ornithology - How do small birds survive the winter?

I live in a region with cold winters (ca. -40 C) and many quite small birds (sparrows, crows, ducks) stay for the winter.

How can the birds survive this?

As I understand it, smaller bodies will be less able to produce and retain heat. Despite this, birds seem to cope much better than humans, sitting in the cold all winter and even swimming in cold water. In comparison, humans lose mobility in their muscles when cold, and can suffer severe frostbite causing them to lose fingers, toes, or limbs from relatively short exposure to the same conditions.

What specific adaptations allow birds to cope so well in these conditions?

Answer

There are a variety of physiological, anatomical and behavioral adaptations that keep birds warm in winter.

For starters, birds are endothermic ("warm-blooded"), similar to mammals. You suggested that the coats humans wear are superior to feathers as insulation. Yet some of the finest coats and sleeping bags were long filled with feathers (e.g. goose down). Animals that live in cold regions tend to have smaller extremities. For example, you probably won't find many long-legged flamingos or ibises in the Arctic during the winter (though food supply is another reason they couldn't survive there).

As someone else suggested, water temperature is a relative constant, which means water (or better yet, snow) can actually insulate animals from colder temperatures.

Countercurrent heat exchange is a strategy that helps endothermic animals conserve heat. The page I linked to is part of a book titled Animal Adaptations to Cold, which includes a chapter titled "Avian [Bird] Adjustments to Cold."

reproduction - How only one follicle develops into graffian follicle?

I've studied that one out of many follicle develops into mature or graffian follicle. The fact which confuses me is that, since all follicles are in same ovary, close to each other with equal supply of nutrients. What causes the other follicles to give up the race? Why our body cannot develop mature follicle from a single one?

graduate admissions - Should I emphasize my existing PhD in my master's application?

Should the fact that I already have a PhD in another (useful) subject be downplayed on the personal statement? I'm concerned that it would make me look unfocused, but I also think I may want to emphasize it because it demonstrates prior success.

In case it's relevant, my PhD is in physics, and the Masters is in Computer Game Engineering. I am applying to a one year, full time taught Masters at a UK institution.

Answer

A person qualified in another area (such as a Phd in Physics) who wanted to learn a new topic (like computer game development) would likely be welcomed on a full-time taught masters course. Full-time taught masters courses are often designed for those who want a change in direction and have the motivation to focus for the year to achieve that goal.

There are people who want to be an astronaut, for example, who go back and learn new skills and knowledge and collect several degrees in the process.

You do have to have an interregnum in employment, as a full-time course is exactly that. A lot of daily, weekly and monthly time needs to be devoted to it to learn all that material that others will have picked up in a three year Bachelor's degree.

I teach on such a course and we have many "career change" applicants who are well qualified in other fields. It is quite normal.

Can I use images showing up in Google search for my presentation slides without violating any copyright?

I am teaching a freshman science course for the first time and I am doing also outreach activities in high schools. To be able to attract the young generation to science one has to connect the concepts with everyday applications.

So I build my power point slides using pictures from the textbooks which we officially use. Unfortunately when one does a Google search on any subject by images, one gets much more appealing and fascinating pictures. Some of these pictures are even related to simple applications which are explained in popular science sites on very recent discoveries. The problem is that I cannot use those pictures from Google sites in my slides because they are copyrighted.

What should I do then? Should I stick to the boring-looking textbook pics to avoid copyright problems, or bring life to my course by using images Google shows up (but then I might go to the jail!)?

Is there something that says one can use images shown by Google for educational purposes with no copyright issues?

professors - How widespread is sharing of slides/assignments among educators?

Often, when taking a course at the university level, I amuse myself by Googling phrases from the instructors' slides, assignments, and other materials. I have found, without exception from any instructor, that the material is more or less identical to some resource I can find online, often course materials posted by a professor at a highly prestigious university (e.g. Stanford). In some cases I will find material that is 10 - 15 years old; other times it is undated. Sometimes I can find the same material posted by a dozen different professors at a dozen different universities.

A few times in the past, I've entertained the idea of reporting the professor for possible plagiarism, but I've never followed through on it because

1. If the material is undated, there's no way to know who published it first


2. For all I know these slides and assignments can be purchased from vendors. I have occasionally had a professor use a complete course package, where the publisher of a textbook also offers the assignments and tests to accompany the textbook.


3. I have been unwilling to risk having to re-take the course, if the instructor is suddenly fired mid-semester for plagiarism

(In some cases the materials are sprinkled with enough informal language that it's obvious that they were not purchased from a vendor.)

Since it seems like all of my professors get all of their slides and assignments from somewhere else, I am curious how common it is to share course materials between instructors. Do college professors commonly purchase their lesson plans and assignments from vendors? Do instructors and universities share premade courses with each other?

publications - Is it reasonable to submit a paper to a journal that I have uploaded to the Arxiv 4 years ago?

I have a paper submitted to the Arxiv 4 years ago (with another co-author). At that time, the only reason that we put the article online was that someone asked us to do that in order to cite it. Since then it has been cited some times, including authors that claim that have found (independently) the same proof as ours. The paper is the solution of a combinatorics problem.

I have been thinking lately that it would help my career to get this paper published in a Journal, but I'm not quite sure if this is a good idea, since it is certainly not a new result (and it is not super-interesting, just a nice solution for a problem).

What should I do? Has anyone been in the same situation?

Any advice is very welcome!

PS: In case that is a good idea to get it published it would be nice to have some kind of advise of which journal might consider articles of the types I described, as I guess that lots of Journals won't even consider it.

evolution - Can two humans with 44 chromosomes produce viable offspring?

It is known that there are very few individuals having 44 chromosomes, not the usual 46 chromosomes.

One example is a male in China: the first article, the second article.

The other is a female in Turkey, unfortunately the article is in Turkish.

It is claimed in the links that they might reproduce and make healthy children if they mate. So I wonder if this already happened and such a couple is living, or if it would be theoretically possible?

Edit: As requested, here is the Karyotype of Turkish female, which the professor in the video call her HomoNeoSapiens, with Robertsonian translocation between 13 and 14 chromosomes. So, this translocation is different from Chinese Man's translocation, which is between 14 and 15 chromosomes. So in this case they can't breed a healthy children? Gosh, I was about to create a new species :((

teaching - Is "read the syllabus" a sufficient transfer of responsibility?

In my experience, most instructors spend a large portion of the first period in a term talking about the syllabus. This seems to serve to pass responsibility onto students:

• Students see the deadlines. No student can claim to not know about an assignment or deadline.


• Students see the course rules. No student can claim they did not know they were breaking a rule.

In the past, some students have tried various methods, such as skipping lessons, then claiming to not know about requirements, in an attempt to get the support of the administrators to back their case of "I didn't know".

I have lots of material to cover within the term, so do not like to waste lots of time with talking about the course and would rather get started. Is "here is the syllabus, read it" sufficient for passing responsibilities onto students? If students do not read it (many won't) is the responsibility nevertheless still passed?

ethics - Is it appropriate for a PI to appoint someone who is a family member?

I am a junior faculty in one of the top-tier research US institutions. I just joined the department and hired two GRAs meanwhile. In addition, I would like to appoint one more individual in my research group who could be appointed as a research engineer/technician. His/her role would be to support my research program and assist my GRAs on their PhD work. I am wondering whether there are any legal issues/conflict of interests if he/she is one of my family members. How will the department see this recruitment?

publications - How to discourage irrelevant self-citation?

I once reviewed a manuscript whose authors cited many of their own published papers, which were not relevant to the subject of the manuscript. This kind of practice is evidently frowned upon by the academic community. In my comments, I advised the authors to remove those references, which they did afterwards to some extent. The manuscript eventually got published, after two rounds of review.

With hindsight, did I do the right thing to discourage this practice of irrelevant self-citation, or is there anything else that I should have done?

Answer

Did I do the right thing to discourage this practice of irrelevant self-citation?

Yes. In fact, as a reviewer, you should point out irrelevant citations of any kind (self- or otherwise), and suggest that these be removed. Conversely, you should not complain about relevant and appropriate self-citations. The issue is the lack of relevance, not the self-citing.

Is there anything else that I should have done?

This is exactly what should happen: reviewers should call out this kind of thing, so the authors will have to remove the irrelevant citations before the paper is published. This anecdote is a triumph of diligent reviewing :)

Avoid spam filters when applying for academic/research internships

CASE

I am a student from India and have been looking for internships outside India. Now, a lot of Indian students apply for summer internships without serious thought. So they end up spamming professors. See: What is behind the “Indian Undergrad Research Experience”-spam? is just an example for that.

It is normal for me to assume that a lot of professors by now may have applied spam filter for undergraduates from Indian universities. These would activate as soon as I send them a mail. As a result I might miss a good opportunity. Hence, I turn to you for a possible solution.

This problem does not apply to just Indian students or Indian under graduate students rather people from other countries applying for internships(including students from masters and other degree courses).

EDIT

I understand why the question is heavily down-voted.

PROBLEM

There are students(I used to) who believe that such practices can be followed to increase a chance of getting through. I quote from the link:

Always remember to attach your CV as a Google doc link and NOT as an attachment. Why? Because usually profs receive a huge number of mails for internship applications that they make their Spam filters keeping this in account. One criteria is attachments and their size (Though not a strong one, can help if your CV is really huge, despite all the cut-downs). So a Google doc link to your CV is a good call.( Make sure you change the privacy settings for this particular document, a mistake many people have committed)

Another pointer to avoid the spam filter as much as possible : Avoid words like "internship" , "applications" and other such words in your subject. They can trigger the spam filter.

I believe that the question could be helpful for students having false assumptions.

The answers I now expect should discourage students to spam professors and suggest an alternative pathway. I could have edited the question for a more appropriate title but didn't because ultimately I feel somewhere in future, some one is bound to look for an approach/hack to spam filters. Further, I think the title is all the more apt because people basically search a related title.

Answer

Adding to the answer that aeismail has already given, thinking about this from a technology perspective is wrong. Even if your email gets through, how will a professor differentiate you from a spamming student?

A better way to go about dealing with this problem is to obtain an introduction to a potential supervisor from somebody who already knows that person, knows they might be interested in interns, and can also vouch for you as being worth their time.

funding - What is a soft-money research position?

I have read the term "soft-money research position" a few times.

E.g. Path of a postdoc.

Another consideration for interviewees is whether to pursue a "soft-money" position. A tenure-track university professor is typically paid a nine-month salary to teach one or more courses, conduct research and train graduate students. During the summer months, the professor can optionally pay his or her salary from grant money. In contrast, non-tenure-track research professors often hold soft-money positions, which require them to cover 100 percent of their salary from research grants, teaching and/or administrative responsibilities. Soft-money positions offer the advantage of few teaching responsibilities, which frees time for grant writing and conducting research, but at the expense of job security, since winning grants is a necessity. The Hutchinson Center and some other private institutions offer a compromise between these systems, covering up to half of a faculty member's salary from institutional funds, so research grants only have to cover the remainder.

Advice for stats students on the academic job market gives a clear distinction between soft and hard money:

Before listing the options I should explain the concept of hard versus soft money. Revenue in academia comes from tuition (in public schools the state kicks in some extra $), external funding (e.g. NIH grants), services (e.g. patient care), and philanthropy (endowment). The money that comes from tuition, services, and philanthropy is referred to as hard money. Every year roughly the same amount is available and the way its split among departments rarely changes. When it does, it’s because your chair has either lost or won a long hard-fought zero-sum battle. Research money comes from NIH, NSF, DoD, etc.. and one has to write grants to raise funding (which pay part or all of your salary). These days about 10% of grant applications are funded, so it is certainly not guaranteed. Although at the school level the law of large numbers kicks in, at the individual level it certainly doesn’t. Note that the break down of revenue varies widely from institution to institution. Liberal arts colleges are almost 100% hard money while research institutes are almost 100% soft money.

I'm still confused regarding the exact definition of a soft-money research position: what is the threshold soft-money : hard-money above which a position is regarded as a soft-money position?

Conversely, what is a hard-money research position? Is it any research position that is not a soft-money research position?

peer review - Will it be considered duplicate submission in a venue, if we knew that the article will be rejected for sure in another venue?

The reviewers have already commented on our article and the conference management system shows us each of their comments. Based on the comments, we know that the article will definitely be rejected. The final verdict is scheduled on 15 days from today.

We are interested in improving (based on the presently seen reviews) the manuscript and submitting it to another venue.

Will it be called duplicate submission in the new venue, if we submit now?

grading - How do teachers learn to grade?

I teach math with about two years of experience now. In general I have found that all the cliches about graduate school teaching you "how to research but not how to teach" are true. But I have also found many great resources (at my institution, online, in print, etc.) that are helping me, over time, work through my teaching deficits.

...in all things but grading.

I struggle with many grading decisions: from small things, like grading individual homework problems, all the way up to life-changing things like evaluating master's degree defenses. What I lack is a coherent philosophy of grading that might motivate my various grading policies/strategies/choices.

Interestingly, I have not found good resources for this. Yes, my institution provides a tiny bit of guidance, but it is very broad. This forum contains a hundred or so questions tagged with "grading", which is a good start, but I wonder if there are resources that provide a more cohesive treatment of the subject.

I want to hear about theories of grading. I want principles which flow naturally from the theories. I want applications and strategies which build on the principles. I want to hear different viewpoints on the issues so I can evaluate their relative strengths and weaknesses as I come to understand my own thoughts better. In short, I want it all.

Do any such resources exist? Can anyone point me in the right direction? If these don't exist, why not?

citations - Got accused of plagiarism due to a reference lost during copying my own writing

Summary

I was assigned to write an autobiography for a course and copied some sentences from a personal statement for an application. Those sentences in turn included material by somebody else, which I referenced in the application, but I failed to reference in the autobiography. Due to this I was accused of plagiarism by my professor, who I feel is making a mountain out of a molehill.

What happened

I am a mathematics PhD student. I am taking a course outside of the math department in the education department. For the first week of class we have to submit an assignment essentially showing that we're in the class for financial aid purposes and what not, creating the impression that the assignment is not necessarily for credit. My professor wanted us to write a short autobiography for this assignment. It was about 1% of the total grade.

I had previously done an intense personal statement for NSF-GRFP, a prestigious fellowship. I took one paragraph from that personal statement for this autobiography assignment and forgot a reference that I had included in the NSF-GRFP personal statement. Unfortunately, the plagiarized portion was not in quotations and just merely had a footnote in my original NSF-GRFP proposal that I mistakenly overlooked.

Thus, two sentences (out of the five paragraphs) came up flagged as plagiarism and my professor indicated that they were going to submit this to the student-conduct office. Now needless to say I'm freaking out. I understand what plagiarism is, and I understand it does not matter whether it is intentional or not, and I do not what kind of sanctions will be placed on me for this oversight. This all happened today and I'm meeting with my graduate adviser tomorrow to discuss what actions need to be taken.

What the professor and the rules say

I went to explain my situation to the professor. Before I could even finish explaining I was interrupted and told that I committed self-plagiarism as well by taking material from my NSF-GRFP personal statement. This professor is now completely unwilling to hear me out and told that I will be assigned an "F" for their course in addition to whatever penalties the university places on me.

Upon reviewing my institution's self-plagiarism statement, it says that the assignment/paper must be submitted for academic credit. Clearly an NSF-GRFP grant proposal is not for academic credit. So the self-plagiarism issue should be resolved rather quickly, I hope. I emailed my professor and she said that she will still be reporting me to student conduct for plagiarism and that she would give me a 0% on this assignment and take 30% off of my final course grade, i.e. if I get a 100% on every assignment for the entire term I can pull off a 70% "C" passing grade. I'm confident in my abilities but I'm sure I would end up losing a point or two along the way and end up with a "D" or worse. So that much has been retracted.

What my graduate advisor says

I met with my graduate program adviser, and he indicated that there is nothing that he personally can do about the matter as the instructor of record has the right to submit any form of plagiarism to student conduct at their own free will if they have any form of evidence. He indicated that there is nothing the department can really do about the matter and that I need "roll with the punches." I found this quite discouraging.

On the other hand, he mentioned that I will not lose my position (graduate teaching assistant) in the department due to this, and that as far as he is aware, the grade I receive in the course won't impact my graduation or progression through the department. However, he fears that if the university places severe sanctions on me (i.e. semester probation, expulsion) that there is nothing that can be done. All in all, his advice was to simply go through the procedure and do not fight it.

This conflicts with advice I have received from some other professors that I am in good terms with in the department, they said at worst I should receive a failing grade for that assignment and nothing more. However, it all boiled down to their mere opinion of the matter. I still have not heard from the student-conduct board, but I anticipate to receive that email on Monday if not sooner.

If I choose to appeal I have seven business days to put in a formal appeal plea. I guess my new crossroad is whether to: appeal or not? If the accusation is self-plagiarism, I will certainly appeal it because I have a strong case for that. However, if it is merely plagiarism I don't know... I guess it comes back to the title of this question: where's the line between plagiarism and missing a reference? The student handbook at my university defines plagiarism as:

whereby another’s work is used or appropriated without any indication of the source, thereby attempting to convey the impression that such work is the student’s own.

Taking away all the circumstances of this event, I have done that. Considering how this actually happened, it was more of a clerical error. I will update again after I receive the official email from the student conduct board.

Question

I do not know what to do or what I even can do right now.

I actually have aspirations to one day become faculty at a university. Moreover, I am on an assistantship through my university teaching courses and I fear that I could lose that position and thus my stipend money.

physiology - Why is thrombin time (TT) normal range longer than prothrombin time (PT)?

Reference range for the TT is longer than that of the PT.

human biology - At what age do babies begin to synthesize their own antibodies?

When babies are first born, they receive their antibodies from their mother (I assume because they do not yet have the capacity to synthesize their own). So my question is, at what age do babies begin synthesizing their own antibodies?

vision - Can "red" cone cells actually see much red light?

In electronics, the most common color scheme is the "red-green-blue" (RGB) scheme. This choice is often justified by claiming that the long- (L), medium- (M), and short- (S) type cones in the human eye are most sensitive to red, green, and blue light respectively. But this seems clearly wrong if you look at the actual normalized frequency receptivity spectra for the three types of cone cells:

It's clear that the L-type cones are actually most sensitive to yellow-green light and are actually relatively insensitive to red light. (Presumably the brain distinguishes between yellow, orange, and red light by the rapidly decreasing ratios of M-type to L-type signal.)

My question is threefold: (1) The L-type cones are usually called "red" cones. Is this simply incorrect, or is there some justification for this name that I can't see from the receptivity spectra? (2) Does the RGB color scheme give a better color range than, say, a "yellow-green-blue" scheme (which would more closely correspond to the actual cone sensitivities) simply because red is at one end of the visible spectrum, so you can more easily get a wide color range? (3) If this is the case, do we not use a "red-green-violet" color scheme (which would give an even wider color range) simply because the human eye is so much more sensitive to blue than to violet light?

Answer

This is a good question. The first thing to note is that human colour vision is very complex and still poorly understood. If you visit the wikipedia page on RGB, you will find that this correctly mentions that the S, M and L cones are most responsive to violet, green and yellow wavelengths respectively (which answers your first question - calling the cones red, green and blue is primarily for historical reasons, because there aren't any real wavelengths that only activate a single cone, it's hard to say what colour a cone 'is'). So why do we use red, green and blue phosphors? A practical answer can be found by looking at the CIE 1931 colour space: this was essentially an attempt to find how one could add together different amounts of a small number of wavelengths to make the result indistinguishable from any desired wavelength (read the linked page if you want more information, also have a look here). The result found was that the colour matching functions should look like the following graph (what this is showing is how much of a red, green and blue light are required to simulate a wavelength):

You can see that this is similar to the responses of the cones except for the peak in the red (which corresponds to violet looking like red-blue):

To answer the question in your title, red cells do see the most red light of any cone, but that is not where they see the most light. Here is an example set of spectra of the red, green and blue phosphors in a CRT:

To answer your question about why we use red, green and blue in the first place (rather than yellow-green-blue or red-green-violet), it's good to understand why the CIE 1931 functions are that shape in the first place. The wikipedia RGB page mentions that:

...good primaries are stimuli that maximize the difference between the responses of the cone cells of the human retina to light of different wavelengths, and that thereby make a large color triangle.

This gets at the fundamental reason, which is that it is generally believed that we do not perceive colours in terms of the activities of each cone, but in terms of the differences between those signals (as it says here), an opponent process. The following image illustrates a simplified version of how the opponent signals in colour vision processing are thought to function, so that the resulting signals are a black-white, a yellow-blue and a red-green axis:

This image shows the theorized shapes of the response curves of these opponent functions (see here for an interesting historical paper on this theory and here for more details and some predictions of the theory):

It is possibly apparent from the last graph why the CIE 1931 colour graph is the shape that it is, since we see red as a bimodal distribution with a distribution of green in between, and a large distribution of blue at short wavelengths and yellow is red + green. (Incidentally this also explains why we also perceive yellow as a primary colour - see the 4 highlighted points R, Y, G and B where one curve passes through 0). Additional information on the neurological and psychological correlates of colour vision can be found here and here and more technical theoretical details here.

The upshot of all of this is that red, green and blue are the best 3 colours to use as the basis for additive colour mixing, but not because they are what L, M and S cones are most sensitive to. Rather it is because it has been shown that these particular colours fall where there is maximal difference between the cone signals and because they can accurately represent all of the colours in our colour space as illustrated by CIE 1931 (due to being widely spaced and all perceived easily as you have mentioned in points 2 and 3 of your question). Effectively, the reasons are complicated and to do with the neurological processing of the colour signals and the differences between the signals rather than the straightforward signals themselves.

Pros and Cons of Enrolling in coursework units during a PhD

In my university PhDs are assessed purely on dissertation, there is no coursework component or oral defence or anything else (this is not unusual for Australia, as I understand).

There are no units for PhD students, but they can get into Masters, Honours or Bachelor level units, assuming they meet the conditions or get exceptions.

However the federal government will pay for up to 4 coursework units to be completed over the first 3 years of the PhD. They will outright pay the course fees for the units -- which is a nice change from undergraduate where the fees go into your HECs debt.

Some advisors/departments strongly advise students to take particular units (though not normally 4 as I understand it). I doubt mine will.

So I guess the purpose of these 4 "free" units is to let shore up any areas of knowledge -- particularly for students embarking on something multidisciplinary.

But what is the advantage in actually enrolling in the units? the alternative to enrolling is to go up to the lecturer and say: "Hi, ... I'm doing a PhD on X, and I know this course covers Y which is kind of relevant to it, do you mind if I sit in on your lectures?"

I suspect more lecturers wouldn't mind at all, so long as you didn't cause trouble -- they are paid the same either way. If you were extra friendly (say you'ld taken some units with them before), you could probably convince them to let you have the digital course notes, and maybe even to mark a assignment so you could see how you are going.

The Advantages I am seeing to not formerly enrolling are:

• No pressure to do well in exams/tests


• Attend only the subset of the unit relevant to your research

The Disadvantages I can see:

• 'Robbing' the university of income (but also not generating any extra expense for it)


• Less access to resources, like online notes


• Not having the unit on your transcript

The Pros seem to outweigh the Cons, but I suspect I am missing something. Perhaps lecturer pay is generally directly proportional to number of students?

---

I have gone through the (large) university policy base and have found no rule forbidding this, except if there is a shortage of seating.

publications - What are the differences between Peer Reviewed Journals and Refereed Journals?

I would be interested to know the differences between peer reviewed journals and refereed journals in these aspects:

1. 
   

   Conditions for the acceptance of papers for publications.

   
   


2. 
   

   The time length of paper stage after submission.

   
   



3. 
   

   Amount payable by authors.

   
   

Answer

To expand on Yuichiro Fujiwara's comment, "peer review" and "refereeing" are exact synonyms, and no differences at all are implied by the names. For historical reasons, some fields are more likely to use one term than the other (for example, mathematicians talk more often about refereeing than peer review). Publishing practices also differ between fields in other ways, such as the length of the reviewing process. There might be a weak correlation with the use of terms like peer review and refereeing, since both issues are heavily influenced by which field you are looking at. However, I'd bet that any correlations are small, and in any case this is not a productive way to investigate journal differences (since knowing the field would tell you enormously more than just knowing which term the journal uses for peer review).

terminology - What does confluency mean?

Since as long as I have been doing cell culture, the word confluency is used to describe the % growth of cells or area covered by them. However, no dictionary that I have found uses this word. I was wondering if anyone could reliably state where the meaning comes from or how the association began, and truly what it means. I don't believe I can post this on another stack exchange because the word doesn't have even a resembling meaning in the dictionary. Cell culture is such an integral part of cell biology, medical research and biological manufacturing. And this term is an integral part of cell culture. I was surprised to be unable to reliably verify it's meaning.

Answer

Besides the etymologic explanation that @aandreev gave, in cell culture this term is commonly used to describe the density of adherent cells and it is used as a measure of their proliferation. It is usually combined with an estimated (or counted) percentage, so 10% confluency means that 10% of the surface the dish or flask used is covered with cells, 100% means that it is entirely covered. The cells grow twodimensional on the surface of the flask in this case. The picture below (from here) illustrates different levels of confluency:

The level of confluency is important as the cells change their growth with changing densities. Low density cells (10-20%) usually grow slower than 50% confluent cells. If the plate is complete grown by cells, they tend to grow much slower again. This influences their genetic program, behaviour in experiments and transfections.

As @Roland pointed out it is important to say that confluency is not a hard measure, but rather an estimate of the cell density. Different people will get different estimations, but the trend should be the same.

rna - What makes DNA helical?

Why isn't DNA like RNA; why isn't RNA like DNA, that is, helical? Why are RNA chains straight?

Answer

The helix shape of DNA molecule is a consequence of its secondary structure. This refers to the bases contained in the molecule which pair, thus determining tertiary structure [1].

Basepairing also occurs in RNA, so it can form a double helix. In fact, RNA is composed of short helices packed together [2]. Base pairs maintain DNA's helical structure no matter the nucleotide sequence [3].

A nucleic acid strand is composed of nucleotides joined together by covalent bonds between the sugar of one nucleotide and the phosphate of the next. Adenine pairs with thymine and cytosine pairs with guanine by hydrogen bonds and form the double-stranded structure [3]. Because covalent bonds are stronger than hydrogen bonds, the double helical structure of DNA is easily broken by heat [4], but the nucleotides remain bonded together.

Here is the tRNA molecule (you can see it has short helices):

"TRNA-Phe yeast 1ehz" by Yikrazuul - Own work. Licensed under CC BY-SA 3.0 via Wikimedia Commons.

Here is the DNA structure:

"ADN animation" by brian0918™ - Own work. Licensed under Public domain via Wikimedia Commons.

---

References:

1. 
   

   Wikipedia contributors, "Nucleic acid double helix," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Nucleic_acid_double_helix&oldid=609435163 (accessed June 26, 2014).

   
   
   


2. 
   

   Wikipedia contributors, "RNA," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=RNA&oldid=612056511 (accessed June 26, 2014).

   
   


3. 
   

   Wikipedia contributors, "DNA," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=DNA&oldid=611891356 (accessed June 26, 2014).

   
   


4. 
   

   Wikipedia contributors, "Nucleic acid thermodynamics," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Nucleic_acid_thermodynamics&oldid=606379256 (accessed June 26, 2014).

   
   

evolution - Why is the heart not in the middle of the body?

All mammals that I can think of have a high degree of bilateral symmetry (In fact, almost every animal I can think of is like this).

So why is the human heart not exactly in the middle of the body? An effect of this is that one lung is slightly smaller. Are there any evolutionary theories on why this came to be?

Answer

First of all, let me make it clear that the heart is at the vertical centre of the body -- it is not shifted towards left (or right). However, it is slightly tilted towards the left in most cases.

In some cases, it is tilted towards the right, and the condition is called Dextrocardia. For why it is so, lets look at what the heart does. Below is a diagram of double circulation (from here).

As you see, the highest pressure needs to be generated for pumping oxygenated blood into the body. Thus, the left ventricle needs the thickest muscles for this purpose. And due to these extra muscles, the heart appears extended and seems shifted towards left.

Coming to the evolutionary perspective, it is important to mention that humans are not the only organisms with this feature. Indeed, displacement of the heart towards the left is a conserved feature in all vertebrates (Fishman et al, 1997). See this answer for more information.

Coming to genes, bending of the heart towards one side is actually controlled by the NODAL gene during development. See this diagram (from Jensen et al, 2013):

Tilting occurs in two phases, one during the first four and a half months of intrauterine life and the other, which is actually a 45° rotation to the median plane, later. During the early development of the heart, a process called cardiac looping happens and the straight heart tube develops a bend (see diagram). The NODAL gene, along with the Lefty1 and Lefty2 genes, regulates the speed and direction of cardiomyocyte movement during the development of the heart, leading to this asymmetry. To confirm it, researchers knocked out the spaw/nodal gene from a zebrafish and found randomized development of heart, even symmetric heart, as the result(!) (see Walmsley, 1958 and Rohr et al, 2008).

Now, talking about why this happened in the first place, and why it is so conserved among vertebrates, we need to ask ourselves a basic question: what good would a symmetrical heart be? External symmetry is preferred (probably) because it helps in locomotion; it would be quite difficult to move with your two legs placed away from your center of gravity. But when we talk about internal symmetry, conditions drastically change. We get a major restrictive factor here: space. And limited space always dominates other factors. Seeing that the structure of the heart is necessarily pointed towards one side, it becomes difficult to make it symmetrical. (The only option IMO is to have another pointed end at the right side.) In this case again, what advantage would a symmetrical heart provide? None. And it might even be harmful since having an even bigger heart would mean making both lungs smaller. Thus, a symmetrical heart would only prove to be a liability rather than an asset. See this question for more information.

plant physiology - How do white Caladiums perform enough photosynthesis to support their mass?

In some white caladiums, there is less than a square inch of green space spread over the whole leaf. How do these plants perform the photosynthesis necessary to support the large leaves, the roots, the flowers, and build a corm?

Answer

There are many different kinds of plants that have independently evolved this sort of variegation (non-green areas) in the leaves. However, the mechanisms by which they effect this vary between species.

Some have little or no chlorophyll in the non-green areas, but many others have changed the architecture of their leaf cell layers in the non-green areas, creating refraction effects that make the leaves appear white, but don't significantly change their photosynthetic efficiency (Sheue et al.) In fact, Arum italicum white areas actually have higher efficiency in certain light conditions! (La Rocca et al.)

I can't find any information on which type of variegation Caladium shows. The genus Caladium is related to the Arum I mentioned above which uses the "architecture" method, but it's also related to Epipremnum, which seems to use the "no-cholorophyl" method.

Sheue et al. mention that with some species that use the architecture method, using transmitted light instead of reflected light reveals that the white spots are actually green; while in no-chlorophyll plants the spots remain white. If you have a Caladium around, you could try holding its leaf up to a bright light, and see!

So, to answer your question: if Caladium is an 'architecture-variegation' plant, its white areas perform photosynthesis at or near the efficiency of the green areas of the leaf. If it's a 'no-chlorophyll-variegation' plant, it would have reduced efficiency, but might make up for this with strategies including:

• Having a larger total leaf area (La Rocca et al. and also see this question)


• Only developing large white areas if there's plenty of light as they grow (Garland et al.)


• Increasing the mitochondrial activity in its white areas, which could lead to other energy efficiencies (Toshoji et al.)


• Using Homo sapiens to help it reproduce and provide plenty of light for it. Many of these extreme variegation patterns are found in horticulturally bred varieties!


• Just using its green areas for photosynthesis, and "accepting" the fact that the white areas are not producing energy. In natural populations, you often don't find varieties as completely white as in that picture: they usually show white spots and plenty of green. This is true of Caladium species in the wild, which may use the variegation to mimic and to prevent herbivory: potential pests think the leaves are already infested, and avoid them (Soltau et al.). In other words, even if the white patches represent decreased photosynthesis efficiency, it could be a trade-off in order to achieve less herbivory.

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• Garland KF, Burnett SE, Stack LB, Zhang D. 2010. Minimum Daily Light Integral for Growing High-quality Coleus. HortTechnology 20: 929–933.


• La Rocca NN, Rascio NN, Pupillo PP. 2011. Variegation in Arum italicum leaves. A structural-functional study. Plant Physiol Biochem 49: 1392–1398.


• Sheue C-RC, Pao S-HS, Chien L-FL, Chesson PP, Peng C-IC. 2012. Natural foliar variegation without costs? The case of Begonia. Ann Bot 109: 1065–1074.


• Soltau U, Dötterl S, Liede-Schumann S. 2009. Leaf variegation in Caladium steudneriifolium (Araceae): a case of mimicry? Evolutionary Ecology 23: 503–512.


• Toshoji HH, Katsumata TT, Takusagawa MM, Yusa YY, Sakai AA. 2012. Effects of chloroplast dysfunction on mitochondria: white sectors in variegated leaves have higher mitochondrial DNA levels and lower dark respiration rates than green sectors. Protoplasma 249: 805–817.

plagiarism - Same literature survey in first and final reports, Is it ok?

Is it considered bad to copy literature survey from 1st/initial report of the dissertation to the final report?

Does it count as self plagiarism?

Generally speaking one should include more recent researches, if any, related to the topic in the final report but what if there is only a 2-3 months period between two reports that happens for masters students in some countries (and in my case too).

graduate school - Rankings for university departments

The Internet is littered with information about university rankings and comparisons that it is very easy for an applicant to lose track of what exactly he wants to know. Apparently rankings which compare all departments of a university and have a single rank are not very useful from an applicant's perspective. Yet these are the most common rankings one can find. I know of the FT rankings which order MBA schools. It does rank B-schools in terms of research too, but clumps different branches (Accounting, Finance, Operations, etc) into one.

1. 
   

   For other departments are there reputable and reliable portals where one can get to know rankings based on various criteria like published research, number of graduates, time taken for graduation, etc?

   
   


2. 
   

   Are there no well-established ranking systems for academic departments? For example, these ranking systems could be similar to those in cricket or football. Such as periodic updates are made with every publication and every citation, and possibly journal reputation could also be brought into picture. In a way, would that not enhance the competitiveness in academia among similar departments?

   
   

Answer

The big difficulty with devising formal ranking systems based on numerical measures is that, outside of a handful of areas like sports, anything we can measure is at best a proxy for what we really care about. It may start off as a pretty accurate reflection, but anyone judged on this basis will quickly discover how to manipulate it.

For example, universities in the US are often judged partially by the fraction of students they accept. Of course, ambitious universities have adapted by advertising to encourage more applications, with no intention of accepting these applicants, but just to lower the acceptance rate by increasing the denominator.

Similarly, universities are also judged based on "yield," the fraction of admitted students who attend. That sounds at first like a pretty good measure of popularity, but it creates an incentive to game the system by rejecting students you think are likely to choose another university in the end, and universities do just that.

Time taken to graduation can be gamed by kicking out students who are taking too long. Employment rates can be gamed by offering ten-week temporary jobs to unemployed students, timed to coincide with the measurement of employment rate (really!). All sorts of things can be gamed.

And this is not just a theoretical problem. It occurs all the time in practice (if you are in the US, then your school is very likely doing some of these things), and some people are extremely upset about it.

You might think scholarly measures based on citation counts would be less subject to this, but they are not. There are plenty of corrupt journals where editors put pressure on people to cite papers, or even use totally fraudulent methods like publishing review articles that carefully cite every paper they have recently published. People have been caught seriously distorting their journals' impact factors by doing this, and I'm sure there are other, more clever editors who are getting away with it. If professional success depends on influencing a number, then people will discover ways to influence it.

In summary, there's an awful tension between transparency and resistance to fraud: if you explain how your ratings work, then people will manipulate them. Nobody has any idea how to avoid this, and the net effect is that serious scholars do not waste time trying to compile numerical rankings. For the most part, the only people who do are those who are naive, trying to make money in unscrupulous ways, or trying to promote a cause through carefully chosen rating methods. The rankings they produce are not worth paying attention to.

P.S. Polls of expert opinion are generally much better than rankings based on numerical measures, but even they have their problems. For example, the U.S. News college rankings are based partly on asking college presidents to rank other schools. Clemson University manipulated the rankings by rating all competing schools as below average, no matter how good they were. I suspect they weren't the only ones to do this - the amazing thing isn't that it happened, but rather that we ever found out.

publications - How to train students to write high-quality research papers?

As someone supervising postgrad students, I wonder what is the best way to train these students to write high-quality research papers?

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The best way seems to be through coauthorship but ...

On the one hand I can be hands-off and rather give them feedback as best as I can but let them do most of the work themselves, sort of like a "sink or swim" strategy.

On the other hand I can be hands-on and rewrite the paper (or large parts of it) and hope that they learn from the example I give.

On the one hand I want them to learn to write papers without me some day and I want them to learn as quickly as possible to take load off me.

On the other hand I want us to publish in the best place possible with as little stress as possible.

On the one hand I want them to see the peer review comments from what they themselves have written.

On the other hand I do not want them to be discouraged by the peer review system early on and do not want to submit papers I know we could have written better.

On the one hand I want them to get confidence by being published and presenting work at good venues.

On the other hand I wonder if they need to get there themselves to get that confidence boost.

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At the moment I'm very hands on. There's a few factors for this: I don't like submitting papers that are not up to a certain standard, I'm a native English speaker in a non-English speaking country with non-native speaking students, publications are a high priority for me, etc.

But recently a friend/colleague warned me that I should not be so hands-on with the writing of the papers of my students. He pointed to recently graduated researchers in my area that published good work as students but who struggled after leaving their PhD supervisor saying their supervisor did them no favours in the long term ... that by being so hands on, while the students have success getting published and so forth with me, I'm not really doing the most important thing a good supervisor should do: making myself obsolete.

---

My question is how to train students to write good research papers and in what ways can I balance being hands-on and hands-off?

I'm also interested in methods not directly involving coauthorship.

Answer

edit: To clear a misunderstanding that might have arisen (see the answer of Kimball): the papers described here were not solo-papers. Neither me nor my advisor would ever have the idea to write a paper together and then put only one name on it...

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My instructor did a really good job with that (and is still doing it), so I'll explain here approach as I experienced it:

For our first paper, we were sitting in her office, she wrote it and asked my opinion from time to time. I was still really new to everything and agreed most of the time, but I also already learned about some questions that should be considered and, of course, I learned the style she was using first-hand.

For the second paper, we started in the same way. At some point, she told me that I should write a part (the proof of a theorem, a short paragraph,...) myself. Of course we discussed the content first, but I was responsible for writing it down. I already had the first part of the paper that we wrote together to use as a starting point, to adjust my style to it, but I was still ultimately responsible for it myself. Once I finished it, she looked over it, gave me comments and asked me to write a new version. And a new one. And a new one,... until it looked just as good as the rest of the paper she wrote. Of course it would have been easier for her to just write it down herself, but doing it this way I learned how to write myself and I had the success of having something I wrote myself in a paper. (Yes, I had to adjust it a few times, but ultimately I did write the final version that we published)

For the third paper, she told me to write it completely myself. Once again we went through a long process of her commenting on things and me correcting it, but in the end I had a paper that I wrote myself, and I felt really proud of it.

After that, she got me some review jobs, so that I could learn what to look for in a paper, how to recognize strong parts and flaws and (I assume) so that I don't just copy her style but also see other authors and learn from them.

All in all, she did a really good job and with only three publications yet I feel like I am now able to write a paper on my own.

Now let's end with some general disclaimers: The approach given above assumes a motivated student that wants to produce good quality papers and is willing to adjust it until it looks really nice. A lazy student who just wants to increase his paper count with the least effort possible is of course still a problem. Also, your students should be able to produce papers in English. If not, point them towards English courses offered (most likely) at the university, help them install spell-checkers on their computers, etc.

graduate admissions - Can I remind a professor that I submitted a "good" essay in her class? (LOR request)

I would like to ask my former professor for a reference, I'm not sure how to formulate it and am worried the professor won't remember me. I submitted a good essay in her class though (got an A).

Can I write:

Dear Professor,

I studied with you 2 years ago, I don't know if you remember. In any case, I submitted a good essay in your class and wanted to ask you for a letter of recommendation?

Answer

A better outline might be somehting like:

Dear Professor Smith,

I am planning to apply to Teleportation programme at the University of Wonderland for my graduate studies. They require two reference letters, and your area of interest is related to the programme I am applying to.

Would you please be kind enough to write a letter of recommendation?

I have taken your course Introduction to Supernatural Incidents (ISI 101) in 2016 - 2017 Fall semester, and you have noted that one of my assignments were outstanding.

Keep in mind that if you suspect that the professor wouldn't even remember you, it is better not to ask that professor for a letter of recommendation, because chances are they are going to write a mediocre letter.

Why did I pick this outline

Because first of all, the reason for you writing a mail should be explained at the first sentence. An avarage professor mailbox receives around 100 mails per day. Thus, they decide whether or not to read the full mail in a few seconds.

The actual reason for such mail is your application for graduate studies, and you give solid reasons for the letter of recommendation. Note that in your outline, the letter of recommendation is just mentioned. It seems like you wanted to remind the professor that you were his student, and handed in a good essay.

Another reason is, the punctiation and language. Although overly-formal emails are not good, using a proper language helps.

To sum up, the professor wants to know three things very clearly, and as soon as possible:

1. Why are you writing this mail?



2. What do you want from me?


3. Why would I grant your wish?

research process - How can we change things so more researchers are willing to share their source code?

This is a followup to Why are CS researchers reluctant to share code and what techniques can I use to encourage sharing?. That question specifically asked how one can succeed in obtaining researcher's source code.

As discussed in the answers to that question, the reasons largely boil down to competitive advantage and people thinking their code is not good enough. The former issue is difficult to address. However, one could try to address the latter issue, making the reasonable assumption that this behavior stems from the surrounding academic culture. There may be additional aspects of the academic culture that discourage code sharing, and which do not relate to competitive advantage.

So, one could instead ask the general questions what concrete actions one can take to change this culture? Or, to put it a little differently, how can I help change the academic world so that more researchers are willing to share their source code?

ethics - Is it acceptable to submit a postdoc fellowship application (same lab, same project) to two funding agencies at the same time?

I've already applied for one post-doc fellowship with one project with the consent of my possible future supervisor. I will know whether I've been succesfull in 6 months.

Now I realised that there is another fellowship to which I could apply - my potential host supervisor agreed that she would support me for both fellowships.

From my view I see no obstacles to ask for both, nevertheless I want to ask, what would be the opinion of a potential reviewer if he/she will get the same project for review twice from different agencies? If I will apply for both fellowships, both the review process and the results anouncement would run more or less in the same time period.

Answer

It's quite common to submit proposals to multiple funding agencies at the same time. Most grant applications ask you if you are submitting the proposal to multiple funding agencies. You should note this in your application. If both agencies are interested in funding your proposal then they'll coordinate awards so that you don't get funded twice.

publications - Is h-index important? Can h-index be used to classify yourself to know whether you are at a given academic rank?

Of all the statistical factors that are used for judging publication record, the h-index seems to be the most commonly used

Wikipedia says

Hirsch suggested (with large error bars) that, for physicists, a value for h of about 12 might be typical for advancement to tenure (associate professor) at major research universities. A value of about 18 could mean a full professorship, 15–20 could mean a fellowship in the American Physical Society.

I am an organic chemistry with an h-index of 16. I assume physics should be similar to (organic) chemistry. I am now applying for a tenure-track position.
I mean to be overqualified for research funds, academic and scientific honors, etc.

Questions

• How important is the Hirsch index (h-index)?


• How much is the h-index really relied upon?


• Can the h-index be used to categorize yourself?


• Can I really set a goal that by reaching h-index 20, I am at the level of fellows of my professional society?


• Can the h-index be used to indicate whether I am ahead of my rivals?


• Can we claim something by h-index or is it just a number?


• What should be the h-index of assistant/associate/full professor in chemistry to be a leader of his own rank?

publications - How to make a paper anonymous for reviewers when it heavily extends on your own previous work?

I am writing a paper that continues and extends my previous paper (the usual situation), and I plan to submit it to a journal that conducts a double-blind review. It is a research that started recently, so I have only one paper published.

The published paper represents a strong foundation of the research, which means that I would have to refer to it in the new paper at least a few times (basically the new paper extends it). While the peer-review is double-blind, the reviewers would then easily realize who is the author.

Therefore, I can't just cite it as it's someone else's research because it's obvious that I am talking about a paper of mine.

How can I refer to my previous paper completely anonymously so that the reviewers cannot realize who is the author of the new paper?

I am insisting on this because I don't believe that there is such a thing as a completely unbiased peer-review process, even when double-blind. I am new in the field, and I can imagine that this is where a reviewer could have prejudices. Stupid reason, but I already have an unpleasant experience with this.

I cannot cite the paper by removing the author and retaining the title, as it would take 5 seconds for a computer-literate person to find the full record.

On the bright side, while the previous paper is easily accessible, the reviewers probably would not be aware of it because it is from a conference that is not really in that field. But still, they would manage to find it with some effort.

Would it be acceptable that I mention that this paper extends my previous research that cannot be cited in order to accomplish the anonymity of a double-blind peer-review, and that the citation will be added later?

Answer

Disclaimer: I work in a field in which double-blind reviewing is either completely absent or so rare that I have never encountered it.

Would it be acceptable that I mention that this paper extends my previous research that cannot be cited in order to accomplish the anonymity of a double-blind peer-review, and that the citation will be added later?

No, I don't see how that's possible. The principle that you must cite work that you use or build on -- no less so if it's yours -- seems much more basic than your desire to get genuinely double-blind refereeing. Moreover, if a paper continues previous work, can anyone sensibly evaluate its added value without having access to that previous work? I can't see how.

I am a new guy in the field, and I can imagine that this is where a reviewer could have prejudices. Stupid reason, but I already have an unpleasant experience with this.

When you self-identify your reasoning as "stupid", there's a clear opportunity to think it through again. The process of journal submission and publication has a non-negligible random component: it would be unwarranted to assume that an experience that you had once or twice will necessarily recur. Your desire to circumvent an unfair refereeing process seems premature. If you feel like you're being treated unfairly as a new researcher, there are more productive ways to react to this: make it more clear why your work is competitive with or superior to the work done by more established researchers. I don't know of any academic field in which journals systematically don't want to publish work by new researchers that they believe is better than prior work just because those researchers are new. It is also true, unfortunately, that new researchers can overestimate (and also underestimate!) the value of their work. It is hard to hear that the thing you slaved over for months and years is not good enough for a second-rate journal in your field. But it may be true nevertheless.

Let me say finally that I see a little irony in your approach: you lament your treatment as an unestablished researcher, but you are in fact more established than most people: you have published a paper that your present work builds on. My experience is that it is much easier to publish a second paper on the same topic in a reasonable journal than a first paper, just as it is easier for an artist to sell their second painting for a reasonable price than their first. In publishing the first paper, the journal has conferred on your work the important imprimatur of publishable value. Insisting on throwing that away will probably increase your chance of receiving "anti-newbie bias" in the evaluation of your followup work!

mathematics - Why subscribe to printed versions of math journals?

This question follows from a MathOverflow question, "Why should one subscribe to print Journals".

It seems obvious to me that having print journals in a library is beneficial. Yes, Arxiv, MathSciNet, Blogs and lecture notes by Mathematicians, Math Overflow, Wikipedia and Scholarpedia all of these have been extremely helpful in dissemination of research mathematics. Amongst other things electronic copies of articles helped immensely in increasing accessibility.

Most journals these days have an online version. Which probably only a few would argue is not beneficial.

What I can't get myself agree is the opinion that one should stop subscribing to print copies of journals altogether. The arguments against subscribing both print and online I have come across are cost, space constraint, and redundancy.

The difference between online and print+online versions of journals are often marginal. If space constraint is an issue then one can argue against having a library as well. Why subscribe to the journals at all as most of the articles are available in the internet free.

What I can't fathom is the argument that print version of journals have become redundant.

I am asking this as in a discussion regarding journal subscription many faculty members expressed the opinion that we should stop subscribing to print version of the journals. How does one defend the case for need of print journals?

Am I overly emotional and just nostalgic for old times? So many times I chanced upon a result while browsing through the pages of a journal; sometimes relevant to my own area, and sometimes totally unrelated but so exciting that it got me interested in that area.

I am sure this issue or debate is not limited to my university and I am asking this question here hoping to benefit from the comments and thoughts you may share.

My question is what are the benefits of subscribing print version of journals, even if online versions are available. How it helps the research of faculty and graduate students.

bacteriology - "Most bacteria have at least one cell wall"

In the first answer to How do we find antibiotics? @Ashafix claims that

Most bacteria have at least one cell wall

Does this mean that there are bacteria with more than one cell membrane? Which are those and how does that look/work? Are there different milieus in the different compartments?

Cheers

Answer

The phrase you quote is a little unclear, but in looking at the page you link to I believe that @Ashafix was referring to Gram-positive (one cell membrane) and Gram-negative bacteria (two cell membranes).

Each type has only one cell WALL, which refers to the structural peptidoglycan layer, which is between the two membranes in gram-negative bacteria, and is much larger in gram-positive bacteria.

The differences between these two cell types are of some interest with regard to the biology of what structures can sit in the cell membrane and how easy they are to work with in the lab, and how easy things are to get across the cell wall (w/r/t @Ashafix's original point).

authorship - Can co-first authors’ positions be swapped in a CV?

Some papers have co-first authors, which are supposed to have contributed equally. However, there is still an order issue.

Imagine a paper co-authored by A, B, and C. The paper goes like:

                                     A Very Long Paper Title
                                         A*, B*, and C

Our work is good.
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* A and B contributed equally to the work.

In this case, is it acceptable for B to cite this paper as follows in his/her CV?

B*, A*, and C. A Very Long Paper Title. Journal of Stack Exchange. Jan. 2015. (* indicates the co-first authorship)

Note the position swap.

Answer

No. The reference is the reference, changing it to move yourself higher could be misinterpreted as willful deceit.

Add a parenthetical statement at the end of the references saying "first n authors are co-first authors, listed in this order because..."

On my "internal" CV I have parentheticals after many papers, for example, listing contributions, nominations for best paper, etc.

career path - How much will dropping out of a Master's program hurt job prospects?

I am extremely dissatisfied with the Master's program I just began and plan on dropping out ASAP. I currently have no interest in finding another graduate program and instead wish to pursue a job outside of academia. As I see it my two choices are to either stick it out for the rest of the semester and just try to maintain C's, or to simply walk away from it and accept the F's because the drop deadline has passed.

The main question I have is how much more damaging is the option of just walking away mid-semester?

I realize that certain employers will view the situation differently, but I am just seeking opinions here. I have no idea of what industry I would want to work in or how that might affect your answers. Or if anyone has advised students in similar situations, I would greatly appreciate similar advice.

As for my records before this program, I got my BS in applied math and graduated with honors. I am hoping that I can bank on this earlier performance and explain the reasoning behind dropping out to potential employers.

Is attending an academic conference beneficial if you are not presenting any paper? Does it reflect well in your CV?

I have recently been given an opportunity to attend a conference on Robotics although I don't have any paper to present. The registration fee is around 7k. Before spending such an amount, I wanted to know if it is worth attending conference sessions just for its sake. Please help.

publications - Is it wise to contact the editor of a journals with my concerns regarding the length of the acceptance process?

I have finished writing my first paper to be published in a journal. My intent is to try to publish in a high-impact journal (there are two candidates from the IEEE Transactions class). However, my advisor and another professor, who is close to our research, both suggest that I should refrain from trying to aim that high, i.e. first publish in a lower ranked journal. They state that the reason is not the insufficient quality of the paper, but rather the length of the acceptance process, which is in their experience particularly for first-time authors very prolonged. The argument is, that I would lose many months, perhaps even more than a year in the back and forward process of rejections and resubmitions, when all this could be cut significantly, if a l. All that seems a bit pessimistic to me, of course, I don't want to wait so long, but I was under the impression that such a process would take at most 3-4 months.

Are those considerations regarding first-time authors deemed accurate? Would it be appropriate/advisable to contact the editors of the journals with my concerns regarding the length of the acceptance process?

PS: the field is computer science

Answer

I was under the impression that such a process would take at most 3-4 months.

No. 3-4 months would be, in my experience, extremely quickly for Computer Science transactions. That would mean that your submission would get accepted without modifications in the first revision, which almost never happens (and even then 3 months would be very fast). 1 to 2 years for the entire process is more common.

However, this has nothing to do with it being your first paper. It is the same for every submission. Those journals have pretty rigours peer review, which simply takes some time.

That being said, it will also be similar for other non-spam journals. I am not aware of any reputable CS journal that would suit your 3-4 months expectation.

Would it be appropriate/advisable to contact the editors of the journals with my concerns regarding the length of the acceptance process?

The answer would very likely be "deal with it or submit somewhere else". Frankly, if a journal had a reasonable way to cut down on the time required for the review process without hampering review quality, they would arguably do it anyway. They are not going to "make an exception" or anything of this ilk.

my advisor and another professor, who is close to our research, both suggest that I should refrain from trying to aim that high, i.e. first publish in a lower ranked journal. They state that the reason is not the insufficient quality of the paper, but rather the length of the acceptance process

I would assume they meant not "a lower ranked journal", but rather "a conference". Review durations for conferences are indeed much more predictable (and, generally, shorter, in the 2-month range on average).

Submitting to a weaker journal to get your notification a little bit faster does not seem like overly good advice to me. If they indeed were speaking about a lower-ranked journal, you should consider the possibility that they were sugar-coating their judgement that your paper is not good enough for a very strong journal.

sweden - Why do Swedish postdoc ads typically have a requirement that PhD date must not be more than 5 years ago?

Ads for postdocs in Sweden appear to always have a rule like PhD degree obtained preferable not longer than three-five years ago:

Example 1, 2. I've seen it many times in the past but job opening links are particularly temporary.

Is this to protect people from becoming career postdocs? Is it a requirement from a funding agency? Or is it just a habit?

united states - Why is PhD GPA considered irrelevant?

The importance of a recent PhD’s GPA was recently dismissed in another question (What does an industry recruiter want to know my Ph.D. GPA for?).

Why isn’t GPA considered relevant for graduate study?

molecular genetics - Can you detect if a mutation is spontaneous or induced?

Is it possible to determine if a certain specific mutation had a spontaneous origin (for example from a mistake of the DNA polymerase) as opposed to an induced origin (for example, from some genotoxic agent)?

Answer

Here's a quick answer; hopefully someone will give a more complete one. But meanwhile you've got something.

Some genotoxic agents have predictable results. For example, they cause Gs to substitute for Cs, or they cause mutations at specific spots on the genome. So if you had a bunch of mutations in a single cell (or collection of related cells) that matched the modus operandus of a known genotoxic agent, then it would be reasonable to conclude that the mutations were induced. But not all genotoxic agents are like that. And if you only have 1 or 2 mutations, that's not enough to prove they were induced. Also, of course, it depends on your sample size and your controls.

sleep - Is it possible to live without health problems sleeping one day and not the other?

Basically, I want to know if it would be humanely possible to sleep one day, skip the next, sleep, skip, sleep, skip, etc, with a 8 hour sleep time.

If you need any extra information, let me know.

Answer

(too long to be a comment)

You may be interested in http://en.wikipedia.org/wiki/Phase_response_curve.

This graph shows how the body's circadian rhythm normally works: http://en.wikipedia.org/wiki/File:Body_Temp_Variation.png. Body temperature decreases during the night (apparently due to more melatonin production.

I conjecture that the proposed schedule would interfere with the Circadian rhythm. Melatonin is the hormone that regulates sleep--it causes drowsiness. It is suppressed by blue light (because we get exposed to blue light in the daytime).

Aside from this, I am also very interested in the effects because I have personally wondered about the same question. The thing I am worried about is significant immunosuppression.

A larger question might be--"Why is sleep necessary?" Does it serve only to conserve food (which is very useful if you are living on subsistence) or does it serve a greater purpose? (whenever I have asked anyone about it, they always cite "regeneration" and some have cited the recycling of neurotransmitters. Personally, I'm a little skeptical.)

One final study: there was a study by Dement on the effect of dream deprivation: he took several people and woke them up whenever they went into REM sleep. Then, there was a period when the patients were not woken up. He found that there was a "REM rebound"--that they would go into more REM sleep after they had been deprived of it. This seems to indicate that dreaming, specifically, may serve a significant purpose.

Pathogenesis of Chronic Venous Congestion in Lungs?

I am thinking how CVC in lungs lead to the left-sided heart failure.

Answer

I think CVC lead to Pulmonary congestion and edema. They produce heavy, wet lungs.

Pulmonary changes include

1. perivascular and interstitial edema, particularly in the interlobular septa;


2. progessive edematous widening of alveolar septa; and



3. accumulation of edema fluid in alveolar spaces which contain Hemosiderin and microhemorrhages

Now, the progression of the disease to heart should be discussed. I am not sure if hemosiderin can go directly from lungs to heart or if it has to travel through circulation and then to left-side of lung.

exams - Falsely accused of cheating in college

I finished up a final exam right before the holidays, it was 10 questions, fully mathematically explained questions, and just after the holidays, I got an email from my professor saying that I am being investigated for cheating and have a meeting with my professor next week.

Apparently the guy I'm being accused of cheating from is a guy that sat in the same row as I did and he had some questions that had NEARLY the exact same text. This guy was my friend, but that's because we entered the classroom and sat in the same row, I had absolutely no plans of cheating,

I don't have that kind of thick skin and would never pull that mess - especially in college. Apparently my friend and I had some similarities between questions that suggested that we cheated, whether it was a collaboration or whether one cheated from another.

The problem is that I have no clue if my friend looked at my paper or was trying to cheat from me but I can be sure that I was not cheating from his work. I was doing my own thing during the exam period. If I get the exact same test with the same questions, I would get about 90-95% of the same answers I did for that final exam if I remember my material still, which I hope I do because I actually studied my best for it.

Anyways, I'm just curious, what exactly should I do when confronted - should I just tell the professor everything I just wrote here - Like what was going on. I'm getting anxiety over the fact that I might fall in to deeper pit if I sound aggressive or say things that might turn against my favor. I am willing to retake the same test in front of the professor on the spot to prove to the professor that I will get more or less the same result. On top of that, the professor allowed everyone to bring in a double sided piece of paper with information about the course on it to help us (like a legal cheat-sheet) during the final exam, and my cheat sheet covered about 9/10 questions on the test. What fricking reason would I have to cheat off of someone else?!

On top of all that, I took 3 different courses last year that pretty much covered 90% of the math course I took this year, and a lot of people didn't take those courses in my field. I took a course that covered probability, another that covered linear algebra and another course that covered proofs, all of which combined to create 9 out of 10 questions from that test. I knew all my material going in. What should I say or do? I don't want to spook the professor in to contacting the dean because this is phase 1 in the scholastic offence book - to contact the student first before deciding anything else to make sure there is enough evidence to continue further. Should I just say everything I wrote here?

zoology - Why are cancer rates low in large animals?

Large animals generally have more cells and live longer than smaller animals. For example, bowhead whales live up to 200 years and weigh up to 100 tonnes, as opposed to humans (living ~71 years and weigh ~75 kg) and mice (10–25 g, <1 year in the wild). Hence, whales have an immense number of cells and those cells are subjected to environmental carcinogenic influences (chemicals, UV) for a longer period of time.

Cancer is caused by random mutations and those random mutations are basically stochastic processes. Given their long life span and larger number of cells, shouldn't larger animals have a substantially higher chance to develop cancer? In fact, story goes that bowhead whales in fact only very rarely contract cancer, and less so compared to humans?

graduate school - What is the purpose of the weekly research meetings that advisers often have with their research group?

Does it usually happen even if all of the adviser's students have very different research interests?

Answer

These meetings can serve a variety of purposes, but many of them fall into the broad category of keeping the adviser and all the group members updated on what everyone in the group is doing. Below are some of the secondary benefits of a group meeting:

• saves the adviser time (compared to meeting with students individually)


• motivates the students to keep doing work, so they have something to report at the meeting


• fosters a sense of community with the group


• provides the students experience giving informal presentations


• often leads to the more senior students mentoring the junior students

To answer your follow-up question in the description, no, some faculty meet with each student individually; in fact these separate meetings are common, for example, in mathematics.

graduate school - What are the signs that it is time to switch from thesis to capstone track?

The Master's program (Software Engineering) I'm enrolled in offers both a thesis track and capstone track. Currently I'm enrolled in the thesis track and I've completed all of the required coursework for the thesis track, but I've been stuck in the thesis proposal process for over a year now¹ and I'd like to just graduate and be done. I suspect that I'm being "encouraged" to switch over to the capstone track without the Research Advisor outright saying it. What should I take as the signs that it's time to make the switch?

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1. By stuck I don't mean that I don't have a proposal, I mean that I've been submitting revisions about once a month for the past year with conflicting feedback being received and no real progress towards having a Thesis Director.

Answer

This answer might not be applicable to everyone; however, today I met with the Associate Director of Professional Programs at [tier-one university]. I was informed that barring extenuating circumstances, if a student doesn't have an accepted proposal and a Thesis Director assigned after a year then they should switch over to the capstone track to ensure they are able to successfully finish their degree.