Simulating perfect channels with probabilistic lossy channels

We consider the problem of deciding whether an infinite-state system (expressed as a Markov chain) satisfies a correctness property with probability 1. This problem is, of course, undecidable for general infinite-state systems. We focus our attention on the model of probabilistic lossy channel systems consisting of finite-state processes that communicate over unbounded lossy FIFO channels. Abdulla and Jonsson have shown that safety properties are decidable while progress properties are undecidable for non-probabilistic lossy channel systems. Under assumptions of “sufficiently high” probability of loss, Baier and Engelen have shown how to check whether a property holds of probabilistic lossy channel system with probability 1. In this paper, we consider a model of probabilistic lossy channel systems, where messages can be lost only during send transitions. In contrast to the model of Baier and Engelen, once a message is successfully sent to channel, it can only be removed through a transition which receives the message. We show that checking whether safety properties hold with probability 1 is undecidable for this model. Our proof depends upon simulating a perfect channel, with a high degree of confidence, using lossy channels.     

RNA amplification chip with parallel microchannels and droplet positioning using capillary valves

We present results from the MicroActive project which develops an instrument for molecular diagnostics. The instrument is first tested for patient screening for a group of viruses causing cervical cancer. Two disposable polymer chips with reagents stored on-chip are developed and will be inserted into the instrument for each patient sample analysis. The first chip will perform nucleic acid extraction from patient epithelial cervical cells, while mRNA amplification and fluorescent detection takes place in the second chip. This paper reports results on the amplification chip. Purified sample is inserted into the chip and split into ten smaller droplets for simultaneous amplification and detection of ten viruses. The droplets move in parallel channels, each with two chamber extensions containing dried reagents. Experimental results on parallel droplet movement using one external pump combined with hydrophobic restrictions show that the parallel droplet positions can be controlled. There are four valves with increasing burst pressures between 800 and 4,500 Pa in each parallel channel, positioning the droplets in metering zones and reaction chambers. The re-hydration times for the dried reagents in micro chambers have been monitored. After sample insertion, uniform concentration of the reagents in the droplet was reached after respectively 60 s and 10 min. These times are acceptable for successful amplification. Finally we show positive amplification of HPV type 16 viruses in a micro chamber.     

Dual setting α-tricalcium phosphate cements

An extension of the application of calcium phosphate cements (CPC) to load-bearing defects, e.g. in vertebroplasty, would require less brittle cements with an increased fracture toughness. Here we report the modification of CPC made of alpha-tricalcium phosphate (α-TCP) with 2-hydroxyethylmethacrylate (HEMA), which is polymerised during setting to obtain a mechanically stable polymer-ceramic composite with interpenetrating organic and inorganic networks. The cement liquid was modified by the addition of 30–70 % HEMA and ammoniumpersulfate/tetramethylethylendiamine as initiator. Modification of α-TCP cement paste with HEMA decreased the setting time from 14 min to 3–8 min depending on the initiator concentration. The 4-point bending strength was increased from 9 MPa to more than 14 MPa when using 50 % HEMA, while the bending modulus decreased from 18 GPa to approx. 4 GPa. The addition of ≥50 % HEMA reduced the brittle fracture behaviour of the cements and resulted in an increase of the work of fracture by more than an order of magnitude. X-ray diffraction analyses revealed that the degree of transformation of α-TCP to calcium deficient hydroxyapatite was lower for polymer modified cements (82 % for polymer free cement and 55 % for 70 % HEMA) after 24 h setting, while the polymerisation of HEMA in the cement liquid was quantitative according to FT-IR spectroscopy. This work demonstrated the feasibility of producing fracture resistant dual-setting calcium phosphate cements by adding water soluble polymerisable monomers to the liquid cement phase, which may be suitable for an application in load-bearing bone defects.     

Growth and structure of aggregates of heat-denatured β-Lactoglobulin

Summary The aggregation of the globular protein β-lactoglobulin after heat-denaturation was studied in aqueous solution at pH 7 using static and dynamic light scattering. The structure of the aggregates is self-similar with fractal dimension 2.0. Size exclusion chromatography and dynamic light scattering measurements show that the aggregates have a broad size distribution. Initially clusters of about 85 proteins and 15 nm radius are formed which are the elementary units of the larger fractal aggregates. At low ionic strength the formation of the larger aggregates is impeded by electrostatic interactions.
The structure of the aggregates is independent of the concentration and the temperature. The rate of aggregation has an Arrhenius temperature dependence with an activation energy of about 350 kJ/mol weakly dependent on the concentration. The apparent reaction order of the aggregation is 1.5. In the mixture both variants A and B have the same aggregation rate. The gel time increases with decreasing concentration and diverges at about 0.7g L⁻¹. At lower concentration the aggregate growth stagnates when all protein has aggregated.     

Evidence that atypical protein kinase C-lambda and atypical protein kinase C-zeta participate in Ras-mediated reorganization of the F-actin cytoskeleton

Liver fatty acid binding protein (L-FABP) appears to contain several different forms that may result from post-translational modification or bound ligand. To further assess this possibility, L-FABP was purified from rat liver homogenate and two putative isoforms separated using a sulfonyl column, a strong cation exchange resin. Fraction I eluted at 0.2 M NaCl, had a pI of 7.59, and following a final size exclusion step contained > 98% L-FABP. Fraction II eluted at 1.0 M NaCl, had a pI of 7.59, and following a final size exclusion step contained > 99% L-FABP. Both fractions contained approx. 0.15 moles of endogenous bound fatty acid per mole of protein, while L-FABP not subjected to the cation exchange step contained 0.75 moles of fatty acid per mole of protein. Fractions I and II had a greater proportion of saturated and monounsaturated fatty acids with a large reduction in polyunsaturated fatty acids compared to L-FABP not fractionated by cation exchange. Mass spectral analysis indicated the molecular mass of Fraction I was 14,315.02 +/- 0.35 Da and Fraction II was 14,315.86 +/- 0.34 Da. The peptide map for each fraction was determined by limited digestion of each fraction with either trypsin, Asp-N, or chymotrypsin to yield overlapping peptide fragments. Mass spectral analysis of these digests indicated the two proteins had identical amino acid fragments and that Cys69 was reduced and there were no Asn to Asp exchanges. Hence, these two forms of L-FABP were not isoforms and were not the result of differences in bound fatty acid. It is proposed that these two distinct forms of rat L-FABP were structural conformers based on two alternative folding pathways.     

The effect of binary cosolvent systems (glycerol–sucrose mixtures) on the heat-induced gelation mechanism of bovine serum albumin

The influence of cosolvent composition on the thermal denaturation and gelation of bovine serum albumin (BSA) has been studied. Cosolvent composition was varied by changing the ratio of glycerol to sucrose in 40 wt% cosolvent solutions containing BSA. Differential scanning calorimetry measurements on 0.5 wt% BSA solutions showed that the thermal denaturation temperature of the protein increased with increasing sucrose content. Temperature scanning dynamic shear rheology and turbidity measurements on 4 wt% BSA solutions showed that the gelation temperature and final gel strength increased with increasing sucrose concentration. These observations were attributed to the fact that sucrose was more effective than glycerol at increasing the thermal stability and attraction between globular BSA molecules through a steric exclusion effect. The molecular origin of these effects is the tendency for the system to minimize the contact area of the protein molecules with the surrounding cosolvent solution.