Tuesday, 22 May 2007

terminology - What does "Activation" refer to in the context of the symptoms of Schizophrenia and Schizoaffective Disorder?

The authors use the Positive and Negative Syndrome Scale (PANSS) to assess symptoms. One of its cluster scores is activation factor.



Summary:
http://en.wikipedia.org/wiki/Positive_and_Negative_Syndrome_Scale



Original publication of the article, which doesn't list activation factors:
http://schizophreniabulletin.oxfordjournals.org/content/13/2/261.long



Marketed currently here:
http://www.mhs.com/product.aspx?gr=cli&id=overview&prod=panss



None of the sources I saw specified what is meant by activation factor, and many didn't even mention it. It's possible that it's the hyperactivity mentioned in the original publication. Also, it's possible that it's a modified category in the version sold at the last link. Hopefully this is enough information to get you started, if you want to hunt down the details.

Thursday, 17 May 2007

human biology - HSL Lightness vs Eye sensitivity

No, the L axis in the HSL color space does not really correspond to lightness as perceived by the human eye, except in the very crudest sense that, for given values of the H and S components, increasing L produces an increase in the perceived lightness.



The L component of the standard HSL color space is simply calculated as the average of the lowest and the highest RGB component of the color (in whichever RGB color space in being used): $$L = \frac{\min(R, G, B) + \max(R,G,B)}2$$



This definition alone should make it obvious that the L value cannot correspond to perceived lightness, since it completely ignores the middle one of the three RGB channels. Thus, the color (R=0, G=0, B=1), i.e. pure $\color{#0000ff}{\rm blue}$, has exactly the same L value (0.5) as the color (R=0, G=1, B=1), i.e. $\color{#00ffff}{\rm cyan}$, yet it's obvious at a glance that the latter color is visually much brighter.



Indeed, the HSL color space doesn't even try to match the perceptual lightness of the colors; rather, the definition of the L channel is chosen because it has the convenient feature that it maps black to L=0, white to L=1, and all the six maximally saturated pure RGB colors (red, yellow, green, cyan, blue and magenta), despite their wide perceptual lightness differences, to L=0.5.




A much better approximation to the perceived lightness of a color is the luma Y', which is defined as a weighted average of the RGB channels. The precise weights depend on the definition and the RGB color space used, but a common choice (from ITU-R Rec. 709) is: $$Y' = 0.2126\, R + 0.7152\, G + 0.0722\, B$$



The weighs are chosen to account for the different perceived lightness of the different RGB primary colors. A striking feature is the that the green component alone accounts for over 70% of the luma, nearly ten times as much as the blue component. Yet a visual comparison of $\color{#0000ff}{\rm 100\%\ blue}$ with $\color{#00ff00}{\rm 100\%\ green}$ does clearly confirm that this choice of weights is justified: the pure green appears much brighter than the blue, and almost as bright as the cyan (which is their sum) above.




However, the definition of the luma still ignores the non-linearity of both the standard RGB color spaces (such as sRGB) and the human eye. While these two effects partly cancel out each other, allowing luma to be used as a reasonable approximation of perceptual lightness, for truly accurate results they need to be accounted for. This involves several steps:



  1. Convert the RGB color into a linear color space. For sRGB, the following formula may be used: $R_L = f(R), G_L = f(G), B_L = f(B)$, where: $$f(C) = \begin{cases}C / 12.92 & \text{if } 0 \le C \le 0.04045 \\ ((C + 0.055) / 1.055)^{2.4} & \text{if } 0.04045 < C \le 1 \end{cases}$$ (Here, $R$, $G$ and $B$ are the sRGB component values, and $R_L$, $G_L$ and $B_L$ the linear ones, both scaled to the range from 0.0 to 1.0.) Alternatively, a very close approximation to the formula above is given by simple gamma-expansion with $\gamma = 2.2$: $f(C) = C^{2.2}$.


  2. Calculate the relative luminance as a weighted average of the linear RGB component values: $$Y = 0.2126\, R_L + 0.7152\, G_L + 0.0722\, B_L$$ (The weights are exactly the same as for the luma formula above, because that's where they come from; the luma calculation just blindly applies them to the gamma-compressed RGB values.)


  3. Convert the relative luminance value into an approximation of the percieved lightness, using something like the CIELAB formula: $\ell^* = 1.16\, g(Y) - 0.16$, where: $$g(Y) = \begin{cases} \tfrac13 \left(\tfrac{29}{6}\right)^2 Y + \tfrac{4}{29} & \text{if } 0 \le Y \le \left(\tfrac{6}{29}\right)^3\\ Y^{1/3} & \text{otherwise} \end{cases}$$ (Note: In the CIELAB standard, the $L^*$ value ranges from 0 to 100, but for the sake of consistency, in the formula above I chose to define $\ell^* = L^* / 100$, so that its range is also from 0 to 1.)


Wednesday, 16 May 2007

neuroscience - If a non-mammal is starved of oxygen for some time, how long would it take the animal's neurons to die?

Medically, recovery of brain function after 3 minutes of oxygen deprivation at body temperature is rare.



Further down here in 1 it indicates that at lower temperatures the time can be much longer. At 13C, the record is 80 minutes for people. Animals cooled to 0C have a record of recovery of three hours! Not sure how much like themselves they feel after that though...

Tuesday, 15 May 2007

botany - Any food crops that could grow in a desert provided that they get fertilizer and water

I am working on an idea to provide nearly unlimited amounts of water in desert regions. To make this commercially viable. I would use the water to irrigate desert sand and grow crops. Given my extremely limited understanding of biology, I cannot find an answer to the following question:



Are there any food crops (preferably high valuable/low maintenance ones), that can grow in a desert, given that I can just provide the seed, water and fertilizer and stop sandstorms.



My motivation for investigating this is the following map showing regions that are either already deserts or at risk of becoming deserts:
enter image description here



Source: http://en.wikipedia.org/wiki/Desertification

proteins - How to bind antibodies to study their properties?

Like any other protein, antibodies will aspecifically bind nitrocellulose or PVDF membranes, but any other protein present in your antibody preparation will also do.



Depending on the antibody class, more specific binding can be obtained with protein A or protein G, that recognize the Fc domain. It's usual to have protein A/G immobilized on a stationary phase like agarose.



If you know the antigen used to develop the antibody, you can also use the immunizing peptide crosslinked to CnBr activated sepharose as a probe to bind your antibodies.



Knowing something more about your antibody preparation and what exactly is the 'behavior' your want to study could help obtain better answers.

vision - Why do we squint?

Recently, I was having an eye exam and admitted to squinting my eyes to sharpen blurred edges. Later, while waiting for the dilation to set in, my brother (a would-be pharmacist fresh off an anatomy course) was telling me about how vision works.



As a non-scientist, here's as much as I gathered:



  • The pupil allows light into our eyes.

  • The lens bends and shifts to focus that light against our retina.

  • The retina translates this light-information into signals via the optic nerve.

  • Something about brains, and then sight!

So, my question is, if the lens being bent and shifted inside of our eye by muscles is how our eyes focus, why do those of us with poor vision squint? Surely it can't be that by narrowing my field of vision I'm consciously bending my lens.

Friday, 11 May 2007

microbiology - How to learn biomathematics?

MathsBio is quite a large field. It is an interdisciplinary branch having utility in a lot of branches in biology like biophysics, biomedical, genetics and molecular biology. Applied Mathematics is generally used in modelling and understanding biological phenomena where we have to deal with large amount of data, for example the use of graph theory for analysing biochemical networks. Systems biology is an emerging field which uses a lot of mathematics.



You should pick a book depending on the field in which you want to use mathematics, though having knowledge of elementary biology is necessary. I am suggesting some books which cover wide application of mathematics in biology.



Mathematical Biology: I. An Introduction by JD Murray



For systems biology:



Mathematical Modelling in Systems Biology: An Introduction by Brian Ingalls