Diffusion-reaction modelling of DNA hybridization kinetics on biochips

An analytical expression for the rate of DNA hybridization on the surface of DNA biochips is established for the case of a finite 1-D diffusion space. The expression allows to account for the diffusion-limited supply of unreacted probe DNA and was obtained by solving the continuous 1-D reaction-diffusion mass balance using a Finite Fourier Transform technique. The extrapolation of the presently considered 1-D case to the full 3-D case is outlined as well. By bringing the obtained result into concurrence with the results of a stochastic random walk study, the kinetic constant k of the continuous reaction-diffusion model could be expressed as a function of the basic physico-chemical parameters (persistence length and jump frequency of the Brownian motion, collision frequency, binding probability) of the individual molecules. With the availability of an analytical expression describing the full time course of the 1-D hybridization process, and by using the Damköhler number Da=kh/D_mol, the different reaction- and diffusion-limited regimes occurring during the course of a hybridization process can now be described in general, dimensionless terms, allowing to establish some very simple rules for the design of DNA biochips and flow-through biosensors.     

X-masking during logic BIST and its impact on defect coverage

We present a technique for making a circuit ready for logic built-in self test by masking unknown values at its outputs. In order to keep the silicon area cost low, some known bits in output responses are also allowed to be masked. These bits are selected based on a stuck-at n-detection based metric, such that the impact of masking on the defect coverage is minimal. An analysis based on a probabilistic model for resistive short defects indicates that the coverage loss for unmodeled defects is negligible for relatively low values of n.     

On properties of multicast routing trees

In the last several years we witnessed the proliferation of multimedia applications on the Internet. One of the unavoidable techniques to support this type of communication is multicasting. However, even a decade after its initial proposal, multicast is still not widely deployed. One of the reasons is the lack of a solid business model. If the gain and the cost of multicast could be predicted, network operators might be encouraged to deploy multicast on a larger scale. In this paper we propose analytical expressions that could be used to estimate the gain of network‐layer multicast. We show that the theoretical model matches extensive simulation and Internet measurement results remarkably well. Furthermore, we examine the reliability of traceroute data and of traceroutes‐based conclusions. We investigate the node degree distributions in the Internet maps obtained from CAIDA and RIPE and we show the divergency of our results with those obtained by other researchers. We further focus on the analysis of multicast trees based on traceroute data. Only few results have been available on the node degree distribution of multicast routing trees which provided contradictory conclusions. Our results seem to indicate that the node degrees follow power laws only for a large number of multicast users. Copyright © 2005 John Wiley & Sons, Ltd.     

Block position dithering in DCT-coded sequences

An attempt has been made to hide the false edges perceived at block borders in DCT-coded image sequences. The standard H.261 codec is extended by simple pre- and postprocessing: shifting the input image over small pseudo-random horizontal and vertical distances and shifting back the output image by the same amount. A subjective comparison by a panel of 20 observers has established a quality improvement for interframe coding, if both the current image and the previous image are subjected to the same shift. Masking the block borders by adding a time-invariant noise image to the output is found to be a desirable option.     

The influence of lactoperoxidase,heat and low pH on survival of acid-adapted and non-adapted Escherichia coli O157:H7 in goat milk

In hot climates where quality of milk is difficult to control, a lactoperoxidase (LP) system can be applied in combination with conventional preservation treatments at sub-lethal levels to inhibit pathogenic microbes. This study investigated the effect of combined heat treatments (55 °C, 60 °C and 72 °C) and milk acidification (pH 5.0) on survival of acid-adapted and non-adapted Escherichia coli O157:H7 strains UP10 and 1062 in activated LP goat milk. Heat treatment at 72 °C eliminated E. coli O157:H7. Acid-adapted strains UP10 and 1062 cells showed resistance to combined LP and heat at 60 °C in fresh milk. The inhibition of acid-adapted and non-adapted E. coli O157:H7 in milk following combined LP-activation, heat (60 °C) and milk acidification (pH 5.0) suggests that these treatments can be applied to reduce E. coli O157:H7 cells in milk when they occur at low numbers (<5 log₁₀ cfu mL^?1) but does not eliminate E. coli O157:H7 to produce a safe product.     

Extraction and fractionation of wheat flour proteins

Extraction of wheat flour with 1.5% sodium dodecyl sulphate (SDS) solution dissolved 65–67% of the total flour nitrogen. The SDS-insoluble proteinaceous material was separated into glycoproteins-I, II and III by ultracentrifugation. Part of the SDS-soluble proteinaceous material was precipitated by addition of ethanol and separated into glycoproteins-IV, glutenins and globulins. The rest of the dissolved proteinaceous material was separated into glycoproteins-V, gliadins, glycoproteins-VI, and albumins by (NH₄)₂SO₄-precipitation and gel filtration chromatography.     

A New Technique for the Suppression of the MECG

After a review of the different techniques in use up to now for the detection of an interference-free abdominal fetal electrocardiogram (FECG), with the limitations of these techniques indicated, a new technique is described which does not suffer from these limitations. This technique is based on an optimization procedure applied to the multiplication coefficients of six independent abdominal signals which are added together. The theoretical background of this method is given, as well as the required operational conditions and electrode positions, leading to an FECG reading guaranteed free of maternal electrocardiogram (MECG).     

Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains

Although the conformational states of protein side chains can be described using a library of rotamers, the determination of the global minimum energy conformation (GMEC) of a large collection of side chains, given fixed backbone coordinates, represents a challenging combinatorial problem with important applications in the field of homology modelling. Recently, we have developed a theoretical framework, called the dead-end elimination method, which allows us to identify efficiently rotamers that cannot be members of the GMEC. Such dead-ending rotamers can be iteratively removed from the system under study thereby tracking down the size of the combinatorial problem. Here we present new developments to the dead-end elimination method that allow us to handle larger proteins and more extensive rotamer libraries. These developments encompass (i) a procedure to determine weight factors in the generalized dead-end elimination theorem thereby enhancing the elimination of dead-ending rotamers and (ii) a novel strategy, mainly based on logical arguments derived from the logic pairs theorem, to use dead-ending rotamer pairs in the efficient elimination of single rotamers. These developments are illustrated for proteins of various sizes and the flow of the current method is discussed in detail. The effectiveness of dead-end elimination is increased by two orders of magnitude as compared with previous work. In addition, it now becomes feasible to use extremely detailed libraries. We also provide an appendix in which the validity of the generalized dead-end criterion is shown. Finally, perspectives for further applications which may now become within reach are discussed.     

The use of thermal analysis techniques for the validation of phase transformation models

In the study of the phase transformation of steel several methods can be used to obtain information about the behaviour of steel during heating and cooling. In this research several conventional methods, e.g. dilatometry, were studied together with an in-situ thermal analysis method (ISTA). This method, which can be applied to any cooling curve, enables us to draw conclusions as to the transformation behaviour of the steel. Using a continuous annealing simulator (Casim) a range of cooling rates can be investigated with the resulting mechanical properties. It will be demonstrated that ISTA can be performed on the results of a variety of experimental techniques and therefore under very different experimental conditions. It is possible to investigate transformation behaviour and mechanical properties on a single test piece. Using the pressurized air cooling of the Casim proves to be a good compromise between the possibilities of determining the mechanical properties and flexibility in cooling conditions of the specimens.