Linkage disequilibrium assessment via log-linear modeling of SNP haplotype frequencies

Analyses of high-density single-nucleotide polymorphism (SNP) data, such as genetic mapping and linkage disequilibrium (LD) studies, require phase-known haplotypes to allow for the correlation between tightly linked loci. However, current SNP genotyping technology cannot determine phase, which must be inferred statistically. In this paper, we present a new Bayesian Markov chain Monte Carlo (MCMC) algorithm for population haplotype frequency estimation, particulary in the context of LD assessment. The novel feature of the method is the incorporation of a log-linear prior model for population haplotype frequencies. We present simulations to suggest that 1) the log-linear prior model is more appropriate than the standard coalescent process in the presence of recombination (>0.02cM between adjacent loci), and 2) there is substantial inflation in measures of LD obtained by a "two-stage" approach to the analysis by treating the "best" haplotype configuration as correct, without regard to uncertainty in the recombination process. Genet Epidemiol 25:106-114, 2003. (C) 2003 Wiley-Liss, Inc.

Taxonomic free sorting: a successful method with older consumers and a novel approach to preference mapping

Taxonomic free sorting (TFS) is a fast, reliable and new technique in sensory science. The method extends the typical free sorting task where stimuli are grouped according to similarities, by asking respondents to combine their groups two at a time to produce a hierarchy. Previously, TFS has been used for the visual assessment of packaging whereas this study extends the range of potential uses of the technique to incorporate full sensory analysis by the target consumer, which, when combined with hedonic liking scores, was used to generate a novel preference map. Furthermore, to fully evaluate the efficacy of using the sorting method, the technique was evaluated with a healthy older adult consumer group. Participants sorted eight products into groups and described their reason at each stage as they combined those groups, producing a consumer-specific vocabulary. This vocabulary was combined with hedonic data from a separate group of older adults, to give the external preference map. Taxonomic sorting is a simple, fast and effective method for use with older adults, and its combination with liking data can yield a preference map constructed entirely from target consumer data.

Influence of short-term solar disturbances on the fair weather conduction current

The fair weather atmospheric electrical current (Jz) couples the ionosphere to the lower atmosphere and thus provides a route by which changes in solar activity can modify processes in the lower troposphere. This paper examines the temporal variations and spectral characteristics of continuous measurements of Jz conducted at the Wise Observatory in Mitzpe-Ramon, Israel (30°35′ N, 34°45′ E), during two large CMEs, and during periods of increased solar wind density. Evidence is presented for the effects of geomagnetic storms and sub-storms on low latitude Jz during two coronal mass ejections (CMEs), on 24–25th October 2011 and 7–8th March 2012, when the variability in Jz increased by an order of magnitude compared to normal fair weather conditions. The dynamic spectrum of the increased Jz fluctuations exhibit peaks in the Pc5 frequency range. Similar low frequency characteristics occur during periods of enhanced solar wind proton density. During the October 2011 event, the periods of increased fluctuations in Jz lasted for 7 h and coincided with fluctuations of the inter-planetary magnetic field (IMF) detected by the ACE satellite. We suggest downward mapping of ionospheric electric fields as a possible mechanism for the increased fluctuations.

An automatic correction method for the heel effect in digitized mammography images

The most significant radiation field nonuniformity is the well-known Heel effect. This nonuniform beam effect has a negative influence on the results of computer-aided diagnosis of mammograms, which is frequently used for early cancer detection. This paper presents a method to correct all pixels in the mammography image according to the excess or lack on radiation to which these have been submitted as a result of the this effect. The current simulation method calculates the intensities at all points of the image plane. In the simulated image, the percentage of radiation received by all the points takes the center of the field as reference. In the digitized mammography, the percentages of the optical density of all the pixels of the analyzed image are also calculated. The Heel effect causes a Gaussian distribution around the anode-cathode axis and a logarithmic distribution parallel to this axis. Those characteristic distributions are used to determine the center of the radiation field as well as the cathode-anode axis, allowing for the automatic determination of the correlation between these two sets of data. The measurements obtained with our proposed method differs on average by 2.49 mm in the direction perpendicular to the anode-cathode axis and 2.02 mm parallel to the anode-cathode axis of commercial equipment. The method eliminates around 94% of the Heel effect in the radiological image and the objects will reflect their x-ray absorption. To evaluate this method, experimental data was taken from known objects, but could also be done with clinical and digital images.

Damping behavior of continuous fiber/metal composite materials by the free vibration method

Fiber metal laminates (FML) offer significant improvements over current available materials for aircraft structures due to their excellent mechanical characteristics and relatively low density. Non-destructive testing techniques are being used in the characterization of composite materials. Among these, vibration testing is one of the most used tools because it allows the determination of the mechanical properties. In this work, the viscoelastic properties such as elastic (E') and viscous (E) responses were obtained for aluminum 2024 alloy; carbon fiber/epoxy; glass fiber/epoxy and their hybrids aluminum 2024 alloy/carbon fiber/epoxy and aluminum 2024 alloy/glass fiber/epoxy composites. The experimental results were compared to calculated E modulus values by using the composite micromechanics approach. For all specimens studied, the experimental values showed good agreement with the theoretical values. The damping behavior, i.e. The storage modulus and the loss factor, from the aluminum 2024 alloy and fiber epoxy composites can be used to estimate the viscoelastic response of the hybrid FML. (c) 2005 Elsevier Ltd. All rights reserved.

Evaluation of postural balance in postmenopausal women and its relationship with bone mineral density- a cross sectional study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Short report: Application of an alternative Aedes species (Diptera : Culicidae) surveillance method in Botucatu City, São Paulo, Brazil

One of the main problems with dengue is the control of Aedes aegypti, its major vector. In Brazil, the current control program for Ae. aegypti and Aedes albopictus populations includes larval density surveys. An interesting alternative is the use of a distinct index, the Premise Condition Index (PCI). This tool relates conditions of property, such as houses and yards, and the degree of shade with the occurrence of Aedes sp. oviposition, and is calculated as scores from 3 to 9. The lowest score indicates property in good condition and an unfavorable breeding environment, while the highest score indicates property at high risk for infestation by Aedes sp. The present study is based on the application of the PCI in an urban area of Botucatu, Brazil to confirm its effectiveness.

Characterization of lanthanum-doped bismuth titanate thin films prepared by polymeric precursor method

Lanthanum-modified bismuth titanate, Bi4-xLaxTi3O12 (BLT), with x ranging from 0 to 0.75 was grown on Pt/Ti/SiO2/Si substrates using a polymeric precursor solution and spin-coating method. The dielectric constant of highly doped bismuth titanate was equal to 148 while dielectric losses remained low (tan delta = 0.0018), and the films showed well-saturated polarization-electric field curves (2P(r) = 40.6 muC/cm(2) and V-c = 0.99 V). The leakage current densities improve for the lanthanum-doped system. For five-layered BLT films with x = 0.75, a charge storage density of 35 fC/mum(2) and a thickness of 320 nm were found. (C) 2004 Elsevier B.V. All rights reserved.

Determination of density of states in PPS from space-charge-limited current measurements

Space-charge-limited currents measurements have been carried out on undoped amorphous poly p-phenylene sulfide. The scaling law is checked for different samples with varying thickness, and J-V data analyzed. The position of the quasi-Fermi level and the density of states was obtained.

Energy method to calculate the density of liquids using ultrasonic reflection techniques

In this work it is introduced a new approach to calculate the density of liquids in terms of the energies of the acoustic signals. This method is compared to other methods in the time domain (peak-to-peak amplitudes) and frequency domain magnitudes at a single frequency. It is used a measurement cell based on a multiple reflection technique, and it is developed an acoustic model for the cell. Simulations and experiments using several liquids are presented, showing that the energy method a less sensitive to noise than the other techniques. The relative errors in the density are smaller than 0.2% when compared to the values measured with a pycnometer.

Early and current physical activity: relationship with intima-media thickness and metabolic variables in adulthood

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A novel automated alternating current biosusceptometry method to characterization of controlled-release magnetic floating tablets of metronidazole

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Experimental and theoretical studies of photoluminescence in Zns obtained by microwave-assisted solvothermal method

A shift of the photoluminescence (PL) emission was observed in ZnS prepared by microwave assisted solvothermal method with the increase of the time in microwave. In this work we reported a study of the optical behavior linking with the structural disorder according to XRD and FEG-TEM results. The reduction of intrinsic defects in the lattice is responsible for the decrease of electronic levels in the band gap changing the PL profile. This effect was confirmed by electronic structure calculations.

A New Method of Current Switching for Linear Wide-Range Measurement Systems

This new and general method here called overflow current switching allows a fast, continuous, and smooth transition between scales in wide-range current measurement systems, like electrometers. This is achieved, using a hydraulic analogy, by diverting only the overflow current, such that no slow element is forced to change its state during the switching. As a result, this approach practically eliminates the long dead time in low-current (picoamperes) switching. Similar to a logarithmic scale, a composition of n adjacent linear scales, like a segmented ruler, measures the current. The use of a linear wide-range system based on this technique assures fast and continuous measurement in the entire range, without blind regions during transitions and still holding suitable accuracy for many applications. A full mathematical development of the method is given. Several computer realistic simulations demonstrated the viability of the technique.

Translocation capture sequencing: A method for high throughput mapping of chromosomal rearrangements

Chromosomal translocations require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are involved in producing leukemias, lymphomas and sarcomas. Translocations are frequent, clonal and recurrent in mature B cell lymphomas, which bear a particularly high DNA damage burden by virtue of activation-induced cytidine deaminase (AID) expression. Despite the ubiquity of genomic rearrangements, the forces that underlie their genesis are not well understood. Here, we provide a detailed description of a new method for studying these events, translocation capture sequencing (TC-Seq). TC-Seq provides the means to document chromosomal rearrangements genome-wide in primary cells, and to discover recombination hotspots. Demonstrating its effectiveness, we successfully estimate the frequency of c-myc/IgH translocations in primary B cells, and identify hotspots of AID-mediated recombination. Furthermore. TC-Seq can be adapted to generate genome-wide rearrangement maps in any cell type and under any condition. (C) 2011 Elsevier B.V. All rights reserved.