Light scattering by arbitrarily oriented rotationally symmetric particles

We use the T-matrix approach and the analytical orientation-averaging technique to formulate the problem of light scattering by an ensemble of rotationally symmetric particles in arbitrary orientation. The mathematical formulation yields analytical expressions for the elements of the ensemble-averaged scattering matrix that involve no more than four nested summations. An expansion into generalized spherical functions is used in the particular case where the scatterers are partially aligned along the direction of incidence. A computer code that implements the analytical expressions derived is publicly available on the World Wide Web at http://irctr.et.tudelft.nl/ -Skaropoulos/T-matrix.htm.     

Application of Mismatch Detection Methods in DNA Computing

In many implementations of DNA computing, reliable detection of hybridization is of prime importance. We have applied several well-established DNA mutation scanning methods to this problem. Since they have been developed for speed and accuracy, these technologies are very promising for DNA computing. We have benchmarked a heteroduplex migration assay and enzymatic detection of mismatches on a 4 variable instance of 3SAT, using a previously described blocking algorithm. The first method is promising, but yielded ambiguous results. On the other hand, we were able to distinguish all perfect from imperfect duplexes by means of a CEL I mismatch endonuclease assay.     

Rapid detection of stressed Salmonella spp. in dairy and egg products using immunomagnetic separation and PCR

The rapid detection of an average of 5.9 stressed Salmonella cells in 25 g of food product using immunomagnetic separation (IMS) and PCR is described. For pasteurised egg yolk, egg yolk powder, ice-cream, whole egg, egg white and cheeses made from pasteurised milk PCR was applied after 16 h of preenrichment in buffered peptone water (BPW) using IMS and alkaline lysis as sample preparation method. For whole egg and egg white the BPW was supplemented with iron. For milk powder, and raw milk cheeses, the 16-h preenrichment in BPW was followed by IMS and a 4-h enrichment in Rappaport-Vassiliadis broth. In the latter case, PCR was applied on the enrichment medium after centrifugation and alkaline lysis. For PCR the primers ST11 and ST15 (Aabo et al., 1993) producing a fragment of 429 bp were used. An internal PCR control, designed to be co-amplified with the target DNA using the same primers but producing a smaller fragment of 240 bp, was used.     

A rapid turnaround design of a high speed VLSI search processor

Performance of relational database systems is a major impediment to their use in many applications. We have designed and implemented a customized RISC processor to accelerate associative search and aggregation operations for relational database systems. Since the processor is programmable and supports many queries concurrently, a system utilizing tens of such processors is capable of handling thousands of complex search requests simultaneously.

While the design of a VLSI programmable processor is a complex process, research prototyping requires a fast turnaround design process. We took advantage of the logic programming paradigm and the silicon compiler technology to explore and simulate architecture alternatives prior to the actual implementation. The prototyping process allowed us to complete the chip design in nine months. The resulting processor, fabricated in 2 Itm CMOS technology, consists of 91,000 transistors, executes over 18 million predicate evaluations per second, and searches database contents at 74 megabytes per second.     

Comparison of the pharmacological profile of S-nitrosothiols, nitric oxide and the nitrergic neurotransmitter in the canine ileocolonic junction

1. In organ bath experiments, hydroquinone (30-100 microM) and hydroxocobalamin (30-100 microM) concentration-dependently inhibited the relaxations induced by NO (0.3-30 microM) but not those by nitroglycerin (GTN, 1 microM) in the canine ileocolonic junction (ICJ). Hydroxocobalamin reduced the relaxation to low frequency (2 Hz) stimulation of the non-adrenergic, non-cholinergic (NANC) nerves, whereas hydroquinone only reduced the NANC nerve-mediated relaxations to electrical stimulation at 16 Hz, 0.5 ms. 2. Relaxations to S-nitroso-L-cysteine (CysNO, 1-30 microM), or S-nitroso-N-acetyl-D,L-penicillamine (SNAP, 1-30 microM) were not inhibited by hydroquinone (30-100 microM), hydroxocobalamin (30-100 microM), pyrogallol (30-100 microM) or L-cysteine (1-3 microM). Hydroquinone (100 microM) only reduced the relaxation to 10 microM CysNO. Hydroxocobalamin, but not hydroquinone, pyrogallol or L-cysteine, potentiated the relaxations to the lowest concentration (1 microM) of S-nitrosoglutathione (GSNO, 1-30 microM). 3. In the superfusion bioassay, hydroquinone (100 microM) and hydroxocobalamin (1 microM) concentration-dependently inhibited the biological activity of authentic NO (1-4 pmol) to the same extent as that of the transferable nitrergic factor, released from the canine ICJ in response to NANC nerve stimulation (8-16 Hz, 2 ms). Responses to GTN (10 pmol) or adenosine 5'-triphosphate (10 nmol) were not affected. 4. In conclusion, the nitrosothiols CysNO, SNAP and GSNO relax the canine ileocolonic junction, but these relaxations, pharmacologically, behave differently from the NANC nerve-mediated relaxations. From the bioassay experiments, we conclude that the nitrergic factor, released in response to NANCnerve stimulation of the canine ICJ, behaves pharmacologically like NO but not like a nitrosothiol.Therefore, we suggest NO, and not CysNO, SNAP or GSNO as the inhibitory NANC neurotransmitter in the canine ICJ.     

Trisomy 18 anomalies on sonography and calculated risk of chromosomal abnormalities during first trimester

Trisomy 18 is a chromosomal disorder giving multiple anomalies. Its frequency depends on maternal age. We report a 28-year-old woman in her first pregnancy, who underwent first trimester scanning for screening. Due to increased nuchal translucency and exomphalos, chorionic villous sampling was performed. Cytogenetic diagnosis was trisomy 18 and termination of pregnancy was carried out immediately.     

Structure prediction of subtilisin BPN' mutants using molecular dynamics methods

In this paper we describe the achievements and pitfalls encounteredin doing structure predictions of protein mutants using moleculardynamics simulation techniques in which properties of atomsare slowly changed as a function of time. Basically the methodconsists of a thermodynamic integration (slow growth) calculationused for free energy determination, but aimed at structure prediction;this allows for a fast determination of the mutant structure.We compared the calculated structure of the mutants Met222Ala,Met222Phe and Met222Gln of subtilisin BPN' with the respectiveX-ray structures and found good agreement between predictedand X-ray structure. The conformation of the residue subjectto the mutation is relatively easy to predict and is mainlydetermined by packing criteria. When the side chain has polargroups its exact orientation may pose problems; long-range Coulombinteractions may generate a polarization feedback involvingsystem relaxation times beyond the simulation time. Changesinduced in the environment are harder to predict using thismethod. In particular, rearrangement of the hydration structurewas difficult to predict correctly, probably because of thelong relaxation times. In all conversions made the changes observedin the environment were found to be history-dependent and inparticular the hydrogen bonding patterns provided evidence formetastable substates. In all cases the structure predicted wascompared with available kinetic data and the reduced activitycould be explained in terms of changes in the configurationof the active site.     

Cross section measurements of the 23Na(n, 2n)22Na, 58Ni(n, 2n)57Ni and 115In(n,n′)115mIn reactions

Cross sections for two high energy threshold reactions ²³Na(n, 2n)²²Na and ⁵⁸Ni(n, 2n)⁵⁷Ni were measured by the activation method in the neutron energy range from 14 to 18 MeV. Inelastic scattering cross section for ¹¹⁵In was measured in the threshold region, i.e. from 0.5 to 1.3 MeV. The results of measurements are compared with scarce and divergent earlier data.     

Molecular interaction of quinoline with coal-liquid fractions

A direct calorimetric method has been used to determine simultaneously the molar enthalpy, ΔH^o, and equilibrium constant, K, for the interaction of quinoline (Qu) with coal-derived asphaltenes (A), acid/neutral (AA) and base (BA) components of A, silylated asphaltenes (A(TMS)) and heavy oil (HO) fractions in solvent C₆H₆. Solvent fractionated A and HO fractions were from three centrifuged-liquid product (CLP) samples prepared in the 450 kg ($\text{≈}\text{1}\text{2}$ U.S. ton) per day Process Development Unit at Pittsburgh Energy Research Center, at different process conditions from the same feed coal, Kentucky hvAb. For a given system, Qu-A (AA or BA), Qu-HO, the almost constant value of K and rectilinear variation of ΔH^o with the phenolic oxygen content of coal-liquid fractions have been attributed to the dominance of hydrogen-bonding effects, involving phenolic OH, over other types of molecular interactions in solution. In the Qu-A(TMS) system, ?ΔH^o values increase with decrease in molecular weight of A(TMS), while ?ΔS^o values increase with increase in aromaticity of the A fraction. The degree of complexation, in absence of OH groups, is much smaller than with the Qu-A system.