A Modeling Framework for Generation of Positional and Temporal Simulations of Transcriptional Regulation.

We present a modeling framework aimed at capturing both the positional and temporal behavior of transcriptional regulatory proteins in eukaryotic cells. There is growing evidence that transcriptional regulation is the complex behavior that emerges not solely from the individual components, but rather from their collective behavior, including competition and cooperation. Our framework describes individual regulatory components using generic action oriented descriptions of their biochemical interactions with a DNA sequence. All the possible actions are based on the current state of factors bound to the DNA. We developed a rule builder to automatically generate the complete set of biochemical interaction rules for any given DNA sequence. Off-the-shelf stochastic simulation engines can model the behavior of a system of rules and the resulting changes in the configuration of bound factors can be visualized. We compared our model to experimental data at well-studied loci in yeast, confirming that our model captures both the positional and temporal behavior of transcriptional regulation.

Structural (XRD) and thermal (DSC, TGA) and BET analysis of materials derived from non-metal cation pentaborate salts.

The synthesis, structural characterization (XRD), and thermal properties of nine non-metal cation (NMC) pentaborate anion salts, [NMC][B(5)O(6)(OH)(4)] (1a-1i) is described (NMC = [NH(3)CMe(2)(CH(2)OH)](+) (a), [O(CH(2)CH(2))(2)NH(2)](+) (b), [NH(3)CMe(CH(2)OH)(2)](+) (c), [2-(2-CH(2)CH(2)OH)PyH](+) (d), [(CH(2))(4)NH(CH(2)CH(2)OH)](+) (e), [(CH(2))(5)NH(CH(2)CH(2)OH)](+) (f), [2-MeImid](+) (g), [Me(3)NCMe(2)(CH(2)OH)](+) (h), [O(CH(2)CH(2))(2)NMe(2)](+) (i). Single-crystal X-ray diffraction studies on all compounds show that they contain isolated pentaborate anions, H-bonded together in a supramolecular array, with the cations occupying the cavities within the network. Compound 1c was obtained as a partial hydrate (0.16H(2)O). TGA and DSC analysis (in air, 25-1000 degrees C) indicate that compounds 1a-1i thermally decompose via a 2 stage process to B(2)O(3). The first stage (<250 degrees C) is dehydration to condensed polymeric pentaborates {approximate composition: [NMC][B(5)O(8)] (2a-2i)}. Five condensed pentaborates (2a-c, 2e, 2g) were synthesised and characterized by powder XRD and BET analysis. These condensed pentaborates were amorphous. The isolated pentaborates intumesced at approximately 600 degrees C (occupying approximately 10 times their original volume), and then contracted back to black glassy B(2)O(3) solids at 1000 degrees C. The intumescent materials (3a), (3b), (3e), (3g), and a final B(2)O(3) sample (4b) were synthesised and isolated and their porosities determined. BET surface area analysis on the isolated pentaborates (1a-c, 1e, 1g), the condensed pentaborates (2a-c, 2e, 2g), intumesced materials (3a, 3b, 3e, 3g), and B(2)O(3) (4b) showed that they were all 'non-porous' (<1.59 m(2) g(-1)).

Evidence that in vivo wear damage alters kinematics and contact stresses in a total knee replacement.

Polyethylene wear after a total knee arthroplasty is inevitable. The effects of the wear particles on the surrounding soft tissue causing inflammatory responses and eventual aseptic loosening are well documented, but the biomechanical changes from polyethylene wear have been less understood. This study investigated how wear from a retrieved polyethylene insert from a total knee arthroplasty changed the kinematics and contact stresses. A cruciate-retaining total knee implant (Natural-Knee, Intermedics Orthopedics, Inc., Austin, Texas) was retrieved from a donor program. The polyethylene insert was then scanned and modeled. KneeSIM (LifeMOD/KneeSIM, San Clemente, California) was used to simulate one cycle of gait of three second duration (100% of cycle). A threefold increase in contact stress as well as resulting kinematic changes were seen when the model was used to compare the retrieved versus a modeled off-the-shelf new polyethylene insert. Total knee designs should take into account the wear patterns that result from years of use and how they may affect the biomechanics of the knee long term.