what other enzymes will create DNA loops with no DNA motif biases from a DNA extraction.

This is a follow-up question to this one, as ultimately I would like to know if there could be any ways of optimizing the process of DNA circularization of very long stretches of human (or mammalian) double-stranded DNA, from several kilobases to megabases, by first creating stable DNA loops that leave two DNA ends close by for a more effective ligation process.

Any ideas?

neuroscience - What in neurons and their connections changes during the process of learning?

I'm not sure if this question belongs more in physics or biology (or maybe even computer science)... but biology seemed to fit more.

What changes in the state of our brains when we learn things? Because I looked on the internet and I learned about artificial neural networks, and every resource I've found teaches of neural networks that have weights that are trained/evolved and then are static at runtime; you simply train the weights and then once you use them in simulations, they never change.

Purely feedforward neural networks that rely on this can't react to new situations differently if they've experienced it before. They react exactly the same each time.

I suppose that theoretically, a recurrent neural network that was big enough could really learn, but in practice, these have been used as purely memory slots for an existing method defined by the weights, not as storage of new methods of doing things.

So my question is, physically, chemically, biologically, what changes in the neurons and the connections between them when we learn things? I don't think we really understand how it comes together on a grand scale yet, but I'm pretty sure we've figured out that much. I want to learn how to model a simplified version of it mathematically/programmatically.

Answer

What changes in the process of learning:

1. 
   

   The connections (the way one neuron is connected to another). New synapses can form or dissolve in the process of learning. The glial cells such as astrocytes and microglia can facilitate this process.

   
   


2. 
   
   

   Strength of connections: Existing connections can be made weaker or stronger in the process of triggering the same circuit. This happens by up/down regulation of the ion channels at the synaptic junctions.

   
   

This process is not fully understood and is an active area of research. You can find some mathematical models too for learning processes such as Long Term Potentiation etc.

evolution - Why don't we keep evolving until we are super-human?

Humans (homo sapiens) have been on the earth for thousands of generations, and we have kept evolving throughout that time. Why don't we just keep evolving so that, let's say, we live for an average of 300 years? Or why don't we evolve so that we don't need to sleep?

This could also apply to many other species.

publications - Can something published on arXiv or optimization-online.org be mentioned in my CV?

I was thinking about submitting one of my papers in arXiv or www.optimization-online.org and hence I was just wondering if mentioning the same in my CV would be appropriate. Is it done usually? If yes, how should I actually mention something like this in my CV? Kindly guide me (I have no previous experience in publishing papers and I'm an undergraduate student).

graduate admissions - Applying for MS in USA after completing 3 years degree in India

I have completed my Bachelor of Computer Applications (BCA) from India. The minimum requirement for admission into the MS in Computer Science program requires a 4 year college degree. My BCA degree was a 3 year degree and I am planning on pursuing a 1 year Post Graduate Diploma in Computer Applications (PGDCA) from Indira Gandhi National Open University (IGNOU) and would like to find out if these total 4 years satisfy as minimum requirements for admission consideration.

When can scientific publications have a dedication?

Under which circumstances can a scientific publication have a dedication?

It is not uncommon for theses (Bachelor, Master, PhD, ...) to have a dedication. Furthermore, some big publications in high impact journals happen to have a dedication.

However, what about regular journals? Can I include a dedication in the 'Average Journal of okay results'? It is assumed that I will not have a top journal hit publication in the near future. Would such a request be turned down immediately?

biochemistry - How many RNA-binding proteins can simultaneously bind on a single mRNA?

Typically, how many RNA-binding proteins can simultaneously bind to a single mRNA? Or said differently, how many "binding sites" does an mRNA have? What order of magnitude?

I am interested in RNA granules like stress granules or P-bodies. They contain, inter alia, mRNA and RNA-binding proteins. I am not a biologist and I didn't come across this information so far in the related literature.

Answer

See this paper. They have studied RBP-protected sites in the entire human transcriptome by RNA-protein crosslinking followed by RNAse digestion and sequencing: PIPseq.

Figure 1 of the paper shows distribution of protein protected sites in RNAs. They also correlate it with different regions of mRNA and its expression.

They show number of protein protected sites (PPS) per transcript but that is not a proper metric in my opinion. The number should be normalized with transcript length so that you get density of protected sites. From figure 4 (see below) you can roughly estimate that average PPS density is close to 0.6 which means that 60% of any RNA is expected to be protein bound.

                

Figure 4

Other points to be noted:

• Highly translated mRNAs will have multiple ribosomes on their CDS and are likely to be more protected.


• Sequestered RNAs in stress granules will also have high density of PPS


• Footprint of different RBPs will be different. So number of proteins that can bind to a mRNA will differ between different RBPs.

Further reading: