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How can sequence entropy of a protein be found?
To find the sequence entropy of a protein (say, pdb code 4ICB) / DNA , I am using some codes written in C program. For this, I need to use BLAST and ClustalW2 , and resulting aligned sequences are fed into the program. I am curious to know whether there is any handy way of finding sequence entropy of a protein / DNA.
Thank you for help,
Is Chalmers' so-called "hard problem" in consciousness real?
In his 2014 book "Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts" Stanislas Dehaene wrote "Chalmers, a philosopher of the University of Arizona, is famous for introducing a distinction between the easy and the hard problems. The easy problem of consciousness, he argues, consists in explaining the many functions of the brain: how do we recognize a face, a word, or a landscape? How do we extract information form the senses and use it to guide our behavior? How do we generate sentences to describe what we feel?
“Although all these questions are associated with consciousness,” Chalmers argues, “they all concern the objective mechanisms of the cognitive system, and consequently, we have every reason to expect that continued work in cognitive psychology and neuroscience will answer them. By contrast the hard problem is the “question of how physical processes in the brain give rise to subjective experience … the way things feel for the subject. When we see for example, we experience visual sensations, such as that of vivid blue. Or think of the ineffable sound of a distant oboe, the agony of an intense pain, the sparkle of happiness or the meditative quality of a moment lost in thought … It is these phenomena that poses the real mystery of the mind”."
Stanislas Dehaene's opinion is "that Chalmers swapped the labels: it is the “easy” problem that is hard, while the “hard” problem just seems hard because it engages ill-defined intuitions. Once our intuition is educated by cognitive neuroscience and computer simulations, Chalmers’ “hard problem” will evaporate".
Personally, I agree with Stanislas Dehaene's opinion.
"Your concept of subjectivity does not require an internal perspectival representation of the space in which the organism exists".
Yes, as you probably remember, according to me the 'subjectivity' of a given organism entirely depends on this organism.Following
Qualitative Research Into Acting and other Performing Arts?
I am looking for first-person and ethnographic reports on the work of actors as they encounter texts, work together, and present to audiences. References to analogous work in music would be welcome as well.Following
What is the simplest way to "walk" out from a short (about 200 nt) known sequence?
I only need to go a few hundred nt in both directions. I am working with environmental genomic DNA. I have the 200 nt sequence in a vector and I have environmental genomic DNA from which the short segment was amplified and sequenced.
It will depend on the abundance of your target and the complexity of the eDNA sample. If you cloned the same sequence multiple times from the eDNA, then hopefully this will work.Following
Does anyone has interview guidelines asking for data quality for health promotion efforts?
My current research project is about the data quality in child injury prevention. In the course of my study, I predominately make use of qualitative methods.
I'm currently drafting the interview questions for expert interviews, asking about perceptions and expectations of stakeholders, working in child injury prevention, on current data systems in terms of quality (utility). I wondered if anyone had any great interview questions for this type of interview which they are willing to share?
Thanks for your help.
How is "unpublished data" defined?
Are data that are used in a dissertation considered "published" or "unpublished" data? Or is the term "published" data only associated with data that have been used in studies that have been published in peer-reviewed journals? Thanks for any clarification.
Can anyone tell me why the phytochemist use n-hexane and ethyl acetate combination in column chromatography.. why not the n-pentane and ethyl acetate?
For isolation of secondary metabolites from various fractions of plant extract, n-hexane is employed along with ethyl acetate or chloroform etc... my question is that why don't they use the n-pentane instead of n-hexane..?? In my opinion the n-pentane will be more efficient being non polar than n-hexane...
n-pentane polarity = 0.00
n-hexane polarity = 0.10Following
Why am I getting Large Standard deviation (SD) between CT value of technical replica?
I am getting large SD between the CT of the target gene technical replica. Can anyone explain this? The SD of the control Ct value is very small as expected.
If indeed you are talking about the difference in Cq values between technical replicates of a single sample, what were the Cq values of the 2nd sample you speak of? If the technical replicate Cq values for the 2nd sample were above 30, then one would expect a higher impact of sampling/Poisson distribution/Monte Carlo effect. If your technical replicate Cq values for the 2nd sample are below 30, then you would expect better agreement of the Cq values. Pipetting error could explain the latter, whereas expected sampling effect of samples with low target would explain the former.Following
What decides the volume of low temperature plasma?
I am studying the properties of lab-made low temperature plasma. During my study, one question confused me a lot: what decides the volume of low temperature plasma? If the plasma was confined in a cavity, the dimension of which was on the order of hundreds of micrometers, the plasma volume might be decided by the cavity dimensions. But if the plasma was sustained in a large cavity, what affected the volume of the plasma?
And was the sheath generated between the plasma and the wall of the cavity, no matter how large the cavity dimension was?
Dear Professor Pu,
Thank you so much for your answer.
Based on your answer, I understood that the dimension of plasma depended on the pressure and power mainly. When the dimension of plasma is larger than the chamber dimension, the plasma extends to the wall and sheath formed. Otherwise, there is no sheath forming between the plasma and the wall. I'm afraid if I have get your point?Following
Does anyone have access to keys/ID guides to Lepidopteran?
Give me detail , i am working on identification of Lepidopteran insects..specially butterflies
Please check this site http://butterfliesofamerica.com/ the most complet web site of butterflies from North, Central and South America). It contains over 160,500 full color images and list over 8,300 species. It is useful for identification at species level.Following
Is there anybody who knows about nonlinear time history analysis in Midas GTS?
I need some information about the new version of the program (2015) as it has changed a bit.Following
Can anyone suggest an instrument for assessing the attachment style in 8 to 12 year old children?
I want to assess the mother-child attachment style in 8 to 12 year old children. It should be not too long because it will be used before a 2 hour experimental setting.
Dear Jean, it should be a tool to assess attachment of the child. The goal is to find out how the attachment style influences the link between acute stress induction and pain perception in children. It will be an experiental setting that will take 2 hours. Therefore I searched for a relatively short intrument to assess attachment.
Thank you all already for your very interesting suggestions. It helps a lot already.Following
Can you suggest some literature on infrared image processing,...?
infrared image processing
take a look at:
Infrared thermography in nondestructive testing...
Can anyone recommend a DNA FISH probe sequence targeting the GFP sequence in a reporter plasmid?
I would like to localize a GFP reporter plasmid in mammalian cells by using DNA FISH. Can anyone recommend a probe sequence targeting GFP DNA?
Many thanks in advance.
Should professors jointly publish papers with students?
At what point should/could a student be encouraged to publish a worthwhile, viable paper on his own vs. the professor adding his name? Consider the academic level of the professor/student collaboration: undergraduate, master's, doctoral. What is the amount and value of the professor's contribution--a minor edit, a substantial rewrite, repeating an experiment, etc.--that determines when the professor and student should publish jointly? Whose name goes first? Is joint publishing a misuse of a student's work? Should professors give students with potentially publishable papers all the help they need without requiring their names be used?
Brigette@ presicely illustrated the both sides of supervisors co-authoring.Following
How can I do yeast one hybrid assay?
I am working on TFs and want to do yeast one hybrid assay to know the intracting partners. This is first time I am doing this experments. Could you suggest me the best way how to do it? or share the protocols you do in your lab. Your help will be highly appreciable.
Thanks in advance.
How split-ubiquitin screening works?Following
What are the rights of refugees under international law?
The greatest challenge facing refugees arriving in the developed world is to convince authorities that they are, in fact, entitled to recognition of their refugee status.
Sure dear Miranda that nothing could be hidden in our present days through the numerous media communication and connection. But out of political activism or opinion, ethnic discrimination or minorities differences, some scientists are persecuted only on the basis of their scientific work (may be gender.too). How could they claim for refugee rights in another country, since no mean is available in their country for their rights, where if they ask for , different form of persecution is organized against them (insidious, morale, professional, physical etc...)Following
Who is using Design Thinking processes and techniques to improve education in general?
We are researching in witch way Design Thinking can provide a methodology to improve educational and learning experiences.
Hi Katja, sorry for the broken link; we'll repair it asap. Did you get my PDF?
if there is anything else you'd like to know, please contact me.Following
How to avoid "double dipping" in fMRI analysis, when you try to correlate brain activation to behavior response?
When you define a contrast, it may reveal the same psychological processing as the behavior response does. Then it's dangerous to correlate brain activation resulted by the contrast and participants' behavior response. How can we justify it?
sorry, for the english.. because of my tablet.Following
Talking this week at the Methods in Ecology and Evolution conference on new methods in monitoring. Any really novel methods that I should mention?
I have the well known methods but wondering if I have missed anything really novel. Will credit in the talk anything new to me. Thanks. BillFollowing
What kind of characteristics do you have that may either positively or negatively influence your teaching?
I have often thought that it is who we are that most powerfully influences our teaching. But you may never have given much thought to which of your characteristics in particular influence your teaching either positively or negatively. Do you have specific examples? I wrote the following article on this topic some time ago, but never asked for feedback on this topic before now. Can you enhance this idea for me now?
Jacono, B. and J. Jacono (1993). "The impact of teacher characteristics on teaching." Journal of Nursing Staff Development. 11(3), 146-149.
Great answer Patrick. I am sure your perspective is very valuable. I liked the part about not hiding your struggles or confusion. When I was first diagnosed with fibromyalgia, I was so tired I had to sit down to teach a class (never my previous behaviour), and lost track of the thread I was discussing quite often and had to stop to regroup and sometimes lost my place in the notes I had to bring with me to be sure I was remembering to cover things in the course. I could also be short and testy with student questions depending on how I was thinking and feeling. Fibromyalgia plays havoc with your thinking and your mood because of the constant pain and the constant firing of the nerve fibres in very fast and erratic patterns. Fortunately with treatment all of this improved, but my thinking was never quite as good as previously (but quite adequate for the job), and my mood improved tremendously.Following
What could be the effect of ferrite and carbide on the pitting behavior?
The Fe-Mn matrix microstructure has carbides and the Fe-Mn-Al matrix has ferrite on the grain boundaries. What could be the effect of ferrite and carbide on the pitting behavior?
Pitting corrosion sometimes starts on the grain boundaries. To decrease corrosion, including pitting, dissolve carbides and create compressive residual stresses at the surface of hardened samples. Our investigations in this field will be published soon.Following
What is global cooling?
Explain this phenomena and if possible add references about positive and negative effects of it on biosphere.
Dear @Shankhadeep, I am not an expert as You are in this field, but I have watched 30 Top Scientists Predict Global Cooling 2015-2050!
"A new paper claims that declining solar activity since 1998 could mean falling global temperatures in the years ahead — contrary to predictions of rapid warming made by virtually all climate models."Following
Is there any hourly rainfall-runoff data source?
I am doing some analysis for which hourly rainfall-runoff data is needed for at least 5 years. Can anybody help me finding a source?
Thanks in advance
How can I solve non linear PDE with one dependent variable and two independent (space and time) variables using finite difference method?
I want to solve a second order non-linear PDE equation. It has one dependent variable and two independent variables ( space(x,y, and z directions) and time).I have no idea about how to solve this non-linear PDE equations. I want to know how to form the element matrix for non-linear PDE equation. Kindly suggest some specific books or references that talk about it
Go with MOL semidiscretization approach using central difference scheme and convert given PDE to system of ODE and use your preferred time stepping scheme in time direction. The best elementary book is Numerical Solution of Partial Differential Equations,Finite Difference Methods,Third Edition by G.D. Smith.Following
Fungal dna extraction kit
Can anyone suggest best kit for fungal dna extraction. I am having issues in obtaining clean dna. I am using CTAB method at present. I get good concentrations but the dna is not clean, which is affecting the library preparation for next generation sequencing.
You can use FAST DNA Spin Kit from mpbio, or Master pure DNA from epicentreFollowing
Why is the first coulombic efficiency is low for Li-S battery in carbonate electrolyte?
One reason is the SEI formation, the other is for the contribution of carbon substrate.
The carbonate electrolyte is not compatible to conventional S8 cathode because of the irreversible reaction between carbonates and generated high-order polysulfides (J. Phys. Chem. C 2011, 115, 25132–25137). As a result, the coulombic efficiency is very low.
If sulfur can be confined in micropores with size less than 0.5 nm, sulfur will be in form of short-chain S2-S4, and thus avoid formation of high-order polysulfides and the corresponding reversible reaction (J. Am. Chem. Soc. 2012, 134, 18510−18513).
Can anyone give me the example of the term acid what you Mean in the nucleic acid ?
what is mean the word acid in the nucleic acid ?
That mean the elctronic couple in the phosphate its responsible of acidty in Nucleic acidFollowing