Similarity by state/descent and genetic vector spaces: analysis of a longitudinal family study

Using the genome-wide screening data of the Framingham Heart Study (394 nuclear families, 1328 genotyped subjects, 397 marker loci) we have quantified the underlying genetic diversity through high-dimensional genetic feature vectors and constructed a genetic vector space for the analysis of population substructure. Adaptive clustering procedures led to three major subgroups that were regarded as being related to "biological" ethnicity and that included more than 70% of the subjects. Based on these subgroups we addressed the question of ethnicity-related and ethnicity-independent risk factors for coronary heart disease (CHD). To this end, we relied upon hypertension as an endophenotype of CHD and applied a multivariate sib-pair method in order to search for oligogenic marker configurations for which the sib-sib similarities deviated from the parent-offspring similarities. Indeed, the latter similarities are always "0.5" irrespective of the affection status of parents and offspring. Loci with significant contributions to the oligogenic marker configuration constituted a CHD-specific genetic vector space. We found several ethnicity-independent signals. One signal on chromosome 8 may relate to the CYP11B1/CYP11B2 genes

A transimpedance amplifier using a novel current mode feedback loop

We present a transimpedance amplifier stage based on a novel current mode feedback topology. This circuit employs NMOS and PMOS transistors exclusively and requires neither capacitor for stabilizing the transimpedance loop nor resistor for the transresistance feedback and transistor loading. This amplifier circuit is fully compatible with submicron digital CMOS processes. The active feedback network consists of two grounded-gate MOS devices which split the output current in both the feedback and output branches. The transresistance and the phase margin are adjustable through external DC signals. The measured rise time of the impulse response of the amplifier implemented in an industrial 0,7µm CMOS process is 18 ns for a transresistance of 180 k and 30 ns for a transresistance of 560 k. The measured Equivalent Noise Charge (ENC) is 800 rms e¯ for an input capacitance of 20 pF with the transresistance adjusted to 560 k

The difficulties of reproducing conventionally derived results through 500k-chip technology

Based on a "training" sample of 1,042 subjects genotyped for 5,728 single-nucleotide polymorphisms (SNPs) of a conventional 0.4-Mb genome scan and a "test" sample of 746 subjects genotyped for 545,080 SNPs on a 500k-chip, we investigated the extent to which the subjects' immunoglobulin M levels can be reproducibly predicted from a multilocus genotype. We were specifically interested in the reproducibility of predictors across populations (1,042 versus 746 subjects) and across SNP sets (conventional genome scan versus anonymous 500k-chip) because this is a prerequisite for clinical application. For the training sample, neural network (NN) analysis yielded classifiers that predicted immunoglobulin M levels from the subjects' multilocus genotypes at acceptable error rates through a configuration of 15 genomic loci (61 SNPs). With the test sample (746 subjects) we addressed the question of reproducibility across populations and across SNP sets by means of a novel "competitive SNP set" approach. However, the chip data contained several sources of distortion, including greatly elevated noise levels and artifact-prone SNP regions, thus complicating attempts to verify the reproducibility of NN predictors. Though 5 of 15 genomic loci from the training samples appeared to be reproducible, the NN classifiers derived so far from the test samples are insufficiently compatible with the training samples. Nonetheless, our results are promising enough to justify further investigations. Because the underlying algorithm can easily be split into parallel tasks, the proposed "competitive SNP set" approach has turned out to be well suited for computers with today's 64-bit multiprocessor architectures and to offer a valuable extension to genome-wide association analyses

Minority-carrier effects in poly-phenylenevinylene as studied by electrical characterization

Electrical measurements have been performed on poly[2-methoxy, 5 ethyl (2' hexyloxy) paraphenylenevinylene] in a pn junction with silicon. These included current-voltage measurements, capacitance-voltage measurements, capacitance-transient spectroscopy, and admittance spectroscopy. The measurements show evidence for large minority-carrier injection into the polymer possibly enabled by interface states for which evidence is also found. The shallow acceptor level depth (0.12 eV) and four deep trap level activation energies (0.30 and 1.0 eV majority-carrier type; 0.48 and 1.3 eV minority-carrier type) are found. Another trap that is visible at room temperature has point-defect nature. (C) 2001 American Institute of Physics

Non-invasive measurement of cholesterol in human blood by impedance technique: an investigation by 2D finite element field modelling

This paper concerns detection of solid particles suspended in conductive media by impedance technique. The technique is based on changes in impedance measured between two electrodes placed across a given volume of conducting medium. It presents a methodology for modelling and investigation of the feasibility of such a technique for particle detection by 2D finite element (FE) field modelling. This is based on modelling and computation of electric field distribution between the above electrodes. It establishes the modelling approach, the complexity involved and justifies the need for modelling in 3D to incorporate some of the effects that cannot be taken into account in 2D models. It reports on the modelling investigation for a specific case of detecting, by impedance technique cholesterol particles suspended in human blood and points to a possible instrument for non-invasive measurement of blood cholesterol level

Uncertainty quantification for kinetic models in socio-economic and life sciences

Kinetic equations play a major rule in modeling large systems of interacting particles. Recently the legacy of classical kinetic theory found novel applications in socio-economic and life sciences, where processes characterized by large groups of agents exhibit spontaneous emergence of social structures. Well-known examples are the formation of clusters in opinion dynamics, the appearance of inequalities in wealth distributions, flocking and milling behaviors in swarming models, synchronization phenomena in biological systems and lane formation in pedestrian traffic. The construction of kinetic models describing the above processes, however, has to face the difficulty of the lack of fundamental principles since physical forces are replaced by empirical social forces. These empirical forces are typically constructed with the aim to reproduce qualitatively the observed system behaviors, like the emergence of social structures, and are at best known in terms of statistical information of the modeling parameters. For this reason the presence of random inputs characterizing the parameters uncertainty should be considered as an essential feature in the modeling process. In this survey we introduce several examples of such kinetic models, that are mathematically described by nonlinear Vlasov and Fokker--Planck equations, and present different numerical approaches for uncertainty quantification which preserve the main features of the kinetic solution.Comment: To appear in "Uncertainty Quantification for Hyperbolic and Kinetic Equations

Combined analysis of 635 patients confirms an age-related association of the serotonin 2A receptor gene with tardive dyskinesia and specificity for the non-orofacial subtype

Tardive dyskinesia (TD) is an important limiting factor in the use of typical antipsychotic drugs. Genetic variability in the serotonin 2A (5-HT2A) receptor may influence risk for TD but the results of prior studies are not confirmatory. The objective of this study was to determine association of T102C and His452Tyr polymorphisms in the 5-HT2A receptor gene (HTR2A) with TD in a large, multicentre patient sample. The design employed case-control analysis controlling for possible confounders using pooled, original data from published and available unpublished samples and employing logistic regression, analysis of variance and meta-analysis. The study sample consisted of 635 patients with schizophrenia or schizoaffective disorder (256 with TD and 379 without TD) drawn from five research centres, divided into six groups based on population origin. The main outcome measure was association of a categorical diagnosis of TD based on the Research Diagnostic Criteria for TD with HTR2A T102C and His452Tyr genotypes and haplotypes. The findings indicate significant association of TD with HTR2A T102C genotype (p = 0.002) over and above the effect of population group, also when controlling for age and gender (p = 0.0008), but not with His452Tyr genotype. The T102C genotype was significantly associated with TD in older (> median age 47 yr, p = 0.002) but not younger patients and in patients with non-orofacial (limb-truncal) (p=0.001) but not orofacial TD. By meta-analysis the Mantel-Haenszel (M-H) pooled odds ratio (OR) across all the available data was 1.64. A T102C-His452Tyr haplotype was significantly associated with TD (p = 0.0008). These findings confirm that genetic variability in HTR2A contributes a small but significant degree of risk for the expression of TD, particularly in older patients and specifically for the non-orofacial (limb-truncal) type. Together with other genetic variants associated with TD the findings could be used to assess risk in patients who are candidates for treatment with typical antipsychotic medications