Stability of the Kauffman Model

Random Boolean networks, the Kauffman model, are revisited by means of a novel decimation algorithm, which reduces the networks to their dynamical cores. The average size of the removed part, the stable core, grows approximately linearly with N, the number of nodes in the original networks. We show that this can be understood as the percolation of the stability signal in the network. The stability of the dynamical core is investigated and it is shown that this core lacks the well known stability observed in full Kauffman networks. We conclude that, somewhat counter-intuitive, the remarkable stability of Kauffman networks is generated by the dynamics of the stable core. The decimation method is also used to simulate large critical Kauffman networks. For networks up to N=32 we perform full enumeration studies. Strong evidence is provided for that the number of limit cycles grows linearly with N. This result is in sharp contrast to the often cited $\sqrt{N}$ behavior.Comment: 12 pages, 4 figure

Three-helix-bundle Protein in a Ramachandran Model

We study the thermodynamic behavior of a model protein with 54 amino acids that forms a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid and has the Ramachandran torsional angles $\phi_i$, $\psi_i$ as its degrees of freedom. The force field is based on hydrogen bonds and effective hydrophobicity forces. For a suitable choice of the relative strength of these interactions, we find that the three-helix-bundle protein undergoes an abrupt folding transition from an expanded state to the native state. Also shown is that the corresponding one- and two-helix segments are less stable than the three-helix sequence.Comment: 15 pages, 7 figure

Five month persistence of Helicobacter pylori infection in guinea pigs

Seven Dunkin-Hartley guinea pigs were infected with the Sydney strain of H. pylori (SS1). Gastric histopathology was evaluated and serum antibody response to H. pylori cell-surface proteins was analysed by enzyme immunoassay (EIA) and immunoblot. Tissue and faecal samples from five control animals were analysed for the presence of naturally occurring Helicobacter spp. infection by culture and Helicobacter genus-specific PCR. The H. pylori infection persisted for 5 months, in most animals accompanied by a histologically severe antral gastritis, exhibiting focal degeneration and necrosis of gastric crypt epithelium. Increased numbers of mitotic figures were observed in the gastric epithelium, indicating a regenerative process. Infected animals displayed specific antibodies towards H. pylori cell-surface proteins in immunoblot, whereas EIA was of dubious value creating false-positive results. Serum complement C3 and cholesterol levels appeared to be elevated in infected animals. Helicobacter spp. infection was not detected in the control animals. The persistent infection, accompanied by severe gastritis and a prominent serum antibody response, and the apparent absence of a natural Helicobacter spp. infection makes the guinea pig model useful in H. pylori research

Single layer centrifugation-selected boar spermatozoa are capable of fertilization in vitro

BACKGROUND: Good quality spermatozoa are important to achieve fertilization, viable embryos and offspring. Single Layer Centrifugation (SLC) through a colloid (Androcoll-P) selects good quality spermatozoa. However, it has not been established previously whether porcine spermatozoa selected by this method maintain their fertility. METHODS: The semen was prepared either by SLC or by standard centrifugation (control) and used for in vitro fertilization (IVF) at oocyte:spermatozoa ratios of 1:50; 1:100 and 1:300 (or 4 x 103, 8 x 103 and 24 x 103 spermatozoa/ml) to evaluate their subsequent ability to generate blastocysts. In addition, sperm motility was assessed by computer assisted sperm motility analysis. RESULTS: Total and progressive motility were significantly higher in sperm samples prepared by SLC compared to uncentrifuged samples. Sperm binding ability, polyspermy, cleavage and blastocyst rates were affected by the oocyte:sperm ratio, but not by sperm treatment. CONCLUSION: The use of SLC does not adversely affect the in vitro fertilizing and embryo-generating ability of the selected spermatozoa compared to their unselected counterparts, but further modifications in the IVF conditions would be needed to improve the monospermy in IVF systems. Since SLC did not appear to have a negative effect on sperm fertilizing ability, and may in fact select for spermatozoa with a greater potential for fertilization, an in vivo trial to determine the usefulness of this sperm preparation technique prior to artificial insemination is warranted

Comparison of LES Models Applied to a Bluff Body Stabilized Flame

Present-day demands on combustion equipment are increasing the need for improved understanding and prediction of turbulent combustion. Large Eddy Simulation (LES), in which the large-scale flow is resolved on the grid, leaving only the small-scale flow to be modeled, provides a natural framework for combustion calculations as the transient nature of the flow is resolved. In most situations, however, the flame is thinner than the LES grid, and subgrid modeling is required to handle the turbulence-chemistry interaction. Here, we examine the predictive capabilities and the theoretical links between LES flamelet models, such as the G-equation model (G-LES), and LES finite rate chemistry models, such as the Thickened Flame Model (TFM-LES), the Partially Stirred Reactor model (PaSR-LES), the Eddy Dissipation Concept (EDC-LES) model, a Presumed Probability Density Function (PPDF-LES) model and the Implicit LES (QL-LES) model. The models are described, and theoretical links between these are discussed in terms of the turbulent flame speed and flame thickness. In addition, the different models are used to study a bluff-body stabilized flame and the resulting predictions are compared with experimental data for two operating conditions