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Selected AbstractsDynamic Textures for Image-based Rendering of Fine-Scale 3D Structure and Animation of Non-rigid MotionCOMPUTER GRAPHICS FORUM, Issue 3 2002Dana Cobza The problem of capturing real world scenes and then accurately rendering them is particularly difficult for fine-scale 3D structure. Similarly, it is difficult to capture, model and animate non-rigid motion. We present a method where small image changes are captured as a time varying (dynamic) texture. In particular, a coarse geometry is obtained from a sample set of images using structure from motion. This geometry is then used to subdivide the scene and to extract approximately stabilized texture patches. The residual statistical variability in the texture patches is captured using a PCA basis of spatial filters. The filters coefficients are parameterized in camera pose and object motion. To render new poses and motions, new texture patches are synthesized by modulating the texture basis. The texture is then warped back onto the coarse geometry. We demonstrate how the texture modulation and projective homography-based warps can be achieved in real-time using hardware accelerated OpenGL. Experiments comparing dynamic texture modulation to standard texturing are presented for objects with complex geometry (a flower) and non-rigid motion (human arm motion capturing the non-rigidities in the joints, and creasing of the shirt). Categories and Subject Descriptors (according to ACM CCS): I.3.3 [Computer Graphics]: Image Based Rendering [source] Evidence for low-titre infections in insect symbiosis: Wolbachia in the bark beetle Pityogenes chalcographus (Coleoptera, Scolytinae)ENVIRONMENTAL MICROBIOLOGY, Issue 8 2009Arthofer Wolfgang Summary Wolbachia are obligatory endosymbiotic ,-proteobacteria found in many insect species. They are maternally transmitted and often exhibit reproductive phenotypes like cytoplasmic incompatibility. Pityogenes chalcographus is a bark beetle causing severe damage in spruce stands. Its European populations are divided into several mitochondrial clades separated by partial crossing barriers. In this study, we tested a large sample set covering the natural range of the beetle in Europe for the presence of Wolbachia and associations between infection pattern and mitotypes using a highly sensitive nested PCR technique. 35.5% of the individuals were infected with the endosymbiont and two distinct strains were identified. Both strains occur in low titre not accessible by conventional detection methods. The infections are present all over Europe, unlikely to cause the partial crossing barriers in this host and uncoupled from mitochondrial clades. This pattern is indicative for populations evolving towards endosymbiont loss and for repeated intraspecific horizontal transfer of Wolbachia. Alternatively, the low-titre infections found in P. chalcographus are yet another example for Wolbachia that can persist in host species at low densities and frequencies. [source] Commercial Runner peanut cultivars in the USA: Fatty acid compositionEUROPEAN JOURNAL OF LIPID SCIENCE AND TECHNOLOGY, Issue 2 2010Eui-Cheol Shin Abstract Though peanuts are classified as a high-fat food, they possess good proportions of fatty acids deemed as heart healthy. The fatty acid compositions of Runner peanuts were determined for commercially grown cultivars over two recent crop years. GC-FID analyses revealed that the fatty acid levels for Runner peanuts were significantly (p,<0.05) different among the normal, mid-, and high-oleic peanuts investigated. Oleic acid-to-linoleic acid (O/L) ratios were found to be 1.93,±,0.30, 5.25,±,1.12, and 16.9,±,5.20 for normal, mid-, and high-oleic peanut lipids, respectively. Tamrun OL01 possessed a fatty acid profile characteristic of a mid-oleic cultivar. From the sample set (n,=,151), mean %,weights for oleic acid and linoleic acid were 52.09,±,2.84 and 27.38,±,2.60 in normal, 69.33,±,3.18 and 13.66,±,2.35 in mid-oleic, and 78.45,±,2.05 and 5.11,±,1.67 in high-oleic peanuts, respectively. Cluster analysis segregated cultivars based on fatty acids into normal, mid-, and high-oleic groups. Factorial analysis revealed that cultivar effects were significant (p,<0.01) for all fatty acids, except for lignoceric acid. Cultivar effects were also highly significant (p,<0.001) for O/L, IV, unsaturated/saturated fatty acid (U/S) ratio, and %,saturation. Significant crop year effects were shown for palmitic, oleic, arachidic, gondoic, and lignoceric acids, as well as U/S ratio and %,saturation. Healthy unsaturated fats accounted for ,80% in all crop years and cultivars. [source] The impact of HLA-A and -DRB1 on age at onset, disease course and severity in Scandinavian multiple sclerosis patientsEUROPEAN JOURNAL OF NEUROLOGY, Issue 8 2007C. Smestad The human leucocyte antigen (HLA) class II haplotype DRB1*15,DQB1*06 (DR15,DQ6) is associated with susceptibility to multiple sclerosis (MS), and HLA class I associations in MS have also been reported. However, the influence of HLA class I and II alleles on clinical phenotypes in MS has not yet been completely studied. This study aimed at evaluating the impact of HLA-A and -DRB1 alleles on clinical variables in Scandinavian MS patients. The correlation between HLA-A or -DRB1 alleles and age at onset, disease course and Multiple Sclerosis Severity Score (MSSS) were studied in 1457 Norwegian and Swedish MS patients by regression analyses and Kruskal,Wallis rank sum test. Presence of HLA-DRB1*15 was correlated with younger age at onset of disease (corrected P = 0.009). No correlation was found between HLA-A and the variables studied. This study analysed the effect of HLA-A on clinical variables in a large Scandinavian sample set, but could not identify any significant contribution from HLA-A on the clinical phenotype in MS. However, associations between HLA-DRB1*15 and age at onset of MS were reproduced in this extended Scandinavian MS cohort. [source] Estimating the number of independent components for functional magnetic resonance imaging dataHUMAN BRAIN MAPPING, Issue 11 2007Yi-Ou Li Abstract Multivariate analysis methods such as independent component analysis (ICA) have been applied to the analysis of functional magnetic resonance imaging (fMRI) data to study brain function. Because of the high dimensionality and high noise level of the fMRI data, order selection, i.e., estimation of the number of informative components, is critical to reduce over/underfitting in such methods. Dependence among fMRI data samples in the spatial and temporal domain limits the usefulness of the practical formulations of information-theoretic criteria (ITC) for order selection, since they are based on likelihood of independent and identically distributed (i.i.d.) data samples. To address this issue, we propose a subsampling scheme to obtain a set of effectively i.i.d. samples from the dependent data samples and apply the ITC formulas to the effectively i.i.d. sample set for order selection. We apply the proposed method on the simulated data and show that it significantly improves the accuracy of order selection from dependent data. We also perform order selection on fMRI data from a visuomotor task and show that the proposed method alleviates the over-estimation on the number of brain sources due to the intrinsic smoothness and the smooth preprocessing of fMRI data. We use the software package ICASSO (Himberg et al. [ 2004]: Neuroimage 22:1214,1222) to analyze the independent component (IC) estimates at different orders and show that, when ICA is performed at overestimated orders, the stability of the IC estimates decreases and the estimation of task related brain activations show degradation. Hum Brain Mapp, 2007. © 2007 Wiley-Liss, Inc. [source] D90A- SOD1 mediated amyotrophic lateral sclerosis: A single founder for all cases with evidence for a Cis -acting disease modifier in the recessive haplotype,,HUMAN MUTATION, Issue 6 2002Matthew J. Parton Abstract More than 100 different heterozygous mutations in copper/zinc superoxide dismutase (SOD1) have been found in patients with amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease. Uniquely, D90A- SOD1 has been identified in recessive, dominant and apparently sporadic pedigrees. The phenotype of homozygotes is stereotyped with an extended survival, whereas that of affected heterozygotes varies. The frequency of D90A- SOD1 is 50 times higher in Scandinavia (2.5%) than elsewhere, though ALS prevalence is not raised there. Our earlier study indicated separate founders for recessive and dominant/sporadic ALS and we proposed a disease-modifying factor linked to the recessive mutation. Here we have doubled our sample set and employed novel markers to characterise the mutation's origin and localise any modifying factor. Linkage disequilibrium analysis indicates that D90A homozygotes and heterozygotes share a rare haplotype and are all descended from a single ancient founder (alpha 0.974) c.895 generations ago. Homozygotes arose subsequently only c.63 generations ago (alpha 0.878). Recombination has reduced the region shared by recessive kindreds to 97-265 kb around SOD1, excluding all neighbouring genes. We propose that a cis -acting regulatory polymorphism has arisen close to D90A- SOD1 in the recessive founder, which decreases ALS susceptibility in heterozygotes and slows disease progression. © 2002 Wiley-Liss, Inc. [source] Real exchange rate fluctuations and monetary shocks: a revisitINTERNATIONAL JOURNAL OF FINANCE & ECONOMICS, Issue 1 2004Shiu-Sheng Chen Abstract In this paper, I first estimate a structural VAR model by following Clarida and Gali (1994) and obtain results indicating that the variance of real exchange rates can be attributed more to monetary shocks when the sample span is extended. In order to further investigate this aspect, I then employ a VAR model with long-run US,UK annual data from 1889 to 1995. According to the variance decompositions, I find that monetary shocks can explain nearly 50% of real exchange rate variance in the long-run sample periods. All the evidence suggests that monetary shocks are indeed more important in a larger sample set. Copyright © 2003 John Wiley & Sons, Ltd. [source] Genetic and morphometric characterization of a local Vietnamese Swamp Buffalo populationJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2010C. Berthouly Summary The water buffalo plays a key role in the socio-economy of South-East Asia as it is the main draught power for paddy rice cultivation. While in the Indian subcontinent the water buffalo is the riverine type, in South-East Asia the majority of buffaloes are of the swamp type. In the poor remote northern province of Ha Giang in Vietnam, improvement of the swamp buffalo breed may be one of the best ways to increase sustainability of farming systems. Therefore, analysis of the genetic structure of the province buffalo population is a prerequisite to any conservation or improvement project. A total of 1122 animals were described for 11 body and horn measurements for morphometric characterization. From this sample set, 744 animals were genotyped for 17 microsatellite markers. Also 17 animals from southern provinces of Vietnam were genotyped as a comparative sample. The results showed that genetic diversity as well as inbreeding value in the Ha Giang was high. The FST values within the province and across Vietnam were low indicating that most of the population variation is explained by individual variability. Bayesian clustering analysis did not highlight the presence of subdivided populations. These results are useful for the implementation of a conservation and improvement strategy of the swamp buffalo in order to guarantee the householders' needs for sustainability of the farming system in the Ha Giang province. [source] A new family of genetic algorithms for wavelength interval selection in multivariate analytical spectroscopyJOURNAL OF CHEMOMETRICS, Issue 6 2003Héctor C. Goicoechea Abstract A new procedure is presented for wavelength interval selection with a genetic algorithm in order to improve the predictive ability of partial least squares multivariate calibration. It involves separately labelling each of the selected sensor ranges with an appropriate inclusion ranking. The new approach intends to alleviate overfitting without the need of preparing an independent monitoring sample set. A theoretical example is worked out in order to compare the performance of the new approach with previous implementations of genetic algorithms. Two experimental data sets are also studied: target parameters are the concentration of glucuronic acid in complex mixtures studied by Fourier transform mid-infrared spectroscopy and the octane number in gasolines monitored by near-infrared spectroscopy. Copyright © 2003 John Wiley & Sons, Ltd. [source] A phenomenological study of ripening of salted herring.JOURNAL OF CHEMOMETRICS, Issue 2 2002Assessing homogeneity of data from different countries, laboratories Abstract Data from ripening experiments of herring carried out at three Nordic fishery research institutions in the period 1992,1995 were collected and analyzed by multivariate analysis. The experiments were carried out at different times, with different stocks as raw material, using different types of treatments and analyzed in different laboratories. The question considered here is whether these data can be assumed to be one homogeneous set of data pertaining to ripening of salted herring or whether data from different labs, stocks, etc. must be considered independently. This is of importance for further research into ripening processes with these and similar data. It is shown in this paper that all data can be considered as one homogeneous data set. This is verified using resampling where latent structures are compared between different sample sets. This is done indirectly by testing regression models, that have been developed on one sample set, on other sample sets. It is also done directly by monitoring the deviation in latent structure observed between different sample sets. No formal statistical test is developed for whether samples can be assumed to stem from the same population. Although this can easily be envisioned, it was exactly the need for a more intuitive and visual test that prompted this work, developing different exploration tools that visually make it clear how well the data can be assumed to derive from the same population. Subsequently analyzing the data as one homogeneous group provides new information about factors that govern the ripening of salted herring and can be used in new strategic research as well as in industrial practice. Copyright © 2002 John Wiley & Sons, Ltd. [source] Authentication of Green Asparagus Varieties by Near-Infrared Reflectance SpectroscopyJOURNAL OF FOOD SCIENCE, Issue 2 2001D.P. Perez ABSTRACT: Near-infrared reflectance spectroscopy (NIRS) was used for the authentication of 2 green asparagus varieties (Taxara and UC-157), grown in Huetor-Tajar (Granada, Spain) protected by the Quality Specific Appellation "Espárragos de Huétor-Tájar". To develop the prediction model, the method chosen was modified partial least square (MPLS) regression. Two sample sets (N = 219 and N2 = 145 samples, respectively) were used to obtain the calibration equations. The standard error of cross-validation (SECV) and the r2 value were 0.082 and 0.97, respectively, for the 1st calibration set and 0.077 and 0.97 for the 2nd calibration set. The 2nd chemometric model obtained was tested with independent validation sample set (N3 = 74 samples), and the resulting values for standard error of prediction (SEP) and for r2 were 0.07 and 0.96, respectively. These results prove that NIRS is an accurate technology for identification and authentication of asparagus varieties and easily implemented in industry. [source] Use of mid-infrared spectroscopy in the diffuse-reflectance mode for the prediction of the composition of organic matter in soil and litterJOURNAL OF PLANT NUTRITION AND SOIL SCIENCE, Issue 3 2008Bernard Ludwig Abstract Mid-infrared spectroscopy (MIRS) is assumed to be superior to near-infrared spectroscopy (NIRS) for the prediction of soil constituents, but its usefulness is still not sufficiently explored. The objective of this study was to evaluate the ability of MIRS to predict the chemical and biological properties of organic matter in soils and litter. Reflectance spectra of the mid-infrared region including part of the near-infrared region (7000,400,cm,1) were recorded for 56 soil and litter samples from agricultural and forest sites. Spectra were used to predict general and biological characteristics of the samples as well as the C composition which was measured by 13C CPMAS-NMR spectroscopy. A partial least-square method and cross-validation were used to develop equations for the different constituents over selected spectra ranges after several mathematical treatments of the spectra. Mid-infrared spectroscopy predicted well the C : N ratio: the modeling efficiency EF was 0.95, the regression coefficient (a) of a linear regression (measured against predicted values) was 1.0, and the correlation coefficient (r) was 0.98. Satisfactorily (EF , 0.70, 0.8 , a , 1.2, r , 0.80) assessed were the contents of C, N, and lignin, the production of dissolved organic carbon, and the contents of carbonyl C, aromatic C, O-alkyl C, and alkyl C. However, the N mineralization rate, the microbial biomass and the alkyl,to,aromatic C ratio were predicted less satisfactorily (EF < 0.70). Limiting the sample set to mineral soils did generally not result in improved predictions. The good and satisfactory predictions reported above indicate a marked usefulness of MIRS in the assessment of chemical characteristics of soils and litter, but the accuracies of the MIRS predictions in the diffuse-reflectance mode were generally not superior to those of NIRS. [source] Effects of component properties and orientation on corrugated container endurancePACKAGING TECHNOLOGY AND SCIENCE, Issue 4 2010Roman E. Popil Abstract Experiments are performed to determine the impact of several physical properties on the creep behavior of three different sets of corrugated containers subjected to static loading and a cyclic humidity environment ranging from 50% to 80% relative humidity in a 24,h period. One sample set had basis weights of the fluted medium varied from 68 to 205,g/m2 while keeping the basis weight of the linerboard facings at 205,g/m2. This varied the out-of-plane shear rigidity of the single wall board by a factor of three. Another set of corrugated samples investigated effects of lateral or linear corrugating by rotation of either linerboards, fluted medium or both. This equalizes hygroexpansivity and affects lifetime. A third series of boxes had barrier coatings applied to their surfaces to determine the effect on lifetime. Creep and lifetime are determined to be inversely related and a multiple regression model for lifetime was sought based on the data set. Homogenization of the corrugated board properties through either increased medium basis weight or component rotation (lateral or linear corrugating) and application of barrier coating will in general, increase the endurance of edge loaded corrugated board in cyclic humidity. Copyright © 2010 John Wiley & Sons, Ltd. [source] Structural flyby characterization of nanoporosityPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue S2 2004R. R. Rosa Abstract Recently, Ferreira da Silva et al. [3] have performed a gradient pattern analysis of a canonical sample set (CSS) of scanning force microscopy (SFM) images of ,-Si. They applied the so-called Gradient Pattern Analysis to images of three typical ,-Si samples distinguished by different absorption energy levels and aspect ratios. Taking into account the measures of spatial asymmetric fluctuations they interpreted the global porosity not only in terms of the amount of roughness, but rather in terms of the structural complexity (e.g., walls and fine structures as slots). This analysis has been adapted in order to operate in a OpenGL flyby environment (the StrFB code), whose application give the numerical characterization of the structure during the flyby real time. Using this analysis we compare the levels of asymmetric fragmentation of active porosity related to different materials as ,-Si and "porous diamond-like" carbon. In summary we have shown that the gradient pattern analysis technique in a flyby environment is a reliable sensitive method to investigate, qualitatively and quantitatively, the complex morphology of active nanostructures. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] C-peptide microheterogeneity in type 2 diabetes populationsPROTEOMICS - CLINICAL APPLICATIONS, Issue 1 2010Paul E. Oran Abstract Purpose: The purpose of this study was to investigate naturally occurring C-peptide microheterogeneity in healthy and type 2 diabetes (T2D) populations. Experimental design: MS immunoassays capable of simultaneously detecting intact C-peptide and variant forms were applied to plasma samples from 48 healthy individuals and 48 individuals diagnosed with T2D. Results: Common throughout the entire sample set were three previously unreported variations of C-peptide. The relative contribution of one variant, subsequently identified as C-peptide (3-31), was found to be more abundant in the T2D population as compared to the healthy population. Dipeptidyl peptidase IV is suspected to be responsible for this particular cleavage product, which is consistent with the pathophysiology of T2D. Conclusions and clinical relevance: C-peptide does not exist in the human body as a single molecular species. It is qualitatively more heterogeneous than previously thought. These results lay a foundation for future studies devoted to a comprehensive understanding of C-peptide and its variants in healthy and diabetic populations. [source] Analysis of Gene Polymorphisms Associated with K+ Ion Circulation in the Inner Ear of Patients Susceptible and Resistant to Noise-induced Hearing LossANNALS OF HUMAN GENETICS, Issue 4 2009Malgorzata Pawelczyk Summary Noise-induced hearing loss (NIHL) is one of the leading occupational health risks in industrialized countries. It results from an interaction between environmental and genetic factors, however the nature of the genetic factors contributing to NIHL has not yet been clarified. Here, we investigated whether genetic variations in 10 genes putatively involved in the potassium recycling pathway in the inner ear may influence susceptibility to noise. 99 SNPs were genotyped in Polish noise-exposed workers, categorized into susceptible and resistant subjects. The most interesting results were obtained for KCNE1 and KCNQ4 as we replicated associations that were previously reported in a Swedish sample set, hence confirming that they are NIHL susceptibility genes. Additionally we report significant associations in GJB1, GJB2, GJB4, KCNJ10 and KCNQ1, however due to the lack of replication in the Swedish sample set, these results should be seen as suggestive. [source] Candidate Gene Association Study for Noise-induced Hearing Loss in Two Independent Noise-exposed PopulationsANNALS OF HUMAN GENETICS, Issue 2 2009A. Konings Summary Millions of people are daily exposed to high levels of noise. Consequently, noise-induced hearing loss (NIHL) is one of the most important occupational health hazards worldwide. In this study, we performed an association study for NIHL based on a candidate gene approach. 644 Single Nucleotide Polymorphisms (SNPs) in 53 candidate genes were analyzed in two independent NIHL sample sets, a Swedish set and part of a Polish set. Eight SNPs with promising results were selected and analysed in the remaining part of the Polish samples. One SNP in PCDH15 (rs7095441), resulted in significant associations in both sample sets while two SNPs in MYH14 (rs667907 and rs588035), resulted in significant associations in the Polish sample set and significant interactions with noise exposure level in the Swedish sample set. Calculation of odds ratios revealed a significant association of rs588035 with NIHL in the Swedish high noise exposure level group. Our studies suggest that PCDH15 and MYH14 may be NIHL susceptibility genes, but further replication in independent sample sets is mandatory. [source] The Y-chromosomal Heritage of the Azores Islands PopulationANNALS OF HUMAN GENETICS, Issue 2 2005P. R. Pacheco Summary The Azores, a Portuguese archipelago located in the north Atlantic Ocean, had no native population when the Portuguese first arrived in the 15th century. The islands were populated mainly by the Portuguese, but Jews, Moorish prisoners, African slaves, Flemish, French and Spaniards also contributed to the initial settlement. To understand the paternal origins and diversity of the extant Azorean population, we typed genomic DNA samples from 172 individuals using a combination of 10 Y-biallelic markers (YAP, SRY-1532, SRY-2627, 92R7, M9, sY81, Tat, SRY-8299, 12f2 and LLY22g) and the following Y-chromosomal STR systems: DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 and DYS385. We identified nine different haplogroups, most of which are frequent in Europe. Haplogroup J* is the second most frequent in the Azores (13.4%), but it is modestly represented in mainland Portugal (6.8%). The other non-European haplogroups, N3 and E3a, which are prevalent in Asia and sub-Saharan Africa, respectively, have been found in the Azores (0.6% and 1.2%, respectively) but not in mainland Portugal. Microsatellite data indicate that the mean gene diversity (D) value for all the loci analysed in our sample set is 0.590, while haplotype diversity is 0.9994. Taken together, our analysis suggests that the current paternal pool of the Azorean population is, to a great extent, of Portuguese descent with significant contributions from people with other genetic backgrounds. [source] Assessing Ceramic Compositional Data: A Comparison of Total Reflection X-ray Fluorescence and Instrumental Neutron Activation Analysis On Late Iron Age Spanish Celtiberian CeramicsARCHAEOMETRY, Issue 3 2001M. García-Heras A solid-phase, non-chemical processing protocol was recently developed as a means of chemically characterizing archaeological ceramics by total reflection X-ray fluorescence (TXRF). Following this methodology, TXRF can provide semi-quantitative determinations for 18 elements with comparable levels of precision and accuracy for the majority of them in comparison with a clay reference material analysed by instrumental neutron activation (INAA). In order critically to assess the analytical capabilities of TXRF, a large sample set of Late Iron Age Spanish Celtiberian ceramics and modern clays was analysed both by TXRF and INAA. Semi-quantitative chemical data provided by TXRF and quantitative data provided by INAA were subjected to commonly used multivariate statistical methods as a way of evaluating the ability of the new technique to discriminate among different compositional groups. The comparison of the two data sets shows no significant discrepancies, thereby allowing support for the same archaeological interpretation. These results suggest that TXRF has potential applicability for compositional characterization of archaeological ceramics, providing data that are useful for provenance studies. [source] Role of the urate transporter SLC2A9 gene in susceptibility to gout in New Zealand M,ori, Pacific Island, and Caucasian case,control sample setsARTHRITIS & RHEUMATISM, Issue 11 2009Jade E. Hollis-Moffatt Objective To examine the role of genetic variation in the renal urate transporter SLC2A9 in gout in New Zealand sample sets of M,ori, Pacific Island, and Caucasian ancestry and to determine if the M,ori and Pacific Island samples could be useful for fine-mapping. Methods Patients (n= 56 M,ori, 69 Pacific Island, and 131 Caucasian) were recruited from rheumatology outpatient clinics and satisfied the American College of Rheumatology criteria for gout. The control samples comprised 125 M,ori subjects, 41 Pacific Island subjects, and 568 Caucasian subjects without arthritis. SLC2A9 single-nucleotide polymorphisms rs16890979 (V253I), rs5028843, rs11942223, and rs12510549 were genotyped (possible etiologic variants in Caucasians). Results Association of the major allele of rs16890979, rs11942223, and rs5028843 with gout was observed in all sample sets (P = 3.7 × 10,7, 1.6 × 10,6, and 7.6 × 10,5 for rs11942223 in the M,ori, Pacific Island, and Caucasian samples, respectively). One 4-marker haplotype (1/1/2/1; more prevalent in the M,ori and Pacific Island control samples) was not observed in a single gout case. Conclusion Our data confirm a role of SLC2A9 in gout susceptibility in a New Zealand Caucasian sample set, with the effect on risk (odds ratio >2.0) greater than previous estimates. We also demonstrate association of SLC2A9 with gout in samples of M,ori and Pacific Island ancestry and a consistent pattern of haplotype association. The presence of both alleles of rs16890979 on susceptibility and protective haplotypes in the M,ori and Pacific Island sample is evidence against a role for this nonsynonymous variant as the sole etiologic agent. More extensive linkage disequilibrium in M,ori and Pacific Island samples suggests that Caucasian samples may be more useful for fine-mapping. [source] Association of the autoimmunity locus 4q27 with juvenile idiopathic arthritisARTHRITIS & RHEUMATISM, Issue 3 2009H. M. Albers Objective Juvenile idiopathic arthritis (JIA) is characterized by chronic arthritis and an autoimmune etiology. In several autoimmune diseases, including rheumatoid arthritis (RA), an association with the 4q27 locus has been reported. We undertook this study to investigate the possible role of the 4q27 locus in JIA. Methods A case,control association study was conducted, with a total of 655 Caucasian JIA patients and 791 healthy controls divided into 2 independent sample sets. The rs6822844 marker in the 4q27 locus was genotyped. Results In the first and larger sample set, a 5% decrease in T allele frequency was observed in patients compared with controls (allelic odds ratio [OR] 0.72 [95% confidence interval 0.55,0.95], P = 0.019), and in the second set, a 3% decrease was observed (allelic OR 0.81 [95% confidence interval 0.61,1.09], P = 0.169). The combined data set generated an OR of 0.76 (95% confidence interval 0.62,0.93, P = 7.08 × 10,3). When the different JIA subtypes were analyzed individually, significant decreases were seen in the subtypes with a polyarticular course of disease (extended oligoarthritis [P = 0.019] and rheumatoid factor,negative polyarthritis [P = 0.038]). Conclusion Our findings suggest that the 4q27 locus, previously reported to be associated with RA, type 1 diabetes mellitus, celiac disease, and psoriatic arthritis, is also associated with susceptibility to JIA. [source] Comparative performances of selected chiral HPLC, SFC, and CE systems with a chemically diverse sample setCHIRALITY, Issue S1 2003Phil Borman Abstract Pharmaceutical companies have a continuous need to resolve new racemates. Analysis may be required in aqueous and nonaqueous media, or in the presence of several different sets of potentially interfering compounds. There is often a preparative requirement. For these reasons analysts may require a number of different separation systems capable of resolving a given pair of enantiomers. We wished to improve upon existing approaches that address this situation and undertook a program of work to screen over 100 racemates, selected for their chemical diversity, on over 100 different chiral HPLC, SFC, and CE systems. Here we report results of this comparison and illustrate the use of rapid gradient screening as a valuable tool for chiral method development. Chirality 15:S1,S12, 2003. © 2003 Wiley-Liss, Inc. [source] Examining the relationships between the Pro12Ala variant in PPARG and Type 2 diabetes-related traits in UK samplesDIABETIC MEDICINE, Issue 12 2005E. Zeggini Abstract Aims The Pro12Ala polymorphism in the PPARG gene alters amino acid sequence and has shown consistent association with susceptibility to Type 2 diabetes in several populations. The present study makes use of large, well-characterized case-control resources to enhance understanding of this susceptibility effect by examining related traits, such as body mass index (BMI), waist,hip ratio and age at diagnosis. Methods The Pro12Ala variant was genotyped in two UK case samples, ascertained for positive family history and/or early onset of Type 2 diabetes (combined n = 971); and in 1257 ethnically matched control subjects. Results There were significant associations of the Pro12Ala single nucleotide polymorphism (SNP) genotypes with diabetes in both case-control comparisons (P = 0.025 and P = 0.039). Comparing individuals homozygous for the Pro allele, with those carrying an Ala allele, the combined odds ratio for diabetes was 1.40 (95% CIs, 1.12,1.76, P = 0.0031). There was no association between the variant and either waist,hip ratio or age at diagnosis. Proline homozygosity was associated with increased BMI in one patient group (P = 0.013) and decreased BMI in the other (P = 0.038). Conclusions This study confirms that variation within PPARG influences susceptibility to Type 2 diabetes in UK samples. However, the relationship between PPARG variation and BMI is more complex, and studies in much larger sample sets will be required to more precisely characterize the effect of this variant on adiposity. [source] Prevalence of BRCA1 genomic rearrangements in a large cohort of Italian breast and breast/ovarian cancer families without detectable BRCA1 and BRCA2 point mutationsGENES, CHROMOSOMES AND CANCER, Issue 9 2006Simona Agata The presence of genomic rearrangements of the BRCA1 gene in breast and/or ovarian cancer families has been intensively investigated in patients from various countries over the last years. A number of different rearrangements have been reported by several studies that clearly document the involvement of this mutation type in genetic predisposition to breast and ovarian cancer. Population-specific studies are now needed to evaluate the prevalence of genomic rearrangements before deciding whether to include ad hoc screening procedures into standard diagnostic mutation detection approaches. Indeed, the vast majority of the studies have been performed on small, highly selected, sample sets because of the limitations imposed by the laborious technical approaches. Moreover, prevalence figures are likely to differ across different countries according to the ethnic origin of each specific population. Here we analyze a large cohort of 653 Italian probands, negative for BRCA1 and BRCA2 point mutations, gathered from four National Institutions. We report the identification of BRCA1 genomic rearrangements in 12 independent families. Noteworthy, half of the probands carry mutations that recur in more than one Italian family. Considering the whole spectrum of Italian BRCA1 gene rearrangements identified thus far in consecutive patients, we estimate that alterations of this type account for 19% (95% CI: 0.11 < 0.19 < 0.28) of the BRCA1 mutation positive families. We conclude that the search for major genomic rearrangements is essential for an accurate and comprehensive BRCA1 mutation detection strategy in Italy. © 2006 Wiley-Liss, Inc. [source] Association with replication between estrogen-related receptor , (ESRR,) Polymorphisms and bone phenotypes in women of European ancestryJOURNAL OF BONE AND MINERAL RESEARCH, Issue 4 2010Latifa Elfassihi Abstract Osteoporosis is a bone disease characterized by low bone mineral density (BMD), a highly heritable polygenic trait. Women are more prone than men to develop osteoporosis owing to a lower peak bone mass and accelerated bone loss at menopause. Lack of estrogen thus is a major risk factor for osteoporosis. In addition to having strong similarity to the estrogen receptor 1 (ESR1), the orphan nuclear estrogen-related receptor , (ESRR,) is widely expressed and shows overlap with ESR1 expression in tissues where estrogen has important physiologic functions. For these reasons, we have undertaken a study of ESRR, sequence variants in association with bone measurements [heel quantitative ultrasound (QUS) by measurements of broadband ultrasound attenuation (BUA), speed of sound (SOS), and stiffness index (SI) and dual-energy X-ray absorptiometry (DXA) at the femoral neck (FN) and lumbar spine (LS)]. A silent variant was found to be associated with multiple bone measurements (LS, BUA, SOS, and SI), the p values ranging from .006 to .04 in a sample of 5144 Quebec women. The region of this variant was analyzed using the HapMap database and the Gabriel method to define a block of 20,kb. Using the Tagger method, eight TagSNPs were identified and genotyped in a sample of 1335 women. Four of these SNPs capture the five major block haplotypes. One SNP (rs2818964) and one haplotype were significantly associated with multiple bone measures. All SNPs involved in the associations were analyzed in two other sample sets with significant results in the same direction. These results suggest involvement of ESRR, in the determination of bone density in women. © 2010 American Society for Bone and Mineral Research [source] A combined artificial neural network/residual bilinearization approach for obtaining the second-order advantage from three-way non-linear dataJOURNAL OF CHEMOMETRICS, Issue 11-12 2005Alejandro C. Olivieri Abstract Three-way instrumental data offer the second-order advantage to analysts, a property of great utility in the field of complex sample analysis in the presence of unsuspected components as potential interferents. The available multivariate methodologies for obtaining this advantage are all based on linear models, and hence they are not applicable to spectral information behaving in a non-linear manner with respect to target analyte concentrations. This work describes the combination of a back-propagation artificial neural network model with a technique known as residual bilinearization, applicable to second-order spectral information. The joint model allows one to efficiently extract analyte concentrations from intrinsically non-linear data, even in the presence of unsuspected constituents. Simulations have been performed by mimicking deviations from linearity brought about by: (1) exponential relationship between fluorescence and concentration, (2) kinetic evolution of responsive reaction products and (3) analytes acting as reaction catalysts. In all of these cases, successful prediction of the analyte concentrations was achieved on large test sample sets, which included the presence of overlapping components not included in the training step. The new method not only obtains the second-order advantage, but also correctly retrieves the contribution of the unsuspected components to the total test sample signals. The comparison with a multivariate methodology based on partial least-squares regression with second-order advantage shows that the presently described method displays better predictive ability. Copyright © 2006 John Wiley & Sons, Ltd. [source] A phenomenological study of ripening of salted herring.JOURNAL OF CHEMOMETRICS, Issue 2 2002Assessing homogeneity of data from different countries, laboratories Abstract Data from ripening experiments of herring carried out at three Nordic fishery research institutions in the period 1992,1995 were collected and analyzed by multivariate analysis. The experiments were carried out at different times, with different stocks as raw material, using different types of treatments and analyzed in different laboratories. The question considered here is whether these data can be assumed to be one homogeneous set of data pertaining to ripening of salted herring or whether data from different labs, stocks, etc. must be considered independently. This is of importance for further research into ripening processes with these and similar data. It is shown in this paper that all data can be considered as one homogeneous data set. This is verified using resampling where latent structures are compared between different sample sets. This is done indirectly by testing regression models, that have been developed on one sample set, on other sample sets. It is also done directly by monitoring the deviation in latent structure observed between different sample sets. No formal statistical test is developed for whether samples can be assumed to stem from the same population. Although this can easily be envisioned, it was exactly the need for a more intuitive and visual test that prompted this work, developing different exploration tools that visually make it clear how well the data can be assumed to derive from the same population. Subsequently analyzing the data as one homogeneous group provides new information about factors that govern the ripening of salted herring and can be used in new strategic research as well as in industrial practice. Copyright © 2002 John Wiley & Sons, Ltd. [source] Authentication of Green Asparagus Varieties by Near-Infrared Reflectance SpectroscopyJOURNAL OF FOOD SCIENCE, Issue 2 2001D.P. Perez ABSTRACT: Near-infrared reflectance spectroscopy (NIRS) was used for the authentication of 2 green asparagus varieties (Taxara and UC-157), grown in Huetor-Tajar (Granada, Spain) protected by the Quality Specific Appellation "Espárragos de Huétor-Tájar". To develop the prediction model, the method chosen was modified partial least square (MPLS) regression. Two sample sets (N = 219 and N2 = 145 samples, respectively) were used to obtain the calibration equations. The standard error of cross-validation (SECV) and the r2 value were 0.082 and 0.97, respectively, for the 1st calibration set and 0.077 and 0.97 for the 2nd calibration set. The 2nd chemometric model obtained was tested with independent validation sample set (N3 = 74 samples), and the resulting values for standard error of prediction (SEP) and for r2 were 0.07 and 0.96, respectively. These results prove that NIRS is an accurate technology for identification and authentication of asparagus varieties and easily implemented in industry. [source] Simultaneous determination of iridoids, phenolic acids, flavonoids, and saponins in Flos Lonicerae and Flos Lonicerae Japonicae by HPLC-DAD-ELSD coupled with principal component analysisJOURNAL OF SEPARATION SCIENCE, JSS, Issue 18 2007Chun-Yun Chen Abstract A method, HPLC coupled with diode-array and evaporative light scattering detectors (HPLC-DAD-ELSD), was newly developed to evaluate the quality of Flos Lonicerae (FL) and Flos Lonicerae Japonicae (FLJ), through a simultaneous determination of multiple types of bioactive components. By employing DAD, the detection wavelengths were set at 240 nm for the determination of iridoids, 330 nm for phenolic acids, and 360 nm for flavonoids, respectively. While ELSD, connected in series after DAD, was applied to the determination of saponins. This assay was fully validated with respect to precision, repeatability, and accuracy. Moreover, principal component analysis (PCA) was used for the similarity evaluation of different samples, and it was proven straightforward and reliable to differentiate FL and FLJ samples from different origins. For PCA, two principal components have been extracted. Principal component 1 (PC1) influences the separation between different sample sets, capturing 54.598% variance, while principal component 2 (PC2) affects differentiation within sample sets, capturing 12.579% variance. In conclusion, simultaneous quantification of bioactive components by HPLC-DAD-ELSD coupled with PCA would be a well-acceptable strategy to differentiate the sources and to comprehensively control the quality of the medicinal plants FL and FLJ. [source] SPLASH: Systematic proteomics laboratory analysis and storage hubPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2006Siaw Ling Lo Abstract In the field of proteomics, the increasing difficulty to unify the data format, due to the different platforms/instrumentation and laboratory documentation systems, greatly hinders experimental data verification, exchange, and comparison. Therefore, it is essential to establish standard formats for every necessary aspect of proteomics data. One of the recently published data models is the proteomics experiment data repository [Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D. et,al., Nat. Biotechnol. 2003, 21, 247,254]. Compliant with this format, we developed the systematic proteomics laboratory analysis and storage hub (SPLASH) database system as an informatics infrastructure to support proteomics studies. It consists of three modules and provides proteomics researchers a common platform to store, manage, search, analyze, and exchange their data. (i),Data maintenance includes experimental data entry and update, uploading of experimental results in batch mode, and data exchange in the original PEDRo format. (ii),The data search module provides several means to search the database, to view either the protein information or the differential expression display by clicking on a gel image. (iii),The data mining module contains tools that perform biochemical pathway, statistics-associated gene ontology, and other comparative analyses for all the sample sets to interpret its biological meaning. These features make SPLASH a practical and powerful tool for the proteomics community. [source] | ||||||||||||||||||||||