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Selected AbstractsInitialization Strategies in Simulation-Based SFE Eigenvalue AnalysisCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 5 2005Song Du Poor initializations often result in slow convergence, and in certain instances may lead to an incorrect or irrelevant answer. The problem of selecting an appropriate starting vector becomes even more complicated when the structure involved is characterized by properties that are random in nature. Here, a good initialization for one sample could be poor for another sample. Thus, the proper eigenvector initialization for uncertainty analysis involving Monte Carlo simulations is essential for efficient random eigenvalue analysis. Most simulation procedures to date have been sequential in nature, that is, a random vector to describe the structural system is simulated, a FE analysis is conducted, the response quantities are identified by post-processing, and the process is repeated until the standard error in the response of interest is within desired limits. A different approach is to generate all the sample (random) structures prior to performing any FE analysis, sequentially rank order them according to some appropriate measure of distance between the realizations, and perform the FE analyses in similar rank order, using the results from the previous analysis as the initialization for the current analysis. The sample structures may also be ordered into a tree-type data structure, where each node represents a random sample, the traverse of the tree starts from the root of the tree until every node in the tree is visited exactly once. This approach differs from the sequential ordering approach in that it uses the solution of the "closest" node to initialize the iterative solver. The computational efficiencies that result from such orderings (at a modest expense of additional data storage) are demonstrated through a stability analysis of a system with closely spaced buckling loads and the modal analysis of a simply supported beam. [source] Secretory activity in medullary thyroid carcinoma: A cytomorphological and immunocytochemical studyDIAGNOSTIC CYTOPATHOLOGY, Issue 6 2007D.Sc., Dilip K. Das M.B.B.S., F.R.C.Path., Ph.D. Abstract Medullary thyroid carcinoma (MTC) is a relatively rare thyroid malignancy of C-cell origin that secretes calcitonin. Although its varied cytomorphologic features are well described in literature, very little is mentioned about the morphologic manifestation of its secretory activity. This study, based on nine fine needle aspiration (FNA) samples from eight MTC patients, is an attempt to present the varied cytomorphologic features suggesting secretory activity in MTC as observed in Papanicolaou and MGG stained FNA smears and correlate them with the immunocytochemical (ICC) staining for calcitonin performed on FNA smears and the serum calcitonin values. The average number of cells in these nine samples was as follows: oval/triangular/plasmacytoid (56.7%), small round (23.6%), spindle-shaped (12.7%), and miscellaneous (7.1%). The cytomorphological features suggesting secretory activity, viz., fine cytoplasmic vacuoles, azurophillic granules, marginal vacuoles, and intracytoplasmic lumina (ICL) with secretions were present in eight, eight, five, and six samples, respectively. Material likely to be amyloid, based on morphological features, was present extracellularly in three samples and both intracellularly and extracellularly in six samples. Immunocytochemically, all the nine samples stained for calcitonin and all the three stained for chromogranin showed positive cytoplasmic reaction in the neoplstic cells. The background amyloid (in six samples), the coarse cytoplasmic granules (in two samples), and the contents of ICL (in one sample) were found to be positively stained for calcitonin. The intracytoplasmic secretory material appeared to be diffusing out of some cells both in the routine MGG stained smears and in the smears stained for calcitonin. Histopathology reports of seven samples in six patients confirmed the cytodiagnosis of MTC in all. Baseline serum calcitonin values in three cases and postoperative serum calcitonin levels during follow-up in three others were high. Thus, our study highlighted the morphological manifestations of secretory activity in MTC and the nature of secretory material as calcitonin, supported by immunocytochemical staining and serum calcitonin level. Diagn. Cytopathol. 2007;35:329,337. © 2007 Wiley-Liss, Inc. [source] Universal multiplex PCR and CE for quantification of SMN1/SMN2 genes in spinal muscular atrophyELECTROPHORESIS, Issue 7 2009Chun-Chi Wang Abstract We established a universal multiplex PCR and CE to calculate the copy number of survival motor neuron (SMN1 and SMN2) genes for clinical screening of spinal muscular atrophy (SMA). In this study, one universal fluorescent primer was designed and applied for multiplex PCR of SMN1, SMN2 and two internal standards (CYBB and KRIT1). These amplicons were separated by conformation sensitive CE. Mixture of hydroxyethyl cellulose and hydroxypropyl cellulose were used in this CE system. Our method provided the potential to separate two 390-bp PCR products that differ in a single nucleotide. Differentiation and quantification of SMN1 and SMN2 are essential for clinical screening of SMA patients and carriers. The DNA samples included 22 SMA patients, 45 parents of SMA patients (obligatory carriers) and 217 controls. For evaluating accuracy, those 284 samples were blind-analyzed by this method and denaturing high pressure liquid chromatography (DHPLC). Eight of the total samples showed different results. Among them, two samples were diagnosed as having only SMN2 gene by DHPLC, however, they contained both SMN1 and SMN2 by our method. They were further confirmed by DNA sequencing. Our method showed good agreement with the DNA sequencing. The multiplex ligation-dependent probe amplification (MLPA) was used for confirming the other five samples, and showed the same results with our CE method. For only one sample, our CE showed different results with MLPA and DNA sequencing. One out of 284 samples (0.35%) belonged to mismatching. Our method provided a better accurate method and convenient method for clinical genotyping of SMA disease. [source] Comparative metabolite profiling of carboxylic acids in rat urine by CE-ESI MS/MS through positively pre-charged and 2H-coded derivatizationELECTROPHORESIS, Issue 22 2008Wen-Chu Yang Abstract A new approach to the selective comparative metabolite profiling of carboxylic acids in rat urine was established using CE-MS and a method for positively pre-charged and 2H-coded derivatization. Novel derivatizing reagents, N -alkyl-4-aminomethyl-pyridinum iodide (alkyl=butyl, butyl-d9 or hexyl), containing quaternary amine and stable-isotope atoms (deuterium), were introduced for the derivatization of carboxylic acids. CE separation in positive polarity showed high reproducibility (0.99,1.32% RSD of migration time) and eliminated problems with capillary coating known in CE-MS anion analyses. Essentially complete ionization and increased hydrophobicity after the derivatization also enhanced MS detection sensitivity (e.g. formic acid was detected at 0.5,pg). Simultaneous derivatization of one sample using two structurally similar reagents, N -butyl-4-aminomethyl-pyridinum iodide (BAMP) and N -hexyl-4-aminomethyl-pyridinum iodide, provided additional information for recognizing a carboxylic acid in an unknown sample. Moreover, characteristic fragmentation acquired by online CE-MS/MS allowed for identification and categorization of carboxylic acids. Applying this method on rat urine, we found 59 ions matching the characteristic patterns of carboxylic acids. From these 59, 32 ions were positively identified and confirmed with standards. For comparative analysis, 24 standard carboxylic acids were derivatized by chemically identical but isotopically distinct BAMP and N -butyl-d9-4-aminomethyl-pyridinium iodide, and their derivatization limits and linearity ranges were determined. Comparative analysis was also performed on two individual urine samples derivatized with BAMP and N -butyl-d9-4-aminomethyl-pyridinium iodide. The metabolite profiling variation between these two samples was clearly visualized. [source] First laboratory confirmation of Xylophilus ampelinus in Slovenia,EPPO BULLETIN, Issue 1 2005T. Dreo Bacterial blight of grapevine is caused by a slow-growing bacterium Xylophilus ampelinus. It has been suspected to occur in Slovenia on the basis of visual observation of characteristic symptoms in the 1960s. In the present study, symptoms were recorded in an infected vineyard during three consecutive years (2002/2004). Samples from this vineyard were tested by nested-PCR and isolation of bacteria on media was attempted. In the first year, angular lesions on leaves were highly expressed and an isolate morphologically similar to X. ampelinus was obtained from one sample. It was purified and identified as X. ampelinus using biochemical and nutritional tests, fatty acid analysis, immuno-fluorescence, nested PCR and partial sequencing of the 16S rRNA gene. The 16S rDNA sequence showed 99,100% homology to known sequences of X. ampelinus strains, including the type strain. Pathogenicity of the isolate was confirmed in tissue-cultured and potted grapevine plants. In the following two years, symptoms of bacterial blight were only faintly expressed. Using isolation on media and nested-PCR, 23 and 17 extracts prepared from 10 and 8 grapevines, respectively, were analysed. In 2003, no positive sample was found, but X. ampelinus was again isolated and identified by colony morphology and nested-PCR in 2004. [source] Imaging of Cell-to-Material Interfaces by SEM after in situ Focused Ion Beam Milling on Flat Surfaces and Complex 3D-Fibrous Structures,ADVANCED ENGINEERING MATERIALS, Issue 11 2009Anne Greet Bittermann Detailed analysis of the cell-to-implant interface needs to be performed prior to medical application. As these interfaces are often not accessible for direct visualization SEM after in situ focused ion beam milling was explored that allows selecting the regions of interest and serial sectioning for analysis of large scale implant architecture/topology down to detailed sub-cellular structures in one sample that might be very useful for (bio)material characterization. [source] Sex differences in school performance as a function of conscientiousness, imagination and the mediating role of problem behaviourEUROPEAN JOURNAL OF PERSONALITY, Issue 3 2008Filip De Fruyt The roles of Conscientiousness and Imagination in explaining sex differences in school performance were examined in two Flemish samples of school children using parental and teacher ratings of school performance (N,=,599) and school grades (N,=,448). Both personality domains predicted parental ratings of school performance and grades. In one sample, girls received slightly higher parental ratings of language achievement and overall performance ratings by teachers. However, controlling for Conscientiousness and Imagination facets, boys scored slightly higher for math and history. In this sample, lower externalising behaviour partially mediated the relation between Conscientiousness facets and school performance in girls but not in boys, but this pattern was not replicated in the second sample. We concluded that sex differences in school performance were small and many could be accounted for by personality traits. In some cases, however, personality traits acted to amplify sex differences in school performance. Copyright © 2008 John Wiley & Sons, Ltd. [source] Factors controlling the partitioning of pyrene to dissolved organic matter extracted from different soilsEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 3 2005B. Marschner Summary The mobility of hydrophobic organic compounds (HOCs) in soils can be influenced by the presence of dissolved organic matter (DOM). While numerous studies have determined interactions of HOCs with humic and fulvic acids, only few data exist on the partitioning of HOCs to natural, non-fractionated DOM as it occurs in soil solutions. In this study, DOM was extracted from 17 soil samples with a broad range of chemical and physical properties, originating from different land uses. The partition coefficients of pyrene to DOM were determined in all soil extracts and for two commercial humic acids using the fluorescence quenching method. For the soil extracts, log KDOC values ranged from 3.2 to 4.5 litres kg,1. For the Aldrich and Fluka humic acids, log KDOC was 4.98 and 4.96 litres kg,1, respectively, thus indicating that they are not representative for soil DOM. After excluding these two values, the statistical analysis of the data showed a significant negative correlation between log KDOC and pH. This was also shown for one sample where the pH was adjusted to values ranging from 3 to 9. A multiple regression analysis suggested that ultraviolet absorbance at 280 nm (an indicator for aromaticity) and the E4:E6 ratio (an indicator for molecular weight) had additional effects on log KDOC. The results indicate that the partitioning of pyrene to DOM is reduced at alkaline pH, probably due to the increased polarity of the organic macromolecules resulting from the deprotonation of functional groups. Only within a narrow pH range was the KDOC of pyrene mainly related to the aromaticity of DOM. [source] Sexual or clonal origin?FEDDES REPERTORIUM, Issue 3-4 2005A morpho-ecological, molecular analysis in a patch of Ajuga reptans L. (Lamiaceae) Spatial clonal structure and patch colonisation in Ajuga reptans L. (Lamiaceae), a common stoloniferous semi-rosette plant, were studied using a combined morpho-ecological and molecular genetic approach. Within a natural patch from a forest near Diedorf (Thuringia, Germany), the spatial clonal structure was analysed, correlating both datasets: Morphologically, characteristics of clonal growth and clonal reproduction were studied, the spatial distribution of modules was mapped and merigenet relationships were reconstructed. Samples from the patch and its surroundings, and an additional sample from Berlin were then analysed by AFLP fingerprinting using four different primer combinations to identify genets. Most divergence in banding patterns was already obtained for samples from the Diedorf forest. Within the patch, however, most samples had very similar fingerprints, indicating their belonging to the same genet and hence a clonal origin, although they are morphologically separated into three "plants". Based on AFLP data, the relationships of one sample remained ambiguous; but the correlation with morphological data helped to interpret the pattern and indicated that the sample is probably a dividual of the clone, too. The relevance of the observed vegetative multiplication (clonal growth and subsequent clonal reproduction) for patch colonisation and maintenance are discussed. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) Generativer (sexueller) oder klonaler Ursprung? Eine morpho-ökologische und molekulare Analyse in einem ,patch' von Ajuga reptans L. (Lamiaceae) Die räumliche klonale Struktur und die ,patch' Besiedlung von Ajuga reptans L. (Lamiaceae), einer häufigen Halbrosettenpflanze mit Ausläufern, wurden mit einem morpho-ökologischen und molekular-genetischen Ansatz kombiniert analysiert. Die Untersuchung wurde in einem ,patch' aus einem Wald bei Diedorf (Thüringen) durchgeführt: Morphologisch wurden Merkmale des klonalen Wachstums und der klonalen Reproduktion untersucht, die räumliche Verteilung der Module kartiert und Merigenet-Beziehungen rekonstruiert. Für Proben aus dem ,patch', aus dessen näherer Umgebung und einer Pflanze aus Berlin wurden AFLP Analysen mit vier verschiedenen Primer-Kombinationen durchgeführt, um genetische Individuen (Genets) zu identifizieren. Die meisten Unterschiede in den Fragmentmustern zeigten sich bereits zwischen Proben aus Diedorf. Die ,patch'-Proben (morphologisch aufgeteilt in drei "Pflanzen") hatten jedoch sehr ähnliche fingerprints, was ihre Zugehörigkeit zum selben Genet und eine klonale Abstammung belegt. Für eine Probe ließen sich die Verwandtschaftsbeziehungen mit den AFLP Daten nicht sicher klären. Der Abgleich mit den morphologischen Ergebnissen ermöglichte jedoch eine Interpretation, und deutet auf die Zugehörigkeit zum Klon. Die Bedeutung der "vegetativen Multiplikation" (durch klonales Wachstum und klonale Reproduktion) für die Besiedlung und dauerhafte Besetzung von ,patches' wird diskutiert. [source] Integrated genomic profiling identifies candidate genes implicated in glioma-genesis and a novel LEO1 - SLC12A1 fusion geneGENES, CHROMOSOMES AND CANCER, Issue 6 2010Linda B. C. Bralten We performed genotyping and exon-level expression profiling on 21 glioblastomas (GBMs) and 19 oligodendrogliomas (ODs) to identify genes involved in glioma initiation and/or progression. Low-copy number amplifications (2.5 < n < 7) and high-copy number amplifications (n > 7) were more frequently observed in GBMs; ODs generally have more heterozygous deletions per tumor. Four high-copy amplicons were identified in more than one sample and resulted in overexpression of the known oncogenes EGFR, MDM2, and CDK4. In the fourth amplicon, RBBP5, a member of the RB pathway, may act as a novel oncogene in GBMs. Not all hCNAs contain known genes, which may suggest that other transcriptional and/or regulatory elements are the target for amplification. Regions with most frequent allelic loss, both in ODs and GBMs, resulted in a reduced expression of known tumor suppressor genes. We identified a homozygous deletion spanning the Pragmin gene in one sample, but direct sequencing of all coding exons in 20 other glioma samples failed to detect additional genetic changes. Finally, we screened for fusion genes by identifying aberrant 5,-3, expression of genes that lie over regions of a copy number change. A fusion gene between exon 11 of LEO1 and exon 10 of SLC12A1 was identified. Our data show that integrated genomic profiling can identify genes involved in tumor initiation, and/or progression and can be used as an approach to identify novel fusion genes. © 2010 Wiley-Liss, Inc. [source] Palynological evidence for Pennsylvanian (Late Carboniferous) vegetation change in the Sydney Coalfield, eastern CanadaGEOLOGICAL JOURNAL, Issue 4 2010Tatyana K. Dimitrova Abstract The palynology of clastic samples from seven stratigraphical levels in the late Moscovian Sydney Mines Formation, exposed along the shore at Bras d'Or, Nova Scotia, has been investigated. Most of the samples were from roof shales of major coals; the one sample that was not yielded a much higher proportion of pollen derived from extra-basinal vegetation. The four stratigraphically lower roof shale samples yielded essentially similar palynological spectra, with 39,±,4% lycophytes, 9,±,4% sphenophylls, 23,±,4% tree-ferns, 12,±,4% other ferns and 5,±,3% cordaites. The palynology of the upper part of the investigated succession suggests a shift in vegetation towards one favouring more marattialean tree-ferns, cordaites and conifers, and fewer lycophytes. This correlates with changes in drainage patterns as the alluvial plain migrated seawards and thus changed water tables. No evidence was found to suggest significant climate change at this time. Copyright © 2009 John Wiley & Sons, Ltd. [source] High-Si phengite, mineral chemistry and P,T evolution of ultra-high-pressure eclogites and calc-silicates from the Dabie Shan, eastern ChinaGEOLOGICAL JOURNAL, Issue 3-4 2000Robert Schmid Abstract A suite of coesite,eclogites and associated calc-silicate rocks from the ultra-high-pressure (UHP) belt in the Dabie Shan (eastern China) was investigated petrologically. Field relations and the presence of UHP minerals such as coesite, omphacite and high-Si phengite in the eclogites and the enclosing calc-silicates testify to a common metamorphic evolution for these two lithologies. Except for one sample, all bear phengite with unusually high silica contents (Si up to 3.7 per formula unit). Phengite occupies various textural positions indicating that different metamorphic stages are reflected by these white micas, which correlate with distinct mineral zonation patterns. Using the latest thermobarometric calibrations for eclogite-facies rocks, maximum pressure,temperature (P,T) conditions of 40,48 kbar at <,750°C were estimated for the peak-metamorphic mineral assemblages. These P,T conditions were calculated for both eclogitic garnet porphyroblasts with diffusion-controlled zoning as well as garnet porphyroblasts with prograde growth zonation patterns. Most samples were affected by a strong retrograde overprint mainly under eclogite- and amphibolite-facies conditions. Thermobarometry using mineral sets from different textural positions reveals cooling and decompression of the UHP rocks down to <,20 kbar at <,600°C for the bulk of the samples. Decompression and heating indicated by a few samples is interpreted to result from mineral chemical disequilibrium or late thermal influence. These new data show that subduction of continental crust in the Dabie Shan was deeper than previously thought, and also that some cooling and decompression took place at upper-mantle depths. Copyright © 2000 John Wiley & Sons, Ltd. [source] Palaeomagnetic study of the El Quemado complex and Marifil formation, Patagonian Jurassic igneous province, ArgentinaGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 3 2003Maria P. Iglesia Llanos SUMMARY The upper Jurassic El Quemado Complex was sampled at 36 sites from five localities in the cordilleran foothills of southern Patagonia between Lago Argentino and Lago Posadas,Sierra Colorada, and the middle Jurassic Marifil Formation at 12 sites in the Somuncurá Massif near Camarones. The main lithology was ignimbrite, with minor tuff and lava. Petrographical and SEM observation show that the El Quemado rocks suffered an intense, high-temperature alteration which resulted in transformation of most primary Ti-magnetite in pseudobrookite, rutile and minor Ti-haematite and Fe hydrated oxides. A similar, less pronounced alteration occurred in the Marifil rocks. 40Ar/39Ar dating of El Quemado was possible for one sample from Sierra Colorada and yielded an age of 156.5 ± 1.9 Ma. Magnetic mineralogy measurements (isothermal remanence, hysteresis loop, Curie balance) show that the remanent magnetization is dominated by PSD low-Ti magnetite, often associated to a minor high-coercive mineral (haematite). Secondary magnetization components are usually absent or weak at El Quemado sites, strong at Marifil. They were completely erased by thermal and AF demagnetization and a characteristic remanence (ChRM) stable up to temperatures higher than 550°C or peak-field values of 100 mT was successfully isolated. The virtual geomagnetic pole (VGP) from the Marifil Formation (83°S, 138°E) is in agreement with the literature data for Jurassic rocks from stable South America. The El Quemado VGPs fall in two groups. The localities to the north of latitude 48°S (Lago Posadas, Sierra Colorada) yield a VGP (81°S, 172°E) close to that of Marifil, whereas those south of latitude 49°S (Lago San Martín, Lago Argentino) show a highly elongated VGP distribution consistent with counter-clockwise block-rotation about vertical axes. These rotations were likely caused by thrust sheets which were rotating counter-clockwise at the same time they were advancing towards the foreland. The amount of rotation varies according to the location of the sampling sites in the thrust and fold belt. [source] Frequently discordant results from therapeutic drug monitoring for digoxin: clinical confusion for the prescriberINTERNAL MEDICINE JOURNAL, Issue 1 2010N. M. Rogers Abstract Background: Digoxin remains a commonly prescribed medication for the treatment of congestive cardiac failure or atrial tachyarrhythmias. Its utility is offset by its narrow therapeutic index requiring regular blood concentration monitoring. Recent evidence suggests that a lower therapeutic range (0.5,0.8 µg/L, or 0.6,1.0 nmol/L) is associated with reduced mortality in patients with congestive cardiac failure. Therapeutic drug monitoring for digoxin is carried out by immunoassays that are well established in routine clinical practice. Laboratories using different immunoassays may be involved in monitoring individual patients throughout the protracted course of therapy. These results should be concordant to ensure consistent dose individualization and optimum clinical management. We have investigated the discordance in digoxin measurements involving five different laboratories across the Adelaide metropolitan area. Methods: Aliquots from routine digoxin samples (n= 261) were analysed by accredited laboratories using commercially available immunoassays. Results: The results showed that 119 (46%) of 261 samples were so varied that a different clinical outcome was indicated when reviewed by the treating physician. The differences between the highest and lowest readings from any one sample were also substantial, with 45% of the measurements exceeding 0.3 µg/L. Conclusions: Our study shows the considerable variation in the routine monitoring of digoxin. This makes therapeutic drug monitoring difficult to interpret and complicates clinical management when treating physicians are endeavouring to avoid toxicity and optimize dosing. These results raise a significant concern for the quality of therapeutic drug monitoring of digoxin and have direct repercussions on patient care. [source] Microbial community analysis at crude oil-contaminated soils targeting the 16S ribosomal RNA, xylM, C23O, and bcr genesJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2009Y. Higashioka Abstract Aims:, The analyses targeting multiple functional genes were performed on the samples of crude oil-contaminated soil, to investigate community structures of organisms involved in monoaromatic hydrocarbon degradation. Methods and Results:, Environmental samples were obtained from two sites that were contaminated with different components of crude oil. The analysis on 16S rRNA gene revealed that bacterial community structures were clearly different between the two sites. The cloning analyses were performed by using primers specific for the catabolic genes involved in the aerobic or anaerobic degradation of monoaromatic hydrocarbons, i.e. xylene monooxygenase (xylM), catechol 2,3-dioxygenase (C23O), and benzoyl-CoA reductase (bcr) genes. From the result of xylM gene, it was suggested that there are lineages specific to the respective sites, reflecting the differences of sampling sites. In the analysis of the C23O gene, the results obtained with two primer sets were distinct from each other. A comparison of these suggested that catabolic types of major bacteria carrying this gene were different between the two sites. As for the bcr gene, no amplicon was obtained from one sample. Phylogenetic analysis revealed that the sequences obtained from the other sample were distinct from the known sequences. Conclusions:, The differences between the two sites were demonstrated in the analyses of all tested genes. As for aerobic cleavage of the aromatic ring, it was also suggested that analysis using two primer sets provide more detailed information about microbial communities in the contaminated site. Significance and Impact of the Study:, The present study demonstrated that analysis targeting multiple functional genes as molecular markers is practical to examine microbial community in crude oil-contaminated environments. [source] Identification of human papillomavirus in keratoacanthomasJOURNAL OF CUTANEOUS PATHOLOGY, Issue 7 2003Ola Forslund Background:, Keratoacanthomas are benign, clinically distinct skin tumors that may infiltrate and show cellular atypia. A viral etiology has been suggested, and the aim was to search for human papillomavirus (HPV) in keratoacanthomas. Methods:, From 21 immunosuppressed organ transplant recipients and 11 non-immunosuppressed patients, 72 fresh biopsies with diagnosis of keratoacanthomas were analyzed. For detection of cutaneous and genital HPV DNA, single-tube nested ,hanging droplet' polymerase chain reaction (PCR) and another PCR (GP5+ and 6+) were used, respectively. Results:, Among 21 immunosuppressed patients, 71% (15/21) harbored HPV DNA at least in one sample. Of the keratoacanthoma lesions, 55% (33/60) were HPV DNA positive. Fourteen samples from eight immunosuppressed patients contained HPV types 5, 9, 10, 14, 19, 20, 21, 38, 49, 80, putative HPV types as HPVvs20-4, HPVvs75, and HPVvs92 and FA16.1, FA23.2, FA37, FA75, and FA81. Among 11 non-immunosuppressed patients, 36% (4/11) harbored HPV DNA at least in one sample, and 33% (4/12) of their keratoacanthomas were HPV DNA positive. In total, HPV DNA was detected in 51% (37/72) of the keratoacanthomas. Conclusions:, By the use of PCR, cutaneous HPV DNA was detected in 51% (37/72) of the keratoacanthomas. No predominating HPV type or genital HPV type was identified. The role of HPV in keratoacanthomas remains thus elusive. [source] Distribution of mycobacteria in clinically healthy ornamental fish and their aquarium environmentJOURNAL OF FISH DISEASES, Issue 7 2006V Beran Abstract Some mycobacterial species (particularly Mycobacterium marinum) found in aquarium environments may cause chronic diseases in fish and cutaneous infections in humans, the so-called ,fish tank granuloma'. The presence and distribution of mycobacterial species in clinically healthy aquarium fish and their environment has not been adequately explored. The present study analysed the occurrence of mycobacteria in a decorative aquarium (Brno, South Moravia) and in five aquaria of a professional fish breeder (Bohumin, North Moravia). After Ziehl,Neelsen staining, acid-fast rods (AFR) were observed in six (14.3%) and mycobacteria were detected by culture in 18 (42.9%) of 42 tissue samples from 19 fish. Sixty-five samples of the aqueous environment from all six aquaria were examined; AFR were found in 16 (24.6%) and mycobacteria were detected by culture in 49 (75.4%) samples. Forty-one (70.7%) of 58 selected mycobacterial isolates were identified biochemically as follows: M. fortuitum, M. flavescens, M. chelonae, M. gordonae, M. terrae, M. triviale, M. diernhoferi, M. celatum, M. kansasii and M. intracellulare. The clinically important species for humans and fish, M. marinum, was not detected. Mycobacterium kansasii was isolated from one sample of the aquarium environment from North Moravia, which is a region of the Czech Republic with endemic incidence of M. kansasii in water. The incidence of other conditionally pathogenic mycobacterial species in healthy fish and in all investigated constituents of the aquarium environment including snails and crustaceans used for fish feeding, was quite high. Accordingly, mycobacterial species from aquarium environments may serve as a possible source of infection for both aquarium fish and immunodeficient fish handlers. [source] Consistency, context and confidence in judgements of affective communication in adults with profound intellectual and multiple disabilitiesJOURNAL OF INTELLECTUAL DISABILITY RESEARCH, Issue 1 2001J. Hogg Abstract Twenty-four service providers rated 12 video samples of four service users with whom they were familiar for affective behaviour (i.e. ,like'/,dislike') and confidence (i.e. ,certain'/'uncertain') in their judgement. Each video sample had been recorded as part of a stimulus preference assessment during which a wide range of specific stimuli were presented to each service user. Each video sample was presented twice in a counterbalanced design either with contextual information, i.e. what the presented stimulus was (C) or without such information, i.e. context free (CF). The observers showed considerable individual variation in their judgements, largely uninfluenced by the availability or otherwise of contextual information. However, as a group, observers significantly distinguished between video samples with regard to affective communication (determined through multiple analyses of variance) and the pattern of judgements, i.e. the relative judgement of positive or negative affect, from one sample to another. This showed a good level of consistency between observers (determined through principal components analysis). The impact of contextual information was not apparent for all video samples. However, contextual information significantly influenced judgements in four samples, typically making them more extreme; for example, a response indicative of positive affect in the CF situation became more positive when contextual information was provided, indicating that the stimulus was one that the participant was thought to like. [source] Human caliciviruses detected in Mexican children admitted to hospital during 1998,2000, with severe acute gastroenteritis not due to other enteropathogensJOURNAL OF MEDICAL VIROLOGY, Issue 4 2010Ana Lorena Gutiérrez-Escolano Abstract Few studies exist regarding the frequency of human caliciviruses as single etiologic agents in sporadic cases, or in outbreaks occurring in children hospitalized for acute gastroenteritis. In this study, a total of 1,129 children of <5 years of age and hospitalized due to acute diarrhea were enrolled from three main hospitals in Mexico City during a period of 3 years (March 1998 to December 2000). After analyzing all fecal samples for several enteropathogens, 396 stools that remained negative were further screened for human caliciviruses by RT-PCR using a primer set specific to norovirus and sapovirus. Human caliciviruses were detected in 5.6% (22/396) of the children. The minimum incidence rate for 1999 were 5.3% (7/132) for 1999 and 7.8% (13/167) for 2000, since only fecal specimens that tested negative to other enteric pathogens were examined. Positive samples were further characterized using specific GI and GII primers and sequencing. Norovirus GII was detected in 19/22 samples, most of them were GII/4, while sapovirus GI/2 was detected in one sample. Associations between the presence of human calicivirus and clinical and epidemiological data revealed that diarrhea occurred with a seasonal pattern, and that children hospitalized due to human calicivirus disease scored an average of 13,±,3.2 (SD) points on the Vesikari scale, which corresponded to severe episodes. These results highlight that human caliciviruses, by themselves, are enteropathogens of acute severe diarrhea among young Mexican children requiring hospitalization and that their detection is important in order to reduce the diagnosis gap. J. Med. Virol. 82:632,637, 2010. © 2010 Wiley-Liss, Inc. [source] Microfabric characteristics and rheological significance of ultra-high-pressure metamorphosed jadeite-quartzite and eclogite from Shuanghe, Dabie Mountains, ChinaJOURNAL OF METAMORPHIC GEOLOGY, Issue 2 2010L. WANG Abstract Quantitative analysis of the structural evolution of jadeite-quartzite, a rare ultra-high pressure (UHP) rock type from the Dabie Mountains of eastern China, sheds light on the formation and evolution of UHP orogenic belts worldwide. Geological mapping of the Shuanghe area, where jadeite-quartzites crop out, was carried out to determine the spatial relationships between different UHP rocks within this orogen. The deformation mechanisms of jadeite-quartzite, geodynamical parameters (stress, strain, strain rate), and microstructure including lattice preferred orientation (LPO) were determined from six jadeite-quartzite samples from the Shuanghe area. LPOs of clinopyroxene (jadeite and omphacite), garnet, rutile and quartz from these jadeite-quartzite samples are compared with those of three eclogites preserving different degrees of deformation from the Shuanghe area. Microstructural LPOs of jadeite, omphacite, garnet, rutile and quartz were determined using electron backscattered diffraction (EBSD) analysis. Quartz fabrics were largely recrystallized during late, low-grade stages of deformation, whereas garnet shows no strong LPO patterns. Rutile fabrics show a weak LS fabric along [001]. Jadeite and omphacite show the strongest eclogite facies LPO patterns, suggesting that they may provide important information about mantle deformation patterns and control the rheology of deeply subducted continental crust. Microstructural data show that the jadeite LPO patterns are similar to those of omphacite and vary between L- and S-types, which correlate with prolate and oblate grain shape fabrics (SPO); quartz LPOs are monoclinic. Microstructural analysis using TEM shows that the dominant slip systems of jadeite in one sample are (100)[001], (110)[001] and (1 1 0)1/2[110], while in another sample, no dislocations are observed. Abundant dislocations in quartz were accommodated by the dominant slip system (0001)[110], indicating basal glide and represents regional shearing during the exhumation process. This suggests that dislocation creep is the dominant fundamental deformation mechanism in jadeite under UHP conditions. The protoliths of jadeite-quartzite, metasedimentary rocks from the northern passive continental margin of the Yangtze craton, experienced the same deep subduction and were deformed under similar rheological conditions as other UHP eclogite, marble and paragneiss. Experimental UHP deformation of quartzo-feldspathic gneiss with a chemical composition similar to the bulk continental crust has shown that the formation of a jadeite,stishovite rock is associated with a density increase of the host rock similar to the eclogite conversion from basaltic protoliths. The resulting rock can be denser than the surrounding mantle pyrolite up to depths of 660 km (24 GPa). Thus, processes of deep continental subduction may be better-understood through understanding the rheology and mechanical behaviour of jadeite. Jadeite-quartzites such as those from the Shuanghe may be exhumed remnants of deeply-subducted slabs of continental crust, other parts of which subducted past the ,depth of no return', and remain in the deep mantle. [source] Metastable persistence of pelitic metamorphic assemblages at the root of a Cretaceous magmatic arc , Fiordland, New ZealandJOURNAL OF METAMORPHIC GEOLOGY, Issue 3 2009N. R. DACZKO Abstract Four aluminosilicate-bearing, amphibolite facies pelitic schists sampled from the root of the long-lived eastern Gondwana continental magmatic arc now exposed in southwest Fiordland, New Zealand, record remarkably different P,T,t histories. The four samples were collected from within 20 km of each other within the Fanny Bay Group and Deep Cove Gneiss near Dusky Sound. Integrated petrography, mineral chemistry, mineral equilibria modelling and in situ electron microprobe chemical dating of monazite shows that the sample of the Fanny Bay Group south of the Dusky Fault records a Carboniferous history with peak conditions of 4,4.5 kbar at 570,590 °C, while one sample of the Deep Cove Gneiss from Long Island records a Cretaceous history with apparent peak conditions of 7.5 kbar at 650 °C. Two other samples of the Deep Cove Gneiss from Resolution Island record mixed Carboniferous and Cretaceous histories with apparent peak conditions of 7 kbar at 650 °C and 3,7 kbar at 640,720 °C. The metapelitic schists on Resolution Island were intruded by arc magmas including the voluminous high- P Western Fiordland Orthogneiss, yet they lack mineralogical evidence of the Cretaceous high- P (>12 kbar) event. Analysis of water isopleths in a model system shows that the amount of water accommodated in the rock mineral assemblage increases with pressure. With the exhaustion of all free water, and without the addition of external water, these rocks persisted metastably within the deep arc during the high- P event. The emplacement of large volumes of diorite (i.e. the Western Fiordland Orthogneiss) into the root of the Early Cretaceous continental magmatic arc did not lead to regional granulite facies metamorphism of the country rock schists, as large volumes of amphibolite facies rock metamorphosed under medium- P conditions persisted metastably in the deep arc crust. [source] Small unilateral jaw gap variations: equilibrium changes, co-contractions and joint forcesJOURNAL OF ORAL REHABILITATION, Issue 10 2009H. J. SCHINDLER Summary, After complex prosthetic reconstructions, small differences in vertical distances between the left and right side of the jaw may occur during jaw closing, nevertheless providing bilateral tooth contacts in intercuspation by small deformations of the mandible. Their effects on the co-contraction of the masticatory muscles, the temporomandibular joint reaction forces, and the point of application of the resultant bite force vector in the maxillary occlusion plane , the so-called reduction point , have not been investigated, thus far simultaneously in one sample. The main goal of this study was to investigate variations of these measures in an experimental intercuspation simulated by one anterior and two posterior force transmission points. [source] INTRACELLULAR CYANOBACTERIAL SYMBIONTS IN THE MARINE DIATOM CLIMACODIUM FRAUENFELDIANUM (BACILLARIOPHYCEAE)JOURNAL OF PHYCOLOGY, Issue 3 2000Edward J. Carpenter The diatom Climacodium frauenfeldianum Grunow was collected in the tropical Atlantic and Pacific Oceans. Observations with epifluorescence microscopy revealed that this diatom contained coccoid symbionts (2.5,3.5 ,m) with a typical cyanobacterial fluorescence in addition to that of their own chloroplasts. Mean concentration of C. frauenfeldianum for 28 stations in the SW tropical Pacific Ocean was 530 x 103 (SE = 1372) cells·m,2, with highest concentration (mean 17.5 cells·L,1) at 40-m depth. The symbiosis was only observed at water temperatures between 26.3 and 28.9° C, with highest concentrations at 27.7° C. Three almost complete 16S rDNA sequences from one sample were determined, and they were identical. The phylogenetic analysis of this 16S rDNA sequence and those from other cyanobacteria and plastids revealed that it was closely related to the 16S rDNA sequence from Cyanothece sp. ATCC 51142. Cyanothece sp. ATCC 51142 is a unicellular nitrogen-fixing cyanobacterium isolated from a coastal marine environment and has ultrastructural features similar to the symbionts of C. frauenfeldianum. The close relationship between Cyanothece sp. and the cyanobacterial symbiont in C. frauenfeldianum suggests the potential for nitrogen fixation in the symbiosis. [source] Characterisation of avocado (Persea americana Mill) honeys by their physicochemical characteristicsJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 13 2004Anass Terrab Abstract The quality of 12 avocado (Persea americana Mill) honeys from Spain was evaluated. Eight common physicochemical parameters were analysed, namely water content, pH, acidity (free, lactonic and total), sugar content, ash content and electrical conductivity. In addition, the honey samples were analysed using inductively coupled plasma optical emission spectrometry (ICP-OES), and six minerals were quantified for each honey, namely potassium (K), calcium (Ca), magnesium (Mg), sodium (Na), phosphorus (P) and sulphur (S). Most samples showed proper maturity considering the medium water content (mean 17.7%). The total acidity (below 50 meq kg,1 except for one sample) indicated absence of undesirable fermentation; also, the mean pH of around 4.77 is usual in this kind of honey. The values for ash content and electrical conductivity were high (0.77% and 798 µS cm,1 respectively) and typical of dark honeys. K was the predominant mineral (accounting for 73% of the total minerals quantified), followed by Na (10%). Copyright © 2004 Society of Chemical Industry [source] Identifying residues in natural organic matter through spectral prediction and pattern matching of 2D NMR datasetsMAGNETIC RESONANCE IN CHEMISTRY, Issue 1 2004Andre J. Simpson Abstract This paper describes procedures for the generation of 2D NMR databases containing spectra predicted from chemical structures. These databases allow flexible searching via chemical structure, substructure or similarity of structure as well as spectral features. In this paper we use the biopolymer lignin as an example. Lignin is an important and relatively recalcitrant structural biopolymer present in the majority of plant biomass. We demonstrate how an accurate 2D NMR database of ,600 2D spectra of lignin fragments can be easily constructed, in ,2 days, and then subsequently show how some of these fragments can be identified in soil extracts through the use of various search tools and pattern recognition techniques. We demonstrate that once identified in one sample, similar residues are easily determined in other soil extracts. In theory, such an approach can be used for the analysis of any organic mixtures. Copyright © 2003 John Wiley & Sons, Ltd. [source] Mitochondrial gene diversity in the common vole Microtus arvalis shaped by historical divergence and local adaptationsMOLECULAR ECOLOGY, Issue 11 2004SABINE FINK Abstract The phylogeography of the common vole (Microtus arvalis) was examined by analysing mitochondrial DNA (mtDNA) sequence variation in 1044 base pairs (bp) of the cytochrome b (cytb) gene and in 322 bp of the control region (ctr) among 106 individuals from 58 locations. The geographical distribution of four previously recognized cytb evolutionary lineages in Europe was refined and a new lineage was found in southern Germany. All lineages were distributed allopatrically, except in one sample that was probably located in a contact zone. The occurrence of several lineages in the Alps is in keeping with their recent recolonization from distinct sources. The translation of 84 cytb DNA sequences produced 33 distinct proteins with relationships that differed from those of the DNA haplotypes, suggesting that the mtDNA lineages did not diverge in response to selection. In comparison with M. agrestis, a neutrality test detected no overall evidence for selection in the cytb gene, but a closer examination of a structural model showed that evolutionarily conserved and functionally important positions were often affected. A new phylogeographical test of random accumulation of nonsynonymous mutations generated significant results in three lineages. We therefore conclude that the molecular diversity of cytb in M. arvalis is overall the result of the demographic history of the populations, but that there have been several episodes of local adaptation to peculiar environments. [source] Quantification of algal endosymbionts (Symbiodinium) in coral tissue using real-time PCRMOLECULAR ECOLOGY RESOURCES, Issue 1 2009J. C. MIEOG Abstract Understanding the flexibility of the endosymbioses between scleractinian corals and single-cell algae of the genus Symbiodinium will provide valuable insights into the future of coral reefs. Here, a real-time polymerase chain reaction (PCR) assay is presented to accurately determine the cell densities of Symbiodinium clades C and D in the scleractinian coral Acropora millepora, which can be extended to other coral,symbiont associations in the future. The assay targets single- to low-copy genes of the actin family of both the coral host and algal symbiont. Symbiont densities are expressed as the ratio of Symbiodinium cells to each host cell (S/H ratio, error within 30%), but can also be normalized to coral surface area. Greater accuracy in estimating ratios of associations involving multiple clades is achieved compared with previous real-time PCR assays based on high-copy ribosomal DNA loci (error within an order of magnitude). Healthy adult A. millepora containing ~1.4 × 106 zooxanthellae per cm2 (as determined by haemocytometer counts) had S/H ratios of c. 0.15, i.e. ~15 symbiont cells per 100 host cells. In severely bleached colonies, this ratio decreased to less than 0.005. Because of its capacity to accurately determine both densities and ratios of multiple symbionts within one sample, the assay will open the door for novel research into the mechanisms of symbiont shuffling and switching. [source] Confidence intervals for ratios of AUCs in the case of serial sampling: a comparison of seven methodsPHARMACEUTICAL STATISTICS: THE JOURNAL OF APPLIED STATISTICS IN THE PHARMACEUTICAL INDUSTRY, Issue 1 2009Thomas Jaki Abstract Pharmacokinetic studies are commonly performed using the two-stage approach. The first stage involves estimation of pharmacokinetic parameters such as the area under the concentration versus time curve (AUC) for each analysis subject separately, and the second stage uses the individual parameter estimates for statistical inference. This two-stage approach is not applicable in sparse sampling situations where only one sample is available per analysis subject similar to that in non-clinical in vivo studies. In a serial sampling design, only one sample is taken from each analysis subject. A simulation study was carried out to assess coverage, power and type I error of seven methods to construct two-sided 90% confidence intervals for ratios of two AUCs assessed in a serial sampling design, which can be used to assess bioequivalence in this parameter. Copyright © 2008 John Wiley & Sons, Ltd. [source] Cordocentesis in multifetal pregnanciesPRENATAL DIAGNOSIS, Issue 12 2007Fuanglada Tongprasert Abstract Objective To describe the experiences in diagnostic cordocentesis in twin pregnancies at midpregnancy Methods The database and medical records of pregnant women attending Maternal Fetal Medicine Unit of the hospital for diagnostic cordocentesis at midpregnancy between January 1989 and September 2006 were retrospectively reviewed. Results During 17 years of experience, 4241 cordocenteses at midpregnancy were performed for prenatal diagnosis, including 59 procedures in 30 multiple pregnancies (29 twins and 1 triplet). The mean gestational age at the time of cordocentesis was 19.5 ± 1.6 weeks. Success rate of the samplings was 98.3% with one sample was maternal blood contamination. Averaged-time used of the procedures was 8.2 minutes (range 1,45 minutes). The procedure-related complications included transient bleeding at puncture site (8.5%) and transient fetal bradycardia (22.0%). The total fetal loss rate was 10.5% but there was no cordocentesis-related fetal loss (0.0%), defined as a fetal loss within 2 weeks after the procedure. Conclusion This study may provide a new insight on the safety of cordocentesis in multifetal pregnancies at midpregnancy. The procedure-related fetal loss is not as high as reported in the past. This study suggests cordocentesis be a relatively safe and highly successful in obtaining fetal blood samples. Copyright © 2007 John Wiley & Sons, Ltd. [source] Detection of four oxidation sites in viral prolyl-4-hydroxylase by top-down mass spectrometryPROTEIN SCIENCE, Issue 10 2003Ying Ge Abstract Oxidative inactivation is a common problem for enzymatic reactions that proceed via iron oxo intermediates. In an investigation of the inactivation of a viral prolyl-4-hydroxylase (26 kD), electrospray mass spectrometry (MS) directly shows the degree of oxidation under varying experimental conditions, but indicates the addition at most of three oxygen atoms per molecule. Thus, molecular ion masses (M + nO) of one sample indicate the oxygen atom adducts n = 0, 1, 2, 3, and 4 of 35, 41, 19, 5 ± 3, and <2%, respectively; "top-down" MS/MS of these ions show oxidation at the sites R28,V31, E95,F107, and K216 of 22%, 28%, and 34%, respectively, but with a possible (,4%) fourth site at V125,D150. However, for the doubly oxidized molecular ions (increasing the precursor oxygen content from 0.94 to 2), MS/MS showed an easily observable ,13% oxygen at the V125,D150 site. For the "bottom-up" approach, detection of the ,4% oxidation at the V125,D150 site by MS analysis of a proteolysis mixture would have been very difficult. The unmodified peptide containing this site would represent a few percent of the proteolysis mixture; the oxidized peptide not only would be just ,4% of this, but the uniqueness of its mass value (,1,2 kD) would be far less than the 11,933 Dalton value used here. Using different molecular ion precursors for top-down MS/MS also provides kinetic data from a single sample, that is, from molecular ions with 0.94 and 2 oxygens. Little oxidation occurs at V125,D150 until K216 is oxidized, suggesting that these are competitively catalyzed by the iron center; among several prolyl-4-hydroxylases the K216, H137, and D139 are conserved residues. 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