Whose Entropy: A Maximal Entropy Analysis of Phosphorylation Signaling

High throughput experiments, characteristic of studies in systems biology, produce large output data sets often at different time points or under a variety of related conditions or for different patients. In several recent papers the data is modeled by using a distribution of maximal information-theoretic entropy. We pose the question: ‘whose entropy’ meaning how do we select the variables whose distribution should be compared to that of maximal entropy. The point is that different choices can lead to different answers. Due to the technological advances that allow for the system-wide measurement of hundreds to thousands of events from biological samples, addressing this question is now part of the analysis of systems biology datasets. The analysis of the extent of phosphorylation in reference to the transformation potency of Bcr-Abl fusion oncogene mutants is used as a biological example. The approach taken seeks to use entropy not simply as a statistical measure of dispersion but as a physical, thermodynamic, state function. This highlights the dilemma of what are the variables that describe the state of the signaling network. Is what matters Boolean, spin-like, variables that specify whether a particular phosphorylation site is or is not actually phosphorylated. Or does the actual extent of phosphorylation matter. Last but not least is the possibility that in a signaling network some few specific phosphorylation sites are the key to the signal transduction even though these sites are not at any time abundantly phosphorylated in an absolute sense.     

Proliferative reactive gliosis is compatible with glial metabolic support and neuronal function

Background

Trail-making tests, such as the Concept Shifting Task (CST), can be used to test the effects of treatment on cognitive performance over time in various neuropsychological disorders. However, cognitive performance in such experimental designs might improve as a result of the practice obtained during repeated testing rather than the treatment itself. The current study investigated if practice affects the accuracy and duration of performance on the repeatedly administered Concept Shifting Task modified to make it resistant to practice (mCST). The mCST was administered to 54 healthy participants twice a day, before and after a short break, for eight days. Results. The ANOVA and meta-analysis showed that there was no improvement in the mCST accuracy on the last vs. the first trial (Hedges' g = .14, p = .221) or within the session (after vs. before the break on all days; g = .01, p = .922). However, the participants performed the task faster on the last vs. the first trial (g = -.75, p < .001) and after vs. before the break on all days (g = -.12, p = .002). Conclusions. Repeated administration of the mCST does not affect the accuracy of performance on the test. However, practice might contribute to faster performance on the mCST over time and within each session.     

Determination of anionic surfactants during wastewater recycling process by ion pair chromatography with suppressed conductivity detection

A direct approach utilizing ion pairing reversed-phase chromatography coupled with suppressed conductivity detection was developed to monitor biodegradation of anionic surfactants during wastewater recycling through hydroponic plant growth systems and fixed-film bioreactors. Samples of hydroponic nutrient solution and bioreactor effluent with high concentrations (up to 120 mS electrical conductance) of inorganic ions can be analyzed without pretreatment or interference. The presence of non-ionic surfactants did not significantly affect the analysis. Dynamic linear ranges for tested surfactants [Igepon TC-42, ammonium lauryl sulfate, sodium laureth sulfate and sodium alkyl (C10-C16) ether sulfate] were 2 to approximately 500, 1 to approximately 500, 2.5 to approximately 550 and 3.0 to approximately 630 microg/ml, respectively.     

SURFACE POTENTIAL AND PHOTO-ADSORPTION ONTO SEMICONDUCTORS

Abstract— A theory of photo-adsorption onto semiconductors is developed using the kinetic expressions and the relations for steady state carrier concentrations in terms of the quasien Fermi levels. Expressions are derived which emphasize the importance of the surface potential. In particular it is shown that a significant quantity is the ratio of the surface potential to a critical quantity, Y_sc . An expression for the latter is given and it is shown that photoadsorption occurs if the ratio is greater than unity while desorption occurs if the ratio is less than unity. The theory also suggests a useful graphical representation of the effects of impurities and surface potential on adsorption.     

Dynamics of competitive evolution on a smooth landscape

We study competitive DNA sequence evolution directed by in vitro protein binding. The steady-state dynamics of this process is well described by a shape-preserving pulse which decelerates and eventually reaches equilibrium. We explain this dynamical behavior within a continuum mean-field framework. Analytical results obtained on the motion of the pulse agree with simulations. Furthermore, finite population correction to the mean-field results are found to be insignificant.     

Blow-up and pattern formation in hyperbolic models for chemotaxis in 1-D

In this paper we study finite time blow-up of solutions of a hyperbolic model for chemotaxis. Using appropriate scaling this hyperbolic model leads to a parabolic model as studied by Othmer and Stevens (1997) and Levine and Sleeman (1997). In the latter paper, explicit solutions which blow-up in finite time were constructed. Here, we adapt their method to construct a corresponding blow-up solution of the hyperbolic model. This construction enables us to compare the blow-up times of the corresponding models. We find that the hyperbolic blow-up is always later than the parabolic blow-up. Moreover, we show that solutions of the hyperbolic problem become negative near blow-up. We calculate the zero-turning-rate time explicitly and we show that this time can be either larger or smaller than the parabolic blow-up time. The blow-up models as discussed here and elsewhere are limiting cases of more realistic models for chemotaxis. At the end of the paper we discuss the relevance to biology and exhibit numerical solutions of more realistic models.     

Blow-up and pattern formation in hyperbolic models for chemotaxis in 1-D

In this paper we study finite time blow-up of solutions of a hyperbolic model for chemotaxis. Using appropriate scaling this hyperbolic model leads to a parabolic model as studied by Othmer and Stevens (1997) and Levine and Sleeman (1997). In the latter paper, explicit solutions which blow-up in finite time were constructed. Here, we adapt their method to construct a corresponding blow-up solution of the hyperbolic model. This construction enables us to compare the blow-up times of the corresponding models. We find that the hyperbolic blow-up is always later than the parabolic blow-up. Moreover, we show that solutions of the hyperbolic problem become negative near blow-up. We calculate the zero-turning-rate time explicitly and we show that this time can be either larger or smaller than the parabolic blow-up time. The blow-up models as discussed here and elsewhere are limiting cases of more realistic models for chemotaxis. At the end of the paper we discuss the relevance to biology and exhibit numerical solutions of more realistic models.     

Analysis of electronically nonadiabatic chemical reactions: An information theoretic approach

A practical procedure for the determination of branching ratios for reactions which lead to either excited or electronically ground state products is outlined. The method is applied to four reactions which could (on energetic grounds) produce an electronically excited iodine atom. No case of a complete inversion is found, but one reaction (F + HI) is predicted to yield a statistical, (one half), I^*(²P_1/2) to I(²P_3/2) ratio.